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Savaia, Bharat S., 2011, “Synthesis and Characterization of New Heterocyclic
Compounds & Their Application”, thesis PhD, Saurashtra University
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Synthesis and Characterization of New
heterocyclic compounds & their
applications
A THESIS SUBMITTED TO
THE SAURASHTRA UNIVERSITY
IN THE FACULTY OF SCIENCE
FOR THE DEGREE OF
Doctor of Philosophy
UNDER THE GUIDANCE OF
PROF. ANAMIK SHAH
DEPARTMENT OF CHEMISTRY
(DST-FIST FUNDED AND UGC-SAP
SPONSORED)
SAURASHTRA UNIVERSITY
RAJKOT – 360 005
GUJARAT (INDIA)
IN
CHEMISTRY
BY
Bharat S. Savalia
UNDER THE CO-GUIDANCE OF
PROF. ERIK VAN DER EYCKEN
LABORATORY FOR ORGANIC &
MICROWAVE-ASSISTED CHEMISTRY
(LOMAC).
DEPARTMENT OF CHEMISTRY,
UNIVERSITY OF LEUVEN
(K.U.LEUVEN), BELGIUM

JANUARY-2011
Statement under O. Ph. D. 7 of Saurashtra University
The work included in the thesis is done by me under the supervision of
Prof. Anamik K. Shah and Co-supervision of Prof. Erik Van der Eycken
and the contribution made thereof is my own work. The work was carried
out at Department of Chemistry, Saurashtra University, Rajkot under
UGC meritorious Fellowship and at Laboratory for Organic &
Microwave-Assisted Chemistry (LOMAC), Department of Chemistry,
University of Leuven (K.U.Leuven), Belgium under Erasmus Mundus
Scholarship.
Date:
Place: Bharat S. Savalia

The Blessed Lord said: Fearlessness, purification of one's existence, cultivation of
spiritual knowledge, charity, self-control, performance of sacrifice, study of the
Vedas, austerity and simplicity; non-violence, truthfulness, freedom from anger;
renunciation, tranquillity, aversion to faultfinding, compassion and freedom from
covetousness; gentleness, modesty and steady determination; vigour, forgiveness,
fortitude, cleanliness, freedom from envy and the passion for honour--these
transcendental qualities, O son of Bharata, belong to godly men endowed with
divine nature.
Bhagvad Gita, Chapter-16, Verses-1-3.
To my Family,
With Love

Acknowledgment
This thesis arose in part out of years of research that has been done since I came to Prof.
Anamik Shah’s group. By that time, I have worked with a great number of people whose
contribution in assorted ways to the research and the making of the thesis deserved special
mention. It is a pleasure to convey my gratitude to them all in my humble acknowledgment.
In the first place I would like to record my gratitude to Prof. ANAMIK SHAH for his
supervision, advice, and guidance from the very early stage of this research as well as giving me
extraordinary experiences through out the work. Above all and the most needed, he provided
me unflinching encouragement and support in various ways. His truly scientific intuition has
made him as a constant oasis of ideas and passions in science, which has exceptionally, inspire
and enrich my growth as a student, a researcher and a scientist want to be. I am indebted to
him for more than he knows.
I gratefully acknowledge My Co-Supervisor Prof. ERIK VAN DER EYCKEN Laboratory
for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry,
University of Leuven (K.U.Leuven), Belgium, for his advice, supervision, and crucial
contribution, which made him a backbone of this research and so to this thesis. His
involvement with his originality has triggered and nourished my intellectual maturity that I
will benefit from, for a long time to come. Erik, I am grateful in every possible way and hope
to keep up our collaboration in the future.
I am very thankful to the faculties of Department of Chemistry namely, Professor and Head
Dr. P.H. Parasaniya, Prof. V. H. Shah, Dr. H. S. Joshi, Dr. Shipra Baluja, Dr. M. K. Shah,
Dr. Yogesh Naliapara, Dr.U.C.Bhoya and Dr. R. C. Khunt for their encouragement and ever
green support.
The Department of Chemistry and LOMAC has provided the support and equipment I have
needed to produce and complete my thesis and the UGC and Erasmus Mundus has funded my
studies. Many Thanks.

Many thanks go in particular to Dr.Denis Ermolet’v. I am much indebted to Denis for his
valuable advice in scientific discussion and synthetic part of this thesis.
To the role model for hard workers in the lab, Dr. Vaibhav Mehta, I would like to thank him
for many reasons. I would also acknowledge Sachin, Rupesh, Ripula, Dipak, Punit, Bari, Jigo,
Nigam, Nick, Prof. BK, and Claudia (Lab Mummy) for their advice and their willingness to
share their bright thoughts with me, which was very fruitful for shaping up my ideas and
research. Thanks to each and every members of LOMAC.
Collective and individual acknowledgments are also owed to my colleagues at Saurashtra
University whose presence somehow perpetually refreshed, helpful, and memorable. Many
thanks go in particular to Vaibhav, Bunty, Ravi, Sailesh, Shrey, Dhiru, Abhay, Bapu, Nilay,
Manisha, Harshad, Ronny, Mrunal, Rakshit, Ashish, Priti, Fatema, Ketaki, Dilip, Pratik,
Vishwa and Paresh. I was extraordinarily fortunate in having Rahul, Matre, Jigo, Bharat,
Suresh, Pankaj, Atul, Raju, Naval, Naimish, Dodia, Ghetiya Satish and Mahesh as my
friends. Thank s to all dear.
To Prashant Shah, thank for giving me the opportunity to work on your O2h in Ahmedabad.
To Cnp, Tusharbhai, Jigo, Pradip, Hemal, Nileshwari, Shabu, PP, Hiral, Tejas, Pareshbhai
and Vikas thank for your technical assistances and fun during the work we had in O2h. It is
also a pleasure to mention.
I am tempted to individually thank all of my friends which, from my childhood until graduate
school, have joined me in the discovery of what is life about and how to make the best of it.
However, because the list might be too long and by fear of leaving someone out, I will simply
say thank you very much to you all.
It is a pleasure to express my gratitude wholeheartedly to Anamik Shah’s family for their kind
hospitality during my stay in Rajkot for Ph.D. Specially thanks to Ranjanmam and Aditya.
Where would I be without my family? My parents deserve special mention for their
inseparable support and prayers. My Father Savdasbhai, in the first place is the person who
put the fundament of my learning character, showing me the joy of intellectual pursuit ever

since I was a child. My Mother Hansaben, is the one who sincerely raised me with her caring
and gently love. My special gratitude is due to my dadi, my brother Kalpesh, Bhabhi
Jayshreeben, my sisters Manisha, Jiju Rajnibhai, Sweet Miral, Mahek, Nancy, & Man, my
uncle Manshukhbhai and his family for their loving support.
Words fail me to express my appreciation to my wife Trupti whose dedication, love and
persistent confidence in me, has taken the load off my shoulder. I owe her for being unselfishly
let her intelligence, passions, and ambitions collide with mine. Therefore, I would also thank
Tupi’s family for letting me take her hand in marriage, and accepting me as a member of the
family, warmly. Furthermore, to Sorathiya family with their thoughtful support, thank you.
I would like to thank everybody who was important to the successful realization of thesis, as
well as expressing my apology to those whose name I could not mention individually.
Finally, I bow my head before almighty GOD, who has inspired ME in each and every stage
of my life.
BHARAT SAVALIA

CONTENTS
CHAPTER – 1
Microwave Assisted Organic Synthesis
1. Microwave Assisted Organic Synthesis 1
1.1 Introduction 1
1.2 Microwave Frequency 2
1.3 Principle 2
1.4 Heating Mechanism 3
1.4.1 Dipolar Polarisation 3
1.4.2. Conduction Mechanism 4
1.5 Effects of solvents 5
1.6 Conventional vs Microwave Heating 6
1.7 Application of microwave in organic synthesis 7
1.8 Studies on 2-Aminoimidazoles 8
1.9 2-Aminoimidazole Alkaloids 11
1.10 Methods for the preparation of 2-aminoimidazoles 15
1.11 The 2-Aminoimidazole as a Pharmacophore 21
1.11.1 Antibiotics Activity 21
1.11.2 Sodium Hydrogen Exchanger-1 (NHE-1) Antagonists. 22
1.11.3 Anti HIV Activity 22
1.11.4 α-adrenoreceptor agonists. 24
1.11.5 Anti Cancer Activity 24
1.11.6 BACE-1 Inhibitors 25
1.11.7 Anti Biofilm Activity 26
1.12 Introduction to Biofilm 29
1.12.1 Properties of biofilms 30
1.12.2 Biofilm Growth Cycle 31
1.12.3 Biofilm Drug Resistance 31
1.13 Recent Publications on 2-aminoimidazoles 33
1.14 Conclusion 33
1.15 References 34

CHAPTER – 2
Microwave Assisted Synthesis & Structure Activity Relationship of 2-Hydroxy-2phenyl-2,3-dihydro-imidazo[1,2-a]pyrimidinium
Salts and 2N-Substituted 4(5)-
Phenyl-2-Amino-1H-imidazoles as Inhibitors of the Biofilm Formation by
Salmonella Typhimurium and Pseudomonas aeruginosa
2.1 Introduction 40
2.2 Reaction scheme 41
2.3 Proposed Mechanism 42
2.4 Results and discussion 43
2.5 Biofilm activity 50
2.5.1 2N-substituted 2-aminopyrimidines 48
2.5.2 2-hydroxy-2,3-dihydro-imidazopyrimidinium salts 48
2.5.2.1 n-Alkyl or iso-alkyl substituents at 1-position 48
2.5.2.2 Further Modification in the most active core structure 51
2.5.2.3 Cyclo-alkyl substituents at 1-position 53
2.5.3 2N-substituted 2-aminoimidazoles 54
2.6 Conclusion 56
2.7 Experimental 57
2.8 Biological Assays 58
2.9 Experimental Protocols 60
2.10 Spectral Characterization 62
2.11 Representative NMR spectra 87
2.12 References 90
CHAPTER – 3
Structure Activity Relationship of N1-Substituted 2-Aminoimidazoles as
Inhibitors of Biofilm Formation by Salmonella Typhimurium and Pseudomonas
aeruginosa
3.1 Introduction 93
3.2 Reaction scheme 94
3.3 Proposed Mechanism 95
3.4 Results and discussion 96

3.5 Biofilm activity 98
3.5.1 N1-alkyl 2-aminoimidazoles 99
3.5.2 Further Modification in the most active core structure 102
3.5.3 Cyclo-alkyl 2-aminoimidazoles 104
3.6 Conclusion 106
3.7 Experimental 107
3.8 Experimental protocols 108
3.9 Spectral Characterization 109
3.10 Representative NMR spectra 122
3.11 References 124
CHAPTER – 4
Copper Catalyzed Microwave Assisted One Pot Synthesis of 2-Aminoimidazole-
Triazole Framework via Dimorth Rearrangement and Click Reaction.
4.1 Introduction 127
4.2 Optimization Study 128
4.3 Results and discussion 130
4.4 Possible Mechanism 133
4.5 Conclusion 134
4.6 Experimental 134
4.7 Experimental Protocols 135
4.8 Spectral Characterization 136
4.9 Representative NMR spectra 149
4.10 References 151
CHAPTER – 5
Synthesis, Characterization, Crystal and molecular structure analysis of DP-7: A
new Multi Drug Resistance Reverter Lead Molecule
5.1 Introduction 154
5.2 Reaction Scheme 155
5.3 Method of crystallization 155
5.4 Crystal structure determination 155

5.5 Results and discussion 156
5.6 Conclusion 160
5.7 Experimental 161
5.8 Spectral Characterization 161
5.9 Representative NMR spectra 163
5.10 References 165
SUMMARY
CONFERENCES/SEMINARS/WORKSHOPS ATTENDED
LIST OF PUBLICATIONS

Abbreviations
Ac Acetyl
2-AI 2-aminoimidazole
aq Aqueous
Boc tert-butyloxycarbonyl
n-BuLi n-butyllithium
t-BuOK potassium tert-butoxide
Cbz Benzyloxycarbonyl
CI chemical ionization
m-CPBA m-chloroperoxybenzoic acid
DAST diethylaminosulfur trifluoride
DBBA 5,5-dibromobarbituric acid
DCM Dichloromethane
DIBAL diisobutylaluminium hydride
DIEA Diisopropylethylamine
DIPA Diisopropanolamine
DMAP 4-dimethylaminopyridine
DMF Dimethylformamide
DMSO dimethyl sulfoxide
EDCI 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
ESI electrospray ionization
equiv Equivalent
h Hour
HMBC heteronuclear multiple bond correlation
HRMS high resolution mass spectrometry
LAH lithium aluminium hydride
MAOS microwave-assisted organic synthesis
MeCN Acetonitrile
min Minute
MS mass spectrometry

Ms Mesyl
MW Microwave
NBS N-bromosuccinimide
NCS N-chlorosuccinimide
NMM N-methylmorpholine
NOESY nuclear Overhauser effect spectroscopy
PCC pyridinium chlorochromate
Pd Palladium
Pd2(dba)3
tris(dibenzylideneacetone)dipalladium
PDC pyridinium dichromate
PPA polyphosphoric acid
rt room temperature
SPOS solid-phase organic synthesis
TBDMS tert-butyldimethylsilyl
TBDPS tert-butyldiphenylsilyl
TEA Triethylamine
TFA trifluoroacetic acid
THF Tetrahydrofuran
TLC thin layer chromatography
TMS Tetramethylsilane
Ts Tosyl
W Watt

Microwave Assisted Organic
Synthesis

1. Microwave Assisted Organic Synthesis:
1.1 Introduction
Synthesis of new chemical entities is major bottleneck in drug discovery.
Conventional methods for various chemical synthesis is very well documented and
practiced. 1 The methods for synthesis (Heating process) of organic compounds has
continuously modified from the decade. In 1855, Robert Bunsen invented the burner
which acts as energy source for heating a reaction vessel, this was latter superseded
by isomental, oil bath or hot plate, but the drawback of heating, though method
remain the same. Microwave Assisted Organic Synthesis (MAOS), which has
developed in recent years, has been considered superior to traditional heating.
Microwave assisted organic synthesis 2 (MAOS) has emerged as a new “lead” in
organic synthesis. The technique offers simple, clean, fast, efficient, and economic for
the synthesis of a large number of organic molecules. In the recent year microwave
assisted organic reaction has emerged as new tool in organic synthesis. Important
advantage of this technology include highly accelerated rate of the reaction,
Reduction in reaction time with an improvement in the yield and quality of the
product. Now day’s technique is considered as an important approach toward green
chemistry, because this technique is more environmentally friendly. This technology
is still under-used in the laboratory and has the potential to have a large impact on the
fields of screening, combinatorial chemistry, medicinal chemistry and drug
development. Conventional method of organic synthesis usually need longer heating
time, tedious apparatus setup, which result in higher cost of process and the excessive
use of solvents/ reagents lead to environmental pollution. This growth of green
chemistry holds significant potential for a reduction of the by product, a reduction in
waste production and a lowering of the energy costs. Due to its ability to couple
directly with the reaction molecule and by passing thermal conductivity leading to a
rapid rise in the temperature, microwave irradiation has been used to improve many
organic syntheses.

1.2 Microwave frequency
Microwave heating refers the use of electromagnetic waves ranges from 0.01m to 1m
wave length of certain frequency to generate heat in the material. These microwaves
lie in the region of the electromagnetic spectrum between millimeter wave and radio
wave i.e. between I.R and radio wave. They are defined as those waves with
wavelengths between 0.01metre to 1meter, corresponding to frequency of 30GHz to
0.3GHz.
1.3 Principle
The basic principle behind the heating in microwave oven is due to the interaction of
charged particle of the reaction material with electro magnetic wavelength of
particular frequency. The phenomena of producing heat by electromagnetic
irradiation are ether by collision or by conduction, some time by both.
All the wave energy changes its polarity from positive to negative with each cycle of
the wave. This cause rapid orientation and reorientation of molecule, which cause
heating by collision. If the charge particles of material are free to travel through the
material (e.g. Electron in a sample of carbon), a current will induce which will travel
in phase with the field. If charge particle are bound within regions of the material, the
electric field component will cause them to move until opposing force balancing the
electric force. 3-9

1.4 Heating Mechanism
In microwave oven, material may be heated with use of high frequency
electromagnetic waves. The heating arises from the interaction of electric field
component of the wave with charge particle in the material. Two basic principal
mechanisms involve in the heating of material
1.4.1 Dipolar Polarisation
Dipolar polarisation is a process by which heat is generated in polar molecules. On
exposure to an oscillating electromagnetic field of appropriate frequency, polar
molecules try to follow the field and align themselves in phase with the field.
However, owing to inter-molecular forces, polar molecules experience inertia and are
unable to follow the field. This results in the random motion of particles, and this
random interaction generates heat. Dipolar polarisation can generate heat by either
one or both the following mechanisms:
1. Interaction between polar solvent molecules such as water, methanol and ethanol
2. Interaction between polar solute molecules such as ammonia and formic acid
The key requirement for dipolar polarisation is that the frequency range of the
oscillating field should be appropriate to enable adequate inter -particle interaction. If
the frequency range is very high, inter-molecular forces will stop the motion of a
polar molecule before it tries to follow the field, resulting in inadequate inter-particle
interaction. On the other hand, if the frequency range is low, the polar molecule gets
sufficient time to align itself in phase with the field. Hence, no random interaction
takes place between the adjoining particles. Microwave radiation has the appropriate
frequency (0.3-30 GHz) to oscillate polar particles and enable enough inter-particle
interaction. This makes it an ideal choice for heating polar solutions.
In addition, the energy in a microwave photon (0.037 kcal/mol) is very low, relative
to the typical energy required to break a molecular bond (80-120 kcal/mol).
Therefore, microwave excitation of molecules does not affect the structure of an
organic molecule, and the interaction is purely kinetic.

1.4.1. a Interfacial Polarization
Interfacial polarization is an effect, which is very difficult to treat in a simple manner,
and easily viewed as combination of the conduction and dipolar polarization effects.
This mechanism is important for system where a dielectric material is not
homogenous, but consists of conducting inclusion of one dielectric in other.
1.4.2. Conduction mechanism
The conduction mechanism generates heat through resistance to an electric current.
The oscillating electromagnetic field generates an oscillation of electrons or ions in a
conductor, resulting in an electric current. This current faces internal resistance, which
heats the conductor.
The main limitation of this method is that it is not applicable for materials that have
high conductivity, since such materials reflect most of the energy that falls on them.

1.5. Effects of solvents
Every solvent and reagent will absorb microwave energy differently. They each have
a different degree of polarity within the molecule, and therefore, will be affected
either more or less by the changing microwave field. A solvent that is more polar, for
example, will have a stronger dipole to cause more rotational movement in an effort
to align with the changing field. A compound that is less polar, however, will not be
as disturbed by the changes of the field and, therefore, will not absorb as much
microwave energy. Unfortunately, the polarity of the solvent is not the only factor in
determining the true absorbance of microwave energy, but it does provide a good
frame of reference. Most organic solvents can be broken into three different
categories: low, medium, or high absorber, as shown in Figure 6. The low absorbers
are generally hydrocarbons while the high absorbers are more polar compounds, such
as most alcohols.
Absorbance level Solvents
High
Medium
Low
DMSO, EtOH, MeOH, Propanols,
Nitobenzen,
Glycol
Formic Acid, Ethylene
Water, DMF, NMP, Butanol,
Acetonitrile, HMPA, Methy Ethyl
Ketone, Acetone, Nitromethane,
Dichlorobenzene, 1,2-Dichloroethane,
Acetic Acid, trifluoroacetic Acid,
Chloroform, DCM, Carbon tetrachloride,
1,4-Dioxane, Ethy Acetate, Pyridine,
Triethyamine, Toluene, Benzene,
Chlorobenzene, Pentane, Nexane and
other hydrocarbons

1.6 Conventional vs Microwave Heating
Microwave heating is different from conventional heating in many respects. The
mechanism behind microwave Synthesis is quite different from conventional
synthesis. Points enlisted in Table 1, differ the microwave heating from conventional
heating. 10-26
No CONVENTIONAL MICROWAVE
1
2
3
4
5
6
7
Reaction mixture heating proceeds
from a surface usually inside surface of
reaction vessels
The vessel should be in physical
contact with surface source that is at a
higher temperature source (e.g. mental,
oil bath, steam bath etc.)
By thermal or electric source heating
take place.
Heating
conduction
mechanism involve-
Transfer of energy occur from the wall,
surface of vessel, to the mixture and
eventually to reacting species
In conventional heating, the highest
temperature (for a open vessels) that
can be achieved is limited by boiling
point of particular mixture.
In the conventional heating all the
compound
equally
in mixture are heated
Reaction mixture heating proceeds
directly inside mixture
No need of physical contact of
reaction with the higher temperature
source. While vessel is kept in
microwave cavities.
By electromagnetic wave heating take
place.
Heating mechanism involvedielectric
polarization and conduction
The core mixture is heated directly
while surface (vessel wall) is source
of loss of heat
In microwave, the temperature of
mixture can be raised more than its
boiling point i.e. superheating take
place
In microwave, specific component
can be heated specifically.
8 Heating rate is less Heating rate is several fold high

1.7 Application of microwave in organic synthesis
Following reactions have been performed through microwave heating.
Sr. Reaction Ref. Sr Reaction Ref.
1 Acetylation reaction 27 18 Diel’s-Alder reaction 44
2 Addition reaction 28 19 Dimerization reaction 45
3 Alkylation reaction 29 20 Elimination reaction 28
4 Alkynes metathesis 30 21 Estrification reaction 46
5 Allylation reaction 31 22 Enantioselective reaction 47
6 Amination reaction 32 23 Halogenation reaction 48
7
Aromatic nucleophillic
substitution reaction
33 24 Hydrolysis reaction 59
8 Arylation reaction 34 25 Mannich reaction 50
9 Carbonylation reaction 35 26 Oxidation reaction 51
10 Combinatorial reaction 36 27 Phosphorylation synthesis 52
11 Condensation reaction 37 28 Polymerization reaction 53
12 Coupling reaction 38 29 Rearrangement reaction 54
13 Cyanation reaction 39 30 Reduction reaction 55
14 Cyclization reaction 40 31 Ring closing synthesis 56
15 Cyclo-addition reaction 41 32 Solvent free reaction 57
16 Deacetylation reaction 42 33 Transestrification reaction 46
17 Dehalogenation reaction 43 34 Transformation reaction 58
Figure 1.2: General View of Monomode CEM Discover (left) and Multimode
MILESTONE Start (right) Systems

1.8 Studies on 2-Aminoimidazoles
Much effort has been dedicated to the study of molecular architecture and its
relationship to biological activity. From decades of high throughput screening of both
natural and synthetic small molecules we have clued in on structural features that
impart a high probability of biological efficacy. 59 Recently natural products have
enjoyed a renaissance in lead generation for discovery based research. This realization
has further been folded into the concept of Biology-oriented synthesis (BIOS) which
relies on the core structures of natural products as valuable pre-validated scaffolds. 60
These so-called “privileged” pharmacophores are often the basis of synthetic
collections aimed at increasing the success rate of small molecule screening ventures.
In particular, marine natural products derived from sponges have provided valuable
leads for therapeutic small molecules. 61-62 Surprisingly the large majority of these
compounds have been isolated from organisms of the class Dermospongiae. In the
mid 1980’s chemists noted that the other major sponge class, Calcarea, had rarely
been subject to chemical investigations. A flurry of efforts through the mid-1990’s
helped to establish biogenetic relationships among these sponges. Isolated to explore
these interconnections and not necessarily for specific biological responses the
activities of these natural products have remained largely uncovered. Since these
initial investigations, an emerging structural class has recurrently been identified
through bioassay guided isolation which contains the 2-aminoimidazole core. From
the viewpoint of small molecule discovery this review will highlight alkaloids isolated
from Leucetta sp. This small skeletal family has been shown to interrogate an
incredibly diverse range of biological processes and thus represents an important
discovery scaffold for both medicinal and discovery based research.
In 1958, a nitrogen rich antibiotic, consequently named azomycin, was isolated from a
presumptive Streptomyces sp. 63 This new antibiotic displayed good antimicrobial
activity against B. subtilis (6 μg/mL) and E. coli (25 μg/mL) and was relatively well
tolerated in mice (LD50 = 80 mg/kg). Eventually the structure of azomycin was
revealed to be 2-nitroimidazole (2) 64 , which along with its synthetic derivative
metronidiazole (3) have become clinically relevant antiprotozoal therapeutics (Fig.
1.8.1). 65 With the parallel observation that several microbes were able to oxidize

aromatic amines, Lancini’s group showed some Streptomyces species are able to
oxidize 2-aminoimidazole itself, along with a series of 4-alkyl-2-aminoimidazoles, to
their corresponding 2-nitroimidazoles. 66 This suggested that the 2-aminoimidazole
might be the direct biosynthetic precursor to azomycin and in 1970 Okami’s group
isolated the parent heterocycle (1) from Streptomyces eurocidicus. 67 This study also
showed that supplementing the growth medium with L-Arg substantially increased the
production of 1, suggesting that arginine catabolism is critical to its biosynthesis. It is
unknown whether a similar pathway exists in marine organisms that produce more
complex 2-aminoimidazoles, however 1 has been discovered in sponges of the family
Halicondriidae. 68
L-Arg
N
NH
NH 2
N
NH
NO 2
N
NO 2
1 2
Me
3
2-Aminoimidazole Azomycin Metronidazole
Fig.1.8.1 Biosynthetic transformations of 2-aminoimidazole.
Studies on azomycin’s (2) and metronidazole’s (3) mechanism of action have
revealed that the nitro group is reduced in vivo to the nitroso radical which is
responsible for its selective anaerobic antiprotozoal activity. 69 Subsequent studies
have shown that hypoxic conditions in tumors are also capable of reducing the 2nitorimidazole,
prompting it to serve as an important prodrug for 2-aminoimidazoles
in hypoxic environments. 70-72
The ambivalent reactivity of the key structural motif 2-amino-1H-imidazole (4) is
responsible for the molecular diversity observed in this group of alkaloids. The
electrophilic or nucleophilic reactivity at the same position C-4(5) is dependent on the
tautomeric isomer involved (Scheme 1.8.1). 73
NH 2
HN N
5
nucleophilic
position
NH
2
3 1
H N N H
4 5
4
NH 2
N N
5
electrophilic
position
Scheme-1.8.1 The Tautomerism and Ambivalent Reactivity of 2-
Aminoimidazole
N
OH

It is understood that the 2-aminoimidazole occupies an important region of chemical
space as its hydrogen bond donor-acceptor pattern is capable of recreating that of the
guanidine. 74 More importantly, it occupies a unique pKa range between the more
acidic 2-aminopyridinium ion 75 and less acidic guanidinium ion 76 (Fig.1.8.2).
Furthermore, the pKa’s of 2-aminoimidazolium ions show a predictable trend with
substitution, allowing it to be finely tuned for medicinal applications as illustrated in
the examples below. 77
2-Aminopyridine 2-aminobenzimidazole
H
N
N NH 2 N
pK a = 6.71 7.18
N
NH 2
NH
2-aminoimidazole
Me
N
NH 2
NH
Me
N
NH 2
pK a = 8.46 8.65 9.21
HN NH 2 HN
NH 2
Me
NH
amidine guanidine
NH 2
pK a = 12.4 13.4
NH 2
Fig.1.8.2 pKa’s of common guanidine mimetics
This dramatic difference in the pKa of 2-aminoimidazoles (~4 pKa units) with that of
guanidine has led to some debate concerning the ability of the 2-aminoimidazole to
directly mimic a guanidine. These arguments, based on a lowered pKa and electronic
dissimilarity are, however, precisely what makes the 2-aminoimidazole a unique
guanidine mimic for medicinal chemistry.- 77-78 Most importantly, their pKa range
(pKa ~7-9) allows a significant fraction of compound to be uncharged at
physiological pH thus increasing the likelihood of cellular penetration. It also permits
this unique heterocycle to cross the blood brain barrier and may decrease the
susceptibility of these compounds to Pgp mediated efflux vide infra. 79

1.9 2-Aminoimidazole Alkaloids
The 2-aminoimidazole framework is emerging as an important pharmacophore, 80 and
is widely found in numerous biologically active marine alkaloids. Over the last 25
years, several hundreds of diverse 1-unsubstituted and 1-substituted 2aminoimidazoles
have been characterized. 1-Unsubstituted 2-aminoimidazole
alkaloids (Fig. 1.9.1) have been isolated essentially from various species of marine
sponges (Phylum Porifera) of Caribbean and South Atlantic regions. 81 Oroidin (1) and
the dimeric sceptrin (3) are the most abundant members of the pyrrole-imidazole
family.
H 2N
H 2N
H 2N
N
N
H
H
N
N
N
Oroidin (1)
HN
O
HN
N
H
O
Sceptrin (3)
H N
HN
H2N HO
N
N
H
HN
N
H
H2N Cl
Palau'amine
(5)
H
N
HN
O
NH 2
O
N
H
N
H
Br
Br
Br
Br
H 2N
N
H
N
HO
O
H 2N
H 2N
Me
HN
H
N
N
N
H
HN
N
N
H
Cl
N
H
OH
Girolline (2)
N
Br
Br
Ageladine A (4)
O
NH 2
NH
Dragmacidin E (6)
Fig.1.9.1 Some representative 1-unsubstituted 2-aminoimidazoles from marine
sponges.
Br

In turn, most of the 1-substituted 2-aminoimidazole alkaloids (Figure 1.9.2) have been
isolated from the Calcarea group of the genera Leucetta and Clathrina from the Red
Sea and the Indo-Pacific regions. 82
N
H2N N
Me
HO
OH
Naamine A (7)
OMe
OMe
OMe
N
H2N N O OMe
Me
Calcaridine A (9)
N
OH
H2N N
OMe
Me
Kealiinine A (11)
H 2N
N
N
OH
Isonaamine A (8)
N
H2N N
Me O
O
O
OH
O
Leucettamine A (10)
N
H2N N
Me O
O
Preclathridine A (12)
Fig.1.9.2 Some representative 1-substituted 2-aminoimidazoles from
marine sponges.
Both classes of 1-substituted and 1-unsubstituted 2-aminoimidazoles possess
interesting biological properties. Due to their high cytotoxicity many polysubstituted
2-aminoimidazole alkaloids are involved in chemical defense of marine sponges
against predators, in the prevention of the settlement of fouling and pathogenic
microorganisms or in the suppression of epibiotic bacteria and spatial competition.

Recently group of Erik 83 described a novel, short and efficient synthesis of diverse 2aminoimidazoles
from readily available polysubstituted secondary propargylamines
and thioureas (Scheme-1.9.1). Both the guanylation and the cyclization steps can be
carried out either in a stepwise manner with a carbodiimide activator and an AgI
catalyst or in a one-pot process with a recoverable AgI salt as a promoter and catalyst.
This protocol was successfully applied to the total synthesis of all trisubstituted 2aminoimidazole
naamine alkaloids. Furthermore, we demonstrated the potential of
polysubstituted 2-aminoimidazoles as inhibitors of bacterial biofilm formation.
R 1
R 2
R 3
R 4
Me
CHO
N
H
Boc
N
N
Boc N
Me
N
H2N N
Me
R 1
R 1
allyl
R 5
R 2
R 4
R 3
1) TFA/DCM
RT, 3h
2) H2-Pd/C
MeOH, RT
R 5
R 2
R 4
R 3
R 5
CuBr (10 mol %)
100 oC, MW
Toluene, 25 min
6a
AgNO3 (1.4 equiv)
Et3N (2 equiv)
MeCN, RT, 5 min
Scheme 1.9.1 Short total synthesis of alkaloid of the naamine family
R 1
R 2
R 1
R 2
R 3
R 3
R 4
R 5
N(Me)Allyl
[Pd(PPh3) 4] (5 mol%)
DMBA (3.5 equiv)
DCM, Reflux, 25 min
R 4
NH(Me)
R 5

Pierre Potier proposed biogenetic scheme, various hypothetical constituents can be
predicted. It is clear that the above chemical pathway suggests that these compounds
may be more widespread than presently known. The isolation and characterisation of
new pyrrole-imidazole metabolites will certainly allow us to explore additional
transformations which could support this hypothesis. As chemical diversity,
enzymatic catalysis variation and mutagenesis are closely related, the ‘‘prebiotic
chemistry’’ presented here can also provide strong evidence for a multifunctional
enzyme-mediated biosynthesis. Such multiprotein systems would be particularly
needed by the living fixed sponges for their adaptation to environmental influences,
and for self-defence.
Fig.1.9.3 Arrangement of all known oroidin alkaloids in structural groups.

1.10 Methods for the preparation of 2-aminoimidazoles
Several methods for the formation of 2-aminoimidazoles are known with widely
differing degrees of synthetic utility, but no current method as of yet has a broad
range of applicability in complex molecule synthesis. Harsh reaction conditions
and/or synthetically difficult and labile precursors are often required for such task.
The methods to prepare 2-aminoimidizoles may be categorized into four main classes:
1) Condensation reactions,
2) Ambivalent addition of 2-aminoimidazole,
3) Direct formation of C-N bond.
4) Heterocyclic exchange reactions.
Functionalized 2-aminoimidazoles can show a wide range of stability issues, the free
base of many substrates is susceptible to nucleophilic or base mediated degredation.
This instability has thus far precluded a unified strategy to access this heterocycle, but
the variety of methods can often lead to success in a complex molecule setting.
1.10.1 Condensations
By far the most common way to prepare the 2-aminoimidazoles originates with the
condensation of α-amino or α -haloketone with cyanamide or a guanidine derivative,
respectively. This strategy was first disclosed by Norris and McKee who explored the
condensation of α -aminoacetophenones with N-cyanoguanidines (scheme-1.10.1). 84
Cl
O
NH 2.HCl
NC
N
H
NH
Scheme-1.10.1 Norris and McKee‘s condensation.
N
R 2
R 1
150-200 o C
Subsequently Lawson was able to show that aminoacetaldehyde diethylacetal can
undergo acid catalyzed addition to cyanamide giving the masked guanidine
acetaldehyde (Scheme-1.10.2). 85
Cl
N
NH
HN
NH
N
R 1
R 2

EtO
OEt
NH 2CN
NH 2
AcOH
EtO
OEt
Scheme-1.10.2 Lawson’s synthesis.
H
N
NH
NH 2
HCl
H 2O
N
H
N
NH 2.HCl
Kruetzberger found that condensation of 1,2-hydrazinedicarboxamidine with benzoin
derivatives in alkali media will yield symmetrically substituted azoimidazoles after
spontaneous oxidation of the bis-imidazolhydrazine (Scheme-1.10.3). 86 Reductive
cleavage of the azo group by hydrogenolysis gives two mole equivalents of the 2aminoimidazole.
This methodology is useful but limited to the preparation of 4,5diaryl
substituted 2-aminoimidazoles.
H 2N
HN
HN NH
NH
NH 2
Ar
O
OH
Ar
NaOH
Scheme-1.10.3 Kruetzberger’s condensation.
Ar
In 1966, Lancini and Lazzari successfully expanded Lawson’s strategy to include α -
aminoketones, including the use of N-alkylamines (Scheme-1.10.4). 87-88 They were
the first to observe the strict pH dependence of this condensation. At very low pH the
cyanamide is quickly converted to urea. At high pH, dimerization of the aminoketone
to the piperazine competes with cyanamide condensation. Having established the
optimum pH of the reaction to be ~4.5, these conditions are now routinely adopted. In
1925 Pyman and Burtles had reported the reaction of α-bromoacetone and guanidine
to give a mixture of uncharacterizable compounds, leading them to abandon this
approach and develop their diazonium coupling described below. 89 Seventy years
later, Weber discovered that N-acetylguanidine smoothly undergoes displacement and
condensation with α -haloketones and aldehydes. 90
O
H
N
NH 2CN
pH = 4.5
N
N
N
NH
Ar
HN
N
N
Ar
N
Ar
NH 2
H 2
Pd/C
Scheme-1.10.4 Lancini and Lazzari’s expanded strategy
Ph
Ar
HN
Ar
N
NH 2

R 1
O
X
R 2
NH 2
H 2N NAc
R 1
HN
R 2
N
NHAc
NH 2NH 2
OR
H 2SO 4
Scheme-1.10.5 Weber’s condensation with N-acetylguanidine.
In the late 1970’s Nishimura reported the condensation of substituted α-diketones
with guanidine to yield a variety of useful products (Scheme-1.10.6). 91 This report
illuminates the variety of chemistry that is possible around this heterocyclic core.
Treatment of a diketone with guanidine in dioxane and methanol yields the substituted
bicyclic bis-guanidine . Alternatively, aprotic reaction conditions can selectively
deliver the 2-aminoimidizo-4-ol. This intermediate can undergo a base catalyzed
pinacol-type rearrangement to form the 2-aminoimidizo-4-one. This same
intermediate can give rise to the 4,5-diol upon exposure to aqueous hydrochloric acid.
A similar hydration reaction with anhydrous HCl affords the di-methoxylated
derivative. Hydrogenolysis of 2-aminoimidizo-4-ol cleanly gives the 4,5-dialkyl-2aminoimidazole.
These laboratory transformations foreshadow potential biosynthetic
relationships between the 2-aminoimidazole natural products isolated from marine
sponges.
R 2
O
R1 R2 NH 2
HN N
HN N
NH 2
N
N
H
R 1
NaOH
MeOH
NH 2
dioxane
MeOH
R1 R2 HO
HO
conc.HCl
N
N
H
R 1
R 2
NH 2
Scheme-1.10.6 Nishimura’s diketone condensation
O
O
H 2N
HN
MeO
R 1
NH 2
MeOH
HCl
N
NH 2
R 1
R 2
R 1
R 1
HN
OH
N
R2 N
R N
MeO H
2 H
N
N
R 2
N
NH 2
NH 2
H2/Pd-C
MeOH
NH 2

1.10.2 Ambi-valent Addition of 2-Aminoimidazole
Depending on reaction conditions, the parent heterocycle, 2-aminoimidazole, can be
influenced to react either at N-2 or C-4. In Potier’s synthesis of girolline, 2aminoimidizole
was added directly to the α-chloroaldehyde. Under the influence of
sodium carbonate, the imidazole adds preferentially through the 4-position (Scheme-
1.10.7 ). 92 As revealed in Horne’s synthesis of stevensine, methanesulfonic acid was
used to add the 2-aminoimidazole across an olefin. 93-94 Horne has also shown that
Friedel-Crafts type alkylation of the activated ethers can proceed with attack by C-4
in the presence of methanesulfonic acid to give stevensine (Scheme-1.10.7).
Alternatively, triflouroacetic acid persuades N-2 addition to give the N-alkylated 2aminoimidazole.
H 2N
H
N
N
O
Cl
N
O
O
Na2CO3 HCl
HCl, H 2O
H 2N
Scheme-1.10.7 Potier’s Ambi-valent additions of 2-aminoimidazole
Br
HN
HN
N
Br
TFA rt.
Br
N
H
NH
O
H2N H
N
N
Br
Scheme-1.10.8 Horne’s Ambi-valent additions of 2-aminoimidazole.
1.10.3 Formation of C-N bond.
Br
Br
MeO
N
H
Br
NH
O
MsOH
90 o C
H
N
N
HO
NH 2
Cl
Girroline
Br
H 2N
HN
N
NH
N
H O
Stevensine
It is now clear that, condensation reactions are applicable to the preparation of monoand
di-substituted 2-aminoimidazoles. To generate more highly substituted 2-amino
imidazole cores, the direct introduction of N-2 on an appropriately substituted
imidazole is frequently applied. The first method for forming 2-aminoimidazoles, in

this manifold, was reported in 1925 by Burtles and Pyman who showed that azobromoaniline
and dimethylimidazole underwent aromatic substitution to form the
hydrazone (Scheme-1.10.9).The aryl hydrazone was then readily reduced by Zn dust
and aqueous acetic acid or stannous chloride and hydrochloric acid.
N 2
HN
N
Br
NaHCO 3
H2O
HN
N
N N
Scheme-1.10.9 Pyman’s synthesis.
Br
SnCl 2
100 o C
HN
N
NH 2.HCl
Hassner was the first to report the reaction of imidazole lithium with a vinyl azide,
hydrolysis of the intermediate triazine gives the aminoimidazole. 95 Since that report,
Potier has popularized the use of lithiated imidazoles. 96 Potier reported that lithiation
with LDA followed by azide transfer from TsN3 efficiently generated the 2azidoimidazoles
(Scheme-1.10.10). Hydrogenolysis of the azide proceeds smoothly to
give the 2-aminoimidazole, exemplified in his synthesis of keramidine. 97
N
N
Tr
HN
O
H
N
Br
LDA, TsN 3
-70 o C
N 3
N
N
Tr
HN
Scheme-1.10.10 Potier’s method via lithiation.
O
H
N
Br
10 % Pd/C
Lithiated imidazoles can also be trapped by disulfides to give the 2-thioimidazoles.
Oxidation to either the sulfone or sulfoxide creates a leaving group capable of
displacement with azide (Scheme-1.10.11). 98 This strategy has been utilized by
Weinreb in the synthesis of ageladine A. 99-100
COOEt
EtOOC
N
N
Me SO2Me NaN 3, DMF
87 o C, 13 h
H 2
COOEt
EtOOC
N
N
Me N3 Scheme-1.10.11 Anderson’s method of synthesis.
H 2N
N
N
Tr
HN
O
H
N
Br

To avoid lithiation, Ohta has shown that 2-bromoimidazoles can undergo palladium
catalyzed coupling with trimethylsilylazide (Scheme-1.10.12). Reduction again
provides the 2-aminoimidazole. This strategy has been implemented by Ohta’s group
to access several Leucetta alkaloids discussed below. Also, noteworthy, Ohta has
shown that during reduction of the azide it can be directly protected as its
benzylidenimine. 101-102
N
N
Br
TMSN 3
PdCl 2(PPH 3) 2
80 o C N
N
N 3
H2, Pd-C
Scheme-1.10.12 Ohta’s palladium catalyzed synthesis.
1.10.4 Heterocyclic Exchange Reactions
The transformation of 3-amino-1,2,4-oxadiazoles to 2-aminoimidazoles can be carried
out by reaction with fluorinated ß-dicarbonyls to give the ß-hemiaminal (Scheme-
1.10.13). 103 This can undergo subsequent conversion to the 2-amidoimidazole through
a Boulton-Katritzky Rearrangement. This intermediate can then be reduced to give
Intermediate. The benzamide can also be removed via acid catalyzed hydrolysis to
give the trifluoromethyl amino-imidazole. An interesting reaction, however the
synthesis of the intermediate ß-enaminocarbonyl is low yielding and initial results
suggest limited substituent scope, as the initial condensation requires the presence of
the trifluoromethyl ketone.
Ph
O
O
N
NH 2
N
O
CF 3
R
Montmorillonite K-10,
PhMe, 100 o C;
Ph
F3C HN
OH O
N
N
O
R
Ph
O
N
H
Ph
N
F3C HN
OH OH
N
N
O
R
NaBH 4
THF
reflux
Scheme-1.10.13 Boulton-Katritzky rearrangment of aminooxadiazoles.
N
H
CF 3
OH
R
N
N
Ph
NH 2
O
N
H
N
N
H N
2N
H
N
H
CF 3
HCl
EtOH
reflux
CF 3
O
R
O
R

Another route to 4(5)-acyl-2-amino-1H-imidazoles is based on the recyclization of 5acyl-2-amino-1,3-oxazoles
(Scheme-1.10.14). 104 For example, 5-acetyl-2-aminooxazole
gave upon heating in water solution with ammonia or aliphatic amines 2amino-1H-imidazoles
in 32% (R = H) and 43-62% (R = alkyl or cycloalkyl) yields.
Me
O
N
O
NH 2
NH 3 or Amine
H 2O, heating
Me
O
N
N
H
NHR
Scheme-1.10.14 Mularski’s recyclization method.
Methodology to prepare 2-aminoimidzoles has greatly advanced due to the rising
demand in natural product synthesis and medicinal chemistry. However, the
development of methods to succinctly generate a highly functionalized 2aminoimidazole
core from stable precursors is warranted.
1.11 The 2-Aminoimidazole as a Pharmacophore
The 2-aminoimidazole has been utilized as a building block has led to the
development of several medicinally relevant small molecules.
1.11.1 Antibiotics Activity
Researchers at Zeneca delivered a series of broad spectrum antibiotics a-c, inspired by
the well studied cephalosporins. 106-106 They were further able to show that substitution
on N1 of the aminoimidazole led to inactive compounds, again suggesting that this
motif may make an acid hydrogen bond contact (Fig. 1.11.1). Interestingly they were
able to correlate the pKa of the 2-aminoimidazole with activity. Against Gram
positive organisms they found that a slight elevation in the pKa led to a dramatic
decrease in activity. For Gram-negative bacteria, there was little difference,
suggesting pKa may alter the membrane permeability.

N N
N
N
S
S
S
H
N
NH
S
S
S
H
N
NH
S
S
S
H
N
NH
HOOC
N NH
HOOC
N NH
HOOC
N NH
O a O b O
c
pKa = 7.1
pKa = 7.4
pKa = 8.05
S.aureus = 8
S.aureus = 16 S.aureus = 256
E Coli = 0.03
E Coli = 0.015 E Coli = 0.03
Fig-1.11.1 2-aminoimidazole modified cephalosporins.
1.11.2 Sodium Hydrogen Exchanger-1 (NHE-1) Antagonists.
Scientists at Bristol-Meyers Squibb have noted the ability of the 2-aminoimidazole to
function as a bioisostere of acylguanidines. 106 Looking to produce novel inhibitors of
the sodium hydrogen exchanger-1 (NHE-1) they aimed at replacing the acylguanidine
in their lead compounds (Fig. 1.11.2). They surveyed a number of heterocyclic
analogues that would conserve the pKa of the acylguanidine as a cationic species,
necessary for antagonism of the Na+ transporter.
Cl
HN N
NH 2
Cl
HN N
NH 2
Cl
HN N
a b NH
Cl
c 2 Cl
d
0.75 0.039 0.18 0.008
Fig.- 1.11.2 NHE-1 antagonists. (NHE-1 Inhibition IC50 (µm))
1.11.3 Anti HIV Activity
N
N
Cl
HN N
Much effort has been dedicated to the development of HIV protease (HIV PR)
inhibitors for the treatment of AIDS. The protease is responsible for the processing of
nascent polypeptides to mature proteins comprising the viral particle. Without the
formation of the mature particle, viral replication of HIV has been shown to be
inhibited. HIV PR has therefore been an active biochemical target for the
development of small molecule therapeutics.
Wilkerson and co-workers at DuPont-Merck had developed a cyclic urea-based HIV
PR inhibitor scaffold which possessed an acceptable pharmacokinetic profile, but
lacking the potency necessary to advance the candidate. 107 Biochemical evaluation of
NH 2

this series of compounds against the HIV PR dimer revealed that a and b were
extremely potent inhibitors Ki = 0.023 and 0.012 nM respectively. The compounds
were also able to inhibit viral replication in vitro as measured by the ability of the
compounds to inhibit RNA synthesis by 90% (a) IC90 = 13.2 nM; (b) IC90 = 26.2 nM).
Interestingly, QSAR on this series of cyclic ureas suggested the optimum lipophilicity
for protease inhibition (ClogP = 4.4) is different from the inhibition of viral
replication (ClogP = 6.36) as revealed by the reversal of Ki and IC90 selectivities for
(a) and (b). This makes it difficult to optimize both parameters within the same
molecule, but suggests that while (a, b) display the same hydrogen bonding pattern at
the terminal urea, the lipophilicity disparity between the 2-aminoimidazole and the
benzimidazole has a significant effect on their pharmacokinetic profile. With these
results, (a) and (b) were advanced for pharmacokinetic studies in female Beagles. As
seen in the pharmacokinetic profiles (Fig. 1.11.3) the decreased lipohilicity of (b) had
a significant impact on the clearance (CL) and half-life (t1/2) of the compound,
advancing its candidacy based on this improved PK profile.
N
NH
H
N
Ph HO OH Ph
O
N
O
N
NH 2
N
NH
H
N
a b
Fig.- 1.11.3 Unsymmetrical HIV PR inhibitors.
Parameter a b
Ki (nM) 0.023 0.012
IC90 (nM) 13.2 26.2
Dose (mg/kg) 5.0 5.0
CL, L/h/kg 0.8 0.5
Vss (L/Kg) 1.0 4.0
T1/2 (h,iv) 0.9 5.6
Ph HO OH Ph
Table-1.13.1: Pharmacokinetic profiles of HIV PR inhibitors
O
N
O
N
NH 2

1.11.4 α-adrenoreceptor agonists.
Agents that can stimulate α-andrenoceptors modulate a variety of physiological
processes including the reduction of blood pressure, sedation and the inhibition of
intestinal fluid secretion. 108 Scientists at Allergan Pharmaceuticals targeted the α –
andrenoceptor to reduce intraocular pressure(IOP), a common condition in patients
suffering from glaucoma. 109 The challenge in designing such agents stems from the
ability of α –andrenoceptor subtypes to modulate different biological processes, most
concerning are those in the central nervous system (CNS). One approach to
minimizing CNS effect is topical application, minimizing access of the compound to
the CNS. From the known α-andrenoceptor agonist clonidine, 110 modifications to
minimize CNS access generated the lead compounds p-aminoclonidine and AGN-
191103 (21) (Fig. 1.13.4). The The alternative approach is to discover compounds
displaying enough selectivity between the α-andrenoceptor subtypes such that they
exhibit an enhanced therapeutic index. This led to replacing the imidazolidin-imine
with a 2-aminoimidazole. This compound (a) was selected for further evaluation.
Binding assays demonstrated (a) bound to the α2A-receptor with a Ki = 1.7 nM and
was 1200-fold selective for the α2A –receptor over the α1-receptor, 50-fold selective
for the α2A –receptor over the α2B –receptor, and 10-fold selective for the α2A –
receptor over the α2C –receptor. Compound (a) was found to be effective in vivo with
an EC50 = 8.7 nM and importantly remained effective when administered
intravenously, demonstrating its capability of crossing the blood-brain barrier.
H
N N
NH
Cl
Cl
H
N N
NH
Cl
Cl
NH 2
Clonidine p-aminoclonidine AGN-191103
Fig.- 1.11.4 α-adrenoreceptor agonists.
H
N
NH
N
N
N
H
N
N
H
N
O
O
Compound (a)
1.11.5 Anti Cancer Activity
Cancer has been the leading cause of death worldwide. Chemotherapy remains one of
the major treatment options available for cancer, andmost of the currently used
anticancer drugs are administered to patients via a parenteral infusion or bolus
injection. Clinical complications with the parenteral administrations have been

documented. Extra care is needed because of inappropriate patient compliances, and
extra cost associated with hospitalization is necessary. Efforts in searching for orally
active anticancer agents have been extensive, including the anticancer drug category
of tubulin binding agents from which only injectable drugs are available such as
taxanes and vinca alkaloids. Recently Chiung-Tong Chen 111 reported the synthesis
and biological functions of 2-amino-1-arylidenaminoimidazoles as orally active
anticancer agents. Selective compounds had shown potent effects in the interference
on the colchicines binding to tubulins, inhibition of tumor cell proliferation, and
induction of human cancer cell apoptosis.
R 2
H 2N
R 1
N
N
N
R 3
R 4
IC 50 = 0.05- >10 (µM)
1.11.6 BACE-1 Inhibitors
Alzheimer’s disease (AD) is the largest unmet medical need in neurobiology and
accounts for the majority of dementia diagnosed in the elderly. AD is characterized by
a progressively slow decline in cognitive function that leaves the end-stage patient
dependent on custodial care with death occurring on the average of 9 years after
diagnosis. The lack of an effective treatment for AD has stirred an intense search for
novel therapies based on the amyloid hypothesis. This hypothesis states that a gradual
and chronic imbalance between the production and clearance of Aß peptides results in
their accumulation in the brain. These secreted peptides polymerize into neurotoxic
oligomers that disrupt neuronal function and lead to cell death and memory loss that is
phenotypical of AD. ß-secretase (BACE-1) is an as partyl protease representing the
ratelimiting step in the generation of these Aß peptide fragments. Given the central
role of Aß in AD pathology, inhibition of BACE-1 has become an attractive target for
the treatment of Alzheimer’s disease. Vacca 112 and Hills 113 developed a series of
aromatic heterocycles as BACE-1 inhibitors. The potency of the weak initial lead
structure was dramatically enhanced using traditional medicinal chemistry. These
inhibitors were shown to bind in a unique fashion that allowed for potent binding in a
non-traditional fashion.

H 2N
N
N
H
R 2
R 1
N
H2N N
Me
Bace-1 IC 50 = 4-6 (µM) Bace-1 IC 50 = 0.47-2 (µM) Bace-1 IC 50 = 0.47-2 (µM)
Fig. 1.11.5 BACE-1 inhibitors
1.11.7 Anti Biofilm Activity
Bacterial biofilms are defined as a surface attached community of ignalling sms
that are protected by an extracellular matrix of biomolecules. Within a biofilm state,
bacteria are more resistant to antibiotics and are inherently insensitive to antiseptics
and basic host immune responses. The NIH has estimated that 65-80% of all
microbial infections are biofilm-based. Biofilm infections of indwelling medical
devices are also of major concern, as once the device is colonized, infection is
virtually impossible to eradicate. Bacterial biofilms 114-116 underlie the persistent
colonization of hospital facilities, which perpetuates nosocomial infections. Hospitalacquired
infections place a $10 billion burden on the U.S. healthcare system annually.
Given the prominence of biofilms in infectious diseases, there has been an increasing
effort toward the development of small molecules that will modulate bacterial biofilm
development and maintenance. This, coupled with the spread of multi-drug antibiotic
resistance across many of these bacteria, has put a tremendous burden on the scientific
and medical community to alleviate biofilm-related problems. In this review, we will
highlight the development of small molecules that inhibit and/or disperse bacterial
biofilms through non-microbicidal mechanisms. The review will be segmented into
providing a general overview of how bacteria develop into biofilm communities, why
they are important, and the difficulties associated with their control. This will be
followed by a discussion of the numerous approaches that have been applied to the
discovery of lead small molecules that mediate biofilm development. These
approaches are grouped into: 1) discovery/synthesis of molecules based upon
naturally occurring bacterial ignalling molecules, 2) chemical library screening, and
3) discovery/synthesis of natural product and natural product analogues.
R 2
R 1
H 2N
N
N
N
R 1
R 2

Very recently the research group of Melander has been studying widely the ability of
simple analogues of the marine natural products bromoageliferin and oroidin (Fig.
1.11.6) to control biofilm development. Bromoageliferin is a sponge-derived alkaloid
that was reported to inhibit the formation of bacterial biofilms from marine sources,
presumably as a defense mechanism against biofouling. 117 They reasoned that core
structures derived from this complex molecule could be used as structural inspiration
for the development of potent and synthetically accessible anti-biofilm agents. One of
these scaffolds developed was based upon an aryl framework. 118 From a medicinal
chemistry stand point, this scaffold was deemed a promising platform to develop
further functionalized 2-aminoimidazole (2-AI) derivatives as diversity could rapidly
be introduced through manipulation of the benzene ring. They described the synthesis
and anti-biofilm activity of these aryl 2-AI derivatives against three commonlystudied
Gram-negative bacteria.
H 2N
H 2N
N
N
H
N
Bromoageliferin
NH
HN
Br
N
H
O
O
NH
H
N
Br
Br
H 2N
N
N
H
H 2N
Fig. 1.11.6 2-Aminoimidazole-based anti-biofilm molecules.
N
H
O
Oroidin
N
N
H
H
N
Br
R
Aryl 2-AI scaffold
The research group of melander has recently developed several novel libraries of 2-
aminoimidazole small molecules inspired by the marine alkaloids bromoageliferin
and oroidin. These natural products were reviously reported to inhibit biofilm
formation of the marine arotobacterium Rhodospirillum salexigens. 119 TAGE and
CAGE were the first documented 2-aminoimidazoles with anti-biofilm activity against
Pseudomonas aeruginosa biofilms.
Analogues of the structurally simpler alkaloid oroidin were also pursued to develop
novel classes of small molecules with anti-biofilm activity. Recently, an oroidin
Br

inspired library was constructed utilizing click chemistry to generate a diverse library
of 2-aminoimidazole/triazole conjugates (2-AIT).These compounds displayed the
widest spectrum of anti-biofilm activity observed within the 2-aminoimidazole class
(Fig. 1.11.7). 120-121
H 2N
H 2N
N
N
H
N
Bromoageliferin
H 2N
N
N
H
NH
HN
Br
N
H
N
H
O
O
NH
O
Oroidin
H
N
H
N
Br
Br
Br
Br
H 2N
N
N
H
H 2N
HN
N
N
H
O
H
N
H
N O
Br
NH
Br Br
Br
H 2N
H 2N
N
N N
R
2-AIT Library
N
N
H
N
N
H
TAGE
CAGE
Fig. 1.11.7 Representative 2-aminoimidazoles derived from the marine natural
products bromoageliferin and oroidin.
The synthetic approach to this 2-AIT derivatization is outlined in (Scheme 1.11.1). In
their previous synthesis of 2-AIT conjugates, they employed the alkyne-derived 2-AI
as a precursor for the CuI-mediated[3+2] alkyne/azide cycloaddition (click reaction).
Although this reaction worked well, purification of the resulting product was
cumbersome, due to the need for copious amounts of ammonia saturated methanol for
column chromatography. Therefore, they decided to revise the route by employing a
Boc-protected 2-AI alkyne that would allow more traditional means of purification
(i.e. methanol/dichloromethane columns). The Boc-protected scaffold was
synthesized from oct-7-ynoic acid by treatment with oxayl chloride followed by
diazomethane and quenching of the resulting α-diazo ketone with HBr to generate the
intermediate a-bromo ketone. Cyclization with Boc-guanidine then delivered the
target 2-AI alkyne..
NH 2
NH 2
NH 2
NH 2

OH
a,b
O
N
H2N N
Boc
N 3
H
N R
N
N
H2N N N
N
H
a) i : (COCl) 2,CH 2Cl 2, DMF (cat.), ii : CH 2N 2,Et 2O/CH 2Cl 2, iii : HBr (82%) ; b) Boc-guanidine, DMF, RT
(59%) ; c) azide, CuSO 4, Na ascorbate, EtOH, CH 2Cl 2,H 2O; d) TFA, CH 2Cl 2 (58-94 % over two steps)
Scheme-1.11.1 Melander’s 2-AI-T conjugate synthesis.
It was explained by earlier work that once target 2-AI alkyne had been synthesized,
assembled a diverse array of azido amides to employ in the click reaction to create
pilot collection of 2-AIT conjugates. Briefly, 2-bromo-ethylamine was treated with
sodium azide to deliver 2-azido-ethylamine, which following acylation (via the
respective acid chloride) generated the azido amides for elaboration into the 2-AIT
collection. Each azido amide was then subjected to the click reaction with target 2-AI
alkyne. Boc-deprotection (TFA/CH2Cl2) followed by counterion exchange
(trifluoroacetate for chloride) delivered the target 2-AIT compounds for antibiofilm
screening.
1.12 Introduction to Biofilm
Biofilms play a significant role in infection disease and account for up
to 80% of microbial infections in the body.
Bacterial biofilms are defined as a surface-attached community of bacteria
that are surrounded by a protective extracellular matrix.
On a global scale, biofilm related costs incur 6-10 billions of Euros to the
agricultural, engineering, and medical sectors of economy.
Despite the focus of modern microbiology research on pure culture,
planktonic bacteria, it is now recognized that most bacteria found in
natural, clinical, and industrial settings persist in biofilms.
Within a biofilm, bacteria are upward of 1000-times more resistant to
conventional antibiotic treatment
Biofilms grow virtually everywhere, in almost any environment where
there is a combination of moisture, nutrients, and a surface.
c,d
H N
R

1.12.1 Properties of biofilms
A biofilm community can be formed by a single bacterial species, but in nature
biofilms almost always consist of rich mixtures of many species of bacteria, as well as
fungi, algae, yeasts, protozoa, other microorganisms, debris and corrosion products.
Biofilms are held together by sugary molecular strands, collectively termed
"extracellular polymeric substances" or "EPS." The cells produce EPS and are held
together by these strands, allowing them to develop complex, three-dimensional,
resilient, attached communities. Biofilms cost the U.S. literally billions of dollars
every year in energy losses, equipment damage, product contamination and medical
infections. But biofilms also offer huge potential for bioremediating hazardous waste
sites, biofiltering municipal and industrial water and wastewater, and forming
biobarriers to protect soil and groundwater from contamination

1.12.2 Biofilm Growth Cycle
1) Planktonic bacteria reversibly attach to a surface suitable for growth and
Bacteria begin secretion of the extra cellular polymeric substances (EPS) and
attachment becomes irreversible.
2) The maturing biofilm begins to take on a 3-dimensional shape. Biofilm
communities can develop within hours.
3) The biofilm fully matures, and complex architecture is observed. Bacteria
disperse from the biofilm to reinitiate biofilm colonization of a distal surface.
1.12.3 Biofilm Drug Resistance

The figure below shows a model of biofilm resistance to killing based on persister
survival.
Initial treatment with antibiotic kills normal cells (coloured green) in both planktonic
and biofilm populations.
The immune system kills planktonic persisters (coloured green), but the biofilm
persister cells (coloured pink) are protected from the host defences by the exopolymer
matrix.
After the antibiotic concentration is reduced, persisters resuscitate and repopulate the
biofilm and the infection relapses.
Biofilm infections are highly recalcitrant to antibiotic treatment. However, planktonic
cells that are derived from these biofilms are, in most cases, fully susceptible to
antibiotics. Importantly, biofilms do not actually grow in the presence of elevated
concentrations of antibiotics, therefore biofilms do not have increased resistance
compared with planktonic cells. 122 But if biofilms are not resistant to antibiotics, how
do biofilm bacteria avoid being killed by antibiotic treatments? The resistance of
biofilms to drug therapy has been one of the more elusive problems in microbiology,
but the analysis of a simple dose-response experiment provided an unexpected insight
into the puzzle. 122-124
Most of the cells in a biofilm are highly susceptible to bactericidal agents such as
fluoroquinolone antibiotics or metal oxyanions, which can kill both rapidly dividing
and slow- or non-growing cells. 124-126 This is important, as cells in the biofilm are
slow-growing, and many are probably in the stationary phase of growth. The
experiment also revealed a small sub-population of cells that remain alive irrespective
of the concentration of the antibiotic (persisters). The number of surviving persisters
was greater in the non-growing stationary phase. In vitro, a stationary culture seems to
be more tolerant than a biofilm to antibiotics. However, this situation is probably
reversed in vivo. Antibiotic treatment will kill most biofilm and planktonic cells,
leaving persisters alive. At this point, the similarity with an in vitro experiment
probably ends. The immune system can mop up and kill remaining planktonic
persisters, just as it eliminates nongrowing cells of a bacterial population that is
treated with a bacteriostatic antibiotic. However, the biofilm exopolymer matrix
protects against immune cells, 127-129 and persisters that are contained in the biofilm

can survive both the onslaught of antibiotic treatment and the immune system. When
the concentration of antibiotic reduces, persisters can repopulate the biofilm, which
will shed off new planktonic cells, producing the relapsing biofilm infection. The
problem of biofilm resistance 72 to killing by most therapeutics probably defaults to
persisters. Interestingly, yeast biofilms also form tolerant persisters.
1.13 Recent publications on 2-aminoimidazoles.
The core structure 2-aminoimidazole has assumed importance in various synthesis
related to heterocyclic in drug synthesis as appeared in Sci-finder search results on the
basis of number of publications in medicinal and synthetic chemistry journals.
Fig.1.10 Sci-finder search results by heating term 2-aminoimidazole.
1.14 Conclusion
Bacterial biofilms pose a serious threat to the healthcare system of our society as they
are responsible for the morbidity and mortality of a myriad of diseases. The
development of antibiotic resistance among many bacterial strains has put a
tremendous pressure on the medical community to find alternative approaches for the
treatment of biofilm-mediated diseases. In this present work of thesis a microwave
assisted synthesis of small molecules which shows ability to controlling bacterial
antibiofilm has been reported.

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[119] A. Yamada, H. Kitamura, K. Yamaguchi, S. Fukuzawa, C. Kamijima, K.Yazawa,
M.Kuramoto, G.Y.S.Wang, Y.Fujitani, D.B.Uemura, (1997), Chem. Soc. Jpn., 70, 3061.
[120] J. J. Richards, T. E. Ballard, R. W. Huigens and C. Melander (2008), ChemBioChem, 9, 1267
[121] For synthesis and antibiofilm activity of 2-AI and 2-AI-T see a) Ballard, T. E., J. J. Richards,
A. Aquino, C. S. Reed, and C. Melander. (2009), J. Org. Chem. 74:1755–1758. b) Ballard, T.
E., J. J. Richards, A. L. Wolfe, and C. Melander. (2008). Chemistry 14:10745–10761. c) .
Huigens, R. W., L.Ma, C. Gambino, A. Basso, P. D. R.Moeller, J. Cavanagh, D. J. Wozniak,
and C. Melander. (2008), Mol. Biosyst. 4:614–621. d) Huigens, R. W., III, J. J. Richards, G.
Parise, T. E. Ballard, W. Zeng, R.Deora, and C. Melander. (2007), J. Am. Chem. Soc.
129:6966–6967. e) Huigens, R. W., III, S. A. Rogers, A. T. Steinhauer, and C. Melander.
(2009), Org. Biomol. Chem. 7:794–802. f) Richards, J. J., T. E. Ballard, R. W. Huigens, and
C. Melander. (2008), Chembiochem 9:1267–1279. g) Richards, J. J., T. E. Ballard, and C.
Melander. (2008), Org. Biomol. Chem. 6:1356–1363. h) Richards, J. J., R. W. Huigens, T. E.
Ballard, A. Basso, J. Cavanagh, and C.Melander. (2008), Chem.Commun. (Camb.)
2008:1698–1700. i) Richards, J. J., and C. Melander. (2008), J. Org.Chem. 73:5191–5193. j)
Richards, J. J., C. S. Reed, and C. Melander. (2008), Bioorg. Med. Chem. Lett. 18:4325–
4327. k) Rogers, S. A., R. W. Huigens, and C. Melander. (2009), J. Am. Chem. Soc.
131:9868–9869. l ) Rogers, S. A., M. Krayer, J. S. Lindsey, and C. Melander. (2009), Org.
Biomol. Chem. 7:603–606. m) Rogers, S. A., and C. Melander. (2008), Angew.Chem. Int. Ed.
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[130] For biofilm resistance mechanism see, http://www.ncbi.nlm.nih.gov/entrez/query.fcg

Microwave Assisted Synthesis & Structure
Activity Relationship of 2-Hydroxy-2-phenyl-
2,3-dihydro-imidazo[1,2-a]pyrimidinium Salts
and 2N-Substituted 4(5)-Phenyl-2-Amino-1H-
imidazoles as Inhibitors of the Biofilm
Formation by Salmonella Typhimurium and
Pseudomonas aeruginosa

Chapter-2
Microwave Assisted Synthesis & Structure Activity Relationship of 2-
Hydroxy-2-phenyl-2,3-dihydro-imidazo[1,2-a]pyrimidinium Salts
and 2N-Substituted 4(5)-Phenyl-2-Amino-1H-imidazoles as Inhibitors
of the Biofilm Formation by Salmonella Typhimurium and
Pseudomonas aeruginosa
Br
N
N
N R 1
OH
R 2
In the current chapter a library of 1-substituted 2-hydroxy-2-phenyl-2,3-dihydro-
imidazo[1,2-a]pyrimidinium salts and 2N-substituted 4(5)-phenyl-2-amino-1H-
imidazoles was synthesized via microwave assisted protocol and tested for the
antagonistic effect against biofilm formation by Salmonella Typhimurium and
Pseudomonas aeruginosa.
Publications:
[1] One-pot microwave-assisted protocol for the synthesis of substituted 2-amino-
R1 HN
1H-imidazoles. Mol Divers. (2010) DOI 10.1007/s11030-010-9270-5
[2] Structure Activity Relationship of 2-Hydroxy-2-phenyl-2,3-dihydro-
imidazo[1,2-a]pyrimidinium Salts and 2N-Substituted 4(5)-Phenyl-2-Amino-
1H-imidazoles as Inhibitors of the Biofilm Formation by Salmonella
Typhimurium and Pseudomonas aeruginosa Bioorganic & Medicinal
Chemistry. Submited (2010)
N
N
H
R 2

2.1 Introduction
As described in chapter-1 the class of 2-aminoimidazoles has recently been given
particular interest due to various biological properties of these compounds. 2-
Aminoimidazole alkaloids and their metabolites, isolated from the marine sponges
Hymeniacidon sp., have been described as potent antagonists of serotonergic 1 and
histaminergic 2 receptors. Naamine and isonaamine alkaloids from the marine sponges
Leucetta sp. exhibit antiviral and anticancer activity. 3,4 Because of these interesting
biological activities, numerous synthetic routes to 1-substituted and 1-unsubstituted 2aminoimidazoles
have been reported. Modern synthetic methods for accessing 1unsubstituted
2-amino-1H-imidazoles can be roughly classified as heterocyclization
of substituted or protected guanidines with 1,2-dielectrophiles, 5a-c heteroaromatic
nucleophilic substitution 5c,6 and recyclization of 2-aminooxazoles. 7 Although different
substituted guanidines are readily available and can be prepared in situ (e.g. from
cyanamines 8 ), the high basicity of guanidines together with non-regioselectivity often
leads to multiple products. 9 Protection by acetyl 5a and Boc-groups 5c requires, in turn,
acidic deprotection conditions. Another procedure is the cyclocondensation of
aldehydes and guanidine nitrate using sodium cyanide and supported aluminum oxide,
which provides symmetric 2-aminoimidazoles. 10
Recently, we described two new approaches to the synthesis of substituted 2-amino-
1H-imidazoles. The first approach is based on the cleavage of imidazo[1,2a]pyrimidines
11 with hydrazine 12 In the second approach we reported microwave
assisted one pot synthesis.(scheme-3) 13

2.2 Reaction scheme:
2.2.1 2-amino pyramidine: (Scheme-1)
N
TEA, EtOH N
R NH2 R
N Cl MW N N
120 H
o +
C, 25 min
2.2.2 Synthesis of substituted 2-amino 1 H-imidazole. (Scheme-2)
N
N N
64% N2H4 100 °C, 10 min
R N
N
+
Br
H
R1 N
MeCN
H MW
O 80 °C, 30 min Br
1
OH
R2 MeCN
MW
R 2
2.2.3 One-Pot approach: (Scheme-3)
N
R1 N N
H
+
Br O
H
R 2
1.MW, 80 °C
MeCN, 30 min
2. N2H4, MW 90 °C
MeCN, 10 min
R 1
HN
N
N
H
R 2
R 1
HN
N
N
H
R 2

2.3 Proposed Mechanism:
Regarding the mechanism of the transformation of 2-hydroxy-2,3-dihydro-1Himidazo[1,2-a]pyrimidinium
salts into 2-amino-1H-imidazoles, we presume that the
reaction proceeds via an unusual Dimroth-type rearrangement 14-16 (Scheme-4).
Scheme-4: Proposed Mechanism for the Dimroth-type Rearrangement of 2-
Hydroxy-2,3-dihydro-1H-imidazo[1,2-a]pyrimidinium Salts III-12
N
N N R1 Br OH
R 2 R3
N N
R 2
NH 2
R1 OH
R 3
N2H4 fast
HN NH R 1
HN
R 2
H 2NHN
O
R 3
N
N
N R1 OH
R 2 R3
R 1HN
N
N
H
H 2NHN
R 2
OH
R 3
N
N
N R1 OH
R 2 R3
1 A B
- H 2O
slow
R 1HN
C D E 2
In the first step, the 2-hydroxy-2,3-dihydroimidazo[1,2-a]pyrimidinium salt (1)
undergoes cleavage of the pyrimidine ring, resulting in the generation of pyrazole and
2-amino-5-hydroxyimidazolidine (C), which is in equilibrium with the open form (D).
This can cyclize again leading to the isomeric 2-amino-5(4)-hydroxyimidazolidines
(E). Both isomers (C) and (E) were detected by mass-spectrometry. Final
dehydratation upon microwave irradiation, results in the rearranged 2-amino-1Himidazoles
2. This dehydratation step, as judged by mass-spectrometry, was found to
be the slowest step of the transformation. While some 2-amino-5(4)hydroxyimidazolidines
(E) lost water spontaneously at room temperature, other
required higher temperature upon microwave irradiation. Therefore all reactions were
run at 100 °C, preventing the sequence from stopping after the first step.
-
N
H
N
N
H
N
R 2
R 3

2.4 Results and discussion:
Initially careful investigation of the formation and dehydratation of salt (3) resulting
in the formation of salt (4) under conventional heating conditions as well as upon
microwave irradiation has been studied. As a proof of concept, the condensation of 2methylaminopyrimidine
(1, R1 = Me) and α-phenacylbromide (2, R2 = Ph) was
studied (Table 1). A sealed vial containing a solution of the starting compounds in
acetonitrile was conventionally heated with an oil bath (Table 1, No-1-6) or irradiated
with microwaves (Table 1, No-7-12) at different temperatures for 30−60 min. The
formation of the 2-hydroxy salt (3) was faster under microwave irradiation and this
compound was obtained in 88% yield within 30 min. Further increase of the
temperature up to 120 °C using conventional heating or microwave irradiation led to a
mixture of salts (3) and (4) (Table 1). Interestingly, using microwave irradiation at
120 °C for 60 min, we were able to drive the reaction completely to the formation of
the imidazo[1,2-a]pyrimidinium salt (4) (Table 1, No-12).
N
N N R N
N
Br O
R1 N N +
1 + N
H H R Br
N
2
OH
1 2 3 R2 R Conditions
Br
1
(R1 = Me, R2 = Ph)
4 R2 No. Conditions Time (min) T (°C) 3 (yield %) b 4 (yield %) b
1
30 80 64 0
2 60 80 77 0
3 30 100 81 Traces
Conventional
4 60 100 85 Traces
5 30 120 68 17
6 60 120 53 28
7
30 80 88 0
8 60 80 85 0
9 Microwave 30 100 48 33
10 60 100 45 35
11 30 120 12 79

No.
12 60 120 traces 84
a
All reactions were carried out on a 1 mmol scale of 2-methylaminopyrimidine (1, R1 = Me) with
1.35 equiv of α-phenacylbromide (2, R2 = Ph) in MeCN (5 Ml); b isolated yield after recrystallization
from MeCN.
Table-1: Investigation of the condensation under conventional heating and
microwave irradiation a
As the transformation of salts (3) into salts (4) is relatively rapid at the temperatures
above 100 °C, the synthesis of salts 3 was conducted at 80 °C. Treatment of
substituted 2-aminopyrimidines (1) with 15 mol % excess of α-bromoketones (2) in
MeCN under microwave irradiation for 30 min generated the intermediate salts (3)
which, in most cases, precipitated from the reaction mixture upon cooling (Table-2).
Reaction progress was monitored by mass-spectrometry. In all cases examined, the
reaction appeared to be complete after 30 min. The cleavage step was performed
under microwave irradiation at 90 °C, using 7 equivalents of hydrazine hydrate. Based
on the data given in (Table-2), the reaction appears to be compatible with both aryl
and alkyl substitutions. All the reactions were clean, smooth, and provided the
products in good and high yields. The compounds were purified by column
chromatography using 5−10% MeOH in CH2Cl2 as the eluent. All the final 2-amino-
1H-imidazoles were characterized by 1 H and 13 C NMR spectroscopy. Their
composition was also confirmed by HRMS.
R1 HN
N
N
H
R 2
Compound
Code
R1 R2 Yield
1 BS-136* CH3 2,4-(di-OCH3) 48
2 BS-137* (benzo[d][1,3]dioxol-6- naphthalen-1-yl 72

yl)methyl
3 BS-140* C3H7 3,4-(di-Cl) 70
4 BS-141* cyclohexane 4-SO2Me 43
5 BS-143* C8H17 4-Cl 43
6 BS-146* C5H11 4-Cl 57
7 BS-147* C6H13 4-F 61
8 BS-148* 4-methoxyphenethyl 3-Br 44
9 BS-154* cyclooctane 4-SO2Me 53
10 BS-139* 2-methoxyethyl 4-CN 55
11 BS-258 C8H17 4-OCH3 78
12 BS-259 C8H17 4-F 69
13 BS-260 C8H17 3,4-(di-Cl) 72
14 BS-261 C8H17 3-Br 79
15 BS-262 C8H17 naphthalen-1-yl 68
16 BS-263 C8H17 4-NO2 66
17 BS-264 C8H17 4-(4-NO2Ph) 75
18 BS-265 C8H17 SO2Me 54
19 BS-292 i-Bu 4-NO2 70
20 BS-293 i-Bu H 71
21 BS-294 i-Bu 4-Br 69
22 BS-295 i-Bu 4-Cl 73
*Compounds have been synthesized via One-pot protocol (Scheme-3).
All compounds are either oily or amorphous solid.
Table-2: Microwave assisted synthesis of substituted 2-amino-1H-imidazoles.
2.5 Biofilm activity:
Bacteria are able to switch between a planktonic life style and a biofilm mode of
growth, in which they live as structured communities of bacterial cells enclosed in a
self-produced polymeric matrix and adherent to an inert or living surface. 17 As
bacteria in biofilms are more resistant to challenges from predators, antibiotics,
disinfectants and host immune systems, 18-21 serious problems and high costs have
been associated with biofilms, both in medicine and industrial settings. According to
the National Institutes of Health, more than 80% of microbial infections are related to
biofilms. 22 Especially the use of indwelling medical devices comprises a high risk for

the development of biofilm related infections. 19 This high prevalence of biofilm
related infections is particularly problematic given the fact that bacteria in biofilms
can be up to 1000-fold more resistant to antibiotics. 23 In industry, biofilms have been
implicated e.g. in the contamination of installations in food industry, mild steel
corrosion, decreased passage through pipelines by colonization of the interior of the
pipes, and enhanced resistance of vessels by initiation of “biofouling” on the vessel
hulls. The yearly economic loss caused by ‘biofouling’ in the marine industry is
estimated at $ 6.5 billion. 24
One way to deal with this problem is the development of small molecules that are able
to prevent or destroy biofilm formation 25 . Only a few molecular scaffolds have been
identified to date, among which the best-studied examples are (1) the halogenated
furanones, which were originally isolated from the seaweed Delisea pulchra, 26-27 (2)
analogues of the homoserine lactone signalling molecules 28 and (3) analogues of the
sponge-derived marine natural alkaloids oroidin and bromoageliferin. 29-36 A
particularly valuable approach is the development of small molecules that specifically
target the biofilm formation in a non-toxic manner, as it is expected that resistance
against these compounds will emerge much slower than against classical
microbiocidal compounds. As a consequence, non-toxic biofilm inhibitors have the
potential to be used in a preventive treatment of a wide diversity of industrial and
medical surfaces. Furthermore, the potential to co-dose biofilm inhibitors and
classical antibiotics for the treatment of biofilm infections is also an attractive
option. 27
Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa are two well
studied organisms in terms of biofilm formation. Salmonella enterica is worldwide
one of the most important causes of foodborne infections. Salmonella is able to form
biofilms on a variety of both biotic surfaces (such as gallstones, 37 plant surfaces, 38-39
and epithelial cell layers 40 ) and abiotic surfaces (such as concrete, plastics, glass,
polystyrene, … ) 41-42 . These biofilms are an important survival strategy in all stages
of infection, from transmission to chronic infection. Severe non-typhoid Salmonella
infections are commonly treated with fluoroquinolones and third-generation
cephalosporins. Unfortunately, there are alarming reports concerning the development
of resistance against these antibiotics 43 , underlining the urgent need of alternative
anti-Salmonella strategies. Given the importance of biofilms in the spread of
Salmonella, the development of Salmonella biofilm inhibitors seems a promising

approach. P. aeruginosa is an opportunistic pathogen implicated in a myriad of
infections. Patients with compromised host defenses, such as burn patients, HIV
patients and cystic fibrosis patients (80% colonization rate of P. aeruginosa 44 ) are
particularly susceptible to P. aeruginosa infections. 45 P. aeruginosa biofilms have
been related to recurrent ear infections, chronical bacterial prostatitis and lung
infections in CF patients, the latter being extremely harmful as P. aeruginosa
colonization and chronic lung infection is the major causative agent of morbidity and
mortality in CF patients. 46 Moreover, P. aeruginosa can colonize as biofilms a
variety of medical devices such as intravascular catheters and urinary catheters.
Obviously there is an urgent need of agents that can prevent or eradicate P.
aeruginosa biofilms on infected tissues and on medical devices.
2.5.1 2N-substituted 2-aminopyrimidines
Some members of the 2-aminopyrimidine class of compounds have previously been
shown to possess antibacterial and antifungal activity. 47-48 These molecules are the
precursors of the N1-substituted diazo[1,2-a]pyrimidinium salts in our synthesis
pathway (scheme-2). The availability of a broad array of 2-aminopyrimidines,
substituted with n-alkyl, cyclo-alkyl and aromatic groups at the N2-position prompted
us to investigate the potential of this class of compounds as biofilm inhibitors. The
influence of compounds on the biofilm formation of S. Typhimurium was tested at
25°C. Remarkably, none of the compounds does have an effect on the biofilm
formation at 400 µM, which was the highest concentration tested.
2.5.2 2-hydroxy-2,3-dihydro-imidazopyrimidinium salts
A broad array of 1-substituted 2-hydroxy-2-phenyl-2,3-dihydro-imidazopyrimidinium
salts were synthesized via previously established chemistry from our laboratory and
their ability to prevent the biofilm formation of S. Typhimurium and P. aeruginosa
was tested. These molecules differ in the substitution pattern of the 2-phenyl ring and
in the nature of the substituent at the 1-position i.e. n-alkyl, iso-alkyl, cyclo-alkyl.
2.5.2.1 n-Alkyl or iso-alkyl substituents at 1-position

In first instance, a series of 2-hydroxy-2-phenyl-2,3-dihydro-imidazopyrimidinium
salts with a broad variety of n-alkyl or iso-alkyl substituents at the 1-position, with
lengths ranging from 1 carbon atom to 14 carbon atoms was synthesized. The 2phenyl
group of these salts is either unsubstituted, para-substituted with a chlorine
atom, a nitro group, a fluorine atom, a bromine atom or a methoxy group, or 3,4disubstituted
with chlorine atoms. Each compound was assayed for the ability to
inhibit S. Typhimurium ATCC14028 biofilm formation at 25 °C. As depicted in
figure 1A, a clear correlation was found between the length of the alkyl substituent
and the biofilm inhibitory activity. In general the activity of the molecules with a
short alkyl chain was found to be very low (IC50 > 400 µM). Within a series of
molecules with the same substitution of the 2-phenyl ring, in general a gradual
increase in biofilm inhibitory activity was observed by raising the length of the alkyl
chain from 1 to 8 carbon atoms. The compounds with an octyl substituent show a
maximal activity with IC50 values in the range of 6-11 µM. By further raising the
alkyl chain length from 8 to 14 carbon atoms, a gradual decrease in biofilm inhibitory
activity was observed. For the molecules with a heptyl, octyl, nonyl and decyl side
chain (which are the most active molecules), the nature of the substituent of the 2phenyl
group does not have a substantial effect on the biofilm inhibitory activity.
Next the influence of a subset of the 2-hydroxy-2-phenyl-2,3-dihydroimidazopyrimidinium
salts for their ability to prevent the biofilm formation of P.
aeruginosa was studied. As represented in table-4 and figure-1B, a similar structure
activity relationship was found as in the case of Salmonella biofilm inhibition.
Compounds with short alkyl substituents (C1-6) in general only have a slight effect on
the biofilm formation (IC50’s >80 µM), while compounds with medium length side
chains (C7-C10) have IC50 values between 20-40 µM and compounds with long side
chains (C11-C14) have IC50 values higher than 800 µM. However, it should be
mentioned that some of the compounds with long side chain do reduce the biofilm
formation to a certain extent, but their dose response curves reach a steady state level
of 25 to 45 % biofilm inhibition starting from concentrations between 25 and 50 µM.

Br
N
N
N R 1
OH
R 2
No. Code R2 R1
S. Typhimurium
IC50
P. aeruginosa
IC50
1 BS-289 H i-Bu 131.2 289.4
2 BS-083 H n-Pen 278.2 565.4
3 BS-058 H n-Hex 102.0 405.8
4 BS-049 H n-Hep 23.4 25.5
5 BS-052 H n-Oct 9.8 14.4
6 BS-061 H n-Non 8.3 26.8
7 BS-055 H n-Dec 15.0 29.9
8 BS-064 H n-Und 24.6 >800
9 BS-067 H n-Dod 27.5 >800
10 BS-070 H n-Trd 81.6 >800
11 BS-073 H n-Tet 179.6 >800
12 BS-291 4-Cl i-Bu 31.4 83.4
13 BS-099 4-Cl n-Pen 32.6 163.9
14 BS-092 4-Cl n-Hex 13.7 79.8
15 BS-089 4-Cl n-Hep 6.7 36.9
16 BS-090 4-Cl n-Oct 7.0 15.7
17 BS-093 4-Cl n-Non 18.3 20.2
18 BS-091 4-Cl n-Dec 51.3 83.3
19 BS-094 4-Cl n-Und 61.9 >800
20 BS-095 4-Cl n-Dod 122.1 >800
21 BS-096 4-Cl n-Trd 316.1 >800
22 BS-097 4-Cl n-Tet >800 >800
23 BS-288 4-NO2 i-Bu 322.5 191.7
24 BS-290 4-Br i-Bu 5.2 6.3
IC50: Concentration of inhibitor needed to inhibit biofilm formation by 50%.
Table-4: Influence of 1-alkylated 2-hydroxy-2,3-dihydro-imidazo[1,2a]pyrimidinium
salts on the biofilm formation of S. Typhimurium ATCC14028 and P.
aeruginosa PA14 at 25°C.

Br
N
N
N R 1
OH
Br
N
N
N R 1
OH
Figure-1A: Effect of the length of the n-alkyl chain at the 1-position of 2-hydroxy-2-
phenyl-2,3-dihydro-imidazo[1,2-a]pyrimidinium salts, substituted with Cl and H at
the para-position of the 2-phenyl ring, on the IC50 (µM) for inhibition of biofilm
formation of S. Typhimurium ATCC14028.
2.5.2.2 Further Modification in the most active core structure
Since the compounds with a n-octyl chain substituted at the 1-position have the
highest activity against Salmonella biofilms and also have a high activity against
Pseudomonas biofilms, we decided to synthesize the additional 1-octyl-2-hydroxy-2phenyl-2,3-dihydro-imidazopyrimidinium
salts with more variation in the substitution
pattern of the 2-phenyl ring. As depicted in Table 5 these compounds generally inhibit
biofilm formation of S. Typhimurium at low concentrations. However, no improved
activity was observed in comparison with the previously described compounds (Table
2). The effect of the n-octyl substituted compounds on the biofilm formation of P.
aeruginosa strongly depends on the substitution pattern of the 2-phenyl ring, as some
Cl

of the compounds have low IC50 values (10-40 µM), while the other compounds only
have a moderate activity (IC50 = 100-400 µM).
Br
N
N
N C 8H 17
OH
R
SR CODE R
S. Typhimurium
IC50
P. aeruginosa
IC50
1 BS-180 4-NO2 6.6 12.1
2 BS-176 4-F 7.6 nd
3 BS-175 4-OMe 10.5 nd
4 BS-177 3,4-diCl 7.1 nd
5 BS-187 4-SMe 13.2 36.5
6 BS-179 Naphtyl 14.7 15.1
7 BS-185 4-(4-NO2Ph) 31 215.2
8 BS-186 4-SO2Me 60.3 99.9
9 BS-188 4-([1,1’-biphenylyl]-4-yl) 52.8 336.1
10 BS-178 3-Br 7.1 29
Table-5: Influence of N1-octyl 2-hydroxy-2, 3-dihydro-imidazo[1,2-a]pyrimidinium
salts on the biofilm formation of S. Typhimurium ATCC14028 and P. aeruginosa
PA14 at 25°C.
2.5.2.3 Cyclo-alkyl substituents at 1-position
A series of 2-hydroxy-2-phenyl-2,3-dihydro-imidazopyrimidinium salts with a broad
variety of cyclo-alkyl substituents at the 1-position was synthesized with lengths
ranging from 3 to 12 carbon atoms (Table 6). The 2-phenyl group of these salts was
either unsubstantiated or para-substituted with a chlorine atom. Similarly to the
structure-activity relationship delineated for the n-alkyl substituted salts, a gradual
increase in the inhibitory activity against Salmonella biofilms was observed by rising
the length of the cyclo-alkyl chain from 3 to 8 carbon atoms. However, in contrast to
the salts with n-dodecyl chain at the 1-position, the salts with a cyclo-dodecyl chain

do have a very strong effect against Salmonella biofilms (IC50 values < 6.25 µM). By
analogy with (1) the effect on Salmonella biofilms and (2) the activity of the n-alkyl
substituted salts, we found that all the cyclo-alkyl substituted salts with a short side
chain do only have a slight effect on the biofilm formation of P. aeruginosa (IC50’s
>150 µM), while the compounds with a medium length side chain have a stronger
biofilm inhibitory activity. The salts with a cyclo-dodecyl chain do drastically reduce
the Pseudomonas biofilm formation (IC50’s ~7 µM), in sharp contrast to the
compounds with n-dodecyl side chain.
Br
N
N
N R 1
OH
R 2
SR CODE R2 R1
S. Typhimurium
IC50
P. aeruginosa
IC50
1 BS-079 H c-Bu 493.0 >400
2 BS-076 H c-Hex 139.0 22.4
3 BS-046 H c-Hep 84.2 191.3
4 BS-043 H c-Oct 58.4 48.6
5 BS-100 4-Cl c-Bu 120.8 371.5
6 BS- 4-Cl c-Pen 41.8 41.9
7 BS-098 4-Cl c- Hex 33.0 16.4
8 BS-088 4-Cl c- Hep 27.9 76.2
9 BS-087 4-Cl c-Oct 12.6 22.7
10 BS-086 4-Cl c-Doc 5.6 6.8
Table-6: Influence of 1-cyclo-alkyl-2-hydroxy-2,3-dihydro-imidazo[1,2-a]
pyrimidinium salts on the biofilm formation of S. Typhimurium ATCC14028 and P.
aeruginosa PA14 at 25°C.
2.5.3 2N-substituted 2-aminoimidazoles
In the present it was interesting to investigate whether introduction of n-alkyl, isoalkyl,
cyclo-alkyl or aromatic group at the 2N-position of the 4(5)-phenyl-2-amino-

1H-imidazoles could also enhance their biofilm inhibitory activity. Therefore a broad
range of 2N-substituted 4(5)-phenyl-2-amino-1H-imidazoles were synthesized.
An array of 4(5)-phenyl-2-aminoimidazoles 2N-substituted with either a short n- or
iso-alkyl chain (C1-C5) or n-octyl chain was synthesized. As depicted in table7, a
broad diversity of (substituted) 4(5)-phenyl groups were included. The compounds
with a iso-butyl substitution at the 2N-position were found to be in general more
active than their 2N-unsubstituted counterparts, with respect to both the Salmonella
and Pseudomonas biofilm formation.
SR R1
R1 HN
R2
N
N
H
R 2
S. Typhimurium
IC50
P. aeruginosa
IC50
1 CH3 2,4-(di-OCH3) Nd Nd
2
(benzo[d][1,3]dioxol-
6-yl)methyl
naphthalen-1-yl 261.0 10.5
3 C3H7 3,4-(di-Cl) 10.9 27.7
4 Cyclohexane 4-SO2Me Nd Nd
5 C8H17 4-Cl >400 Nd
6 C5H11 4-Cl >400 Nd
7 C6H13 4-F >400 12.5
8 C8H17 4-OCH3 >400 >800
9 C8H17 4-F >400 Nd
10 C8H17 3,4-(di-Cl) 118.3 >800
11 C8H17 3-Br 44.6 >800
12 C8H17 naphthalen-1-yl 238.4 >800
13 C8H17 4-NO2 10.9 25.0
14 C8H17 4-(4-NO2Ph) Nd Nd
15 C8H17 SO2Me 41.8 Nd
16 i-Bu 4-NO2 3.8 22.9
17 i-Bu H 4.9 1.2
18 i-Bu 4-Br 2.9 1.2
19 i-Bu 4-Cl 2.0 0.9
Table-7: Influence of 2N-alkylated 2-aminoimidazoles on the biofilm formation and
the planktonic growth of S. Typhimurium ATCC14028 and P. aeruginosa PA14 at
25°C.

2.6 Conclusion
In the present study, the potential of these 1-substituted 2-hydroxy-2,3-dihydroimidazopyrimidinium
salts and 2N-subsituted 2-amino-1H-imidazoles as inhibitors of
the biofilm formation by S. Typhimurium and P. aeruginosa was thoroughly
investigated. We found that 2-hydroxy-2,3-dihydro-imidazopyrimidinium salts with
intermediate length n-alkyl chains (C7-C10) substituted at the 1-position in general
prevent the biofilm formation of both species at low micromolar concentrations (IC50
= 5-50 µM). For these molecules, the nature of the substituent of the 2-phenyl group
does not have a substantial effect on the biofilm inhibitory activity. Salts with a
shorter (C1-C5) or longer (C11-C14) n-alkyl chain at the 1-position were found to be
much less potent. Consistent with this, we observed that salts with an intermediate
length cyclo-alkyl chain are much more active against biofilm formation of both
species as compared to the salts with a short cyclo-alkyl chain. However, remarkably
salts with a long cyclo-dodecyl side chain were found to have even better activities
than salts with an intermediate length cyclo-alkyl side chain.
In the framework of the 2-aminoimidazoles, be the introduction of a butyl, pentyl or
hexyl side chain at the 2N-position of the 2-aminoimdazoles results in an enhanced
biofilm inhibitory activity against both species, while introduction of a shorter n-alkyl
chain reduces the biofilm inhibitory activity. The effect of introduction of longer nalkyl
chains however seems to be strongly dependent on the substitution pattern of the
5-phenyl ring and the bacterial species studied.
In conclusion, the 2N-substituted 2-aminoimidazoles and 2-hydroxy-2-phenyl-2,3dihydro-imidazopyrimidinium
salts of the present study are valuable candidates in the
development of therapeutics and sanitizers for the combat of biofilm formation by S.
Typhimurium, P. aeruginosa and possibly other pathogenic bacteria.

2.7 Experimental
2.7.1 General Methods
All chemical reagents were used without further purification. Solvents for column
chromatography and TLC were laboratory grade and distilled before use. For thinlayer
chromatography (TLC), analytical TLC plates (Alugram SIL G/UV254 (E. M.
Merk) were used. Column chromatography was performed with flash silica gel (100-
200 mesh) or neutral alumina oxide (50-200 micron). 1 H and 13 C NMR spectra were
recorded on a Bruker Avance 300 (300 MHz) or a Bruker AMX-400 (400 MHz)
spectrometers. NMR samples were run in the indicated solvents and were referenced
internally. Chemical shift values were quoted in ppm and coupling constants were
quoted in Hz. Chemical shift multiplicities were reported as s = singlet, d = doublet, t
= triplet, q = quartet, m = multiplet and br = broad. Low-resolution mass spectra were
recorded on a HEWLETT-PACKARD instrument (CI or EI) and LCQ Advantage
instrument (ESI). High-resolution mass spectra (EI) were recorded on a KRATOS
MS50TC instrument. Melting points were determined using Reichert-Jung Thermovar
apparatus and were uncorrected.
2.7.2 Microwave Irradiation Experiments
Microwave irradiation experiments were carried out in a dedicated CEM-Discover
mono-mode microwave apparatus or Milestone MicroSYNTH multi-mode microwave
reactor (Laboratory Microwave Systems). Microwave apparatuses were used in the
standard configuration as delivered, operating at a frequency 2.45 GHz with
continuous irradiation power from 0 to 400 W. The reactions were carried out in 10,
20, 30 and 50 mL glass tubes. The temperature was measured with an IR sensor on
the outer surface of the process vial or fibre optic sensor inside the process vial. After
the irradiation period, the reaction vessel was cooled rapidly (2-5 min) to ambient
temperature by air jet cooling.

2.8 Biological assays
2.8.1 Static peg assay for prevention of Salmonella Typhimurium and
Pseudomonas aeruginosa biofilm formation
The device used for biofilm formation is a platform carrying 96 polystyrene pegs
(Nunc no. 445497) that fits as a microtiter plate lid with a peg hanging into each
microtiter plate well (Nunc no. 269789). Two-fold serial dilutions of the compounds
in 100 µl liquid broth (Tryptic Soy Broth diluted 1/20 (TSB 1/20)) per well were
prepared in the microtiter plate (2 or 3 repeats per compound). Subsequently, an
overnight culture of S. Typhimurium ATCC14028 (grown in Luria-Bertani medium)
or P. aeruginosa (grown in TSB) was diluted 1:100 into the respective liquid broth
and 100 µl (~10 6 cells) was added to each well of the microtiter plate, resulting in a
total amount of 200 µl medium per well. The pegged lid was placed on the microtiter
plate and the plate was incubated for 24 h at 25°C without shaking. During this
incubation period biofilms were formed on the surface of the pegs. After 24 h, the
optical density at 600 nm (OD600) was measured for the planktonic cells in the
microtiter plate using a VERSAmax microtiter plate reader (Molecular Devices). This
gives a first indication of the effect of the compounds on the planktonic growth. For
quantification of biofilm formation, the pegs were washed once in 200 µl phosphate
buffered saline (PBS). The remaining attached bacteria were stained for 30 min with
200 μl 0.1% (w/v) crystal violet in an isopropanol/methanol/PBS solution (v/v
1:1:18). Excess stain was rinsed off by placing the pegs in a 96-well plate filled with
200 μl distilled water per well. After the pegs were air dried (30 min), the dye bound
to the adherent cells was extracted with 30% glacial acetic acid (200 µl). The OD570 of
each well was measured using a VERSAmax microtiter plate reader (Molecular
Devices). The IC50 value for each compound was determined from the concentration
gradient by using the GraphPad software of Prism.

2.8.2 Bioscreen assay for measuring Salmonella Typhimurium and P.
aeruginosa growth inhibition
The Bioscreen device (Oy Growth Curves Ab Ltd) was used for measuring the
influence of the chemical compounds on the planktonic growth of Salmonella
Typhimurium and P. aeruginosa. The Bioscreen is a computer controlled
incubator/reader/shaker that uses 10x10 well microtiter plates and measures light
absorbance of each well at a specified wave length in function of time. An overnight
culture of S. Typhimurium ATCC14028 (grown up in LB medium) or P. aeruginosa
(grown up in TSB) was diluted 1:200 in liquid broth (TSB 1/20). 300 µl of the diluted
overnight culture was added to each well of the 10x10 well microtiter plate.
Subsequently, serial dilutions of the chemical compounds were prepared in DMSO or
EtOH. 3 µl of each diluted stock solution was added to the wells (containing the 300
µl bacterial culture) in 3-fold. As a control 3 µl of the appropriate solvent was also
added to the plate in 3- or 4-fold. The microtiter plate was incubated in the Bioscreen
device at 25°C for at least 24 h, with continuous medium shaking. The absorbance of
each well was measured at 600 nm each 15 min. Excel was used to generate the
growth curves for the treated wells and the untreated control wells.
The effect of each compound concentration on the planktonic growth was classified
into one of the following categories:
1) The planktonic growth is not or only slightly affected, indicated by the symbol
‘-‘.
2) The planktonic growth is retarded, indicated by the symbol ‘+’.
3) The planktonic growth is completely or almost completely inhibited, indicated
by the symbol ‘o’.
The following criterium was used to decide between the first and the second category:
If the absorbance (measured at 600 nm) of the bacterial culture treated with the
compound is at least 0.5 (for Salmonella) or 0.8 (for Pseudomonas) units lower
than the absorbance of the untreated culture during 4 consecutive hours, then the
effect on the planktonic growth is classified in category 2.

2.9 Experimental protocol:
2.9.1 General Procedure for the Preparation of Substituted 2-
Aminopyrimidines
In a 50 mL microwave vial were successively dissolved in EtOH (20 mL) 2chloropyrimidine
(3.43 g, 30 mmol), amine (39 mmol, 1.3 equiv) and triethylamine
(6.2 mL, 45 mmol, 1.5 equiv). The reaction tube was sealed, and irradiated in the
cavity of a Milestone MicroSYNTH microwave reactor at a ceiling temperature of
120 °C at 100 W maximum power for 25 min. After the reaction mixture was cooled
with an air flow for 15 min, it was diluted with water (100 mL), extracted with DCM
(2×150 mL) and dried over Na2SO4. The solvent was evaporated in vacuo, and the
crude mixture was purified by silica gel flash chromatography using 0-5%
MeOH−DCM as the eluent.
13 new substituted 2-aminopyrimidine derivatives were synthesized in similar
manner. (Table-1)
Table-1 Compound synthesized
N
N
N
H R
ENTRY CODE R Yield
1 BS-021 cyclododecane 66
2 BS -024 cyclooctane 60
3 BS -025 cycloheptane 64
4 BS -030 cyclobutane 61
5 BS-029 C6H13 88
6 BS -026 C7H15 87
7 BS -027 C8H17 86
8 BS -033 C9H19 86
9 BS -028 C10H21 87
10 BS -034 C11H23 88
11 BS -035 C12H25 89
12 BS -036 C13H27 88
13 BS -037 C14H19 88

2.9.2 General Procedure for the Preparation of Salts.
To a solution of 2-substituted aminopyrimidine (6 mmol) and α-bromoacetophenone
(7.2 mmol, 1.2 equiv) in acetonitrile (12 mL) was added 4-dimethylaminopyridine (6
mg, 0.05 mmol). After being stirred at 85 °C for 5 h, the reaction mixture was diluted
with acetone (20 mL) and the precipitate was filtered and washed with acetone (2×20
mL), ether (2×20 mL) and dried over P2O5 to give salt as a white solid.
10 new compounds were synthesized in similar manner.
2.9.3 General Procedure for the Preparation of Salts. (Microwave)
In a 50 mL microwave vial were successively dissolved 2-substituted
aminopyrimidine (6 mmol) and α-bromoacetophenone (7.2 mmol, 1.2 equiv) in
acetonitrile (12 mL) was added 4-dimethylaminopyridine (6 mg, 0.05 mmol). The
reaction tube was sealed, and irradiated in the cavity of a Milestone MicroSYNTH
microwave reactor at a ceiling temperature of 80 °C at 100 W maximum power for 30
min. After the reaction mixture was cooled with an air flow for 15 min, the reaction
mixture was diluted with acetone (20 mL) and the precipitate was filtered and washed
with acetone (2×20 mL), ether (2×20 mL) and dried over P2O5 to give salt as a white
solid. 34 new compounds were synthesized in similar manner.
2.9.4 General Procedure for the Preparation of 2-Amino-1H-imidazoles.
To a suspension of salt (2 mmol) in MeCN (5 mL) hydrazine hydrate (0.7 mL, 14
mmol of a 64% solution, 7 equiv) was added, and the mixture was irradiated in the
sealed Milestone MicroSYNTH microwave reactor for 10 min at a ceiling
temperature of 100 °C at 150 W maximum power. After cooling down hydrazine
hydrate was evaporated with toluene (3×20 mL). The resulting residue was purified
by column chromatography (silica gel; MeOH−DCM 1:4 v/v with 5% of 6M NH3 in
MeOH) to afford 2-amino-1H-imidazole as an amorphous material.
12 new compounds were synthesized in similar manner.
2.9.5 General procedure for the one-pot two-step microwave-assisted synthesis
of 2-amino-1H-imidazoles.
In a microwave vial (10 mL) were successively dissolved in dry MeCN (3 mL) the
corresponding 2-aminopyrimidine (4 mmol) and α-bromoketone (4.6 mmol). The
reaction tube was sealed and irradiated in a microwave reactor at a ceiling

temperature of 80 °C and a maximum power of 50 W for 30 min. After the reaction
mixture was cooled with an air flow for 15 min, hydrazine hydrate (0.9 mL, 28 mmol
of a 64% solution, 7 equiv) was added, and the mixture was irradiated at a ceiling
temperature of 90 °C and a maximum power of 50 W for another 10 min. After the
reaction mixture was cooled, hydrazine hydrate was removed by distillation with
toluene (3×20 mL). The resulting residue was purified by column chromatography
(silica gel; MeOH-DCM 1:9 v/v with 0.5 % of 6N ammonia in MeOH) to afford 2amino-1H-imidazole
as amorphous solid.
10 new compounds were synthesized in similar manner.
2.10 Spectral Characterization
N-Cyclooctylpyrimidin-2-amine (BS-024)
N
N
N
H
Yield: 60%. 1 H NMR (300 MHz, CDCl3): δ = 8.25 (d, J = 4.77 Hz, 2H), 6.46 (t, J =
4.8 Hz, 1H), 5.07 (br s, 1H), 4.04 (m, 1H), 1.93 (m, 2H), 1.63 (m, 12H). 13 C NMR
(75.5 MHz, CDCl3): δ =161.6, 158.0 (×2), 110.0, 50.6, 31.7 (×2), 27.5 (×2), 25.3,
23.5 (×2). HRMS (EI): C12H19N3, calcd 205.2994, found: 205.2982.
N –Cycloheptylpyrimidin-2-amine (BS-025)
N
N
N
H
Yield: 64%. 1 H NMR (300 MHz, CDCl3): δ = 8.26 (d, J = 4.77 Hz, 2H), 6.47 (t, J =
4.77 Hz, 1H), 5.09 (br s, 1H), 4.01 (m, 1H), 2.02 (m, 2H), 1.55 (m, 10H). 13 C NMR
(75.5 MHz, CDCl3): δ =161.6, 158.0 (×2), 110.0, 51.6, 35.0 (×2), 28.2 (×2), 23.9
(×2). HRMS (EI): C11H17N3, calcd 191.2728, found: 191.2742.
N –Heptylpyrimidin-2-amine (BS-026)
N
N
N
H
C 7H 15
Yield: 87%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.8 Hz, 2H), 6.50 (t, J = 4.8
Hz, 1H), 5.07 (br s, 1H), 3.40 (m, 2H), 1.61 (m, 2H), 1.31 (m, 8H), 0.85 (m 3H). 13 C

NMR (75.5 MHz, CDCl3): δ =162.5, 157.9 (×2), 110.1, 41.5, 31.8, 29.6, 29.0, 26.9,
22.6, 14.0. HRMS (EI): C11H19N3, calcd 193.2887, found: 193.2894.
N –Octylpyrimidin-2-amine (BS-027)
N
N
N
H
C 8H 17
Yield: 86%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.74 Hz, 2H), 6.49 (t, J =
4.77 Hz, 1H), 5.11 (br s, 1H), 3.40 (m, 2H), 1.60 (m, 2H), 1.27 (m, 10H), 0.87 (m
3H). 13 C NMR (75.5 MHz, CDCl3): δ =162.4, 158.0 (×2), 110.1, 41.5, 31.8, 29.6,
29.3, 29.2, 26.9, 22.6, 14.1. HRMS (EI): C12H21N3, calcd 207.3152, found: 207.3131.
N –Decylpyrimidin-2-amine (BS-028)
N
N
N
H
C 10H 21
Yield: 87%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.8 Hz, 2H), 6.50 (t, J = 4.8
Hz, 1H), 5.07 (br s, 1H), 3.38 (m, 2H), 1.60 (m, 2H), 1.26 (m, 14H), 0.87 (t, J = 6.93,
3H). 13 C NMR (75.5 MHz, CDCl3): δ =162.4, 158.0 (×2), 110.1, 41.5, 31.8, 29.6 (×2),
29.5, 29.3 (×2), 26.9, 22.6, 14.1. HRMS (EI): C14H25N3, calcd 235.3684, found:
235.3670.
N –Cyclobutylpyrimidin-2-amine (BS-030)
N
N
N
H
Yield: 61%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (m, 2H), 6.51 (t, J = 4.77 Hz, 1H),
5.29 (br s, 1H), 4.46 (m, 1H), 2.42 (m, 2H), 1.89 (m, 2H), 1.76 (m, 2H). 13 C NMR
(75.5 MHz, CDCl3): δ =161.6, 158.0 (×2), 110.4, 46.3, 31.5 (×2), 15.0. HRMS (EI):
C8H11N3, calcd 149.1930, found: 149.1917
N –Nonylpyrimidin-2-amine (BS-033)
N
N
N
H
C 9H 19
Yield: 86%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.71 Hz, 2H), 6.50 (t, J =
4.77 Hz, 1H), 5.07 (br s, 1H), 3.40 (m, 2H), 1.61 (m, 2H), 1.26 (m, 12H), 0.87 (t, J =
6.9, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =162.5, 158.0 (×2), 110.1, 41.5, 31.8, 29.6,

29.5,29.4, 29.2, 27.0, 22.6, 14.1. HRMS (EI): C13H23N3, calcd 221.3418, found:
221.3400.
N –Undecylpyrimidin-2-amine (BS-034)
N
N
N
H
C 11H 23
Yield: 88%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.62 Hz, 2H), 6.50 (t, J =
4.77 Hz, 1H), 5.07 (br s, 1H), 3.40 (m, 2H), 1.60 (m, 2H), 1.25 (m, 16H), 0.87 (t, J =
6.87, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 162.5, 158.0 (×2), 110.2, 41.5, 31.9,
29.6 (×4), 29.3 (×2), 26.9, 22.6, 14.1. HRMS (EI): C15H27N3, calcd 249.3950, found:
249.3938.
N –Dodecylpyrimidin-2-amine (BS-035)
N
N
N
H
C 12H 25
Yield: 89%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.41 Hz, 2H), 6.50 (t, J =
4.74 Hz, 1H), 5.07 (br s, 1H), 3.40 (m, 2H), 1.61 (m, 2H), 1.25 (m, 18H), 0.88 (t, J =
6.84, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 162.4, 158.0 (×2), 110.2, 41.5, 31.9,
29.6 (×5), 29.3 (×2), 26.9, 22.6, 14.1. HRMS (EI): C16H29N3, calcd 263.4216, found:
263.4202.
N –Tridecylpyrimidin-2-amine (BS-036)
N
N
N
H
C 13H 27
Yield: 88%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.77 Hz, 2H), 6.50 (t, J =
4.8 Hz, 1H), 5.07 (br s, 1H), 3.38 (m, 2H), 1.60 (m, 2H), 1.25 (m, 20H), 0.88 (t, J =
6.9, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 162.4, 158.0 (×2), 110.1, 41.5, 31.9, 29.6
(×6), 29.3 (×2), 27.0, 22.7, 14.1. HRMS (EI): C17H31N3, calcd 277.4481, found:
277.4491.
N –Tetradecylpyrimidin-2-amine (BS-037)
N
N
N
H
C 14H 29

Yield: 88%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 4.77 Hz, 2H), 6.50 (t, J =
4.8 Hz, 1H), 5.07 (br s, 1H), 3.38 (m, 2H), 1.60 (m, 2H), 1.25 (m, 22H), 0.88 (t, J =
6.9, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 162.4, 158.0 (×2), 110.2, 41.5, 31.9, 29.6
(×7), 29.3 (×2), 26.9, 22.7, 14.1. HRMS (EI): C18H33N3, calcd 291.4747, found:
291.4723.
1-Heptyl-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide amine (BS-049)
N
Br
N
N C 7H 15
OH
Yield: 75 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.85 (m, 1H), 7.80 (s,
1H), 7.77 (m, 2H), 7.49 (m, 3H), 7.31 (m, 1H), 4.82 (s, 2H). 3.17 (m, 2H), 1.36 (m,
2H), 1.09 (m, 8H), 0.80 (t, J = 6.84 Hz, 3H).
2-Hydroxy-1-octyl-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-052)
N
Br
N
N C 8H 17
OH
Yield: 73 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.86 (m, 1H), 7.80 (s,
1H), 7.75 (m, 2H), 7.47 (m, 3H), 7.31 (t, J = 5.49 Hz, 1H), 4.83 (s, 2H). 3.17 (m, 2H),
1.36 (m, 2H), 1.09 (m, 10H), 0.83 (t, J = 6.72 Hz, 3H).
1-Decyl-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-055)
N
Br
N
N C 10H 21
OH

Yield: 78 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d, J = 4.62 Hz, 1H), 8.87 (d, J =
6.18 Hz, 1H), 7.81 (s, 1H), 7.74 (m, 2H), 7.47 (m, 3H), 7.31 (m, 1H), 4.83 (s, 2H).
3.17 (m, 2H), 1.09 (m, 16H), 0.85 (t, J = 6.51 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3):
δ =167.5, 154.5, 148.2, 138.2, 129.2, 128.3 (×2), 126.9 (×2), 111.1, 90.6, 62.6, 40.7,
31.2, 28.7, 28.6, 28.5, 28.2, 27.3, 25.8, 22.0, 13.9.
1-Hexyl-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-058)
N
Br
N
N C 6H 13
OH
Yield: 80 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.87 (m, 1H), 7.81 (s,
1H), 7.74 (m, 2H), 7.47 (m, 3H), 7.31 (m 1H), 4.83 (s, 2H). 3.17 (m, 2H), 1.34 (m,
2H), 1.09 (m, 6H), 0.78 (t, J = 6.48 Hz, 3H).
2-Hydroxy-1-nonyl-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-061)
N
Br
N
N C 9H 19
OH
Yield: 75 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.87 (m, 1H), 7.80 (s,
1H), 7.74 (m, 2H), 7.47 (m, 3H), 7.31 (t, J = 6.21 Hz, 1H), 4.83 (s, 2H). 3.17 (m, 2H),
1.09 (m, 14H), 0.84 (t, J = 6.63 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =167.5,
154.5, 148.2, 138.2, 129.2, 128.3 (×2), 126.9 (×2), 111.1, 90.6, 62.6, 40.7, 31.1, 28.5,
28.4, 28.2, 27.3, 25.8, 22.0, 13.9.
2-Hydroxy-2-phenyl-1-undecyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-064)
N
Br
N
N C 11H 23
OH

Yield: 80 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d of d, J = 1.89, 4.68 Hz, 1H),
8.87 (d, J = 6.06 Hz, 1H), 7.80 (s, 1H), 7.75 (m, 2H), 7.47 (m, 3H), 7.31 (m 1H), 4.83
(s, 2H). 3.17 (m, 2H), 1.09 (m, 18H), 0.85 (t, J = 6.42 Hz, 3H).
1-Dodecyl-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-067)
N
Br
N
N C 12H 25
OH
Yield: 78 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.87 (m, 1H), 7.81 (s,
1H), 7.74 (m, 2H), 7.46 (m, 3H), 7.31 (m, 1H), 4.84 (s, 2H). 3.17 (m, 2H), 1.22 (m,
20H), 0.85 (t, J = 6.24 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =167.5, 154.5,
148.2, 138.2, 129.2, 128.3 (×2), 126.9 (×2), 111.1, 90.6, 62.6, 40.7, 31.2, 28.9 (×2),
28.8, 28.6 (×2), 28.2, 27.3, 25.8, 22.0, 13.9.
2-Hydroxy-2-phenyl-1-tridecyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-070)
N
Br
N
N C 13H 27
OH
Yield: 79 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.87 (m, 1H), 7.80 (s,
1H), 7.76 (m, 2H), 7.46 (m, 3H), 7.31 (m 1H), 4.83 (s, 2H). 3.17 (m, 2H), 1.22 (m,
22H), 0.85 (m, 3H).
2-Hydroxy-2-phenyl-1-tetradecyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-073)

N
Br
N
N C 14H 29
OH
Yield: 72 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d, J = 4.65 Hz, 1H), 8.87 (d, J =
6.27 Hz, 1H), 7.81 (s, 1H), 7.77 (m, 2H), 7.46 (m, 3H), 7.32 (m 1H), 4.84 (s, 2H).
3.17 (m, 2H), 1.23 (m, 24H), 0.85 (m, 3H).
1-Cyclobutyl-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4ium
bromide (BS-079)
N
Br
N
N
OH
Yield: 77 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.83 (m, 1H), 7.86 (s,
1H), 7.65(m, 2H), 7.46(m, 3H), 7.34 (m 1H), 4.76 (s, 2H). 3.90 (m, 1H), 2.76 (m,
2H), 1.88 (m, 2H), 1.69 (m, 2H).
2-Hydroxy-1-pentyl-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4-ium
bromide (BS-083)
N
Br
N
N C 5H 11
OH
Yield: 74 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (m, 1H), 8.86 (m, 1H), 7.82 (s,
1H), 7.77 (m, 2H), 7.47 (m, 3H), 7.31 (m 1H), 4.83 (s, 2H). 3.17 (m, 2H), 1.36, (m,
2H), 1.09 (m, 4H), 0.73 (t, J = 6.72 Hz, 3H).
2-(4-Chlorophenyl)-1-cycloheptyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-088)
N
Br
N
N
OH
Cl

Yield: 90 %. 1 H NMR (300 MHz, CDCl3): δ = 9.00 (d of d, J = 1.92, 4.65 Hz, 1H),
8.85 (m, 1H), 7.92 (s, 1H), 7.79 (d, J = 8.64 Hz, 2H), 7.56 (d, J = 8.58 Hz, 2H), 7.28
(m, 1H), 4.74 (m, 2H). 3.10 (m, 1H), 2.19 (m, 2H), 1.40 (m, 10H).
2-(4-Chlorophenyl)-1-heptyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-089)
N
Br
N
N C 7H 15
OH
Cl
Yield: 91 %. 1 H NMR (300 MHz, CDCl3): δ = 9.04 (d, J = 4.65 Hz, 1H), 8.87 (d, J =
5.85 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.61 Hz, 2H), 7.55 (d, J = 8.58 Hz, 2H), 7.32
(m, 1H), 4.82 (s, 2H). 3.17 (m, 2H), 1.09 (m, 10H), 0.81 (t, J = 7.17 Hz, 3H).
2-(4-Chlorophenyl)-2-hydroxy-1-octyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-090)
N
Br
N
N C 8H 17
OH
Cl
Yield: 71 %. 1 H NMR (300 MHz, CDCl3): δ = 9.05 (d, J = 6.51 Hz, 1H), 8.90 (d, J =
6.24 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.61 Hz, 2H), 7.55 (d, J = 8.58 Hz, 2H), 7.32
(m, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.09 (m, 12H), 0.83 (t, J = 6.75 Hz, 3H).
2-(4-Chlorophenyl)-1-decyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-091)
N
Br
N
N C 10H 21
OH
Cl
Yield: 86 %. 1 H NMR (300 MHz, CDCl3): δ = 9.04 (d, J = 3.33 Hz, 1H), 8.86 (d, J =
6.0 Hz, 1H), 7.89 (s, 1H), 7.81 (d, J = 8.37 Hz, 2H), 7.55 (d, J = 8.4 Hz, 2H), 7.32 (m,
1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.09 (m, 16H), 0.85 (t, J = 6.51 Hz, 3H). 13 C NMR

(75.5 MHz, CDCl3): δ = 167.7, 154.6, 148.2, 137.3, 134.1, 129.0 (×2), 126.3 (×2),
111.1, 90.2, 62.5, 40.7, 31.2, 28.8, 28.6 (×2), 28.2, 27.2, 25.8, 22.0, 13.9.
2-(4-Chlorophenyl)-1-hexyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-092)
N
Br
N
N C 6H 13
OH
Cl
Yield: 83 %. 1 H NMR (300 MHz, CDCl3): δ = 9.04 (d, J = 4.47 Hz, 1H), 8.87 (d, J =
6.3 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.55 Hz, 2H), 7.56 (m, 2H), 7.33 (t, J = 5.0 Hz,
1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.05 (m, 8H), 0.79 (t, J = 6.30 Hz, 3H).
2-(4-Chlorophenyl)-2-hydroxy-1-nonyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-093)
N
Br
N
N C 9H 19
OH
Cl
Yield: 82 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d of d, J = 1.86, 4.62 Hz, 1H),
8.86 (m, 1H), 7.89 (s, 1H), 7.78 (d, J = 8.64 Hz, 2H), 7.55 (d, J = 8.58 Hz, 2H), 7.32
(m, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.09 (m, 14H), 0.84 (t, J = 6.63 Hz, 3H).
2-(4-Chlorophenyl)-2-hydroxy-1-undecyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-094)
N
Br
N
N C 11H 23
OH
Cl

Yield: 83 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d, J = 4.56 Hz, 1H), 8.87 (d, J =
6.3 Hz, 1H), 7.89 (s, 1H), 7.78 (d, J = 8.49 Hz, 2H), 7.55 (d, J = 8.49 Hz, 2H), 7.32
(m, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.22 (m, 18H), 0.85 (t, J = 6. 3 Hz, 3H). 13 C
NMR (75.5 MHz, CDCl3): δ = 167.5, 154.6, 148.2, 137.3, 134.1, 129.0 (×2), 128.3
(×2), 111.1, 90.2, 62.5, 40.7, 31.2, 28.9, 28.8, 28.6 (×2), 28.2, 27.2, 25.8, 22.0, 13.9.
2-(4-Chlorophenyl)-1-dodecyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-095)
N
Br
N
N C 12H 25
OH
Cl
Yield: 90 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d of d, J = 1.83, 4.59 Hz, 1H),
8.87 (d, J = 6.06 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.64 Hz, 2H), 7.55 (d, J = 8.61
Hz, 2H), 7.32 (m, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.22 (m, 20H), 0.85 (t, J = 6. 33
Hz, 3H).
2-(4-Chlorophenyl)-2-hydroxy-1-tridecyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-096)
N
Br
N
N C 13H 27
OH
Cl
Yield: 95 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d of d, J = 1.83, 4.65 Hz, 1H),
8.87 (d of d, J = 1.77, 6.27 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.61 Hz, 2H), 7.55 (d, J
= 8.61 Hz, 2H), 7.32 (m, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.23 (m, 22H), 0.85 (t, J =
6. 33 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 167.5, 154.6, 148.2, 137.2, 134.1,
129.0 (×2), 128.3 (×2), 111.2, 90.2, 62.5, 40.7, 31.2, 28.9 (×3), 28.8, 28.6 (×2), 28.2,
27.2, 25.8, 22.0, 13.9.
2-(4-Chlorophenyl)-2-hydroxy-1-tetradecyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-097)

N
Br
N
N C 14H 29
OH
Cl
Yield: 90 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d, J = 4.56 Hz, 1H), 8.87 (d J =
6.12 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.55 Hz, 2H), 7.55 (d, J = 8.55 Hz, 2H), 7.32
(t, J = 4.95 Hz, 1H), 4.82 (m, 2H). 3.17 (m, 2H), 1.23 (m, 24H), 0.85 (t, J = 6. 09 Hz,
3H).
2-(4-Chlorophenyl)-1-cyclohexyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-098)
N
Br
N
N
OH
Cl
Yield: 84 %. 1 H NMR (300 MHz, CDCl3): δ = 9.01 (d of d, J = 1.86, 4.68 Hz, 1H),
8.84 (d of d, J = 1.83, 6.39 Hz, 1H), 7.96 (s, 1H), 7.78 (d, J = 8.64 Hz, 2H), 7.56 (d, J
= 8.58 Hz, 2H), 7.30 (m, 1H), 4.72 (m, 2H). 3.02 (m, 1H), 2.13 (m, 2H), 0.75 (m, 8H).
2-(4-Chlorophenyl)-2-hydroxy-1-pentyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-099)
N
Br
N
N C 5H 11
OH
Cl
Yield: 78 %. 1 H NMR (300 MHz, CDCl3): δ = 9.04 (d of d, J = 1.8, 4.56 Hz, 1H),
8.87 (d of d, J = 1.65, 6.27 Hz, 1H), 7.90 (s, 1H), 7.78 (d, J = 8.64 Hz, 2H), 7.56 (d, J
= 8.61 Hz, 2H), 7.32 (m, 1H), 4.81 (m, 2H). 3.17 (m, 2H), 1.10 (m, 6H), 0.75 (t, J = 6.
81 Hz, 3H).
2-(4-Chlorophenyl)-1-cyclobutyl-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
(BS-100)

N
Br
N
N
OH
Cl
Yield: 81 %. 1 H NMR (300 MHz, CDCl3): δ = 9.06 (d, J = 4.11 Hz, 1H), 8.84 (d, J =
6.21 Hz, 1H), 7.95 (s, 1H), 7.69 (d, J = 8.58 Hz, 2H), 7.55 (d, J = 8.55 Hz, 2H), 7.35
(t, J = 5.22 Hz, 1H), 4.64 (m, 2H), 3.89 (m, 1H), 2.73 (m, 2H), 1.91 (m, 2H), 1.66 (m,
2H).
2-Hydroxy-2-(4-methoxyphenyl)-1-octyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-175)
N
Br
N
N C 8H 17
OH
OMe
Yield: 77 %. 1 H NMR (300 MHz, CDCl3): δ = 9.02 (m, 1H), 8.84 (d, J = 6.3 Hz, 1H),
7.71 (s, 1H), 7.65 (d, J = 8.79 Hz, 2H), 7.30 (m, 2H), 7.01 (d, J = 8.79 Hz, 1H), 4.79
(s, 2H). 3.79 (s, 3H), 3.17 (m, 2H), 1.10 (m, 12H), 0.83 (t, J = 6.66 Hz, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ = 167.4, 159.7, 154.4, 148.2, 129.8, 128.4 (×2), 113.5 (×2),
111.0, 90.5, 62.5, 55.2, 40.5, 31.0, 28.2 (×2), 27.3, 25.8, 22.0, 13.8.
2-(4-Fluorophenyl)-2-hydroxy-1-octyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-176)
N
Br
N
N C 8H 17
OH
F
Yield: 68 %. 1 H NMR (300 MHz, CDCl3): δ = 9.03 (d of d, J = 1.92, 4.71 Hz, 1H),
8.84 (d of d, J = 1.65, 6.3 Hz, 1H), 7.86 (s, 1H), 7.82 (m, 2H), 7.33 (m, 3H), 4.82 (s,
2H). 3.17 (m, 2H), 1.10 (m, 12H), 0.83 (t, J = 6.72 Hz, 3H). 13 C NMR (75.5 MHz,
CDCl3): δ = 167.4, 164.1, 160.8, 154.5, 134.5 (×2), 129.5 (d), 115.3 (d), 111.2, 90.2,
62.5, 40.6, 31.0, 28.2 (×2), 27.3, 25.8, 21.9, 13.8.

2-(3,4-Dichlorophenyl)-2-hydroxy-1-octyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-177)
N
Br
N
N C 8H 17
OH
Cl
Cl
Yield: 82 %. 1 H NMR (300 MHz, CDCl3): δ = 9.05 (d of d, J = 1.86, 4.62 Hz, 1H),
8.88 (d of d, J = 1.74, 6.27 Hz, 1H), 8.07 (s, 1H), 8.02 (s, 1H), 7.78 (s, 2H), 7.33 (m,
1H), 4.83 (m, 2H). 3.23 (m, 2H), 1.11 (m, 12H), 0.83 (t, J = 6.75 Hz, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ = 167.4, 154.6, 148.0, 139.4, 132.1, 131.2, 130.4, 129.4, 127.3,
111.3, 89.6, 62.3, 40.6, 31.0, 28.2 (×2), 27.2, 25.7, 21.9, 13.8.
2-(3-Bromophenyl)-2-hydroxy-1-octyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-178)
N
Br
N
N C 8H 17
OH
Br
Yield: 53 %. 1 H NMR (300 MHz, CDCl3): δ = 9.04 (d of d, J = 1.86, 4.68 Hz, 1H),
8.87 (d of d, J = 1.62, 6.27 Hz, 1H), 8.01 (s, 1H), 7.93 (s, 1H), 7.77 (d, J = 7.86 Hz,
1H), 7.66 (d, J = 8.4 Hz, 1H), 7.46 (t, J = 7.92 Hz, 1H) 7.33 (m, 1H), 4.82 (m, 2H).
3.22 (m, 2H), 1.36 (m, 2H), 1.11 (m, 10H), 0.83 (t, J = 6.72 Hz, 3H). 13 C NMR (75.5
MHz, CDCl3): δ = 167.4, 154.6, 148.1, 140.9, 132.1, 130.4, 129.9, 126.0, 121.7,
111.2, 89.8, 62.5, 40.6, 31.0, 28.2 (×2), 27.2, 25.7, 21.9, 13.8.
2-Hydroxy-2-(naphthalen-1-yl)-1-octyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-179)

N
Br
N
N C 8H 17
OH
Yield: 82 %. 1 H NMR (300 MHz, CDCl3): δ = 9.08 (d, J = 4.11 Hz, 1H), 9.00 (d, J =
5.25 Hz, 1H), 8.38 (s, 1H), 8.02 (m, 4H), 7.86 (d, J = 7. 61 Hz, 1H), 7.60 (m, 2H),
7.38 (t, J = 5.64 Hz, 1H), 4.99 (s, 2H). 3.26 (m, 2H), 1.39 (m, 2H), 1.00 (m, 10H),
0.76 (t, J = 6.6 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 167.4, 154.7, 148.3,
135.4, 132.9, 132.1, 128.4, 128.1, 127.5, 127.0, 126.6 (×2), 124.2, 111.2, 90.8, 62.5,
40.7, 30.9, 28.2 (×2), 27.3, 25.8, 21.9, 13.8.
2-Hydroxy-2-(4-nitrophenyl)-1-octyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4ium
bromide (BS-180)
N
Br
N
N C 8H 17
OH
NO 2
Yield: 75 %. 1 H NMR (300 MHz, CDCl3): δ = 9.06 (m, 1H), 8.89 (m, 1H), 8.37 (d, J
= 8.7 Hz, 2H), 8.12 (s, 1H), 8.05 (d, J = 8.76 Hz, 2H), 7.36 (m, 1H), 4.86 (m, 2H).
3.22 (m, 2H), 1.39 (m, 2H), 1.09 (m 10H), 0.81 (t, J = 6.66 Hz, 3H). 13 C NMR (75.5
MHz, CDCl3): δ = 167.5, 154.7, 148.2, 147.9, 145.2, 128.7 (×2), 123.0 (×2), 111.4,
90.0, 62.3, 40.8, 30.9, 28.2 (×2), 27.2, 25.7, 21.9, 13.8.
2-Hydroxy-2-(4’-nitrobiphenyl-4-yl)-1-octyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-185)

N
Br
N
N C 8H 17
OH
NO 2
Yield: 49 %. 1 H NMR (300 MHz, CDCl3): δ = 9.05 (d, J = 4.11 Hz, 1H), 8.88 (d, J =
6.2 Hz, 1H), 8.32 (d, J = 8.7 Hz, 2H), 8.03 (d, J = 8.76 Hz, 2H), 7.94 (m, 5H), 7.34 (t,
J = 4.98 Hz, 1H), 4.87 (s, 2H). 3.24 (m, 2H), 1.43 (m, 2H), 1.10 (m 10H), 0.76 (t, J =
6.45 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ = 167.5, 154.6, 148.2, 146.9, 145.5,
138.9, 138.4, 127.9 (×3), 127.2 (×2), 124.1 (×3), 111.2, 90.5, 62.6, 40.8, 31.0, 28.2
(×2), 27.3, 25.8, 21.9, 13.8.
2-Hydroxy-2-(4-(methylsulfonyl)phenyl)-1-octyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-186)
N
Br
N
N C 8H 17
OH
SO 2Me
Yield: 48 %. 1 H NMR (300 MHz, CDCl3): δ = 9.06 (d of d J = 1.65, 4.47 Hz, 1H),
8.94 (d of d, J = 1.56, 6.21 Hz, 1H), 8.08 (s, 1H), 8.05 (s, 4H), 7.36 (m, 1H), 4.87 (m,
2H). 3.27 (s, 3H), 3.24 (m, 2H), 1.40 (m, 2H), 1.11 (m, 10H), 0.82 (t, J = 6.66 Hz,
3H). 13 C NMR (75.5 MHz, CDCl3): δ = 167.4, 154.7, 148.2, 143.7 (×2), 141.6, 128.1
(×2), 127.0, 111.4, 90.3, 62.5, 43.3, 40.9, 31.0, 28.2 (×2), 27.4, 25.9, 21.9, 13.8.
2-Hydroxy-2-(4-(methylthio)phenyl)-1-octyl-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-187)

N
Br
N
N C 8H 17
OH
SMe
Yield: 49 %. 1 H NMR (300 MHz, CDCl3): δ = 9.02 (m, 1H), 8.85 (m, 1H), 7.78 (s,
1H), 7.66 (d, J = 8.52 Hz, 2H), 7.33 (m, 3H), 4.79 (m, 2H). 3.33 (s, 3H), 3.22 (m,
2H), 1.39 (m, 2H), 1.10 (m, 10H), 0.83 (t, J = 6.66 Hz, 3H). 13 C NMR (75.5 MHz,
CDCl3): δ = 167.4, 154.7, 148.2, 143.7 (×2), 141.6, 128.1 (×2), 127.0, 111.4, 90.3,
62.5, 43.3, 40.9, 31.0, 28.2 (×2), 27.4, 25.9, 21.9, 13.8.
5-(2,4-Dimethoxyphenyl)-N-methy-1H-imidazol-2-amine (BS-136)
HN
N
N
H
O
O
Yield : 48 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.63 (br, 1H), 7.43 (d, J = 3.0
Hz, 1H), 7.07 (s, 1H), 6.90 (d, J = 8.8 Hz, 1H), 6.63 (d of d, J = 3.1, 3.1 Hz, 1H), 5.73
(q, J = 5.1 Hz, 1H), 3.80 (s, 3H). 3.71 (s, 3H), 2.77 (d, J= 5.1 Hz, 3H). 13 C NMR
(75.5 MHz, DMSO-d6): δ =153.1, 151.0, 149.5, 129.3, 123.4, 114.8, 111.8, 111.2,
110.1, 55.5, 55.2, 29.8. HRMS (EI) C12H15N3O2, calcd 233.1164, found : 233.1173.
N-((Benzol[d][1,3]dioxol-6-yl)-5-(naphthalene-3-yl)-1H-imidazol-2-amine (BS-
137)
O
O
HN
N
N
H
Yield : 72 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.61 (br, 1H), 8.06 (s, 1H), 7.83-
7.79 (m, 4H), 7.44-7.37 (m, 2H), 7.19 (s, 1H), 6.99 (s, 1H), 6.87-6.86 (m, 2H), 6.32 (t,
J = 6.4 Hz, 1H), 5.96 (s, 2H), 4.34 (d, J = 6.4 Hz, 2H). 13 C NMR (75.5 MHz,
DMSO-d6) δ =151.2, 147.0, 145.8, 134.6, 133.5, 131.3, 127.5 (x 2), 127.4, 127.3,
126.0,125.6, 124.6, 123.2, 120.4, 108.0 (x 2),107.8, 100.6 (x 2), 46.1. HRMS EI
C21H17N3O2, calcd 343.1321 , found : 343.1340.
5-(3,4-Dichlorophenyl)-N-propyl-1H-imidazol-2-amine(BS-140)

C3H7 HN
N
N
H
Cl
Cl
Yield : 70 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.55 (br, 1H), 7.82 (s, 1H), 7.58
(s, 1H), 7.50 (d, J = 8.2 Hz, 1H), 7.22 (s, 1H), 5.83 (t, J = 6.0 Hz, 1H), 3.10 (q, J = 8.2
Hz, 2H), 1.54 (m, 2H), 0.90 (t, J = 7.35 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6) δ
=151.6, 130.9 (x 2), 130.3 (x 2), 126.3, 124.6, 123.4, 104.2, 44.7, 22.6, 11.4. HRMS
EI C12H13Cl2N3, calcd 269.0487, found : 269.0480.
N-Cyclohexyl-5-(4-(methylsulfonyl)phenyl)-1H-imidazol-2-amine (BS-141)
HN
N
N
H
S O
O
Yield : 43 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.54 (br, 1H), 7.83-7.76 (m, 4H),
7.31 (s, 1H), 5.75 (d, J = 8.4 Hz, 1H), 3.16 (s, 3H), 2.49 (s, 1H), 1.90 (s, 2H), 1.70 (m,
2H), 1.20 (m, 6H). 13 C NMR (75.5 MHz, DMSO-d6) δ =151.1, 140.1, 136.1, 127.2(x
4), 123.4 (x 2), 104.2, 51.1, 43.7, 33.0(x 2), 25.4, 24.6(x 2). HRMS EI C16H21N3O2S,
calcd 319.1354. , found : 319.1337.
5-(4-Chlorophenyl)-N-octyl-1H-imidazol-2-amine (BS-143)
C8H17 HN
N
N
H
Cl
Yield : 43%. 1 H NMR (300 MHz, DMSO-d6) δ = 10.43 (br, 1H), 7.63 (d, J = 8.3 Hz,
2H), 7.31 (d, J = 8.4 Hz, 2H), 7.09 (s, 1H), 5.71 (t, J = 4.9 Hz, 1H), 3.12 (m, 2H),
1.48-1.51 (m, 2H), 1.25 (m, 10H), 0.85 (t, J = 4.2 Hz, 3H). 13 C NMR (75.5 MHz,
DMSO-d6) δ =151.5, 128.8 (x 2), 128.1 (x 3), 124.9 (x 2), 100.7, 42.9, 31.2, 29.4,
28.8, 28.7, 26.4, 22.0, 13.9. HRMS EI C17H24ClN3, calcd 305.1659, found : 305.1646.
5-(4-Chlorophenyl)-N-pentyl-1H-imidazol-2-amine (BS-146)
C5H11 HN
N
N
H
Cl

Yield: 57 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.44 (br, 1H), 7.65 (d, J = 7.3 Hz,
2H), 7.31 (d, J = 8.3 Hz, 2H), 7.09 (s, 1H), 5.71 (t, J = 5.1 Hz, 1H), 3.12 (m, 2H),
1.51 (t, J = 1.7 Hz, 2H), 1.30 (m, 4H), 0.88 (t, J = 6.7 Hz, 3H). 13 C NMR (75.5 MHz,
DMSO-d6) δ =151.5, 128.9 (x 2), 128.1 (x 3), 124.9 (x 2), 104.1, 42.8, 29.1, 28.6,
21.9, 13.9.HRMS EI C14H18ClN3, calcd 263.1189. , found: 263.1180.
5-(4-Fluorophenyl)-N-hexyl-1H-imidazol-2-amine (BS-147)
C6H13 HN
N
N
H
F
Yield: 61 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.38 (br, 1H), 7.62 (m, 2H), 7.09
(t, J = 8.8 Hz, 2H), 6.99 (s, 1H), 5.66 (m, 1H), 3.13-3.10 (m, 2H), 1.51 (m, 2H), 1.28
(m, 6H), 0.87 (t, J = 6.4 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6) δ =161.6, 158.5,
151.4, 125.0, 124.9, 115.0, 114.7, 104.1 (x 2), 42.9, 31.0, 29.4, 26.1, 22.1, 13.8.,
HRMS EI C15H20FN3, calcd 261.1641. , found: 261.1631.
N-(4-Methoxyphenethyl)-5-(3-bromophenyl)-1H-imidazol-2-amine(BS-148)
O
HN
N
N
H
Br
Yield : 44 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.56 (br, 1H), 7.82 (s, 1H), 7.65
(d, J = 6.5 Hz, 2H), 7.24-7.16 (m, 5H), 6.88 (d, J = 8.4 Hz, 2H), 5.77 (m, 1H), 3.72 (s,
3H), 3.35 (s, 2H), 2.77 (t, J = 7.6 Hz, 2H). 13 C NMR (75.5 MHz, DMSO-d6) δ
=157.5, 151.3, 131.6 (x 2), 130.3, 129.6 (x 3), 127.3, 125.7, 122.1, 121.9, 113.6 (x 3),
54.9, 44.8, 34.6.,HRMS EI C18H18BrN3O, calcd 371.0633. , found : 371.0658.
N-Cyclooctyl-5-(4-(methylsulfonyl)phenyl)-1H-imidazol-2-amine (BS-154)
HN
N
N
H
SO 2Me
Yield : 53 %. 1 H NMR (300 MHz, DMSO-d6) δ = 10.49 (br, 1H), 7.86 (d, J = 8.5 Hz,
2H), 7.79 (d, J = 8.5 Hz, 2H), 7.31 (d, J = 1.5 Hz, 1H), 5.74 (d, J = 8.4 Hz, 1H), 3.64

(s, 1H), 3.16 (s, 3H), 1.80 (m, 2H), 1.53 (m, 12H). 13 C NMR (75.5 MHz, CDCl3) δ =
151.5, 138.8, 136.2, 127.7 (x 3), 124.0 (x 2), 105.1, 53.7, 44.6, 32.3 (x 2), 27.2 (x 2),
25.2, 23.4 ( x 2). HRMS EI C18H25N3O2S, calcd 344.1667. , found : 344.1644.
4-(2-(2-Methoxyethylamino)-1H-imidazole-5-yl)benzonitrile(BS-139)
O
N
H
N
N
H
N
Yield 85 %. 1 H NMR (300 MHz, DMSO d6) δ = 10.6 (br, 1H), 7.7 (m 4H), 7.3 (s 1H),
5.8 (s 1H), 3.5 (t 2H), 3.4 (m 2H), 3.2 (s 3H). 13 C NMR (300 MHz, DMSO d6) δ
=151.3, 140.1, 134.2, 132.2(x 2), 123.8, 119.5, 110.8, 106.4, 104.1, 70.9, 57.9, 54.8,
43.3. HRMS EI C13H14N4O, calcd 242.1168 , found : 242.1167.
5-(4-Methoxyphenyl)-N-octyl-1H-imidazol-2-amine (BS-258 )
C 8H 17
N
H
N
N
H
O
Yield : 78 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.91 (br s, 1H), 7.51 (d, J = 8.57
Hz, 2H), 6.95 (s, 1H), 6.87 (d, J = 8.75 Hz, 2H), 6.05 (m, 1H), 3.74 (s, 3H), 3.16 (m,
2H), 1.51 (m, 2H), 1.28 (m, 10H), 0.85 (t, J = 6.75 Hz, 3H). 13 C NMR (75.5 MHz,
CDCl3): δ =149.2, 131.1, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.4, 43.1, 31.6, 29.5,
29.0, 28.9, 26.4, 22.2, 14.0. HRMS (EI): C18H27N3O, calcd 301.2154, found:
301.2142.
5-(4-Fluorophenyl)-N-octyl-1H-imidazol-2-amine (BS-259)
C 8H 17
N
H
N
N
H
F
Yield : 69% . 1 H NMR (300 MHz, DMSO-d6): δ = 10.44 (br s, 1H), 7.61 (t, J = 5.85
Hz, 2H), 7.08 (t, J = 8.78 Hz, 2H), 6.99 (s, 1H), 5.67 (t, J = 6.03 Hz, 1H), 3.10 (m,
2H), 1.51 (m, 2H), 1.25 (m, 10H), 0.83 (m, 3H). 13 C NMR (75.5 MHz, CDCl3): δ
=163.8, 160.5, 148.7, 130.2, 128.4, 127.0, 122.9, 115.5, 104.7, 43.0, 31.6, 29.5, 29.0,
28.9, 26.4, 22.5, 14.0. HRMS (EI): C17H24FN3, calcd 289.1954, found:. 289.1964.
5-(3,4-Dichlorophenyl)-N-octyl-1H-imidazol-2-amine (BS-260)
C 8H 17
N
H
N
N
H
Cl
Cl

Yield : 72 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.52 (br s, 1H), 7.82 (s, 1H),
7.58 (m, 1H), 7.50 (d, J = 8.13 Hz, 1H), 7.22 (s, 1H), 5.78 (m, 1H), 3.11 (m, 2H), 1.51
(m, 2H), 1.28 (m, 10H), 0.85 (t, J = 6.94 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ
=149.6, 132.8, 131.1, 131.0, 130.6, 129.5, 127.1, 127.0, 124.2, 43.3, 31.6, 29.5, 29.0,
28.9, 26.4, 22.5, 14.0. HRMS (EI): C17H23Cl2N3, calcd 339.1269, found:. 339.1279.
5-(3-Bromophenyl)-N-octyl-1H-imidazol-2-amine (BS-261)
C 8H 17
N
H
N
N
H
Br
Yield : 79 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.49 (br s, 1H), 7.79 (s, 1H),
7.59 (s, 1H), 7.22 (m, 1H), 7.14 (s, 1H), 5.73 (t, J = 5.66 Hz, 1H), 3.11 (m, 2H), 1.51
(m, 2H), 1.25 (m, 10H), 0.84 (t, J = 6.69 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ
=149.2, 133.0, 130.8, 130.1 (×2), 128.0, 126.5, 123.8, 122.6, 43.2, 31.6, 29.5, 29.0,
28.9, 26.4, 22.5, 14.0. HRMS (EI): C17H24BrN3, calcd 349.1154, found:. 249.1138.
5-(Naphthalen-1-yl)-N-octyl-1H-imidazol-2-amine (BS-262)
C 8H 17
N
H
N
N
H
Yield : 68 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.53 (br s, 1H), 8.05 (s, 1H),
7.80 (m, 3H), 7.39 (m, 3H), 7.17 (s, 1H), 5.73 (m, 1H), 3.16 (m, 2H), 1.54 (m, 2H),
1.26 (m, 10H), 0.83 (t, J = 6.86 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1,
133.4, 132.4, 129.5, 128.3, 128.2, 127.9, 127.7, 126.6, 126.4 (×2), 126.0, 123.0, 43.3,
31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI): C21H27N3, calcd 321.4592,
found:. 321.4578.
5-(4-Nitrophenyl)-N-octyl-1H-imidazol-2-amine (BS-263)
C 8H 17
N
H
N
N
H
NO 2
Yield : 66 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.74 (br s, 1H), 8.12 (d, J = 8.92
Hz, 2H), 7.84 (d, J = 8.92 Hz, 2H), 7.43 (s.1H), 5.91 (t, J = 5.54 Hz, 1H), 3.16 (m,
2H), 1.52 (m, 2H), 1.25 (m, 10H), 0.85 (t, J = 6.75 Hz, 3H). 13 C NMR (75.5 MHz,
CDCl3): δ =163.8, 160.5, 148.7, 130.2, 128.4, 127.0, 122.9, 115.5, 104.7, 43.0, 31.6,
29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI): C17H24N4O2, calcd 316.1899,
found:.316.1909.

5-(4’-Nitrobiphenyl-4-yl)-N-octyl-1H-imidazol-2-amine (BS-264)
C 8H 17
N
H
N
N
H
NO 2
Yield : 75 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.53 (br s, 1H), 8.27 (d, J = 8.71
Hz, 2H), 7.96 (d, J = 8.71 Hz, 2H), 7.75 (s.4H), 7.18 (s. 1H), 5.76 (t, J = 5.88 Hz,
1H), 3.16 (m, 2H), 1.53 (m, 2H), 1.26 (m, 10H), 0.86 (t, J = 6.75 Hz, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ =163.8, 160.5, 148.7, 130.2, 128.4, 127.0, 122.9, 115.5, 104.7,
43.0, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI): C23H28N4O2, calcd
392.2212, found:.392.2201.
5-(4-(Methylsulfonyl)phenyl)-N-octyl-1H-imidazol-2-amine (BS-265)
C 8H 17
N
H
N
N
H
O
S
O
Yield : 54 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.62 (br s, 1H), 7.84 (d, J = 8.55
Hz, 2H), 7.76 (d, J = 8.35 Hz, 2H), 7.32 (s.1H), 5.83 (t, J = 5.97 Hz, 1H), 3.16 (m,
5H), 1.52 (m, 2H), 1.25 (m, 10H), 0.85 (t, J = 6. 56 Hz, 3H). 13 C NMR (75.5 MHz,
CDCl3): δ =150.7, 138.1, 136.6, 127.9 (×2), 127.6, 127.4 (×2), 126.0, 44.5, 43.6, 31.6,
29.6, 29.0, 28.9, 26.5, 22.5, 14.0. HRMS (EI): C18H27N3O2S, calcd 349.4909,
found:.249.4918.
N-Isobutyl-5-(4-nitrophenyl)-1H-imidazol-2-amine (BS-292)
N
H
N
N
H
NO 2
Yield : 70 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.69 (br s, 1H), 8.12 (d, J = 9.02
Hz, 2H), 7.84 (d, J = 8.50 Hz, 2H), 7.42 (s, 1H), 5.99 (t, J = 5.93 Hz, 1H), 2.99 (t, J =
6.44 Hz, 2H), 1.83 (m, 1H), 0.89 (d, J = 6.70 Hz, 6H). 13 C NMR (75.5 MHz, DMSOd6):
δ =152.2 (×2), 143.8, 141.6, 123.9 (×2), 123.3, 104.1 (×2), 50.4, 27.9, 20.1 (×2).
HRMS (EI): C13H16N4O2, calcd 260.1273, found: 260.1287
N-Isobutyl-5-phenyl-1H-imidazol-2-amine (BS-293)
N
H
N
N
H

Yield : 71 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.52 (br s, 1H), 7.59 (d, J = 7.47
Hz, 2H), 7.28 (t, J = 7.47 Hz, 2H), 7.09 (t, J = 7.25 Hz,1H), 7.04 (s,1H), 5.92 (t, J =
5.71 Hz, 1H), 2.98 (t, J = 6.37 Hz, 2H), 1.82 (m, 1H), 0.89 (d, J = 6.59 Hz, 6H). 13 C
NMR (75.5 MHz, DMSO-d6): δ =151.2, 134.0, 133.1, 128.2 (×2), 125.1, 123.4(×2),
104.1, 50.5, 27.9, 20.1 (×2). HRMS (EI): C13H17N3, calcd 215.1422, found:215.1411.
5-(4-Bromophenyl)-N-isobutyl-1H-imidazol-2-amine (BS-294)
N
H
N
N
H
Br
Yield : 69 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.46 (br s, 1H), 7.55 (d, J = 8.25
Hz, 2H), 7.42 (d, J = 8.25 Hz, 2H), 7.08 (s, 1H), 5.80 (t, J = 5.75 Hz, 1H), 2.97 (t, J =
6.25 Hz, 2H), 1.82 (m, 1H), 0.89 (d, J = 6.50 Hz, 6H). 13 C NMR (75.5 MHz, DMSOd6):
δ =151.6, 134.1, 133.0 (×3), 125.3 (×2), 117.2, 104.1, 50.6, 27.9, 20.1 (×2).
HRMS (EI): C13H16BrN3, calcd 293.0528, found:293.0529.
5-(4-Chlorophenyl)-N-isobutyl-1H-imidazol-2-amine (BS-295)
N
H
N
N
H
Cl
Yield : 73 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.46 (br s, 1H), 7.60 (d, J = 8.35
Hz, 2H), 7.29 (d, J = 8.35 Hz, 2H), 7.07 (s, 1H), 5.81 (t, J = 5.96 Hz, 1H), 2.97 (t, J =
6.20 Hz, 2H), 1.82 (m, 1H), 0.89 (d, J = 6.68 Hz, 6H). 13 C NMR (75.5 MHz, DMSOd6):
δ =151.5, 133.6, 133.2, 128.9, 128.0 (×2), 124.9 (×2), 104.1, 50.5, 27.9, 20.1
(×2). HRMS (EI): C13H16ClN3, calcd 249.1033, found:249.1047.

2.11 Representative NMR spectra
2.11.1 1 H and 13 C NMR spectra of bs-026
Integral
9.5
9.0
170
8.5
8.2747
8.2590
1.8547
162.5113
157.9984
160
8.0
150
7.5
7.2629
140
7.0
6.5166
6.5003
6.4846
0.9485
6.5
N
130
6.0
N
5.5
5.0793
N
C7H15 N
H
110.1675
N
C7H15 N
H
120
110
0.8893
5.0 4.5
(ppm)
100
3.4260
3.4028
3.3834
3.3790
3.3595
4.0
77.5117
77.0862
76.6644
90 80
(ppm)
1.9702
3.5
70
3.0
60
2.5
2.0
50
1.6316
1.6102
1.5870
1.3698
1.3522
1.3403
1.3058
1.2876
0.9035
0.8959
0.8815
0.8583
0.0003
2.6079
1.5
41.5103
40
8.3061
1.0
3.0000
0.5
31.8118
29.6081
29.0662
26.9680
22.6114
30
20
0.0
14.0875
10
0

2.11.2 1 H and 13 C NMR spectra of bs-091
Integral
170
167.5253
9.5
9.0476
9.0376
8.8882
8.8687
0.9779
0.9465
160
9.0
154.6121
8.5
148.2155
150
7.8977
7.8105
7.7816
7.5826
7.5544
7.3454
7.3284
7.3084
0.9515
1.9910
1.9242
0.9636
8.0
140
7.5
137.3205
134.1059
129.0584
128.3529
N
Br
7.0
N
Br
130
N
120
N
6.5
N C 10H 21
OH
111.2795
6.0
Cl
N C 10H 21
OH
110
Cl
100
5.5
4.8203
1.9070
5.0 4.5
(ppm)
90.2424
90 80
(ppm)
4.0
70
3.5
62.5177
3.3309
3.2179
3.1959
3.1689
3.1520
60
1.7611
3.0
50
2.5024
2.5
40.7023
40
2.0
1.5
1.2025
1.0976
0.8748
0.8535
0.8309
16.214
1.0
31.2220
28.6219
28.2364
27.2800
25.8145
22.0544
30
20
3.0000
13.9231
0.5
10
0.0
0

2.11.3
10.4329
0.7429
151.5720
10.0
150
1 H and 13 C NMR spectra of bs-143
C8H17 HN
C8H17 HN
140
9.0
N
N
H
128.8948
128.1056
124.9601
N
N
H
130
8.0
120
7.6549
7.6273
7.3122
7.2845
7.0969
1.7133
2.0012
0.7988
110
7.0
Cl
100.7882
Cl
100
6.0
90
5.7173
1.3479
5.0
(ppm)
80
(ppm)
70
4.0
60
3.1288
3.1068
50
2.0669
3.0
42.9279
40
2.5024
2.0863
2.0
1.5113
1.4893
1.2584
1.9883
10.174
31.2511
29.4365
28.8183
28.7164
26.4691
22.0835
30
20
1.0
0.8579
0.8353
3.0000
13.9304
10
-0.0001
0.0
0

2.12 References
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3590.
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[6] Stamford AW, Craig CD, Huang Y. (2001) Int. Pat. WO 01/44201
[7] (a) Lamattina JL, Mularski CJ (1984)Tetrahedron Lett. 25, 2957-2960 (b) Lamattina JL.
(1985) Eur. Pat. Appl. EP 138464 A2.
[8] Katritzky AR, Rogovoy B (2005) Arkivoc. Part Iv, 49-87 and references herein.
[9] Beyer H, Pyl T, Lahmer H. (1961) Chem. Ber. 94, 3217.
[10] Thangavel N, Murgesh K. (2005) Asian J. Chem. 17, 2769.
[11] Ermolat’ev DS, Giménez V N, Babaev EV, Van der Eycken E. (2006) J. Comb. Chem. 8, 659-
663.
[12] Ermolat’ev DS, Svidritsky EP, Babaev EV, Van der Eycken E. (2009) Tetrahedron Lett. 50,
5218-5220.
[13] Ermolat’ev D. S., Savaliya B, Shah A, Van der Eycken E, (2010) Molecular Diversity.
accepted.
[14] Ashry EI, Kilany Y, Rashed N, Assafi H. (1999) Adv. Heterocycl. Chem. 75, 79;
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Structure Activity Relationship of N1-
Substituted 2-Aminoimidazoles as Inhibitors of
Biofilm Formation by Salmonella Typhimurium
and Pseudomonas aeruginosa

Chapter-3
Structure Activity Relationship of N1-Substituted 2-Aminoimidazoles
as Inhibitors of Biofilm Formation by Salmonella Typhimurium and
Pseudomonas aeruginosa
H 2N
N
N
R 1
A library of N1-substituted 4(5)-phenyl-2-aminoimidazoles was synthesized and
tested for the antagonistic effect against biofilm formation by Salmonella
Typhimurium and Pseudomonas aeruginosa. The substitution pattern of the 4(5)-
phenyl group and the nature of the N1-substituent were found to have a major effect
on the biofilm inhibitory activity. The most active compounds of this series were
shown to inhibit the biofilm formation at low micromolar concentrations.
Publication:
[1] Structure Activity Relationship of 4(5)-Phenyl-2-amino-1H-imidazoles, N1-
Substituted 2-Aminoimidazoles and Imidazo[1,2-a]pyrimidinium Salts as
Inhibitors of Biofilm Formation by Salmonella Typhimurium and
Pseudomonas aeruginosa. J. Med.Chem. (2010) DOI: 10.1021/jm1011148
R 2

3.1 Introduction
In previous chapter-2 the dimorth rearrangement was performed to generate
substituted 2-aminoimidazoles. The 2-aminoimidazole (2-AI) ring structure is of
particular interest especially within the realms of medicinal chemistry. For example,
several classes of marine natural products possessing this structure were recently
discovered and identified. l Many of these compounds display a broad range of
biological properties including antibacterial, anti-inflammatory, anticancer, and
antiviral activity. Synthetic 2-AI derivatives, including 2-amino-histamine have been
shown to have HI- and H2-receptor agonist and antagonist activity. 2 Other unrelated
2-AI derivatives are selective 5-HT3 receptor antagonists, which may be
potentially useful in the treatment of chemotherapy induced emesis 3 . Novel
cephalosporins with incorporated 2-AI rings display both Gram-positive and Gramnegative
antibacterial activity as well as good ß-lactamase stability 4 . In addition, 2-AI
can serve as an important starting material in the preparation of 2-nitroimidazole
(azomycin) a naturally occurring antibiotic 5 . Other synthetic analogs of 2nitroimidazole
have been found to be cytotoxic toward hypoxic tumor cells and act as
hypoxic cell radiosensitizers. 6
The methods reported to prepare imidazoles are numerous, although only a limited
number describe the direct synthesis of the corresponding 2-amino derivatives. The
preparation of 2-AI was accomplished by the intramolecular cyclization of N-(2,2diethoxyethyl)guanidine
upon acid hydrolysis. 7,8 The reaction of α-amino aldehydes
or ketones with cyanamide appears to be the most commonly used direct approach. 8,9
However, this reaction is pH sensitive and can lead to different products. In one
case the formation of lH-imidazo[l,2-a]imidazoles was observed. 8 The dimerization
and cyclization of a-amino aldehydes or ketones to symmetrical pyrazines is also a
common problem associated with this method. 9a,10 A classical, although indirect
approach to 2-AI's relies upon the formation of 2-arylazo derivatives via diazonium
coupling, followed by reduction. 2a,7,11 The synthesis of 2-amino-4,5-diarylimidazoles
was accomplished by the reduction of symmetrical 2,2'-azoimidazoles. 13 A more
recent procedure was reported where 2-AI's were formed by the reaction of α -
diketones with guanidine, followed by catalytic hydrogenation. 14 Other indirect
approaches to 2-AI's involve ipso type substitutions of appropriate C-2 substituted

imidazoles, where the addition of a suitable nitrogen nucleophile is followed by the
elimination of an activated leaving group such as a halogen or alkyl sulfoxide or
sulfone. This method has been applied with limited success to electron-poor
imidazoles or when fluorine is the leaving group. 4,15 An interesting synthetic route to
functionalized 2-AI's, which were difficult to obtain by other methods, has been
achieved using a base catalyzed rearrangement of 3-amino-1,2,4-oxadiazoles. 16
Another type of heterocyclic rearrangement involves the reaction of 2-aminooxazoles
with ammonia or formamide. 17 Most recently, the synthesis of 2-amino-4(5)-(αhydroxyalkyl)imidazoles
has been demonstrated where 2-AI was reacted with
aldehydes under neutral conditions. 18
The microwave-assisted procedure for the synthesis of 1,4,5-substituted 2aminoimidazoles
(Scheme-1) is two-step protocol based on the cyclocondensation of
2-aminopyrimidines and bromocarbonyl compounds at 130-150 °C, followed by the
cleavage of the intermediary imidazo[1,2-a]pyrimidin-1-ium salts with an excess of
hydrazine.
3.2 Reaction Scheme
Scheme-1
N
N
+
N
H
Br O
H
H 2N
N
N
R 1
R 2
R 1
R 2
MeCN
MW
80 °C, 30 min
MeCN
64% N2H4 MW
100 °C, 10 min
Br
N
N
N
N
N R1 OH
R 2
PPA, 150 °C
aq. HClO4 N R 1
R 2
ClO 4

3.3 Proposed Mechanism
A possible mechanism for the pyrimidine ring cleavage upon reaction of salts (1) with
amines, which involves the formation of azabutadienes (Scheme 2), Initially, the
imidazo[1,2-a]pyrimidinium salt (1) undergoes a nucleophilic attack at its C-5
position by a first molecule of amine. After rearrangement of the intermediate (A) and
isomerisation of the resulting (B), (E, E)-azabutadiene (2) is formed. Initiated by
protonation, the azabutadiene intermediate (C) in turn undergoes 1,4-addition with a
second molecule of amine, finally resulting in the formation of 2-aminoimidazole (3)
together with diazapentadienium salt (4) (Scheme-2).
Consistent with this mechanism, the corresponding imidazo[1,2-a]pyrimidinium salts
(1) can directly be cleaved to 2-aminoimidazoles (3) upon stirring with a large excess
of secondary amine (6 or more equiv) at room temperature, while the isolated
azabutadienes (2) appeared to be stable to 20 and more equivalents of piperidine in
refluxing acetonitrile for 1 h. In contrary, azabutadienes (2) were quantitatively
cleaved to 2-aminoimidazoles (3) in the presence of 1.5 equiv triethylamine
hydrochloride salt (Scheme-3.5).
Scheme-2
N
N N R1 H
1
R' 2N
R 2
R' 2NH
-H
NH
N
N
R1 R 2
R' 2N
N
R' 2NH
A
N
N R 1
R 2
R' 2N
R' 2N
H
C D
R' 2N
NH
N
N
R1 R 2
N
N
N R 1
R 2
B
H 2N
N
N
R 1
3
R' 2N
R 2
N
N
2
N R 1
R 2
NR' 2
+ NR' 2
4

3.4 Result and Discussion
It was found that the cyclocondensation of 2-alkylaminopyrimidines with αbromoacetophenones
at 80 °C first led to stable 2-hydroxy-2,3-dihydroimidazo[1,2a]pyrimidinium
bromides. The bicyclic nature of the structures clearly followed from
1 H NMR data, indicating the doublet of doublets of the methylene fragments, as well
as from 13 C NMR spectra.
The 2-hydroxy-2,3-dihydroimidazo[1,2-a]pyrimidinium salts were obtained in good
yields, and only for sterically hindered 2-alkylaminopyrimidines the yields slightly
decreased. Dehydration of the 2-hydroxy-2,3-dihydroimidazo[1,2-a]pyrimidinium
salts was successfully achieved by short (15 min) heating in polyphosphoric acid
(PPA) at 150 °C. The corresponding imidazo[1,2-a]pyrimidinium salts were isolated
and characterized as perchlorates, and in most cases the yields were almost
quantitative. The structures of aromatic salts were completely consistent with their 1 H,
and 13 C NMR data.
The cleavage step was performed under microwave irradiation at 100 °C, using 7
equivalents of hydrazine hydrate. Resulting 2-amino-1H-imidazoles were obtained in
high yields. Using this protocol we have synthesized library of substituted 2aminoimidazole
(Table-1)
No.
Compound
Code
H 2N
N
N
R 1
R 2
R1 R2 Yield % m.p. o C
1 BS-042 cyclododecane H 53 228-230
2 BS-045 cyclooctane H 53 152-154
3 BS-048 cycloheptane H 54 180-182
4 BS-078 cyclohexane H 64 153-155

5 BS-081 cyclobutane H 47 77-79
6 BS-085 C5H11 H 53 123-125
7 BS-060 C6H13 H 53 -
8 BS-051 C7H15 H 61 -
9 BS-054 C8H17 H 55 -
10 BS-063 C9H19 H 58 -
11 BS-057 C10H21 H 53 -
12 BS-066 C11H23 H 52 -
13 BS-069 C12H25 H 52 -
14 BS-072 C13H27 H 58 44-46
15 BS-075 C14H19 H 64 44-46
16 BS-116 cyclododecane Cl 42 221-223
17 BS-117 cyclooctane Cl 55 207-209
18 BS-118 cycloheptane Cl 51 180-182
19 BS-128 cyclohexane Cl 37 179-181
20 BS-130 cyclobutane Cl 40 156-158
21 BS-129 C5H11 Cl 38 96-98
22 BS-122 C6H13 Cl 53 76-78
23 BS-119 C7H15 Cl 54 80-82
24 BS-120 C8H17 Cl 57 76-78
25 BS-123 C9H19 Cl 50 76-78
26 BS-121 C10H21 Cl 52 89-91
27 BS-124 C11H23 Cl 57 78-80
28 BS-125 C12H25 Cl 57 79-81
29 BS-126 C13H27 Cl 56 83-85
30 BS-127 C14H19 Cl 51 82-83
Yields are isolated yields over 2 steps.
Table-1: compound library of substituted 2-aminoimidazole

No.
H 2N
Compound
Code
N
N
C8H17 R1
R 1
Yield %
1 BS-199 4-OCH3 56
2 BS-200 4-F 71
3 BS-201 3,4-di Cl 64
4 BS-202 3-Br 68
5 BS-203 Naphthalen-1-yl 59
6 BS-204 4-NO2 66
7 BS-205 4-(4-NO2-Ph) 52
8 BS-206 4-SO2Me 61
9 BS-207 4-SMe 40
10 BS-208 4-(4-biphenyl)_ 31
Yields are isolated yields over 2 steps.
Table -2: 2-aminoimidazole with octyl substitution at N-1 position
3.5 Biofilm Activity
The preliminary results from our lab the basic compound (A) with a non-substituted
phenyl group at the C(5) position of the imidazole ring shows a moderate biofilm
inhibitory activity (IC50 = 130 µM). Interestingly, substitution of the para- position of
the phenyl ring with a chlorine (B) atom enhances the biofilm inhibitory activity
about ten times (IC50 = 16 µM).
H 2N
N
N
H
N
H2N N
H
A B
In an attempt to improve their biofilm inhibitory activity, we substituted the N1position
of some of the para-substituted 4(5)-phenyl-2-aminoimidazoles with n-alkyl
and cyclo-alkyl groups by using our previously established chemistry.
Cl

3.5.1 N1-alkyl 2-aminoimidazoles
In first instance a broad variety of alkyl groups, with lengths ranging from one carbon
atom to 14 carbon atoms, were introduced at the N1-position of the 4(5)monosubstituted
2-aminoimidazoles (A) and (B) resulting in compounds A-1 to A-
14, and B-1 to B-13 respectively (Table-3). Each compound was assayed for the
ability to inhibit S. Typhimurium ATCC14028 biofilm formation at 25 °C. As
depicted in figure 1, a clear correlation was found between the length of the alkyl
substituent and the biofilm inhibitory activity. In general, compounds with a short
alkyl chain substitution (C1, C2, C3) on the N1-position have a lower activity as
compared to their respective unsubstituted counterparts. This effect is most
pronounced for the methyl substituent, which causes a reduction in the activity of at
least 4 times. To a lesser extent, ethyl and isopropyl substituents also cause a
reduction in activity. Substitution with a butyl group does not have an unequivocal
effect. In the case of compound A-4, the activity is enhanced three-fold, while in the
other cases the activity is reduced. Remarkably, all the compounds substituted with
an alkyl group with an intermediate length between 5 and 10 carbon atoms are very
active biofilm inhibitors, with IC50 values in general below 12 µM. The effect of
substitution with a longer alkyl chain drastically depends on the nature of the
substituent on the C5-position of the ring (phenyl or p-chlorophenyl). Indeed,
replacement of the N1-hydrogen of compound (A) (phenyl on C5 of the ring) by a
long alkyl chain (C11-C14) raises the activity drastically, from an IC50 of 130 µM for
compound (A) to values below 8 µM for the substituted compounds (A-11 to A-14).
In the case of compound (B) (p-chlorophenyl on C5 of the ring), substitution with an
undecyl (B-10) and dodecyl (B-11) group results in very active compounds IC50
values below 5 µM), while introduction of a tridecyl group (B-12) does not have a
clear effect on the biofilm inhibitory activity and introduction of a tetradecyl (B-13)
group drastically reduces the activity (IC50 = 453 µM). Subsequently, we investigated
the influence of some of the most active representatives of this class of compounds on
the planktonic growth curve of S. Typhimurium at 25°C. Most compounds only show
a very small concentration range with a specific effect on biofilm formation and no
effect on the planktonic growth (Table-3). Therefore we cannot exclude the possibility
that the biofilm inhibitory effect of these compounds (at the higher concentrations) is
partially due to a reduction of the planktonic growth of the bacteria in the growth

medium used in the set-up to monitor biofilm formation. Interestingly, compound A-
14 with a long alkyl chain, does not follow this general trend as no effect on the
growth was observed at 80 µM while the biofilm formation was inhibited at 9 µM.
As depicted in table-3 and figure 1, a similar structure activity relationship was found
for the inhibition of P. aeruginosa biofilm formation at 25°C. Again, introduction of
a short alkyl chain at the N1-position generally results in a decreased activity (except
for compound (A-2), while all the compounds with an intermediate alkyl chain length
show very strong activities. The effect of substitution with a long alkyl chain is in this
case also dependent on the nature of the C5-subsitutent. In the case of compound (A),
substitution with a long alkyl chain results in very active compounds (A-10 to A-14),
The activity of compound (B) is also decreased after introduction of a long N1-alkyl
chain, (compounds B-9 to B-13). Interestingly, growth curve analysis revealed that
these compounds are much less toxic to P. aeruginosa than to S. Typhimurium. Most
compounds show a broad concentration range with only biofilm inhibition and no
effect on the planktonic growth (table -3).
No. Compound
Code
R1
H 2N
N
N
R 1
R2
R 2
S. Typhimurium
IC50
P. aeruginosa
IC50
1 A-1 Me H 431.5 95.1
2 A-2 Et H 206.0 20.6
3 A-3 i-pr H 175.5 4.5
4 A-4 n-Bu H 51.9 2.1
5 A-5 n-Pen H 48.3 2.0
6 A-6 n-Hex H 39.6 19.1
7 A-7 n-Hep H 12.2 6.8
8 A-8 n-Oct H 11.8 18.5
9 A-9 n-Non H 5.9 8.3
10 A-10 n-Dec H 6.1 15.0
11 A-11 n-Und H 7.1 16.2

12 A-12 n-Dod H 7.1 12.8
13 A-13 n-Trd H 5.9 27.2
14 A-14 n-Tet H 8.6 9.7
15 B-1 Me Cl 108.1 111.8
16 B-2 Et Cl 53.1 11.3
17 B-3 n-Bu Cl 57.8 16.9
18 B-4 n-Pen Cl 8.0 6.0
19 B-5 n-Hex Cl 4.9 5.3
20 B-6 n-Hep Cl 9.3 2.6
21 B-7 n-Oct Cl 5.8 3.9
22 B-8 n-Non Cl 3.9 8.0
23 B-9 n-Dec Cl 4.0 22.3
24 B-10 n-Und Cl 4.0 42.9
25 B-11 n-Dod Cl 6.1 49.7
26 B-12 n-Trd Cl 19.5 33.8
27 B-13 n-Tet Cl 453.3 19.0
IC50: concentration of inhibitor needed to inhibit biofilm formation by 50%.
Explanation Note: Number of compound code is also corresponding to the number of
carbon chain at R1 position. (ie. A-1 is Methyl substituted )
Table-3: Influence of N1-alkylated 2-aminoimidazoles on the biofilm formation and
the planktonic growth of S. Typhimurium ATCC14028 and P. aeruginosa PA14 at
25°C.

H 2N
N
N
N
H2N N
R R
Figure-1 Effect of introduction of alkyl chains with different lengths (1-14 C-
atoms; at the N1-postion of compound A (Blue) and B (Red) on the IC50 (µM) for
inhibition of the biofilm formation of S. Typhimurium ATCC14028 at 25°C in TSB
1/20.
3.5.2 Further Modification in the most active core structure
The introduction of a n-octyl side chain at the N1-position of compounds (A) and (B)
does result in very active inhibitors of both the Salmonella and Pseudomonas biofilm
formation, we also decided to introduce an n-octyl chain at the N1-position of some
other 4(5)-phenyl-2-amino-1H-imidazoles and evaluate the biofilm inhibitory activity
of the substituted compounds (table 4). All the compounds (C8-1 to C8-10) are
active inhibitors of both the S. Typhimurium and P. aeruginosa biofilm formation at
25°C, except for compounds C8-7 and C8-10. These compounds have very bulky
C5-substituents, which could diminish the solubility of the compounds in the growth
medium, reduce the uptake into the cell or cause steric hindrance in the putative
Cl

eceptor binding pocket. Growth curve analysis confirmed the previously described
finding that the N1-alkylated 2-aminoimidazoles in general show a broad
concentration range in which they specifically inhibit the biofilm formation of P.
aeruginosa, without reducing the planktonic growth of the bacteria, while this
concentration range is smaller in the case of S. Typhimurium. Compounds C8-7 and
C8-10 are exceptions to this rule as we found them to slow down the planktonic
growth of P. aeruginosa at the IC50 for biofilm inhibition.
Sr.
Compound
Code
H 2N
N
N
C8H17 R1
R 1
S.
Typhimurium
IC50
P. aeruginosa
1 C8-1 4-OCH3 8.5 1.2
2 C8-2 4-F 10.7 4.8
3 C8-3 3,4-di Cl 3.7 -
IC50
4 C8-4 3-Br 11.1 40.6
5 C8-5 Naphthalen-1-yl 6.5 17.6
6 C8-6 4-NO2 35.4 -
7 C8-7 4-(4-NO2-Ph) 116.6 >800
8 C8-8 4-SO2Me 29.1 4.9
9 C8-9 4-SMe 6.6 2.7
10 C8-10 4-(4-biphenyl) >800 >800
IC50: concentration of inhibitor needed to inhibit biofilm formation by 50%.
Table-4: Influence of N1-octyl-2-aminoimidazoles on the biofilm formation and the
planktonic growth of S. Typhimurium ATCC14028 and P. aeruginosa PA14 at 25°C.

3.5.3 Cyclo-alkyl 2-aminoimidazoles
To determine whether the introduction of an intermediate or long cyclo-alkyl chain
could also enhance the activity of the compounds, a broad variety of cyclo-alkyl
groups, with lengths ranging from 4 to 12 carbon atoms, were introduced at the N1position
of the 4(5)-monosubstituted 2-aminoimidazoles (A) and (B) (table 5). The
compounds were tested against biofilm formation of S. Typhimurium and P.
aeruginosa at 25°C. As depicted introduction of an intermediate cyclo-alkyl chain
does improve the biofilm inhibitory activity of compound (A) against S. Typhimurium
and even more drastically against P. aeruginosa. In the case of Salmonella,
introduction of a cyclo-heptyl chain yields the most active compound (compound A-
Cy-5) with an IC50 of 27 µM, as compared to 130 µM for compound (A). In the case
of Pseudomonas, cyclo-hexyl and cyclo-octyl are the best substituents as introduction
of these groups improves the activity drastically from an IC50 of 73 µM. All
compounds derived from (B) by introduction of an intermediate length side chain are
very strong inhibitors of the Salmonella and Pseudomonas biofilm formation (table
5), although their activity is not markedly better than the activity of the unsubstituted
compounds. Introduction of a dodecyl side chain abolishes the activity of all three
compounds against P. aeruginosa biofilm formation, while the effect of a cyclododecyl
substituent on the Salmonella biofilm inhibition depends on the nature of the
C5-group. Indeed, compound A-Cy-7, derived from (A) by introduction of a cyclododecyl
group, is a very strong biofilm inhibitor, while compound B-Cy-6, derived
from (B), is a moderate biofilm inhibitor. As in the case of the n-alkyl substituents,
growth curve analysis revealed that most compounds with cyclo-alkyl substituents
only possess a very small concentration range with a selective effect on the
Salmonella biofilm formation and no effect on the planktonic growth. An exception
is compound A-Cy-7, with a cyclo-dodecyl side chain, which does not affect the
planktonic growth of Salmonella at 80 µM (the highest concentration tested), while
the IC50 for biofilm inhibition is 15 µM. Interestingly, the concentration range
between biofilm inhibition and growth inhibition is much broader in the case of P.
aeruginosa (table-5).

No.
Compound
Code
R1
H 2N
N
N
R 1
R2
R 2
S. Typhimurium
IC50
P. aeruginosa
IC50
1 A-Cy-1 c-Pr H 89.6 35.0
2 A-Cy-2 c-Bu H 116.3 19.9
3 A-Cy-3 c-Pen H 70.7 12.6
4 A-Cy-4 c-Hex H 85.1 4.6
5 A-Cy-5 c-Hep H 26.8 14.2
6 A-Cy-6 c-Oct H 40.4 4.5
7 A-Cy-7 c-Dod H 14.5 >800
8 B-Cy-1 c-Pr Cl 54.8 13.0
9 B-Cy-2 c-Bu Cl 11.5 6.0
10 B-Cy-3 c-Hex Cl 33.2 11.2
11 B-Cy-4 c-Hep Cl 15.6 4.0
12 B-Cy-5 c-Oct Cl 12.8 48.6
13 B-Cy-6 c-Dod Cl 120.2 >800
IC50: concentration of inhibitor needed to inhibit biofilm formation by 50%.
Explanation Note: Number of compound code is also corresponding to the ring size of
cyclic substitution at R1 position. (ie. A-Cy-1 is Cyclopropyl substituted )
Table-5: Influence of N1-cyclo-alkyl-2-aminoimidazoles on the biofilm formation
and the planktonic growth of S. Typhimurium and P. aeruginosa PA14 at 25°C.

3.6. Conclusion
In the present study, we investigated the effect of the different substitution on 2aminoimidazoles
on the biofilm formation of S. Typhimurium and P. aeruginosa. We
found that our simplest 2-aminoimidazole structure, 4(5)-phenyl-2-amino-1Himidazole
(A), showed a moderate biofilm inhibitory activity both against S.
Typhimurium and P. aeruginosa. Substitution of the para-position of the 4(5)-phenyl
ring with a chlorine atom (B) enhanced the biofilm inhibitory activity about ten times.
We were able to delineate a relationship between the length of the N1-alkyl or N1cyclo-alkyl
chain of the N1-substituted 2-aminoimidazoles and their biofilm
inhibitory activity. In general, introduction of a short alkyl chain at the N1-position
resulted in a decreased activity against S. Typhimurium and P. aeruginosa biofilm
formation, while all compounds with an intermediate alkyl or cyclo-alkyl chain length
showed very strong activities in both test systems. The introduction of a long alkyl or
cylco-alkyl chain could either drastically enhance the activity or totally abolish the
activity, depending on the nature of the C5-subsitutent and the bacterial species tested.
Growth curve analysis revealed that the N1-(cyclo-)alkylated 2-aminoimidazoles
show a broad concentration range in which they specifically inhibit the biofilm
formation of P. aeruginosa, without retarding the planktonic growth of the bacteria.
However, these compounds were much more toxic to S. Typhimurium. Therefore, we
cannot exclude the possibility that a part of the inhibitory effect against Salmonella
biofilms (at the higher concentrations) is due to a reduction of the planktonic growth
of the bacteria in the growth medium surrounding the surface on which the biofilms
are formed.
In conclusion, the 2-aminoimidazoles and the imidazopyrimidinium salts of the
present study are valuable candidates in the development of therapeutics and
sanitizers for the combat of biofilm formation by S. Typhimurium, P. aeruginosa and
possibly other pathogenic bacteria.

3.7 Experimental
3.7.1 General Methods
All chemical reagents were used without further purification. Solvents for column
chromatography and TLC were laboratory grade and distilled before use. For thinlayer
chromatography (TLC), analytical TLC plates (Alugram SIL G/UV254 (E. M.
Merk) were used. Column chromatography was performed with flash silica gel (100-
200 mesh) or neutral alumina oxide (50-200 micron). 1 H and 13 C NMR spectra were
recorded on a Bruker Avance 300 (300 MHz) or a Bruker AMX-400 (400 MHz)
spectrometers. NMR samples were run in the indicated solvents and were referenced
internally. Chemical shift values were quoted in ppm and coupling constants were
quoted in Hz. Chemical shift multiplicities were reported as s = singlet, d = doublet, t
= triplet, q = quartet, m = multiplet and br = broad. Low-resolution mass spectra were
recorded on a HEWLETT-PACKARD instrument (CI or EI) and LCQ Advantage
instrument (ESI). High-resolution mass spectra (EI) were recorded on a KRATOS
MS50TC instrument. Melting points were determined using Reichert-Jung Thermovar
apparatus and were uncorrected.
3.7.2 Microwave Irradiation Experiments
Microwave irradiation experiments were carried out in a dedicated CEM-Discover
mono-mode microwave apparatus or Milestone MicroSYNTH multi-mode microwave
reactor (Laboratory Microwave Systems). Microwave apparatuses were used in the
standard configuration as delivered, operating at a frequency 2.45 GHz with
continuous irradiation power from 0 to 400 W. The reactions were carried out in 10,
20, 30 and 50 mL glass tubes. The temperature was measured with an IR sensor on
the outer surface of the process vial or fibre optic sensor inside the process vial. After
the irradiation period, the reaction vessel was cooled rapidly (2-5 min) to ambient
temperature by air jet cooling.

3.8. Experimental protocols
3.8.1 General Procedure for the Preparation of hydroxy Salts. (Microwave)
According to process described in chapeter-2 40 new hydrocy salts were
synthesized
3.8.2 General Procedure for the Preparation of HClO4 Salts.
A mixture of 84% polyphosphoric acid (3 g) and hydroxy salts (3 mmol) was heated
in 50 ml beaker upon intensive stirring at 150 °C for 15 min. After cooling to the
room temperature the resulting viscous mass was dissolved in 30 ml of water and 1 ml
(10 mmol) of 70% HClO4 was added dropwise upon mild stirring. The white
precipitate was washed with distilled water (3×10 mL), ether (2×10 mL) until a
neutral reaction of the pH paper and then dried over P2O5 to give salt as fine white
crystals.
In similar manner 40 new compounds were synthesized.
3.8.3 General Procedure for the Microwave-Assisted Synthesis of 2aminoimidazoles.
To a suspension of HClO4 salt (2 mmol) in MeCN (5 mL) hydrazine hydrate (0.7 mL,
14 mmol of a 64% solution, 7 equiv) was added, and the mixture was irradiated in the
sealed Milestone MicroSYNTH microwave reactor for 10 min at a ceiling
temperature of 100 °C at 150 W maximum power. After cooling down the reaction
was worked up by diluting with DCM (300 mL), washing with sat. NH4Cl solution
(150 mL), brine (150 mL) and water (2×150 mL) and drying over anhydrous Na2SO4.
After filtration and concentration the resulting residue was purified by column
chromatography (silica gel; DCM−MeOH, 9:1 v/v with 3% TEA) to afford the
product as a colourless solid.
40 new compounds were synthesized In similar manner.

3.9 Spectral Characterization
1-Cyclododecyl-5-phenyl-1H-imidazol-2-amine (BS-042)
H 2N
N
N
Yield: 42 %. Mp: 228-230 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.38 (m, 5H), 6.59 (s,
1H), 4.16 (m, 1H), 3.98 (br, 2H), 1.88 (m, 5H), 1.22(m, 14H), 0.90 (m, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ =148.4, 131.4, 131.2, 129.8 (× 2), 128.3 (×2), 127.5, 122.1,
50.0, 29.1(×2), 24.0 (×2), 23.9 (×2), 22.6 (×2), 21.9 (×2), 21.5. HRMS (EI):C21H31N3,
calcd 325.2518, found: 325.2511.
1-Cyclooctyl-5-phenyl-1H-imidazol-2-amine (BS-045)
H 2N
N
N
Yield: 53 %. Mp: 152-154 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.43-7.28 (m, 5H),
6.60 (s, 1H), 4.24 (m, 1H), 3.98 (br, 2H), 2.11 (m, 2H), 1.87 (m, 4H), 1.50 (m, 7H),
1.25 (m, 1H). 13 C NMR (75.5 MHz, CDCl3): δ =148.1, 131.2, 129.5, 129.0 (×2),
128.4 (×2), 127.3, 122.7, 54.5, 33.1(×2), 26.2, 25.8 (×2), 25.3 (×2). HRMS (EI):
C17H23N3, calcd 269.1892, found: 269.1893.
1-Cycloheptyl-5-phenyl-1H-imidazol-2-amine (BS-048)
H 2N
N
N
Yield: 54 %. Mp: 180-182 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.43-7.29 (m, 5H),
6.59 (s, 1H), 4.09 (m, 3H), 2.13 (m, 2H), 1.95 (m, 2H), 1.73 (m, 2H), 1.54 (m, 6H).
13 C NMR (75.5 MHz, CDCl3): δ =148.2, 131.1, 129.6, 128.9 (×2), 128.5 (×2), 127.3,

122.6, 54.6, 33.3(×2), 27.3 (×2), 25.7 (×2). HRMS (EI): C16H21N3, calcd 255.1735,
found: 255.1759.
1-Heptyl-5-phenyl-1H-imidazol-2-amine (BS-051)
H 2N
N
N
C7H15 Yield: 61 %. 1 H NMR (300 MHz, CDCl3): δ = 7.43-7.31 (m, 5H), 6.67 (s, 1H), 3.95
(br, 2H), 3.75(t, J = 7.5 Hz, 2H), 1.59 (m, 2H), 1.17 (m, 8H), 0.84 (t, J = 6.5 Hz, 3H).
13
C NMR (75.5 MHz, CDCl3): δ =149.0, 131.0, 129.4, 128.6 (×2), 128.2 (×2), 127.2,
122.6, 43.1, 31.5, 29.5, 28.6, 26.4, 22.4, 14.0. HRMS (EI): C16H23N3, calcd 257.1892,
found: 257.1908.
1-Octyl-5-phenyl-1H-imidazol-2-amine (BS-054)
H 2N
N
N
C8H17 Yield: 55 %. 1 H NMR (300 MHz, CDCl3): δ = 7.40-7.31 (m, 5H), 6.67 (s, 1H), 4.02
(br, 2H), 3.75(t, J = 7.3 Hz, 2H), 1.59 (m, 2H), 1.17 (m, 10H), 0.85 (t, J = 6.6 Hz,
3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1, 131.0, 129.4, 128.6 (×2), 128.2 (×2),
127.2, 122.6, 43.1, 31.6, 29.5, 29.0, 28.9, 26.4, 22.2, 14.0. HRMS (EI): C17H25N3,
calcd 271.2048, found: 271.2035.
1-Decyl-5-phenyl-1H-imidazol-2-amine (BS-057)
H 2N
N
N
C 10H 21
Yield: 53 %. 1 H NMR (300 MHz, CDCl3): δ = 7.41-7.29 (m, 5H), 6.67 (s, 1H), 4.15
(br, 2H), 3.75(t, J = 7.3 Hz, 2H), 1.58 (m, 2H), 1.21 (m, 14H), 0.87 (t, J = 6.5 Hz,
3H). 13 C NMR (75.5 MHz, CDCl3): δ =148.9, 131.0, 129.4, 128.6 (×2), 128.3 (×2),
127.2, 122.6, 43.1, 31.8, 29.5, 29.4, 28.3, 29.2, 28.9, 26.4, 22.2, 14.1. HRMS (EI):
C19H29N3, calcd 299.2361, found: 299.2365.

1-Hexyl-5-phenyl-1H-imidazol-2-amine (BS-060)
H 2N
N
N
C6H13 Yield: 53 %. 1 H NMR (300 MHz, CDCl3): δ = 7.41-7.30 (m, 5H), 6.67 (s, 1H), 3.98
(br, 2H), 3.75(t, J = 7.4 Hz, 2H), 1.59 (m, 2H), 1.18 (m, 6H), 0.82 (t, J = 6.4 Hz, 3H).
13
C NMR (75.5 MHz, CDCl3): δ =149.0, 131.0, 129.4, 128.6 (×2), 128.2 (×2), 127.2,
122.8, 43.1, 31.1, 29.5, 26.1, 22.4, 13.8. HRMS (EI): C15H21N3, calcd 243.1735,
found: 243.1730.
1-Nonyl-5-phenyl-1H-imidazol-2-amine (BS-063)
H 2N
N
N
C9H19 Yield: 58 %. 1 H NMR (300 MHz, CDCl3): δ = 7.31 (m, 5H), 6.67 (s, 1H), 3.95 (br,
2H), 3.75(t, J = 7.5 Hz, 2H), 1.58 (m, 2H), 1.17 (m, 12H), 0.86 (t, J = 6.6 Hz, 3H).
13
C NMR (75.5 MHz, CDCl3): δ =152.6, 134.6, 132.9, 132.1 (× 2), 131.7 (× 2), 130.7,
126.4, 46.6, 35.3, 33.0, 32.8, 32.6, 32.5, 30.0, 26.1, 17.6. HRMS (EI): C18H27N3, calcd
285.2205, found: 285.2222.
5-Phenyl-1-undecyl-1H-imidazol-2-amine (BS-066)
H 2N
N
N
C 11H 23
Yield: 52 %. 1 H NMR (300 MHz, CDCl3): δ = 7.42-7.31 (m, 5H), 6.67 (s, 1H), 3.99
(br, 2H), 3.75 (t, J = 7.0 Hz, 2H), 1.59 (m, 2H), 1.17 (m, 16H), 0.87 (t, J = 6.4 Hz,
3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1, 131.0, 129.4, 128.6 (×2), 128.2 (×2),
127.1, 122.9, 43.1, 31.8, 29.5 (× 2), 29.4, 29.3, 29.2, 28.9, 26.4, 22.6, 14.1. HRMS
(EI): C20H31N3, calcd 313.2518, found: 313.2512.
1-Dodecyl-5-phenyl-1H-imidazol-2-amine (BS-069)
H 2N
N
N
C 12H 25

Yield: 52 %. 1 H NMR (300 MHz, CDCl3): δ = 7.39-7.30 (m, 5H), 6.67 (s, 1H), 3.99
(br, 2H), 3.75 (t, J = 7.2 Hz, 2H), 1.58 (m, 2H), 1.17 (m, 18H), 0.88 (t, J = 6.4 Hz,
3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.0, 131.1, 129.4, 128.6 (×2), 128.2 (×2),
127.1, 123.0, 43.1, 31.9, 29.5 (× 3), 29.4, 29.3(× 2), 28.9, 26.4, 22.6, 14.1. HRMS
(EI): C21H33N3, calcd 327.2674, found: 327.2663.
5-Phenyl-1-tridecyl-1H-imidazol-2-amine (BS-072)
H 2N
N
N
C 13H 27
Yield: 58 %. Mp: 44-46 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.40-7.31 (m, 5H), 6.67
(s, 1H), 3.99 (br, 2H), 3.75 (t, J = 7.3 Hz, 2H), 1.58 (m, 2H), 1.17 (m, 20H), 0.88 (t, J
= 6.4 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =148.9, 131.0, 129.4, 128.6 (×2),
128.2 (×2), 127.1, 122.7, 43.1, 31.9, 29.5 (× 7), 28.9, 26.4, 22.6, 14.1. HRMS (EI):
C22H35N3, calcd 341.2831, found: 341.2827.
5-Phenyl-1-tetradecyl-1H-imidazol-2-amine (BS-075)
H 2N
N
N
C 14H 29
Yield: 64 %. Mp: 44-46 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.41-7.30 (m, 5H), 6.67
(s, 1H), 4.00 (br, 2H), 3.75 (t, J = 7.4 Hz, 2H), 1.58 (m, 2H), 1.17 (m, 22H), 0.88 (t, J
= 6.3 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =148.8, 131.0, 129.5, 128.6 (×2),
128.3 (×2), 127.2, 122.8, 43.1, 31.9, 29.6 (× 8), 28.9, 26.4, 22.6, 14.1. HRMS (EI):
C23H37N3, calcd 355.2987, found: 355.3016.
1-Cyclohexyl-5-phenyl-1H-imidazol-2-amine (BS-078)
H 2N
N
N
Yield: 64 %. Mp: 153-155 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.42-7.28 (m, 5H),
6.60 (s, 1H), 3.89 (m, 3H), 1.88 (m, 6H), 1.64 (m, 1H), 1.18 (m, 3H). 13 C NMR (75.5

MHz, CDCl3): δ =148.4, 131.2, 130.0, 129.0 (×2), 128.5 (×2), 127.3, 122.6, 55.1,
31.2(×2), 25.9 (×2), 25.1. HRMS (EI): C15H19N3, calcd 241.1579, found: 241.1589.
1-Cyclobutyl-5-phenyl-1H-imidazol-2-amine (BS-081)
H 2N
N
N
Yield: 47%. Mp: 77-79 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.41-7.28 (m, 5H), 6.58
(s, 1H), 4.61 (m, 1H), 4.07 (br, 2H), 2.51 (m, 2H), 2.27 (m, 2H), 1.75 (m, 2H). 13 C
NMR (75.5 MHz, CDCl3): δ =149.1, 131.3, 129.7, 128.6 (×2), 128.3 (×2), 127.1,
122.9, 49.2, 29.5 (×2), 15.0. HRMS (EI): C13H15N3, calcd 213.1266, found: 213.1268.
1-Pentyl-5-phenyl-1H-imidazol-2-amine (BS-085)
H 2N
N
N
C5H11 Yield: 53 %. Mp: 123-125 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.46-7.29 (m, 5H),
6.67 (s, 1H), 4.00 (br, 2H), 3.75 (t, J = 7.5 Hz, 2H), 1.59 (m, 2H), 1.19 (m, 4H), 0.81
(t, J = 6.7 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.0, 131.0, 129.4, 128.6 (×2),
128.2 (×2), 127.2, 122.8, 43.1, 29.2, 28.6, 22.0, 13.8. HRMS (EI): C14H19N3, calcd
229.1579, found: 229.1594.
5-(4-Chlorophenyl)-1-cyclododecyl-1H-imidazol-2-amine (BS-116)
H 2N
N
N
Yield: 42 %. Mp: 221-223 ° C 1 H NMR (300 MHz, CDCl3): δ = 7.38 (m, 5H), 6.59 (s,
1H), 4.16 (m, 1H), 3.98 (br, 2H), 1.88 (m, 5H), 1.22(m, 14H), 0.90 (m, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ =148.4, 131.4, 131.2, 129.8 (×2), 128.3 (×2), 127.5, 122.1,
50.0, 29.1(×2), 24.0 (×2), 23.9 (×2), 22.6 (×2), 21.9 (×2), 21.5. HRMS (EI):C21H31N3,
calcd 325.2518, found: 325.2118.
Cl

5-(4-Chlorophenyl)-1-cyclooctyl-1H-imidazol-2-amine (BS-117)
H 2N
N
N
Yield: 55 %. Mp: 207-209 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.37 (d, J = 8.4 Hz,
2H), 7.20 (d, J = 8.4 Hz, 2H), 6.59 (s, 1H), 4.18 (m, 1H), 4.02 (br, 2H), 2.12 (m, 2H),
1.85 (m, 4H), 1.50 (m, 7H), 1.25 (m, 1H). 13 C NMR (75.5 MHz, CDCl3): δ =148.6,
131.1, 130.0 (× 2), 129.7, 128.7 (×2), 128.3, 123.4, 56.7, 33.3(×2), 27.2 (×3), 25.7
(×2). HRMS (EI): C17H22ClN3, calcd 303.1502, found: 303.1519.
5-(4-Chlorophenyl)-1-cycloheptyl-1H-imidazol-2-amine (BS-118)
H 2N
N
N
Yield: 51 %. Mp: 180-182 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.36 (d, J = 8.4 Hz,
2H), 7.18 (d, J = 8.4 Hz, 2H), 6.59 (s, 1H), 4.00 (m, 3H), 2.12 (m, 2H), 1.92 (m, 2H),
1.75 (m, 2H), 1.55 (m, 6H). 13 C NMR (75.5 MHz, CDCl3): δ =148.6, 131.1, 130.0
(×2), 129.7, 128.7 (×2), 128.3, 123.4, 56.7, 33.3(×2), 27.2 (×2), 25.7 (×2). HRMS
(EI): C16H20ClN3, calcd 289.1346, found: 289.1364.
5-(4-Chlorophenyl)-1-heptyl-1H-imidazol-2-amine (BS-119)
H 2N
N
N
C7H15 Yield: 54 %. Mp: 80-82 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 8.4 Hz, 2H), 6.66 (s, 1H), 4.02 (br, 2H), 3.72(t, J = 7.5 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 8H), 0.84 (t, J = 6.5 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.4,
133.0, 129.6, 129.3 (×2), 128.8 (×2), 128.1, 123.5, 43.1, 31.5, 29.5, 28.6, 26.4, 22.5,
14.2. HRMS (EI): C16H22ClN3, calcd 291.1502, found: 291.1507.
Cl
Cl
Cl

5-(4-Chlorophenyl)-1-octyl-1H-imidazol-2-amine (BS-120)
H 2N
N
N
C8H17 Yield: 57 %. Mp: 76-78 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 9.3 Hz, 2H), 6.67 (s, 1H), 3.95 (br, 2H), 3.73(t, J = 7.2 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 10H), 0.86 (t, J = 6.6 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.2,
131.1, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.4, 43.1, 31.6, 29.5, 29.0, 28.9, 26.4,
22.2, 14.0. HRMS (EI): C17H24ClN3, calcd 305.1659, found: 305.1649.
5-(4-Chlorophenyl)-1-decyl-1H-imidazol-2-amine (BS-121)
H 2N
N
N
C 10H 21
Yield: 52 %. Mp: 89-91 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.33 (d, J = 9.0 Hz, 2H), 6.67 (s, 1H), 3.97 (br, 2H), 3.72 (t, J = 7.4 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 14H), 0.87 (t, J = 6.5 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =148.3,
133.0, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.5, 43.1, 31.8, 29.5, 29.4 (×2), 29.2,
28.9, 26.4, 22.6, 14.1. HRMS (EI): C19H28ClN3, calcd 333.1972, found: 333.1999.
5-(4-Chlorophenyl)-1-hexyl-1H-imidazol-2-amine (BS-122)
H 2N
N
N
C6H13 Yield: 53 %. Mp: 76-78 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 8.4 Hz, 2H), 6.67 (s, 1H), 3.97 (br, 2H), 3.37 (t, J = 7.9 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 6H), 0.83 (t, J = 6.4 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.3,
133.0, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.5, 43.1, 31.1, 29.5, 26.1, 22.4, 13.9.
HRMS (EI): C15H20N3, calcd 277.1346, found: 277.1353.
5-(4-Chlorophenyl)-1-nonyl-1H-imidazol-2-amine (BS-123)
H 2N
N
N
C9H19 Cl
Cl
Cl
Cl

Yield: 50 %. Mp: 76-78 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.5 Hz, 2H),
7.23 (d, J = 8.9 Hz, 2H), 6.67 (s, 1H), 4.00 (br, 2H), 3.73 (t, J = 7.3 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 12H), 0.87 (t, J = 6.6 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =152.2,
133.1, 129.5, 129.3 (× 2), 128.8 (× 2), 128.2, 123.6, 43.1, 31.7, 29.6, 29.3, 29.1, 28.9,
26.4, 22.6, 14.0. HRMS (EI): C18H26ClN3, calcd 319.1815, found: 319.1808.
5-(4-Chlorophenyl)-1-undecyl-1H-imidazol-2-amine (BS-124)
H 2N
N
N
C 11H 23
Yield: 57 %. Mp: 78-80 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 9.1 Hz, 2H), 6.66 (s, 1H), 4.00 (br, 2H), 3.72 (t, J = 7.3 Hz, 2H), 1.57 (m,
2H), 1.18 (m, 16H), 0.88 (t, J = 6.4 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.2,
133.1, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.6, 43.1, 31.8, 29.6, 29.5, 29.4 (×2),
29.3, 28.9, 26.4, 22.6, 14.1. HRMS (EI): C20H30ClN3, calcd 347.2128, found:
347.2136.
5-(4-Chlorophenyl)-1-dodecyl-1H-imidazol-2-amine (BS-125)
H 2N
N
N
C 12H 25
Yield: 57 %. Mp: 79-91 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 8.9 Hz, 2H), 6.67 (s, 1H), 3.99 (br, 2H), 3.72 (m, 2H), 1.58 (m, 2H), 1.17
(m, 18H), 0.88 (m, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1, 133.1, 129.5, 129.3
(×2), 128.8 (×2), 128.2, 123.6, 43.1, 31.9, 29.6 (× 3), 29.4 (× 2), 29.3, 28.9, 26.4,
22.6, 14.1. HRMS (EI): C21H32ClN3, calcd 361.2285, found: 361.2281.
5-(4-Chlorophenyl)-1-tridecyl-1H-imidazol-2-amine (BS-126)
H 2N
N
N
C 13H 27
Yield: 56 %. Mp: 83-85 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.5 Hz, 2H),
7.23 (d, J = 9.3 Hz, 2H), 6.67 (s, 1H), 3.99 (br, 2H), 3.72 (t, J = 7.3 Hz, 2H), 1.57 (m,
2H), 1.17 (m, 20H), 0.88 (t, J = 6.3 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1,
Cl
Cl
Cl

133.1, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.6, 43.1, 31.9, 29.6 (×4), 29.5, 29.4,
29.3, 28.9, 26.4, 22.6, 14.1. HRMS (EI): C22H34ClN3, calcd 375.2441, found:
375.2446.
5-(4-Chlorophenyl)-1-tetradecyl-1H-imidazol-2-amine (BS-127)
H 2N
N
N
C 14H 29
Yield: 51 %. Mp: 82-83 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.5 Hz, 2H),
7.23 (d, J = 8.7 Hz, 2H), 6.67 (s, 1H), 4.00 (br, 2H), 3.72 (t, J = 7.3 Hz, 2H), 1.55 (m,
2H), 1.17 (m, 22H), 0.87 (m, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1, 133.1,
129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.6, 43.1, 31.9, 29.6 (×5), 29.5, 29.4 (×2),
29.0, 26.4, 22.7, 14.1. HRMS (EI): C23H36ClN3, calcd 389.2598, found: 389.2602.
5-(4-Chlorophenyl)-1-cyclohexyl-1H-imidazol-2-amine (BS-128)
H 2N
N
N
Yield: 37 %. Mp: 179-181 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz,
2H), 7.18 (d, J = 8.4 Hz, 2H), 6.60 (s, 1H), 4.00 (br, 2H), 3.81 (m, 1H), 1.87 (m, 6H),
1.66 (m, 1H), 1.23 (m, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =148.8, 133.2, 130.2
(×2), 129.8, 128.9, 128.7 (×2), 123.7, 55.2, 31.2(×2), 25.9 (×2), 25.1. HRMS (EI):
C15H18ClN3, calcd 275.1189, found: 275.1187.
5-(4-Chlorophenyl)-1-pentyl-1H-imidazol-2-amine (BS-129)
H 2N
N
N
C5H11 Yield: 38 %. Mp: 96-98 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.35 (d, J = 8.4 Hz, 2H),
7.23 (d, J = 8.8 Hz, 2H), 6.67 (s, 1H), 4.08 (br, 2H), 3.73 (t, J = 7.3 Hz, 2H), 1.58 (m,
2H), 1.22 (m, 4H), 0.82 (t, J = 6.6 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.3,
133.0, 129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.4, 43.2, 29.3, 28.6, 22.1, 13.8. HRMS
(EI): C14H18ClN3, calcd 263.1189, found: 263.1185.
Cl
Cl
Cl

5-(4-Chlorophenyl)-1-cyclobutyl-1H-imidazol-2-amine (BS-130)
H 2N
N
N
Yield: 40%. Mp: 156-159 ° C. 1 H NMR (300 MHz, CDCl3): δ = 7.33 (d, J = 8.4 Hz,
2H), 7.19 (d, J = 8.5 Hz, 2H), 6.57 (s, 1H), 4.55 (m, 1H), 4.00 (br, 2H), 2.47 (m, 2H),
2.27 (m, 2H), 1.76 (m, 2H). 13 C NMR (75.5 MHz, CDCl3): δ =149.4, 133.0, 129.8,
129.7 (×2), 128.6 (×2), 128.4, 123.5, 49.2, 29.5 (×2), 15.0. HRMS (EI): C13H14ClN3,
calcd 247.0876, found: 247.0874.
5-(4-Methoxyphenyl)-1-octyl-1H-imidazol-2-amine (BS-199)
H 2N
N
N
C8H17 Yield: 56 %. 1 H NMR (300 MHz, CDCl3): δ = 7.25 (m, 2H), 6.95 (d, J = 8.7 Hz, 2H),
6.60 (s, 1H), 3.97 (br s, 2H), 3.84 (s, 3H), 3.70 (t, J = 7.8 Hz, 2H), 1.56 (m, 2H), 1.17
(m, 10H), 0.86 (t, J = 7.05 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.2, 131.1,
129.5, 129.3 (×2), 128.8 (×2), 128.2, 123.4, 43.1, 31.6, 29.5, 29.0, 28.9, 26.4, 22.2,
14.0. HRMS (EI): C18H27N3O, calcd 301.4265, found: 301.4271.
5-(4-Fluorophenyl)-1-octyl-1H-imidazol-2-amine (BS-200)
H 2N
N
N
C8H17 Yield: 71 %. 1 H NMR (300 MHz, CDCl3): δ = 7.27 (m, 2H), 7.09 (m, 2H), 6.63 (s,
1H), 3.96 (br s, 2H), 3.70 (t, J = 6.8 Hz, 2H), 1.56 (m, 2H), 1.17 (m, 10H), 0.86 (t, J =
7.05 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =163.8, 160.5, 148.7, 130.2, 128.4,
127.0, 122.9, 115.5, 104.7, 43.0, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI):
C17H24FN3, calcd 289.3910, found: 289.3901.
5-(3,4-Dichlorophenyl)-1-octyl-1H-imidazol-2-amine (BS-201)
Cl
O
F

H 2N
N
N
C8H17 Yield: 64 %. 1 H NMR (300 MHz, CDCl3): δ = 7.47 (d, J = 8.3 Hz, 1H), 7.40 (d, J =
7.98 Hz, 1H), 7.16 (d of d, J = 2.0, 6.2 Hz, 1H), 6.71 (s, 1H), 4.05 (br s, 2H), 3.73 (t, J
= 7.68 Hz, 2H), 1.59 (m, 2H), 1.19 (m, 10H), 0.86 (t, J = 7.05 Hz, 3H). 13 C NMR
(75.5 MHz, CDCl3): δ =149.6, 132.8, 131.1, 131.0, 130.6, 129.5, 127.1, 127.0, 124.2,
43.3, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI): C17H23Cl2N3, calcd
340.2906, found: 240.2918.
5-(3-Bromophenyl)-1-octyl-1H-imidazol-2-amine (BS-202)
H 2N
N
N
C8H17 Yield: 68 %. 1 H NMR (300 MHz, CDCl3): δ = 7.45 (m, 2H), 7.25 (m, 2H), 6.70 (s,
1H), 4.02 (br s, 2H), 3.74 (t, J = 7.71 Hz, 2H), 1.59 (m, 2H), 1.19 (m, 10H), 0.86 (t, J
= 6.08 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.2, 133.0, 130.8, 130.1 (×2),
128.0, 126.5, 123.8, 122.6, 43.2, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI):
C17H24BrN3, calcd 350.2966, found:250.2978.
5-(Naphthalen-1-yl)-1-octyl-1H-imidazol-2-amine (BS-202)
H 2N
N
N
C8H17 Yield: 68 %. 1 H NMR (300 MHz, CDCl3): δ = 7.85 (m, 4H), 7.46 (m, 3H), 6.78 (s,
1H), 4.04 (br s, 2H), 3.83 (t, J = 7.62 Hz, 2H), 1.62 (m, 2H), 1.15 (m, 10H), 0.82 (t, J
= 6.99 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =149.1, 133.4, 132.4, 129.5, 128.3,
128.2, 127.9, 127.7, 126.6, 126.4 (×2), 126.0, 123.0, 43.3, 31.6, 29.5, 29.0, 28.9, 26.4,
22.5, 14.0. HRMS (EI): C21H27N3, calcd 321.4592, found: 321.4576.
5-(4-Nitrophenyl)-1-octyl-1H-imidazol-2-amine (BS-204)
H 2N
N
N
C8H17 Cl
Cl
Br
NO 2

Yield: 66%. 1 H NMR (300 MHz, CDCl3): δ = 8.27 (d, J = 8.7 Hz, 2H), 7.47 (t, J = 8.7
Hz, 2H), 6.89 (s, 1H), 4.13 (br s, 2H), 3.82 (t, J = 7.8 Hz, 2H), 1.63 (m, 2H), 1.21 (m,
10H), 0.85 (t, J = 6.96 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =163.8, 160.5,
148.7, 130.2, 128.4, 127.0, 122.9, 115.5, 104.7, 43.0, 31.6, 29.5, 29.0, 28.9, 26.4,
22.5, 14.0. HRMS (EI): C17H24N4O2, calcd 316.3981, found: 316.3993.
5-(4'-Nitrobiphenyl-4-yl)-1-octyl-1H-imidazol-2-amine (BS-205)
H 2N
N
N
C8H17 Yield: 52 %. 1 H NMR (300 MHz, CDCl3): δ = 8.33 (m, 1H), 7.78-7.35 (m, 6H), 7.13
(m 1H), 6.77 (s, 1H), 4.07 (br s, 2H), 3.79 (m, 2H), 1.63 (m, 2H), 1.19 (m, 10H), 0.84
(m, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =163.8, 160.5, 148.7, 130.2, 128.4, 127.0,
122.9, 115.5, 104.7, 43.0, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS (EI):
C23H28N4O2, calcd 392.4940, found:392.4928.
NO 2
5-(4-(Methylsulfonyl)phenyl)-1-octyl-1H-imidazol-2-amine (BS-206)
H 2N
N
N
C8H17 SO 2Me
Yield: 61 %. 1 H NMR (300 MHz, CDCl3): δ = 7.97 (d, J = 8.1 Hz, 2H), 7.51 (d, J =
7.98 Hz, 2H), 6.83 (s, 1H), 4.09 (br s, 2H), 3.82 (t, J = 7.68 Hz, 2H), 3.09 (s 3H), 1.62
(m, 2H), 1.21 (m, 10H), 0.86 (t, J = 7.05 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ
=150.7, 138.1, 136.6, 127.9 (×2), 127.6, 127.4 (×2), 126.0, 44.5, 43.6, 31.6, 29.6,
29.0, 28.9, 26.5, 22.5, 14.0. HRMS (EI): C18H27N3O2S, calcd 349.4909, found:
349.4920.
5-(4-(Methylthio)phenyl)-1-octyl-1H-imidazol-2-amine (BS-207)
H 2N
N
N
C8H17 Yield: 40 %. 1 H NMR (300 MHz, CDCl3): δ = 7.33-7.22 (m, 4H), 6.65 (s, 1H), 4.00
(br s, 2H), 3.73 (t, J = 7.98 Hz, 2H), 2.51 (s, 3H), 1.58 (m, 2H), 1.18 (m, 10H), 0.86
(t, J = 6.99 Hz, 3H). 13 C NMR (75.5 MHz, CDCl3): δ =163.8, 160.5, 148.7, 130.2,
SMe

128.4, 127.0, 122.9, 115.5, 104.7, 43.0, 31.6, 29.5, 29.0, 28.9, 26.4, 22.5, 14.0. HRMS
(EI): C18H27N3S, calcd 317.4921, found: 317.4935.
5-(Triphenyl-4-yl)-1-octyl-1H-imidazol-2-amine (BS-208)
H 2N
N
N
C8H17 Yield: 31 %. 1 H NMR (300 MHz, CDCl3): δ = 7.70-7.64 (m, 7H), 7.46-7.40 (m 5H),
6.74 (s, 1H), 4.03 (br s, 2H), 3.80 (m, 2H), 1.63 (m, 2H), 1.20 (m, 10H), 0.86 (m, 3H).
13
C NMR (75.5 MHz, CDCl3): δ =148.9, 140.5, 140.2, 139.2 (×2), 130.0, 129.2, 128.8
(×2), 128.5, 127.5 (×2), 127.4, 127.3, 127.2 (×4), 127.0, 126.9, 123.1, 43.2, 31.7,
29.6, 29.0, 28.9, 26.5, 22.5, 14.0. HRMS (EI): C29H33N3, calcd 423.5924, found:
423.5941.

3.10 Representative NMR spectra
3.10.1 1 H and 13 C NMR spectra of bs-063
Integral
7.4263
7.3999
7.3780
7.3252
7.3171
7.3102
7.2625
8.0
152.6248
150
7.5
4.9005
7.0
134.6350
132.9477
132.1549
131.8022
130.7185
140
6.6762
0.9360
130
6.5
126.4311
H 2N
120
H 2N
6.0
N
N
N
C9H19 5.5
N
C9H19 110
100
5.0
90
4.5
3.9905
3.7821
3.7570
3.7312
1.4513
81.0402
80.6220
80.2038
4.0
(ppm)
80
(ppm)
2.1067
3.5
70
3.0
60
2.5
50
46.6571
2.0
40
1.6110
1.5890
1.5658
1.9669
1.5
12.326
1.0
35.3221
33.0857
32.8639
32.6638
32.5038
30.0128
26.1509
30
0.8917
0.8691
0.8465
3.0000
20
17.6160
0.5
10
-0.0002
0.0
0

3.10.2 1 H and 13 C NMR spectra of bs-125
Integral
9.0
160
8.5
149.1738
150
8.0
7.3853
7.3570
7.2629
7.2334
2.0207
2.6488
7.5
7.0
6.6722
N
H2N N
C12H25 0.9125
133.1114
129.5949
129.3876
128.8857
128.2966
123.6310
140
130
6.5
6.0
5.5
N
H2N N
C12H25 120
110
100
5.0
Cl
Cl
3.9909
3.7536
3.7285
3.7028
1.4687
1.9926
4.5 4.0
(ppm)
77.4765
77.0510
76.6292
90 80
(ppm)
70
3.5
3.0
60
2.5
50
2.0
43.1952
40
1.5750
1.9595
1.5
1.2492
1.1802
0.9021
0.8808
0.8576
18.169
3.0000
1.0
0.5
31.9039
29.6019
29.4965
29.4019
29.3292
28.9983
26.4927
22.6890
14.1359
30
20
10
0.0002
0.0
0.0008
0

3.11 References
[1] (a) Alvi K. A, Peters B. M, Hunter L. M, Crews P. (1993) Tetrahedron. 49,329. (b) Chan G.
W, Mong S, Hemling M. E, Freyer A. J, Offen P. H, DeBrosse C. W, Sarau H. M, Westley J.
W. (1993) J. Nat. Prod. 56, 116. (c) Tsuda M, Shigemori H, Ishibashi M, Kobayashi J. (1992)
Tetrahedron Lett. 33, 2597. (d) Ishibashi M, Tsuda M, Ohizumi Y, Sasaki T, Kobayashi
(1991) J. Ezperientia, 47, 299. (e) Kobayashi J, Tsuda M, Ohizumi Y. (1991) Experientia 47,
301. (f) Keifer P. A, Schwartz R. E, Koker M. E. S, Hughes R. J, Rittschof D, Rinehart K. L.
(1991) J. Org. Chem. 56, 2965. (g) Morales J. J, Rodriguez A. D. (1991) J. Nat. Prod. 54,
629. (h) Alvi K. A, Crews P, Loughhead D. G. (1991) J. Nat. Prod. 54, 1509. (i) Wright A. E,
Chiles S, Cross S. (1991) J. Nat. Prod. 54, 1684. (j) Kobayashi J, Tsuda M, Murayama T,
Nakamura H, Ohizumi Y, Ishibashi M, Iwamura M, Ohta T, Nozoe S. (1990) Tetrahedron
46, 5579. (k) Bedoya-Zurita M, Ahond A Poupat C, Potier P. (1989) Tetrahedron 45, 6713.
(l) Walker R. P, Faulkner D. J, Van Engen D, Clardy J. (1981) J. Am. Chem. SOC. 103,
6772.
[2] (a) Nagai W, Kirk K. L, Cohen L. A. (1973) J. Org. Chem. 38, 971. (b) Dismukes K, Rogers
M, Daily J. W. (1976) J. Neurochem. 26, 785. (c) Lipinski C. A, LaMattina J. L, Hohnke L.
A. (1986) J. Med. Chem. 28, 1628. (d) Impicciatore M, Morini G, Chiavarini M, Plazzi P. V,
Bordi F, Vitali F. (1986) Agents Actions 18, 134. (e) Haaksma J, DonnB-Op den Kelder M,
Timmerman H, Weinstein H, (1991) In New Perspectives in Histamine Research;
BirkhEiuser Verlag: Basel, 315-324.
[3] See Ann. Drug Data Rep. 1993,15, 513.
[4] Jung F, Boucherot D, Delvare C, Olivier A, Davies G. M, Betts M. J, Brown R, Stevenson R,
Joseph M, Kingston F, Pittam, (1993) J. Antibiot. 46, 992.
[5] (a) Beaman A. G, Tautz W, Gabriel T, Duschinsky R. (1966) J. Am. Chem. SOC. 87, 389.
(b) Lancini C, Lazzari E, Arioli V, Bellani P. (1969) J. Med. Chem. 12, 775.
[6] For example see: Jenkins C, Naylor A, O'Neill, Threadgill D, Cole S, Stratford J, Adams
G. E, Fielden M, Suto J, Stier A. J. Med. Chem. lSW, 33, 2603. Adams E, Stratford J.
(1986) Biochem. Pharm. 35, 71.
[7] Storey B. T, Sullivan W. W, Moyer C. L. (1986) J. Org. Chem. 29, 3118.
[8] Lawson, A. (1956) J. Chem. SOC. 307.
[9] (a) Lancini G. C, Lazzari E. (1966) J. Heterocycl. Chem. 3, 1 (b) Cavalleri B, Ballotta R,
Lancini G. C. (1979) J. Heterocycl. Chem. 979.
[10] See: Porter A. E. A. (1984) In Comprehensive Heterocyclic Chemistr Pyrazines and Their
Benzo Derivatives; Boulton A. J, McKillop A Eds.; Pergamon Press: New York. 3, 184-185.
[11] Fargher R. G, Pyman F. L. (1919) J. Chem. SOC. 217.
[12] Kirk K. L. (1978) J. Org. Chem. 43, 4381.
[13] Kreutzberger A. (1962) J. Org. Chem. 27, 886.
[14] Nishimura T, Kitajima K. (1979) J. Org. Chem. 44, 818.

[15] Takahashi K, Kirk K. L, Cohen L. A. J. Org. Chem. 1984, 49, 1951. Jarosinski M. A,
Anderson K. (1991) J. Org. Chem. 56, 4058.
[16] (a) Ruccia M, Vivona N, Cusmano G. (1974) Tetrahedron 30, 3859. (b) Braun M, Buchi G,
Bushey F. (1978) J. Am. Chem. SOC. 100, 4208. (c) Sehgal K, Agrawal C. (1982) J. Pharm.
Sci. 71, 1203. (d) Berry A, Gilbertsen B, Cook D. (1986) J. Med. Chem. 29, 2034.
[17] LaMattina L, Mularski C. J. (1984) Tetrahedron Lett. 25, 2957.
[18] Xu Y, Yakushijin K, Horne A. (1993) Tetrahedron Lett. 34, 6981

Copper Catalyzed Microwave Assisted One Pot
Synthesis of 2-Aminoimidazole-Triazole
Framework via Dimorth Rearrangement and
Click Reaction

Chapter-4
Copper Catalyzed Microwave Assisted One Pot
Synthesis of 2-Aminoimidazole-Triazole Framework
via Dimorth Rearrangement and Click Reaction.
Br
R 2
N
N
n
N
OH
R 1
n = 1,2
N 3
ABSTRACT
One-pot Microwave-Assisted Synthesis
Cu(OAc) 2 (5 mol %)
N 2H 4 (2 equiv)
R 3
(1.2 equiv)
MW, 100 o C, 2-5 min
R 2
N
NH
N
H
22 examples,
upto 90% yield
R 1
N
N
n
N
R3 A microwave assisted one-pot Cu(II)-catalyzed protocol was developed for the
construction of 2-AI-T framework. This process combining two consecutive steps of
dimorth rearrangement and click reaction represents a useful protocol for the smooth
synthesis of novel 2-aminoimidazole-triazole derivatives.
Publication
[1] Copper Catalyzed Microwave Assisted One Pot Synthesis of 2-
Aminoimidazole-Triazole Framework Org.lett (manuscript in preparation)

4.1 Introduction
There are only a few approaches that describe the direct synthesis of 2aminoimidazoles
and their biological activity 1-5 . The earliest method involves
condensation of α-aminocarbonyl compounds with cyanamide or their synthetic
equivalents 6,7 . This method is most commonly used for the direct construction of the
2-aminoimidazole ring. Other general applicable strategies are cyclocondensation of
α-bromoketone with N-acetylguanidine in acetonitrile 8 , iminophosphorane-mediated
cyclization of α –azido esters 9 , ammonolysis of 2-amino-1,3-oxazol-3-iumsalts 10 ,
sequential functionalization of 1,2-diprotected imidazole ring with different
electrophiles 11 . Most of them involve long experimental procedures, the use of
unstable precursors and tiresome workup process. Accordingly, the development of
straightforward and general procedures for the synthesis of diversely substituted 2aminoimidazoles
from readily available precursors is highly warranted. Herein, we
report a rapid and highly efficient Cu-mediated synthesis of 2-aminoimidazoletriazole
framework via click reaction and dimorth rearrangement.
“Click chemistry” has emerged as a fast and efficient approach to synthesis of novel
compounds with desired function making use of selected “near perfect” reactions. 12
(very fast, selective, high-yield, and wide scope).
The Dimroth rearrangement 13 is an isomerization of heterocycles that consists in a
translocation of endo- or exocyclic heteroatoms through a ring-opening-ring-closure
sequence. It can be catalyzed by acids, bases, heat or light.
Recently group of Erik 14 reported a new one pot microwave assisted synthesis of
substituted 2-amino-1H- imidazoles from readily available 2-aminopyrimidine (1) and
α-bromoketone (2). The first step was performed by heating N-(3azidopropyl)pyrimidin-2-amine
(1) and 2-bromo-1-phenylethanone (2) at 75 o C for 3
h resulting in the formation of hydroxyl salt (3) which undergoes dimorth type
rearrangement by 7 equiv of NH2NH2.H2O resulting in the formation of N-(2-azido)-
1H-imidazol-2-amine. Final step of click reaction was performed under microwaveirradiation
using phenylacetylene (1.5.equiv), Cu(Oac)2 (10 mol %)as catalyst at 100
o
C 10 min with a maximum power of 40W to obtain 2-AI-T scaffold (5). (Scheme 1)

N
N
Br
R 2
N
N
3
N
H
N
OH
R1 N 3
n
MeCN, 75 o C,
3 Hrs
N
n 3
+
R 2
1 2
Br
O
R 1
One Pot MW ?
o MW. 100 C
MeCN, 10 min
N2H4 (7 equiv)
Scheme-1 Sequential Synthesis of 2-AI-T Framework
R 2
R 1
R 2
R 1
N
N
H
H
N
N
NH
N
N R3 N
n
MW. 100 o C
Cu(OAc) 2
10 min, 80 %
In continuation of earlier work on two step synthesis of 2-AI-T scaffold with excellent
yield. now an ameliorated and convenient one-pot protocol for the synthesis of 2-AI-T
scaffold under microwave conditions has been reported.
4.2 Optimization Study
Looking to the current exploration in the synthesis and microwave-assisted decoration
of the 2-aminoimidazole 14 and click reaction 15 and preliminary success of the
sequence, it was very interesting to investigate whether one-pot protocol for the
construction of 2-AI-T scaffold should be possible. The test reaction was performed
with hydroxy salt {3} and phenyl acetylene as a model system. Different Cu catalyst,
equiv of NH2NH2.H2O, temperature and reaction time were screened to derive an
optimized protocol (Table 1).
First, the application of Cu(OAc)2 as catalyst for click reaction and different
equivalents of aqueous NH2NH2.H2O for simultaneous dimorth rearrangement (Table-
1, No-1-3) was evaluated. However in case of 1 equiv. of hydrazine used, yield was
only 51 %. (Table-1, No-1). Next study of different reaction time (Table-1, No-3-7)
performed. It was observed that reaction could complete even in very short time
4
NH
5
R 3
N 3
n

(Table-1, No- 6). Next reaction temperature (Table-1, No-8-9) was investigated.
Decrease of the reaction temperature resulted in lover yield (Table-1, No-9). Then the
examination the catalyst effect on a reaction (Table-1, No-7-13) was done. However
replacement of Cu(Oac)2 with CuSO4 resulted in lower yield (Table-1, No-11). While
in case of Cu Powder (200 mesh) used only traces amount of desire product observed
(Table-1, No-13). Moreover it was observed that the catalyst was mandatory for
successfully performing the reaction, as no product was formed in the absence of the
catalyst (Table-1, No-12). Finally optimum reaction conditions were achieved when a
mixture of hydroxy salt, 1.2 equiv of phenyl acetylene, 5 mol % of Cu(Oac)2 in 1 ml
of Ethenol : water (4: 1) was irradiated for 2 min at a ceiling temperature of 100 o C
applying a maximum power of 36 W, affording the desired compound in 90 % yield
(Table 1 No-8). The protocol was checked with conventional condition providing
lower yield of 24 % of after 24 hrs.
N
N N
Ph OH
N3 One-Pot microwave-assisted
Cu salt (mol %)
Br
3
N2H4 (equiv.)
Ph (1.2 equiv.)
EtOH : Water (4:1, 1ml)
Ph
No.
time
(min)
N
N
H
NH
5
N N
N
temp ( o C) Cu salt (mol %) yield (%) b
1 c 20 100 °C Cu(Oac)2, 10 51
2 d 20 100 °C Cu(Oac)2, 10 84
3 20 100 °C Cu(Oac)2, 10 86
4 10 100 °C Cu(Oac)2, 10 80
5 5 100 °C Cu(Oac)2, 10 90
6 2 100 °C Cu(Oac)2, 10 90
7 1 100 °C Cu(Oac)2, 10 53
8 2 100 °C Cu(Oac)2, 5 90
9 2 90 °C Cu(Oac)2, 5 73
10 2 100 °C Cu(Oac)2, 2 57
11 2 100 °C CuSO4.5H2O, 5 67
Ph

12 2 100 °C - -
13 2 100 °C Cu Powder (200 mesh) Traces
14 e - f 25 °C Cu(Oac)2, 5 24
a
All reactions were run on a 0.7 mmol scale of 3, applying phenyl acetylene (1.2
equiv) in ethanol: water (4:1, 1 mL) under microwave irradiation. The mixture was
irradiated in a sealed tube (CEM Discover @ ) at a ceiling temperature of 100 o C and 35
W maximum power for the stipulated time. b isolated yields. c 1.0 equiv of
NH2NH2.H2O used. d 5.0 equiv of NH2NH2.H2O used. e reaction carried out at room
temperature. f time 24 h.
Table-1: Copper Catalyzed One-Pot protocol: Catalyst, equiv of hydrazine, reaction
time and Temperature Effects on the model reaction to obtain 2-AI-T scaffold a .
4.3 Results and Discussion
Encouraged by these findings, the scope of this protocol was further explored. An
array of hydroxy salts 3 (a-j) (Table-2) were reacted with various acetylene using our
optimized conditions. In most cases, the reactions proceeded well affording the one
pot product in good to excellent yield (Table-2)
R 2
N
1
+
N
Br
2
N
H
O
R 1
N 3
n
MeCN, 75 o C,
3 Hrs
R 3
N N
n
3
N
Br N
R OH
2 R1 Cu(OAc) 2 (5 mol. %)
MW. 100 o N2H4 C
3 {a-j}
2-5 min, 85-90 %
One-pot Microwave-assisted
R 2
R 1
N
N
H
NH
N
N R3 N
n
4 {a-v}

No. Product, Yield b (%) No. Product, Yield b (%)
1
2
3
4
5
6
7
8
9
Cl
Br
Br
Br
Cl
Br
Br
Cl
Cl
N
N
H
N
N
H
N
N
H
N
N
H
N H
N
N
H
N H
N
N
H
N
N
H
N
N
H
N
H
N
N
N
4-a (66)
N
N
N
N
H
N
N
N
4-c (73)
N
N
N
N
N
H
N
H
4-e (73)
NH
4-f (80)
N
H
N
N
N
4-g (80)
NH
NH
N N
N
OMe
4-b (84)
Bu
Me
4-d (64)
N
N Hep
N
N N
N
N N
N
H 2N
H
N
Pen
Hep
4-h (81)
4-I (75)
12
12
14
15
16
17
18
19
20
Cl
N
N
H
NH
N N
N
Cl 4-l (90)
N
N
H
N H
N
N
N
Br 4-m (95)
O
Br
N
N
N
H
NH
N
N
H
NH
4-n (74)
N N
N
N N
N
O 4-o (29)
O
N
N
N
H
N
H
N
N
N
O 4-p (29)
N
N
H
N H
N
N
N
F 4-q (68)
N
N
H
N H
N
N
N
F 4-r (80)
N
N
H
N H
N
N
N
Cl 4-s (16)
Cl
Cl
N
N
H
NH
4-t (85)
N N
N

10
11
Cl
Cl
N
N
H
N
H
N
N
N
Cl 4-j (85)
N
N
H
N
H
N
N
N
Cl 4-k (80)
21
22
Cl
Cl
N
N
H
N
N
H
NH
N H
N N
N
N
N
N
S
4-u (91)
Br 4-v (80)
a
All reactions were run on a 0.7 mmol scale of 3 {a-j} ethanol: water (4:1) (1 ml) with
phenyl acetylene (1.2 equiv), Cu(OAc)2 (5 mol % ) and hydrazine hydride (2 equiv).
The mixture was irradiated in a sealed tube (CEM Discover @ ) at a ceiling temperature
of 100 o C and 35 maximum power for the stipulated time. b isolated yields. Yields are
shown in ().
Table-2: Microwave assisted one pot decoration of 2-AI-T Framework a .
A diverse set of 2-AI-T scaffold were synthesized with these optimized conditions.
Ten different hydroxy salt 3 {a-j} (n = 1 or 2) were reacted with different (hetero)
aromatic or alkyl acetylenes (Table-2) to test the generality of this new microwaveassisted
one pot method (Table 2). All reactions were completed within 5 min using
microwave irradiation at ceiling temperature of 100 o C and 35W power. The yields
varied from good to excellent, although in some cases lower yields were observed
(Table 2, No-15,16 and 19). However in case of morpholine substitution (table-2, No-
15-16) probably due to decomposition of starting hydroxy salt 3 {h} lower yields
were observed. Interestingly when 4,5-disubstituted hydroxy salt react with acetylene
only 16% of desired product 4{s} was observed due to steric hindrance of 4-Mephenyl
substitution on dimorth rearrangement. Motivated by the importance of the
final target to develop new general method toward widely functionalized 2-AI-T
framework, we next examined the extension of this procedure to other acetylene. The
reaction proceeded effectively with aliphatic and aromatic terminal acetylenes to give
the corresponding 2-AI-T (Table 2). Thus, a variety of substituted 2-AI-T containing
aromatic, aliphatic, cyclic and heterocyclic substitution at the C-4 position of the
triazole ring were obtained.

4.4 Possible Mechanism
Regarding the mechanism of transformation of 2-hydroxy 2,3-dihydro-1Himidazo[1,2-a]pyrimidin-4-ium
salts 3 into 2-amino-1H-imidazole-triazole 4, we
presume that the reaction proceeds via an unusual Dimroth type rearrangement
(Scheme-3).
Br
Br
R 2
N
NH 2NH 2
R 2
N
N
N
N3 n
R2 N
H
N
OH
R1 N
H
3
N
R 1
Ring Opening
N
R 1
OH
25 o C
n
N 3
NH 2NH 2
MW
R 2
N
Cu(OAc) 2
CuNP
NH 2
N
N
H ·HBr
a b
N
R 1
OH
Generation of
"nano-Cu"
R 3 "Click" Reaction
N
n
N
N
R 3
Dimroth Rearrangement
Scheme-3: Proposed mechanism for One-pot reaction:
In the first step the 2-hydroxy-2,3-dihydroimidazo[1,2-a]pyrimidinium salt (3)
undergoes cleavage of the pyrimidine ring (a), resulting in the generation of pyrazole
and 2-amino-5-hydroxyimidazolidine (b), meanwhile copper nanoparticle 16 generated
by reduction of Cu(OAc)2 using 1 equiv of NH2NH2.H2O takes part in click reaction.
This intermediate (b), which is in equilibrium with the open form c can cyclize again
leading by dehydration upon microwave irradiation, results in the rearranged 2amino-1H-imidazoles
triazole (4).
R 2
HN
R 1
NH 2
O
N
H 2O
N
N
n
N
n
c
4
N
N
N
R 3
R 3

4.5 Conclusion
In conclusion microwave-assisted Cu-catalyzed one pot protocol for the synthesis of
2-aminoimidazole-triazole framework via two consecutive steps of dimorth
rearrangement and click reaction was demonstrated. Library of 22 compounds have
been synthesized and were subjected to test for antibiofilm activity. However the
antibiofilm activities of these classes of compounds are under pipeline.
4.6 Experimental
4.6.1 General Methods
All chemical reagents were used without further purification. Solvents for column
chromatography and TLC were laboratory grade and distilled before use. For thinlayer
chromatography (TLC), analytical TLC plates (Alugram SIL G/UV254 (E. M.
Merk) were used. Column chromatography was performed with flash silica gel (100-
200 mesh) or neutral alumina oxide (50-200 micron). 1 H and 13 C NMR spectra were
recorded on a Bruker Avance 300 (300 MHz) or a Bruker AMX-400 (400 MHz)
spectrometers. NMR samples were run in the indicated solvents and were referenced
internally. Chemical shift values were quoted in ppm and coupling constants were
quoted in Hz. Chemical shift multiplicities were reported as s = singlet, d = doublet, t
= triplet, q = quartet, m = multiplet and br = broad. Low-resolution mass spectra were
recorded on a HEWLETT-PACKARD instrument (CI or EI) and LCQ Advantage
instrument (ESI). High-resolution mass spectra (EI) were recorded on a KRATOS
MS50TC instrument. Melting points were determined using Reichert-Jung Thermovar
apparatus and were uncorrected.
4.6.2 Microwave Irradiation Experiments
Microwave irradiation experiments were carried out in a dedicated CEM-Discover
mono-mode microwave apparatus or Microwave apparatuses were used in the
standard configuration as delivered, operating at a frequency 2.45 GHz with
continuous irradiation power from 0 to 400 W. The reactions were carried out in 10,
20, 30 and 50 mL glass tubes. The temperature was measured with an IR sensor on
the outer surface of the process vial or fibre optic sensor inside the process vial. After
the irradiation period, the reaction vessel was cooled rapidly (2-5 min) to ambient
temperature by air jet cooling.

4.7 Experimental protocols
4.7.1 General Procedure for the Preparation 3-Azido-propylamine
To a solution of 3-chloropropan-1-amine hydrochloride (3.2 g, 14.6 mmol) in water
(10 mL) was slowly added NaN3 (3.2 g, 49.2 mmol) as a solution in water (15 mL).
The resulting solution was allowed to stir at reflux overnight. After cooling to room
temperature, about 2/3 of the water was removed by evaporation and the remaining
residue diluted with ether (50 mL). This biphasic mixture was cooled to 0 °C and
KOH pellets (4.0 g) were slowly added. The phases separated and the aqueous layer
extracted with ether (2 x 30 mL). All organics combined, dried over Na2SO4, and
concentrated to afford 3-Azido-propylamine (1.17 g, 80%) as yellow oil
4.7.2 General Procedure for the Preparation of N-(3-azidopropyl)pyrimidin-2amine:
In a 50 mL microwave vial were successively dissolved in EtOH (20 mL) 2chloropyrimidine
(3.43 g, 30 mmol), 3-Azido-propylamine (48 mmol, 1.6 equiv) and
triethylamine (6.2 mL, 45 mmol, 1.5 equiv). The reaction tube was sealed, and
irradiated in the cavity of a Milestone MicroSYNTH microwave reactor at a ceiling
temperature of 120 °C at 100 W maximum power for 60 min. After the reaction
mixture was cooled with an air flow for 15 min, it was diluted with water (100 mL),
extracted with DCM (2×150 mL) and dried over Na2SO4. The solvent was evaporated
in vaccuo, and the crude mixture was purified by silica gel flash chromatography
using 0-5% MeOH−DCM as the eluent.
4.7.3 General Procedure for the Preparation of Salts.
To a solution of N-(3-azidopropyl)pyrimidin-2-amine (6 mmol) and αbromoacetophenone
(7.2 mmol, 1.2 equiv) in acetonitrile (12 mL) was added 4dimethylaminopyridine
(6 mg, 0.05 mmol). After being stirred at 85 °C for 5 h, the
reaction mixture was diluted with acetone (20 mL) and the precipitate was filtered and
washed with acetone (2×20 mL), ether (2×20 mL) and dried over P2O5 to give salt as
a white solid.

4.7.4 General Procedure for the preparation of 2-AI-T.
Cool the suspension of hydrazine hydride (2 equiv), in ethanol (0.8 ml.). To the
suspension were added Cu(OAc)2 (5 mol %) in water (0.2 ml). and stirred it for 2 min
at 0 o C. To this were added acetylene (1.5 eq) and hydroxyl salt (1 eq.) The reaction
mixture was irradiated at 100 0 o C at the maximum power 35 W for 2-5 min. After
completion of the reaction, the solvent was removed under reduce pressure. The crude
product was purifier by column chromatography over silica gel using DCM /
methanol / 7N methanolic NH3 (96:3:1) as the eluent.
4.8 Spectral Characterization
2-Azidoethanamine (BS-167)
H 2N
Yield: 41 %. 1 H NMR (300 MHz, CDCl3): δ = 3.37 (t, J = 5.61 Hz, 2H), 2.88 (t, J =
5.50 Hz, 2H), 1.53 (Br s, 2H).
3-Azidopropan-1-amine (BS-220)
H 2N
Yield: 45 %. 1 H NMR (300 MHz, CDCl3): δ = 3.38 (t, J = 6.93 Hz, 2H), 2.81 (t, J =
6.84 Hz, 2H), 1.73 (m, 2H), 1.36 (Br s, 2H).
N-(2-Azidoethyl)pyrimidin-2-amine (BS-168)
N
N
N
H
Yield: 67 %. 1 H NMR (300 MHz, CDCl3): δ = 8.30 (d, J = 4.74 Hz, 2H), 6.58 (t, J =
4.74 Hz, 1H), 5.44 (Br s, 1H), 3.64 (m, 2H), 3.54 (t, J = 5.58 Hz, 2H), 13 C NMR
(75.5 MHz, CDCl3): δ =162.0, 158.1, 158.0, 111.1, 50.8, 40.7. HRMS (EI) C6H6N6,
calcd 164.0810, found :.
N-(3-Azidopropyl)pyrimidin-2-amine (BS-221)
N
N
N
H
N 3
N 3
N 3
N 3

Yield: 69 %. 1 H NMR (300 MHz, CDCl3): δ = 8.28 (d, J = 4.80 Hz, 2H), 6.54 (t, J =
4.80 Hz, 1H), 5.30 (Br s, 1H), 3.52 (m, 2H), 3.42 (t, J = 6.57 Hz, 2H), 1.90 (m, 2H).
1-(3-Azidopropyl)-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-
4-ium bromide (BS-230)
N
Br
N
N
OH
Yield: 72 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.05 (m, 2H), 7.93 (s, 1H), 7.80
(m, 2H), 7.48 (m, 3H), 7.37 (t, J = 4.86 Hz, 1H), 4.95 (m, 2H), 3.41 (m, 4H), 1.64 (m,
2H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 167.4, 154.6, 148.2, 138.1, 129.3, 128.4
(×2), 126.9 (×2), 111.4, 90.6, 62.7, 47.9, 38.2, 27.0.
1-(2-Azidoethyl)-2-hydroxy-2-phenyl-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-4ium
bromide (BS-227)
N
Br
N
N
OH
Yield: 75 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.02 (m, 2H), 7.99 (s, 1H), 7.80
(m, 2H), 7.49 (m, 3H), 7.41 (t, J = 4.92 Hz, 1H), 4.95 (m, 2H), 3.38 (m, 4H). 13 C
NMR (75.5 MHz, DMSO-d6): δ = 167.5, 154.7, 148.4, 137.8, 129.4, 128.4 (×2), 126.9
(×2), 111.8, 90.6, 62.8, 48.1 (×2).
1-(2-Azidoethyl)-2-hydroxy-2-(naphthalen-1-yl)-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-271)
N
Br
N
N
OH
N 3
N 3
N 3

Yield: 67 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.10 (m, 2H), 8.38 (s, 1H), 8.16
(s, 1H), 8.02 (m, 3H), 7.88 (m, 1H), 7.59 (m, 2H), 7.44 (m, 1H), 5.05 (s, 2H), 3.42 (m,
4H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 167.5, 154.9, 148.5, 135.0, 132.9, 132.1,
128.4, 128.2, 127.5, 127.1, 126.7 (×2), 124.1, 111.9, 90.8, 62.6, 48.2 (×2).
1-(3-Azidopropyl)-2-(4-bromophenyl)-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-272)
N
Br
N
N
OH
Yield: 76 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.06 (d of d, J = 1.62, 4.60 Hz,
1H), 8.98 (d of d, J = 1.62, 6.24 Hz,1H) 8.00 (s, 1H), 7.72 (m, 4H), 7.37 (m, 1H),
4.85 (m, 2H), 3.37 (m, 4H), 1.66 (m, 2H). 13 C NMR (75.5 MHz, DMSO-d6): δ =
167.5, 154.7, 148.2, 137.6, 131.4(×2), 129.3 (×2), 122.9, 111.5, 90.3, 62.5, 47.9, 38.2,
27.0.
1-(2-Azidoethyl)-2-(3,4-dichlorophenyl)-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-273)
N
Br
N
Br
N
OH
Yield: 78 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.12 (m, 2H), 8.20 (s, 1H), 8.09
(s, 1H), 7.79 (m, 2H), 7.43 (m, 1H), 4.93 (m, 2H), 3.42 (m, 4H). 13 C NMR (75.5
MHz, DMSO-d6): δ = 167.5, 154.9, 148.3, 139.0, 132.2, 131.3, 130.5, 129.5, 127.4,
112.1, 89.8, 62.5, 48.0 (×2).
Cl
N 3
N 3
Cl

1-(3-Azidopropyl)-2-(3,4-dichlorophenyl)-2-hydroxy-2,3-dihydro-1Himidazo[1,2-a]pyrimidin-4-ium
bromide (BS-274)
N
Br
N
N
OH
Yield: 81 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.07 (m, 1H), 8.97 (m,1H) 8.12 (s,
1H), 8.08 (Br s, 1H), 7.97 (m, 2H), 7.38 (t, J = 4.92 Hz, 1H), 4.86 (m, 2H), 3.37 (m,
4H), 1.68 (m, 2H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 167.5, 154.7, 148.1, 139.2,
132.2, 131.3, 130.6, 129.3, 127.4, 111.6, 89.8, 62.4, 47.8, 38.3, 26.9.
1-(2-Azidoethyl)-2-(4-chlorophenyl)-2-hydroxy-3-p-tolyl-2,3-dihydro-1Himidazo[1,2-a]pyrimidin-4-ium
bromide (BS-299)
N
Br
N
Cl
N
OH
Yield: 42 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.19 (d, J = 3.06 Hz, 1H), 8.55 (d,
J = 5.43 Hz, 1H), 7.71 (d, J = 8.52 Hz, 2H), 7.70 (s, 1H), 7.55 (d, J = 8.49 Hz, 2H),
7.38 (m, 1H), 7.42 (d, J = 7.80 Hz, 2H), 7.08 (d, J = 7.80 Hz, 2H), 6.10 (s, 1H), 3.36
(m, 4H), 2.33 (s, 3H) 13 C NMR (75.5 MHz, DMSO-d6): δ = 168.2, 156.1, 146.9,
139.5, 135.9, 134.4, 129.4 (×6), 128.4 (×2), 124.4, 112.8, 93.5, 74.9, 47.9, 41.0, 20.7.
1-(2-Azidoethyl)-2-(4-fluorophenyl)-2-hydroxy-2,3-dihydro-1H-imidazo[1,2a]pyrimidin-4-ium
bromide (BS-300)
N
Br
N
N
OH
F
Cl
Cl
N 3
N 3
N 3

Yield: 79 %. 1 H NMR (300 MHz, DMSO-d6) : δ = 9.09 (d, J = 4.53 Hz, 1H), 9.01 (d,
J = 6.00 Hz, 1H), 8.04 (s, 1H), 7.85 (m, 2H), 7.37 (m, 3H), 4.92 (m, 2H), 3.38 (m,
4H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 167.5, 164.1, 160.9, 154.7, 148.4, 134.0
(d), 129.4 (d), 115.4, 115.1, 111.9, 90.3, 62.7, 48.1 (×2).
5-(4-Bromophenyl)-N-(2-(4-(4-methoxyphenyl)-1H-1,2,3-triazol-1-yl)ethyl)-1Himidazol-2-amine
(BS-219)
Br
N
H
N
N
H
N
N
N
Yield: 66 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.62 (br s, 1H), 8.45 (s, 1H), 7.43
(d, J = 8.8 Hz, 2H), 7.57 (d, J = 7.9 Hz, 2H), 7.43 (d, J = 8.8 Hz, 2H), 7.10 (s, 1H),
6.98 (d, J = 8.8 Hz, 2H), 6.02 (m, 1H), 4.60 (t, J = 5.90 Hz, 2H), 3.78 (s, 3H), 3.68
(m, 2H). 13 C NMR (75.5 MHz, DMSO-d6): δ =158.8, 150.0, 146.0, 131.0, 126.4
(×4), 125.5 (×2), 123.4, 120.7, 117.5, 114.2 (×4), 55.0, 49.2. 42.8. HRMS (EI)
C20H19BrN6O, calcd 438.0804, found :438.0811.
5-Phenyl-N-(3-(4-phenyl-1H-1,2,3-triazol-1-yl)propyl)-1H-imidazol-2-amine (BS-
238)
N
N
H
N
H
N
N N
Yield: 90 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.91 (br s, 1H), 8.63 (s, 1H), 7.88
(d, J = 7.2 Hz, 2H), 7.59 (d, J = 7.2 Hz, 2H), 7.44 (t, J = 7.7 Hz, 2H), 7.27 (m, 3H),
7.08 (m, 2H), 6.09 (br s, 1H), 4.50 (t, J = 7.1 Hz, 2H), 3.21 (m, 2H), 2.21 (m, 2H). 13 C
NMR (75.5 MHz, DMSO-d6): δ = 150.3, 146.2, 133.0, 132.3, 130.8, 128.8 (×2),
128.3, 127.7, 125.6, 125.0 (×2), 123.6 (×2), 121.4, 110.4, 104.1, 47.3, 28.8 (×2).
HRMS (EI) C20H20N6, calcd 344.1749, found : 344.1734.
5-Phenyl-N-(2-(4-phenyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-2-amine (BS-
228)
N
H
N
N
H
N
N
N
O

Yield: 84 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.68 (br s, 1H), 8.57 (s, 1H), 7.82
(d, J = 7.3 Hz, 2H), 7.61 (m, 2H), 7.43 (t, J = 7.6 Hz, 2H), 7.28 (m, 3H), 7.06 (m,
2H), 6.01 (br s, 1H), 4.63 (t, J = 6.1 Hz, 2H), 3.70 (m, 2H). 13 C NMR (75.5 MHz,
DMSO-d6): δ = 150.3, 146.1, 130.4, 128.8 (×4), 128.2, 127.7, 125.1, 125.0 (×4),
123.4, 121.7, 104.1, 49.3. 42.9. HRMS (EI) C19H18N6, calcd 330.1593, found :
330.1582.
5-(4-Bromophenyl)-N-(2-(4-p-tolyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-2amine
(BS-231)
Br
N
H
N
N
H
N
N
N
Yield: 73 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.66 (br s, 1H), 8.50 (s, 1H), 7.70
(d, J = 8.07 Hz, 2H), 7.57 (d, J = 8.31 Hz, 2H), 7.43 (d, J = 8.56 Hz, 2H), 7.22 (d, J =
8.07 Hz, 2H), 7.13 (s, 1H), 6.03 (br s, 1H), 4.61 (t, J = 5.80 Hz, 2H), 3.68 (m, 2H),
2.32 (s, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 150.4, 146.1, 136.9 (×2), 130.9
(×2), 129.3 (×4), 128.0, 125.3, 124.9 (×3), 121.2, 117.4, 49.2, 42,8, 20.7. HRMS (EI)
C20H19BrN6, calcd 422.0855, found : 422.0863.
N-(2-(4-(4-Butylphenyl)-1H-1,2,3-triazol-1-yl)ethyl)-5-(naphthalen-1-yl)-1Himidazol-2-amine
(BS-275)
N
H
N
N
H
N
N
N
C4H9 Yield: 64 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.9 (br s, 1H), 8.54 (s, 1H), 8.14
(s, 1H), 7.73 (m, 6H), 7.37 (m, 2H), 7.23 (m, 3H), 6.01 (m, 1H), 4.68 (m, 2H), 3.74
(m, 2H), 2.58 (t, J = 7.4 Hz, 2H), 1.56 (m, 2H), 1.32 (m, 2H), 0.89 (t, J = 7.4 Hz, 3H).
13
C NMR (75.5 MHz, DMSO-d6): δ = 150.7, 146.2, 141.8, 133.5, 131.3, 128.7 (×3),
128.3, 127.5, 127.3 (×3), 126.0, 125.0 (×3), 124.6, 123.2, 121.3, 120.2, 49.3, 42.9,
34.5, 32.9, 21.7, 13.7. HRMS (EI) C27H28N6, calcd 436.2375, found : 436. 2349.

5-(4-Bromophenyl)-N-(2-(4-heptyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-2amine
(BS-277)
Br
N
H
N
N
H
N
N
N
C 7H 15
Yield: 73 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.56 (br s, 1H), 7.82 (s, 1H), 7.59
(d, J = 8.2 Hz, 2H), 7.42 (d, J = 7.9 Hz, 2H), 7.13 (s, 1H), 5.93 (br s, 1H), 4.51 (t, J =
5.90 Hz, 2H), 3.60 (m, 2H), 2.57 (d, J = 7.7 Hz, 2H), 1.57 (m, 2H), 1.25 (m, 8H), 0.85
(t, J = 6.9 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 150.5, 146.7 (×2), 131.0
(×3 ), 125.3, 121.9 (×2), 117.4, 104.1, 48.9, 42.9, 31.1, 28.9, 28.5, 28.4, 25.0, 22.0,
13.9. HRMS (EI) C20H27BrN6, calcd 430.1481, found : 430.1488.
5-(4-Bromophenyl)-N-(3-(4-(4-pentylphenyl)-1H-1,2,3-triazol-1-yl)propyl)-1Himidazol-2-amine
(BS-278)
Br
N
N
H
N
H
N
N N
C 5H 11
Yield: 80 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.58 (br s, 1H), 8.55 (s, 1H), 7.72
(d, J = 8.06 Hz, 2H), 7.53 (d, J = 8.06 Hz, 2H), 7.38 (d, J = 8.27 Hz, 2H), 7.23 (d, J =
8.06 Hz, 2H), 7.11 (s, 1H), 5.96 (m, 1H), 4.47 (t, J = 6.57 Hz, 2H), 3.19 (m, 2H), 2.59
(t, J = 7.63 Hz, 2H), 2.14 (m, 2H), 1.59 (m, 2H), 1.30 (m, 4H), 0.86 (t, J = 6.78 Hz,
3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 146.3, 142.9, 131.0 (×2), 128.7 (×4),
128.3, 125.4, 124.0 (×4), 121.0, 117.3 (×2), 47.3, 39.9, 34.8, 30.8, 30.5, 30.6, 21.9,
13.8. HRMS (EI) C25H29BrN6. calcd.492.1637, found: 492. 1621.
5-(3,4-Dichlorophenyl)-N-(2-(4-(4-heptylphenyl)-1H-1,2,3-triazol-1-yl)ethyl)-1Himidazol-2-amine
( BS-279)
Cl
Cl
N
H
N
N
H
N
N
N
C 7H 15

Yield: 80 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.66 (br s, 1H), 8.50 (s, 1H), 7.86
(s, 1H), 7.71 (d, J = 8.3 Hz, 2H), 7.62 (m, 1H), 7.48 (d, J = 8.3 Hz, 1H), 7.22 (d, J =
8.3 Hz, 3H), 6.06 (m, 1H), 4.61 (t, J = 5.77 Hz, 2H), 3.69 (m, 2H), 2.58 (t, J =
7.58Hz, 2H), 1.57 (m, 2H), 1.28 (m, 8H), 0.86 (m, 3H). 13 C NMR (75.5 MHz,
DMSO-d6): δ = 146.1, 141.8, 130.9 (×2), 130.3, 128.6 (×3), 128.2 (×2), 126.5,124.9
(×3), 124.8, 124.7, 121.2, 49.2, 42.8, 34.8, 31.1, 30.7, 28.5, 28.4, 22.0, 13.8. HRMS
(EI) C26H30Cl2N6, calcd 496.1909, found : 496.1919.
5-(3,4-Dichlorophenyl)-N-(3-(4-((methylamino)methyl)-1H-1,2,3-triazol-1yl)propyl)-1H-imidazol-2-amine
(BS-283)
Cl
Cl
N
N
H
N
H
N
N N
Yield: 81 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.70 (br s, 1H), 7.99 (s, 1H), 7.82
(s, 1H), 7.58 (d, J = 8.7 Hz, 1H), 7.48 (d, J = 8.2 Hz, 1H), 7.23 (s, 1H), 6.01 (m, 1H),
4.41 (t, J = 6.95 Hz, 2H), 3.67 (m, 2H), 3.14 (m, 2H), 2.26 (s, 3H), 2.07 (t, J = 6.5 Hz,
2H), 1.86 (s,1H) 13 C NMR (75.5 MHz, DMSO-d6): δ = 151.4, 145.9, 135.9, 130.9
(×2), 130.3, 126.4 (×2), 124.6, 123.4, 122.6, 47.0 (×2), 41.0, 35.4, 30.3. HRMS (EI)
C16H19Cl2N7, calcd 389.1079, found: 389.1064.
N-(3-(4-(2-Aminopropan-2-yl)-1H-1,2,3-triazol-1-yl)propyl)-5-(4-bromophenyl)-
1H-imidazol-2-amine (BS-287)
Br
N
N
H
N
H
N
N N
Yield: 75 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.57 (br s, 1H), 7.92 (s, 1H), 7.55
(d, J = 8.3 Hz, 2H), 7.42 (d, J = 8.3 Hz, 2H), 7.11 (s, 1H), 5.94 (t, J = 5.6 Hz, 1H),
4.38 (t, J = 7.0 Hz, 2H), 4.10 (m, 2H), 3.16 (m, 2H), 2.07 (m, 2H), 1.37 (s, 6H). 13 C
NMR (75.5 MHz, DMSO-d6): δ = 156.0, 151.3, 134.0, 131.0 (×3), 125.3 (×2), 120.1
(×2), 117.3, 54.8, 48.5, 47.1, 30.8 (×2), 30.1. HRMS (EI) C17H22BrN7, calcd
403.1120, found: 403.1131.
H 2N
H
N

5-(3,4-Dichlorophenyl)-N-(2-(4-cyclohexyl-1H-1,2,3-triazol-1-yl)ethyl)-1Himidazol-2-amine
(BS-301)
Cl
Cl
N
H
N
N
H
N
N
N
Yield: 85 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.64 (br s, 1H), 7.58 (s, 1H), 7.80
(s, 1H), 7.60 (m, 1H), 7.48 (d, J = 8.3 Hz, 1H), 7.24 (s, 1H), 6.00 (m, 1H), 4.50 (t, J =
5.76 Hz, 2H), 3.61 (m, 2H), 2.61 (m, 1H), 1.91 (m, 2H), 1.69 (m, 3H), 1.32 (m,5H).
13
C NMR (75.5 MHz, DMSO-d6): δ = 151.9, 150.6, 131.0 (×2), 130.3, 126.6 (×2),
124.7, 123.4, 120.7, 104.1, 54.8, 49.0, 42.8, 34.5, 32.4 (×2), 25.5 (×2).HRMS (EI)
C19H22Cl2N6, calcd 404.1283., found: 404.1278.
5-(3,4-Dichlorophenyl)-N-(2-(4-propyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-
2-amine (BS-302)
Cl
Cl
N
H
N
N
H
N
N
N
C 3H 7
Yield: 90 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.80 (br s, 1H), 7.84 (d, J = 1.7
Hz, 1H), 7.82 (s, 1H), 7.59 (d of d, J = 8.4, 1.7 Hz, 1H), 7.53 (d, J = 8.4 Hz, 1H), 7.26
(s, 1H), 6.14 (br s, 1H), 4.51 (t, J = 6.04 Hz, 2H), 3.62(m, 2H), 2.56 (t, J = 7.49 Hz,
2H), 1.57 (m, 2H), 0.89 (t, J = 7.25 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ =
150.4, 146.5, 135.0, 131.0 (×2), 130.4 126.8 (×2), 124.8, 123.5, 122.0, 48.8, 42.8,
27.0, 22.0, 13.6. HRMS (EI) C16H18Cl2N6, calcd 364.0970., found: 364.0980.
5-(3,4-Dichlorophenyl)-N-(3-(4-propyl-1H-1,2,3-triazol-1-yl)propyl)-1Himidazol-2-amine
(BS-303)
Cl
Cl
N
N
H
N
H
N
N N
C 3H 7

Yield: 83 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.80 (br s, 1H), 7.88 (s, 1H), 7.83
(d, J = 1.7 Hz 1H), 7.58 (d of d, J = 8.3, 1.7 Hz, 1H), 7.52 (s, 1H), 7.49 (s, 1H), 6.13
(br s, 1H), 4.38 (t, J = 6.98 Hz, 2H), 3.15 (m, 2H), 2.57 (t, J = 7.51 Hz, 2H), 2.06 (m,
2H), 1.58 (m, 2H), 0.89 (t, J = 7.51 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ =
150.0, 146.6, 135.1, 131.0 (×2), 130.3 126.8 (×2), 124.8, 123.5, 121.7, 54.8, 46.9,
30.0, 27.0, 22.2, 13.5. HRMS (EI) C17H20Cl2N6, calcd 378.1127., found : 378.1114.
5-(4-Bromophenyl)-N-(2-(4-propyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-2amine
(BS-304)
Br
N
H
N
N
H
N
N
N
C 3H 7
Yield: 95 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.63 (br s, 1H), 7.87(s, 1H), 7.62
(m, 2H), 7.48 (d , J = 8.6 Hz, 2H), 7.17 (s, 1H), 5.98 (t, J = 5.3 Hz, 1H), 4.59 (t, J =
6.04 Hz, 2H), 3.66 (m, 2H), 2.61 (t, J = 7.44 Hz, 2H), 1.62 (m, 2H), 0.94 (t, J = 7.21
Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 150.5, 146.5, 134.6, 131.0 (×3),
125.4 (×2), 122.0 (×2), 117.4, 48.9, 42.9, 27.0, 22.2, 13.6. HRMS (EI) C16H19BrN6,
calcd 374.0855., found: 374.0844.
5-(4-Bromophenyl)-N-(3-(4-propyl-1H-1,2,3-triazol-1-yl)propyl)-1H-imidazol-2amine
(BS-305)
Br
N
N
H
N
H
N
N N
C 3H 7
Yield: 74 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.59 (br s, 1H), 7.89 (s, 1H), 7.55
(d , J = 8.1 Hz, 2H), 7.42 (d , J = 8.4 Hz, 2H), 7.11 (s, 1H), 5.93 (t, J = 5.25 Hz, 1H),
4.38 (t, J = 6.83 Hz, 2H), 3.14 (m, 2H), 2.48 (t, J = 7.62 Hz, 2H), 2.06 (m, 2H), 1.58
(m, 2H), 0.90 (t, J = 7.35 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 151.1,
146.6, 134.6, 131.0 (×3), 125.4 (×2), 121.7 (×2), 117.4, 47.9, 30.0, 27.0 (×2), 22.2,
13.5. HRMS (EI) C17H21BrN6, calcd 388.1011., found: 388.1023.

(2-(3-(4-Propyl-1H-1,2,3-triazol-1-yl)propylamino)-1H-imidazol-5yl)(morpholino)methanone
(BS-306)
O
O
N
N
H
N
N
H
N
N N
C 3H 7
Yield: 29 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.02 (br s, 1H), 7.85 (s, 1H), 7.10
(s, 1H), 6.05 (m, 1H), 4.35 (t, J = 6.8 Hz, 2H), 3.75 (m, 4H), 3.57 (t, J = 4.31 Hz, 4H),
3.10 (m, 2H), 2.57 (t, J = 7.42 Hz, 2H), 2.05 (m, 2H), 1.60 (m, 2H), 0.90 (t, J = 7.42
Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 161.2, 150.1, 146.6, 122.8, 121.7
(×2), 66.3 (×2), 54.8 (×2), 46.9, 44.4, 29.9, 27.0, 22.2, 13.5. HRMS (EI) C16H25N7O2,
calcd 347.2070., found: 347.2085.
(2-(2-(4-Propyl-1H-1,2,3-triazol-1-yl)ethylamino)-1H-imidazol-5yl)(morpholino)methanone
(BS-307)
O
O
N
N
H
N
N
H
N
N
N
C 3H 7
Yield: 29 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.89 (br s, 1H), 7.78 (s, 1H), 7.08
(s, 1H), 5.98 (m, 1H), 4.45 (m, 2H), 3.74 (m, 3H), 3.58 (m, 6H), 3.16 (m, 1H), 2.56
(m, 2H), 1.57 (m, 2H), 0.89 (t, J = 7.25 Hz, 3H). 13 C NMR (75.5 MHz, DMSO-d6): δ
= 161.4, 149.7, 146.5 (×2), 121.9 (×2), 66.3 (×2), 48.7 (×2), 44.4, 44.7, 27.0, 22.2,
13.6. HRMS (EI) C15H23N7O2, calcd 333.1913., found: 333.1920.
N-(2-(4-(Cyclopentylmethyl)-1H-1,2,3-triazol-1-yl)ethyl)-5-(4-fluorophenyl)-1Himidazol-2-amine
(BS-308)
F
N
H
N
N
H
N
N
N
Yield: 68 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.63 (br s, 1H), 7.82 (s, 1H),
7.63 (q, J = 2.9, 5.7 Hz, 2H), 7.11 (t , J = 8.7 Hz, 2H), 7.03 (s, 1H), 5.96 (t, J = 5.4
Hz, 1H), 4.51 (t, J = 5.99 Hz, 2H), 3.61 (m, 2H), 2.59 (d, J = 7.08 Hz, 2H), 2.07 (m,

1H), 1.66 (m, 6H), 1.70 (m, 2H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 161.8, 158.6,
150.3, 146.2, 146.1, 130.9, 125.2, 125.1, 122.2, 115.1, 114.8, 48.9, 42.9, 31.8 (×3),
31.0, 24.5 (×2). HRMS (EI) C19H23FN6, calcd 354.1968., found: 354.1974.
N-(2-(4-Cyclopropyl-1H-1,2,3-triazol-1-yl)ethyl)-5-(4-fluorophenyl)-1H-imidazol-
2-amine (BS-309)
F
N
H
N
N
H
N
N
N
Yield: 80 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.55 (br s, 1H), 7.79 (s, 1H),
7.64 (m, 2H), 7.10 (t , J = 8.7 Hz, 2H), 7.02 (s, 1H), 5.90 (m, 1H), 4.99 (t, J = 5.85
Hz, 2H), 3.61 (m, 2H), 1.91 (m, 1H), 0.85 (m, 2H), 0.69 (m, 2H). 13 C NMR (75.5
MHz, DMSO-d6): δ = 161.8, 158.6, 150.4, 148.6 (×2), 131.1, 125.1, 125.0, 120.9,
115.1, 114.8, 48.9, 42.9, 7.6(×2), 6.5. HRMS (EI) C16H17FN6, calcd 312.1499., found:
312.1487.
5-(4-Chlorophenyl)-N-(2-(4-cyclopentyl-1H-1,2,3-triazol-1-yl)ethyl)-4-p-tolyl-1Himidazol-2-amine(BS-310-B)
Cl
N
H
N
N
H
N
N
N
Yield: 16 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.89 (br s, 1H), 7.84 (s, 1H), 7.40
(m, 2H), 7.29 (m, 4H), 7.14 (m, 2H), 5.87 (m, 1H), 4.52 (t, J = 5.87 Hz, 2H), 3.64 (m,
2H), 3.06 (m, 1H), 2.29 (s, 3H), 1.95 (m, 2H), 1.60 (m, 6H). 13 C NMR (75.5 MHz,
DMSO-d6): δ = 150.9, 150.1, 135.7, 130.0, 128.9 (×3), 128.1 (×3), 128.0 (×2), 127.2
(×3), 121.1, 104.1, 49.0, 42.7, 36.1, 32.7 (×2), 24.6 (×2), 20.7. HRMS (EI)
C25H27ClN6. calcd.446.1986, found: 446.1990.

N-(3-(4-(4-Tert-butylphenyl)-1H-1,2,3-triazol-1-yl)propyl)-5-(3,4dichlorophenyl)-1H-imidazol-2-amine
(BS-340):
Cl
Cl
N
N
H
N
H
N
N N
Yield: 91 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.68 (br s, 1H), 8.53 (s, 1H), 7.82
(s, 1H), 7.73 (d, J = 7.9 Hz, 2H), 7.57 (m, 1H), 7.43 (m, 3H), 7.25 (s, 1H) 6.02 (m,
1H), 4.48 (t, J = 6.73 Hz, 2H), 3.20 (m, 2H), 2.14 (m, 2H), 1.30 (s, 9H). 13 C NMR
(75.5 MHz, DMSO-d6): δ = 150.2, 146.2, 131.0, 130.3, 128.0, 126.6, 125.5 (×3),
124.8 (×3), 124.7, 123.4, 121.0 (×2), 104.1, 47.3, 39.6, 34.2, 31.0 (×3), 29.9.HRMS
(EI) C24H26Cl2N6, calcd 468.1596, found: 468.1602.
5-(3,4-Dichlorophenyl)-N-(3-(4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl)propyl)-1Himidazol-2-amine
(BS-341):
Cl
Cl
N
N
H
N
H
N
N N
Yield: 80 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.67 (br s, 1H), 8.46 (s, 1H), 7.82
(m, 2H), 7.63 (m, 1H), 7.58 (m, 1H), 7.51 (m, 2H), 7.26 (s, 1H) 6.02 (m, 1H), 4.47 (t,
J = 6.8 Hz, 2H), 3.19 (m, 2H), 2.14 (m, 2H). 13 C NMR (75.5 MHz, DMSO-d6): δ =
151.3, 142.8, 132.1 (×2), 131.0, 130.0, 127.0, 126.5, 125.7, 124.7, 123.4, 121.1, 120.6
(×2), 104.1, 47.3, 39.5, 29.9. HRMS (EI) C18H16Cl2N6S, calcd 418.0534, found:
418.0522.
5-(4-Bromophenyl)-N-(2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazol-
2-amine(BS-342):
Br
N
H
N
N
H
N
N
N
Yield: 78 %. 1 H NMR (300 MHz, DMSO-d6): δ = 10.56 (br s, 1H), 7.80 (s, 1H), 7.60
(d, J = 7.3 Hz, 2H), 7.43 (d, J = 7.3 Hz, 2H), 7.14 (s, 1H), 5.93 (m, 1H), 4.49 (t, J =
S

5.48 Hz, 2H), 3.59 (m, 2H), 3.16 (d of d, J = 5.2, 1.4 Hz, 1 H), 0.87 (m, 2H), 0.69 (m,
2H). 13 C NMR (75.5 MHz, DMSO-d6): δ = 150.4, 148.7 (×3), 131.0, 130.9, 125.3,
120.9 (×3), 117.4, 48.9, 42.8, 7.5 (×2), 6.5. HRMS (EI) C16H17BrN6, calcd 372. 0698,
found: 372.0689.
4.9 Representative NMR spectra
4.9.1 1 H and 13 C NMR spectra of bs-272
170
167.5180
9.0686
9.0591
9.0535
8.9901
8.9844
8.9694
8.9637
Integral
160
1.9907
9.0
154.7139
148.2373
150
140
137.6005
8.0015
7.7800
7.7505
7.7216
7.6921
7.3908
7.3745
7.3701
7.3544
1.0890
8.0
3.9124
131.4039
129.3129
0.9792
122.9491
N
Br
130
N
Br
7.0
N
120
N
111.5523
N
OH
110
N
OH
Br
Br
6.0
N 3
100
N 3
90.3697
90
(ppm)
4.9593
4.9109
4.8569
4.8086
2.0000
5.0
(ppm)
80
4.0
70
62.5832
8.6996
60
3.4617
3.4378
3.3788
3.3437
3.3217
3.2991
3.0
50
47.9135
40.0332
39.7568
39.4768
39.2005
38.9205
27.0036
40
2.0
30
1.6835
1.6609
1.6377
1.9439
20
1.0
10
0.0
0

4.9.2
1 H and 13 C NMR spectra of bs-304
Integral
160
11.0
10.6535
0.7987
150.5865
146.5318
150
10.0
140
134.0549
131.0403
130
9.0
125.4219
122.0327
120
Br
117.4725
Br
7.8767
7.6231
7.5139
7.4857
0.9951
1.8738
1.9716
8.0
110
7.1731
N
H
0.9264
N
7.0
N
N
H
100
N
H
N
H
6.0069
5.9887
5.9705
90
N
N
N
0.9433
6.0
(ppm)
N
N
N
C 3H7
80
(ppm)
C 3H 7
5.0
4.5890
4.5689
4.5488
70
1.9449
60
3.6965
3.6764
3.6569
3.6368
4.0
1.9690
3.0
2.6414
2.6169
2.5918
1.9586
48.9026
42.9570
40.3132
39.7568
39.4805
39.2005
38.6441
50
40
2.0
30
27.0764
1.6773
1.6528
1.6283
1.6032
0.9724
0.9479
0.9235
1.9563
22.2144
20
3.0000
1.0
13.6286
10
0.0
0

4.10 References
[1] For a general review of the synthesis and activity of 2-aminoimidazole alkaloids, see: (a) S.
M. Weinreb, (2007) Nat. Prod. Rep. 24, 931–948. (b) H. Hoffmann, T. Lindel, (2003)
Synthesis. 1753–1783. (c) J. D. Sullivan, R. L. Giles, R. E. Looper. (2009) Curr. Bioactive
Cmpds. 5, 39-78.
[2] For the anti-biofilm activity of 2-aminoimidazoles, see: (a) R. W. Huigens III, J. J. Richards,
G. Parise, T. E. Ballard, W. Zeng, R. Deora, C. Melander, (2007) J. Am. Chem. Soc. 129,
6966–6967. (b) S. A. Rogers, C.Melander, (2008) Angew. Chem. 120, 5307–5309., (2008)
Angew. Chem. Int. Ed. 47, 5229–5231. (c) T. E. Ballard, J. J. Richards, A. L. Wolf, C.
Melander, (2008) Chem. Eur. J. 14, 10745–10761.
[3] (a) M. S. Malamas, J. Erdei, I. Gunawan, J. Turner, Y. Hu, E. Wagner, K. Fan, R.Chopra, A.
Olland, J. Bard, S. Jacobsen, R. L. Magolda, M. Pangalos, A. J. Robi- chaud. (2010) J. Med.
Chem. 53, 1146–1158. (b) M. S. Malamas, J. rdei, I. Gunawan, K. Barnes, M. Johnson, Y.
Hui, J. Turner, Y.Hu, E. Wagner, K. Fan, A. Olland, J. Bard,A. J. Robichaud. (2009) J. Med.
Chem. 52, 6314–6323.
[4] (a) R. S. Coleman, E. L. Campbell, D. J. Carper. (2009) Org. Lett. 11, 2133–2136. (b) M.
Nodwell, A. Pereira, J. L. Riffell, C. Zimmermann, B. O. Patrick, M. Roberge, R. J. Andersen.
(2009) J. Org. Chem. 74, 995–1006.
[5] (a) A. G. Beaman, W. Tautz, T. Gabriel, R. Duschinsky. (1966) J. Am. Chem. SOC. 87, 389.
(b) G. C. Lancini, E. Lazzari, V. Arioli, P. Bellani. (1969) J. Med. Chem. 12, 775
[6] (a) A. Lawson. (1956) J. Am. Chem. Soc. 307–310. (b) B. T. Storey, W. W. Sullivan, C. L.
Moyer. (1964) J. Org. Chem. 29, 3118–3120. (c) G. C. Lencini,; E. Lazzari. (1966) J.
Heterocycl. Chem. 3, 152–154.
[7] (a) N. S. Aberle, L. Guillaume, K. G. Watson. (2006) Org. Lett. 8, 419–421. (b) N. Aberle, J.
Catimel, E. C. Nice, K. G. Watson. (2007) Bioorg. Med. Chem. Lett. 17,3741–3744.
[8] C. H. Soh, W. K. Chui, Y. Lam. (2008) J.Comb.Chem. 10,118.
[9] P. Molina, P. Fresneda, M. Sanz. (1999) J. Org. Chem. 64, 2540–2544.
[10] T. Moschny, H. Hartmann. (1999) Helv. Chim. Acta 82, 1981–1993.
[11] S. Ohta, N. Tsuno, S. Nakamura, N. Taguchi, M. Yamashita, I. Kawasaki, M. Fujieda. (2000)
Heterocycles. 53, 1939–1955.
[12] (a) H. C. Kolb, M. G. Finn, K. B. Sharpless. (2001) Angew. Chem., Int. Ed. 40, 2004-2021.
(b) H. C. Kolb, K. B. Sharpless. (2003) Drug Discovery Today. 8, 1128 1137. (c) C. W.
Tornøe, C. Christensen, M. Meldal. (2002) J. Org. Chem., 67, 3057-3064.
[13] (a) E. Lieber, T. S. Chao, C. N. R. Rao. (1963) Organic Syntheses. Coll. Vol. 4, 380., 1957.
Vol. 37, 26. (b) El. Ashry, Y. El Kilany, N. Rashed, H. Assafir, (1999) Adv. Heterocycl.
Chem. 75, 79. (c) D. J. Brown, Mechanisms of Molecular Migrations. Thyagarajan, B. S.,
(1968) Wiley-Interscience: New York, Vol. 1, 209.
[14] For synthesis and anti biofilm activity see (a) D. S. Ermolat’ev, J. B. Bariwal, H. P. L.
Steenackers, S. C. J. De Keersmaecker, E. V. Van der Eycken, (2010) Angew. Chem. Int. Ed.

49, 9465–9468. (b) D. S. Ermolat'ev, E. V. Babaev, E. V. Van der Eycken. (2006) Org Lett. 8,
5781-5784. (c) D. S. Ermolat'ev, E. V. Van der Eycken. (2008) J. Org Chem. 73, 6691-6697.
(d) D. S. Ermolat’ev, B. Savaliya, A. Shah, E. Van der Eycken. (2010) Molecular Diversity.
DOI 10.1007/s11030-010-9270-5 (e) H. P. L. Steenackers, D. S. Ermolat’ev, B. Savaliya, A.
De Weerdt, D. De Coster, A. Shah, E. V. Van der Eycken, D. E. De Vos, J. Vanderleyden, S.
C.J. De Keersmaecker. (2010) J. Med Chem. DOI: 10.1021/jm 1011148.
[15] For microwave-assisted procedure see: P. Appukkuttan, W. Dehaen, V. V. Fokin, E. Van der
Eycken. Org. Lett., 2004, 6, 4223-4225. (b) For click chemistry under non-classical conditions
see: C. O. Kappe, E. Van der Eycken. Chem. Soc. Rev., 2010, 39, 1280–1290, and references
cited therein.
[16] (a) D. Raut, K. Wankhede, V. Vaidya, S. Bhilare, N. Darwatkar, A. Deorukhkar, G. Trivedi,
M. Salunkhe. (2009) Catalysis Communications. 10 1240–1243. (b) A. Sarkar, T. Mukherjee,
S. Kapoor. (2008) J. Phys. Chem. C 112, 3334 3340.

Crystal and Molecular Structure Analysis of
DP-7: A New Multi Drug Resistance Reverter
Lead Molecule

Chapter-5
“Crystal and Molecular Structure Analysis of DP-7: A New
Multi Drug Resistance Reverter Lead Molecule”
O
N
H
O
O
The synthesis of this 3,5-Dibenzoyl-4-(3-methoxyphenyl)-1,4-dihydro-2,6-dimethyl
pyridine DP7, bearing dibenzoyl groups at C(3) and C(5), respectively, has been
achieved by applying the modified Hantzsch-type condensation of 1,3-Diketone (2
equiv) and aromatic aldehydes (1 equiv) using ammonium carbonate as nitrogen
source. The product obtained was characterized by spectroscopic techniques & in
order to correlate structure activity relationship, the X-ray crystallographic study of
DP-7 has been carried out.
Publication:
[1] Synthesis, Characterization, Crystal and molecular structure analysis of DP-7:
A new Multi Drug Resistance Reverter Lead Molecule Cryst. Res. Technol. (2010)
Manuscript in preparation.

5.1 Introduction
The membrane efflux protein P-glycoprotein, a member of the ATP binding cassette
(ABC) family, recognizes and transports structurally, chemically, and
armacologically diverse hydrophobic compounds, giving rise to a phenomenon known
as multidrug resistance (MDR). Development of MDR is one of the main reasons of
failure in cancer chemotherapy, as tumour cells, by increasing drug efflux, acquire
cross-resistance to many structurally and functionally unrelated anticancer agents,
which therefore never achieve effective intracellular concentrations 1 . In the past few
years, extensive studies have been performed with the aim of developing effective
chemo sensitizers to overcome MDR of human cancer cells. Potent P-glycoprotein
inhibitors have been tested in clinical trials so far, including Ca2+ channel blockers
such as verapamil and dihydropyridines 2,3 . However, clinical application of these
agents has not been extensively pursued to date, owing to their unwanted and
sometimes life threatening cardiovascular side effects such as atria-ventricular block
and hypotension. As a consequence, in the last few years, much attention has been
focused on congeners of these first generation-MDR inhibitors, in order to develop
compounds characterized by appropriate potency and selectivity but also by reduced
cardiovascular toxicity.
Very recently, 3,5-Dibenzoyl-4-(3-phenoxyphenyl)-1,4-dihydro-2,6-dimethylpyridine
(DP7) was proposed as a new MDR reverter. It was found that DP7, at a
concentration two order of magnitude higher than its IC50 as a P-glycoprotein
inhibitor, was devoid of cardiovascular effects in in vitro rat preparations 4,5 . These
data were not considered sufficient evidence of DP7 safety before this drug could be
subjected to clinical investigation. Several 1,4 dihydropyridine calcium antagonists
are substrate of CYP enzymes. In particular, CYP3A4 metabolizes dihydropyridines
into the corresponding pyridines 6 . The dihydropyridine can also inhibit the activity of
CYP3A4. For example, Katoh 7 reported that nicardipine, benidipine, maidipine and
barnidipine strongly inhibited human CYP3A4 activity, while nivaldipine, nifedipine,
nitrendepine and amlodipine exhibited a weak inhibition.
The DP-7 was very well explored for variety of biological activity 8 . It was very
important to study the X-ray Crystal structure of this molecule which was not studied

so far and therefore development of single crystal was taken up in the current work.
Thus the synthesis was optimized and studied.
5.2 Reaction Scheme
5.2.1 Scheme-1 1-phenylbutane-1,3-dione
5.2.2 Scheme-2 DP-7
Ph
O
O
O
(NH 4) 2CO 3
Ph
O
Ph
5.3 Method of Crystallization
O
O
O
O
O
Ph
CH 3ONa
0 o C
Ph
MeOH
18 Hrs reflux
O O
Ph
O
N
H
O Ph
0.1gm of DP-7 was taken in 25 ml of methanol into 50ml single neck RBF and
Charcoal (2 g) was added. The solution was heated up to reflux temperature on a
water bath for 45 min. The solution was filtered, while hot through Whatmann 42
filter paper. The resulting solution was kept in a stopper conical flask slightly opened.
After 10 days, crystals grew in cubic shape due to thin layer evaporation. They were
filtered and washed with chilled methanol.
5.4 Crystal structure determination:
A single crystal of suitable size was chosen for X-ray diffraction studies. The data
were collected at room temperature on a DIPLabo Image Plate system with graphite
monochromated radiation MoKα. Each exposure of the image plate was set to a period
of 400 s. Thirty-six frames of data were collected in the oscillation mode with an
O
Ph

oscillation range of 5˚ and processed using Denzo 9 . The reflections were merged with
Scalepack. All the frames could be indexed using a primitive trilinic lattice. The
structure was solved by direct methods using SHELXS-97 10 . Least-squares refinement
using SHELXL-97 10 with isotropic displacement parameters for all the non-hydrogen
atoms converged the residual to 0.1999. Subsequent refinements were carried out with
anisotropic thermal parameters for the non-hydrogen atoms. After eight cycles of
refinement the residuals converged to 0.0578. The hydrogen atoms were fixed at
chemically acceptable positions, and were allowed to ride on their parent atoms.
5.5 Results and discussion:
The details of crystal data and refinement are given in Table 1. The bond lengths and
bond angles of all the non-hydrogen atoms (Table 2 and 3.) and are in good agreement
with the standard values 10 . Figure 1 represents the ORTEP 12 diagram of the molecule
with thermal ellipsoids drawn at 50% probability.
In the title compound C33H27NO3, the 1,4-dihydropyridine ring is in boat
conformation, with atoms N1 and C4 deviating from the plane 13 (Cremer and Pople,
1975) defined by the atoms N1/C2/C3/C4/C5/C6 by 0.1793(2)Å and 0.271(2)Å,
respectively. The 1,4-dihydropyridine ring is puckered. The puckering parameters are
Q = 0.406(2)Å, θ =106.0(3)˚ and Φ =2.4(3)˚. The dihedral angle between the least
squares planes of the ring 1 and 2 is 87.70(1)˚, indicating that the ring 2 is nearly
orthogonal to the dihydropyridine ring. The dihedral angles between the plane (1,3),
(1,4) and (3,4) are 60.74(1)˚, 53.54˚ and 79.49˚, respectively. The structural
conformation of carbomyl groups at C3 and C5 position is described by the torsion
angle values of 50.09˚ and 161.10˚ and have -syn-periplanar and -anti-periplanr
conformations. The structure exhibits coplanarity of the carbomyl group (C=O) with
the conjugated double bond of the 1,4-dihydropyridine ring. The structure exhibit
both inter and intramolecular hydrogen bonds of the type N–H. . .O and C–H. . .O, the
hydrogen bonds bind the molecules into infinite one- dimensional chain. The
observed hydrogen bonds are listed in Table 4. The packing of the molecules down b
axis is shown in the Figure 2.

Empirical formula C33H27NO3
Formula weight 485.56
Temperature 293 k
Wavelength 0.71073 Å
Crystal system Triclinic
Space group Pī
a = 7.4310(6Å), b =12.2580(16)Å, c =
Cell dimensions 14.4180(17)Å, α = 92.066(3)˚, β=95.319(7)˚, γ=
96.235(7)˚
Volume 1298.5(3)Å 3
Z 2
Density(calculated) 1.242Mg/m 3
Absorption coefficient 0.079 mm -1
F000
Crystal size 0.30 x 0.27 x 0.25 mm
Theta range for data collection 3.07˚ to 25.02˚
Index ranges -8

C12-C13 1.372(4) C32-C37 1.390(3)
C13-C14 1.383(4) C33-C34 1.382(3)
C13-O15 1.392(3) C34-C35 1.372(4)
O15-C16 1.387(3) C35-C36 1.379(4)
C16-C17 1.353(4) C36-C37 1.378(3)
C16-C21 1.362(5)
Table-2: Bond lengths (Å)
Atoms Angle(˚) Atoms Angle(˚)
C2-N1-C6 122.62(2) C21-C16-O15 117.5(3)
N1-C2-C3 118.10(2) C16-C17-C18 118.2(3)
N1-C2-C8 113.33(2) C19-C18-C17 119.5(4)
C3-C2-C8 128.53(2) C20-C19-C18 121.0(4)
C2-C3-C30 126.66(2) C19-C20-C21 120.7(4)
C2-C3-C4 118.06(2) C20-C21-C16 119.1(3)
C30-C3-C4 115.09(2) O23-C22-C5 123.7(2)
C3-C4-C5 108.93(1) O23-C22-C24 119.5(2)
C3-C4-C9 114.15(2) C5-C22-C24 116.65(2)
C5-C4-C9 109.54(2) C25-C24-C29 118.8(3)
C6-C5-C22 122.16(2) C25-C24-C22 121.4(2)
C6-C5-C4 118.62(2) C29-C24-C22 119.7(2)
C22-C5-C4 119.04(2) C26-C25-C24 120.6(3)
C5-C6-N1 117.99(2) C27-C26-C25 119.9(3)
C5-C6-C7 127.0(2) C26-C27-C28 120.0(3)
N1-C6-C7 114.96(2) C27-C28-C29 120.9(3)
C10-C9-C14 117.8(2) C28-C29-C24 119.8(3)
C10-C9-C4 123.18(2) O31-C30-C3 118.58(2)
C14-C9-C4 118.97(2) O31-C30-C32 117.36(2)
C9-C10-C11 120.7(2) C3-C30-C32 123.99(2)
C12-C11-C10 121.3(3) C33-C32-C37 119.10(2)
C11-C12-C13 118.6(2) C33-C32-C30 118.92(2)
C12-C13-C14 121.0(2) C37-C32-C30 121.67(2)
C12-C13-O15 116.8(2) C34-C33-C32 120.4(2)
C14-C13-O15 122.0(3) C35-C34-C33 120.1(2)
C13-C14-C9 120.5(2) C34-C35-C36 119.9(2)
C16-O15-C13 119.0(2) C37-C36-C35 120.6(2)
C17-C16-C21 121.5(3) C36-C37-C32 119.9(2)
C17-C16-O15 120.8(3)
Table-3: Bond angles (˚)
Atoms Length (Å) Angle(˚) Symmetry codes
N1–H1. . .O31 2.999(2) 156 1 + x, y, z
Table-4: Hydrogen bonding geometry

Fig.-1: ORTEP of the molecule with thermal ellipsoids drawn at 50%
probability.
Fig.-2: Packing of the molecules when viewed down the a axis. The dashed line
represents the hydrogen bond.

Fig.-3: Packing of the molecules when viewed down the b axis. The dashed line
represents the hydrogen bond.
Fig.-4: Packing of the molecules when viewed down the c axis. The dashed line
represents the hydrogen bond.
5.6 Conclusion:
3,5-Dibenzoyl-4-(3-methoxyphenyl)-1,4-dihydro-2,6-dimethyl pyridine (DP-7) has
been shown to be a powerful P-gp inhibitor, almost devoid of cardiovascular effects,
but capable of inhibiting liver CYP3A, thus it can be conclude that DP-7 is a good
lead compound for the synthesis of new dihydropyridines. As DP-7 shown promising
MDR activity and looking to the scientific publications of DP-7, studied of X-ray
crystal structure of DP-7 performed.

5.7 Experimental:
5.7.1 Preparation of 1-phenylbutane-1,3-dione
Cool peaces of freshly prepared sodium methoxide (6 gm) at 0 o C using ice cold
water. To that added ethyl acetate (100 ml) slowly and stirred at 0 o C for 10 min. to
that solution added acetophenone (30 ml) drop wise over 45 min and stirred for
another 12 hrs. After completion of reaction filtered the reaction mass, washed with
diethyl ether and dried in rotavap. After that dissolved the crude product in to water
and filter it to removed unwanted crude material. To that filtrate added gl. acetic acid
to set Ph 3. Solid formed was filtered and dried to give titled compound as white
powder (mp. 61 o C).
5.7.2 Synthesis of 3,5-Dibenzoyl-4-(3-methoxyphenyl)-1,4-dihydro-2,6-dimethyl
pyridine(DP-7)
To a solution of 1-phenylbutane-1,3-dione (20mmol) in dry methanol (25ml), 3phenoxybenzaldehyde
(10mmol) and ammonium carbonate (1.5g) was added and the
reaction mixture was refluxed for 18hrs with vigorous stirring. After completion of
the reaction, reaction mixture was cooled to RT and was poured on to ice-water
mixture (100ml) and extracted with dichloromethane (2 x 100ml). The organic
extracts were combined and dried over sodium sulfate and the solvent was removed at
reduced pressure. The residue was subjected to the column chromatography (silica
gel; Hexane-Ethyl acetate, 5:5 v/v) to give titled compound as light yellow crystals
(M.P. 190-192°C).
5.8 Characterization
3,5-Dibenzoyl-4-(3-methoxyphenyl)-1,4-dihydro-2,6-dimethyl pyridine(DP-7)
Ph
O
N
H
O Ph
O
Ph

1
H NMR (400 MHz CDCl3): δ = 7.57-7.53 (m 4H), 7.46-7.42 (m 2H), 7.36-7.31 (m
4H), 7.28-7.24 (m 2H), 7.10-7.02 (m 2H), 6.86-6.84 (m 2H), 6.72-6.70 (d of d 2H, J =
2,2), 6.67 (t 1H, J =2), 5.68 (s 1H), 5.15 (s 1H), 1.92 (s 6H). 13 C NMR (400 MHz
CDCl3): δ = 197.8 (×2), 157.2 (×2), 147.8 (×2), 140.3 (×2), 131.5, 129.8 (×3), 129.2
(×2), 128.4 (×4), 128.2 (×4), 122.8, 122.3, 118.5, 117.9 (×2), 117.1, 112.6 (×2), 43.7,
19.0 (×2). MS (m/z): 485 (M+, 62%), 316 (100%). IR (KBr, cm-1): 3396(N–H
stretching), 3030(C-H stretching, Asymmetric), 2930(C–H stretching, Symmetric),
1703(C=O stretching, ester), 1670(C=O stretching, ketone), 1589(N–H deformation).

5.9 Representative NMR spectra
5.9.1
1 H NMR spectra of bs-DP-7

5.9.2 13 C spectra of bs-DP-7

5.10 References
[1] Fusi F., Saponara S., Valoti M., Dragoni S., D'Elia P., Sgaragli T., Alderighi D., Kawase M.,
Shah A., Motohashi N., Sgaragli G. (2006)Curr. Drug Targets. 8, 949–959.
[2] Bates, S.E., Regis, J.I., Robey, R.W., Zhan, Z., Scala, S., Meadows, B.J. (1994)
Chemoresistance in the clinic: overview. Bull. Cancer 81 (suppl 2), 55–61.
[3] Bellamy, W.T. (1996) Annu. Rev. Pharmacol. Toxicol. 36, 161–183
[4] Saponara S., Kawase M., Shah A., Motohashi N., Molnar J., Ugocsai K., Sgaragli G., Fusi F.
(2004) Br. J. Pharm. 141, 415-422.
[5] Saponara S., Ferrara A., Gorelli B., Shah A., Kawase M., Motohashi N., Molnar J., Sgaragli
G., Fusi F. (2007) Eur. J. Pharmacol. 563, 160–163.
[6] Guengerich, F.B., Brian, W.R., Iwasaki, M., Sari, M.A., Baarnhielm, C., Berntsson, P. (1991)
J. Med. Chem. 34, 1838–1844.
[7] Katoh, M., Nakajima, M., Shimada, N., Yamazaki, H., Yokoi, T. (2000) Eur. J. Clin.
Pharmacol. 55, 843–852
[8] For synthesis and biological activity see (a) Paolo D'Elia , Francesco De Matteis , Stefania
Dragoni , Anamik Shah ,Giampietro Sgaragli, Massimo Valoti. (2009) European Journal of
Pharmacology. 614, 7–13 (b) Masami Kawase, Anamik Shah, Harsukh Gaveriya, Noboru
Motohashi, Hiroshi Sakagami, Andreas Vargae, Joseph Molnar. (2002) Bioorganic &
Medicinal Chemistry. 10, 1051–1055. (c) Prashant S. Kharkar, Bhavik Desai, Harsukh
Gaveria, Bharat Varu, Rajesh Loriya, Yogesh Naliapara, Anamik Shah, Vithal M. Kulkarni.
(2002) J. Med. Chem. 45, 4858-4867
[9] Otwinowski, Z. Minor, W. In: Methods in Enzymology, 276, Carter, C. W. Jr., Sweet, R. M.,
(1997) New York: Academic Press, 307-326.
[10] Sheldrick, G.M. (2008) Acta Cryst., A64, 112-122.
[11] Allen, F.H., Kennard, O., Watson, D.G., Brummer, L., Orpen, A.G., Taylor, R. (1987) J.
Chem. Soc. Perkin Trans, II:S1.
[12] Spek, A.L. (2003) J. Appl. Cryst. 36, 7-13.
[13] Cremer, D., and Pople, J.A. (1975) J. Am. Chem. Soc. 97, 1354-1358.

SUMMARY
The work represented in the thesis entitled “Synthesis and Characterization of New
heterocyclic compounds & their application” is divided into five chapters which can
be summarized as under.
Chapter-1 covers basic introduction to Microwave assisted organic synthesis
including comparison of conventional vs microwave assisted reaction and
introduction of 2-aminoimidazole and their presence as naturally occurring marine
alkaloids described. In this part various synthetic approaches toward 2aminoimidazole
and short review on 2-aminoimidazole as pharmacophores also
presented. Finally basic concept of anti biofilm activity described.
Chapter-2 deals with microwave assisted one pot synthesis and Structure Activity
Relationship of 2-Hydroxy-2-phenyl-2,3-dihydro-imidazo[1,2-a] pyrimidinium Salts
and 2N-Substituted 4(5)-Phenyl-2-Amino-1H-imidazoles as Inhibitors of the Biofilm
Formation by Salmonella Typhimurium and Pseudomonas aeruginosa.
Chapter-3 entitled “Structure Activity Relationship of N1-Substituted 2-
Aminoimidazoles as Inhibitors of Biofilm Formation by Salmonella Typhimurium
and Pseudomonas aeruginosa.” In this chapter a library of N1-substituted 4(5)-phenyl-
2-aminoimidazoles was synthesized and tested for the antagonistic effect against
biofilm formation by Salmonella Typhimurium and Pseudomonas aeruginosa. The
substitution pattern of the 4(5)-phenyl group and the nature of the N1-substituent were
found to have a major effect on the biofilm inhibitory activity. The most active
compounds of this series were shown to inhibit the biofilm formation at low
micromolar concentrations.
Chapter-4 deals with microwave-assisted Cu-catalyzed one pot protocol for the
synthesis of 2-aminoimidazole-triazole framework via two consecutive steps of
dimorth rearrangement and click reaction was demonstrated. Library of 22
compounds have been synthesized and were subjected to test for antibiofilm activity.
However, the antibiofilm activities of these classes of compounds are under pipeline.

After careful study of Structure Activity Relationship, a fresh libraries of N1substituted
2-aminoimidazoles and N1-unsubstituted 2-aminoimidazoles have been
synthesized and tested for anti biofilm activity. In Chapter-4 microwave assisted one
pot protocol for synthesis of 2-aminoimidazole-triazoel framework has been described
and all newly synthesized compounds were tested for antibiofilm activity. However
activities of these calls of compounds are under pipeline.
Chapter-5 entitled “Crystal and molecular structure analysis of DP-7: A new Multi
Drug Resistance Reverter Lead Molecule” deal with crystal and molecular structure
analysis. 3,5-Dibenzoyl-4-(3-methoxyphenyl)-1,4-dihydro-2,6-dimethyl pyridine
(DP-7) has been shown to be a powerful P-gp inhibitor, almost devoid of
cardiovascular effects, but capable of inhibiting liver CYP3A, thus it can be conclude
that DP-7 is a good lead compound for the synthesis of new dihydropyridines. As DP-
7 demonstrated promising MDR activity, several scientific publications on this
molecule appeared. However study of X-ray crystallography was done first time and
presented in the current work.
All newly synthesized compounds have been characterized by 1 H NMR, 13 C NMR
and HRMS. Some representative copy of 1 H and 13 C NMR spectra also presented.

CONFERENCES/SEMINARS/WORKSHOPS ATTENDED
“International Conference On The Interface of Chemistry-Biology In
Biomedical Research” jointly organized by ISCBC and Birla Institute of
Technology & Science, Pilani. February, 22-24, 2008
“National Workshop On Management And Use Of Chemistry Database
And Patent Literature” organized by GUJCOST & Dept. of Chemistry of
Saurashtra University, Rajkot, (Gujarat), February, 27-29, 2008.
“A National Workshop On Updates In Process And Medicinal Chemistry”
jointly organized by National Facility for Drug Discovery through New
Chemicals Entities Development & Instrumentation support to Small
Manufacturing Pharma Enterprises and DST FIST, UGC-SAP & DST-DPRP
Funded Department of Chemistry, Saurashtra University, Rajkot March, 3-4,
2009.
“National Conference On Selected Topics In Spectroscopy And
Stereochemistry” organized by the Department of Chemistry, Saurashtra
University, Rajkot, March, 18-20, 2009.
“12th Belgian Organic Synthesis Symposium” (BOSS XII) Namur, Belgium
July 11-16, 2010.

Paper/Poster presented at the International Conference:
“Microwave-Assisted One Pot Synthesis Of Anti-Biofilm Active 2-
Aminoimidazole -Triazole Conjugates Using Copper Nanoparticles”
Bharat S. Savalia, Denis S. Ermolat’ev, Anamik K. Shah and Erik V. Van der
Eycken.“12th Belgian Organic Synthesis Symposium” (BOSS XII) Namur,
Belgium (2010)
“A General Approach To 2-Aminoimidazole Marine Sponge Alkaloids
From Leucetta sp.”
Denis S. Ermolat’ev, Bharat S. Savalia, Jitender B. Bariwal and Erik V. Van
der Eycken,“12th Belgian Organic Synthesis Symposium” (BOSS XII)
Namur, Belgium (2010)
“Crystal Structure Of DP-7: A New MDR Reverting Agent Against
Tumor Cells”
Manisha Parmar, Bharat Savaliya, Harsukh Gaveriya, Lakshminarayana B.N.
J. Shashidhara Prasad, M. A. Sridhar and Anamik Shah. ISCBC.
Lucknow,India, 2010.
“Rapid Synthesis Of Fused Bicyclic Thiazolo-Pyrimidine And Purimido-
Thiazine Derivatives Devoid Of Use Of Catalyst By Microwave Assisted
Method.”
Bharat S.Savaliya, Vijay Virsodia, Punit Rasadia, Nikhil Vekaria, Rupesh
Khunt And Anamik Shah.ISCBC., BITS-Pilani, India.2008

PUBLICATIONS
[1] One-Pot Microwave-Assisted Protocol For The Synthesis Of Substituted 2-
Amino-1H-Imidazoles. Denis S. Ermolat’ev, Bharat Savaliya, Anamik Shah
and Erik V. Van der Eycken. Molecular Diversity. (2010) DOI
10.1007/s11030-010-9270-5
[2] Structure Activity Relationship of 2-Hydroxy-2-phenyl-2,3-dihydro-
[3]
imidazo[1,2-a]pyrimidinium Salts and 2N-Substituted 4(5)-Phenyl-2-Amino-
1H-imidazoles as Inhibitors of the Biofilm Formation by Salmonella
Typhimurium and Pseudomonas aeruginosa. P.L. Steenackers, Denis S.
Ermolat’ev, Bharat Savaliya, Ami De Weerdt, David De Coster, Anamik
Shah, Erik V. Van der Eycken, Dirk E. De Vos, Jozef Vanderleyden and
Sigrid C.J. De Keersmaecker. Bio. & Med. Chem. Submitted (2010)
Structure Activity Relationship of 4(5)-Phenyl-2-amino-1H-imidazoles, N1-
Substituted 2-Aminoimidazoles and Imidazo[1,2-a]pyrimidinium Salts as
Inhibitors of Biofilm Formation by Salmonella Typhimurium and
Pseudomonas aeruginosa. Hans P.L. Steenackers, Denis S. Ermolat’ev,
Bharat Savaliya, Ami De Weerdt, David De Coster, Anamik Shah, Erik V.
Van der Eycken, Dirk E. De Vos, Jozef Vanderleyden and Sigrid C.J. De
Keersmaecker. J. Med. Chem. (2010) DOI: 10.1021/jm1011148
[4] Copper Catalyzed Microwave Assisted One Pot Synthesis of 2-
Aminoimidazole-Triazole Framework. Bharat Savaliya, Denis S. Ermolat’ev,
Anamik Shah and Erik V. Van der Eycken. (2010) Manuscript in preparation.
Org. lett.
[5] Crystal And Molecular Structure Analysis Of DP-7: A New Multi Drug
Resistance Reverter Lead Molecule. Bharat Savaliya, Manisha Parmar,
Vaibhav Ramani, Harsukh Gevariya, B.N. Lakshminarayana, J. Shashidhara
Prashad, M. A. Sridhar and Anamik Shah. (2010) Manuscript in preparation.
[6] Catalyst-Free, Rapid Synthesis of Fused Bicyclic Thiazolo-Pyrimidine and
Pyrimido-Thiazine Derivatives by a Microwave-Assisted Method.
Vijay R. Virsodia, Nikhil R. Vekariya, Atul T. Manvar,Rupesh C. Khunt,
Bhavin R. Marvania, Bharat S.Savalia and Anamik K. Shah. Phosphorus,
Sulfur, and Silicon, 184:34–44 (2009)

Mol Divers
DOI 10.1007/s11030-010-9270-5
FULL-LENGTH PAPER
One-pot microwave-assisted protocol for the synthesis
of substituted 2-amino-1H -imidazoles
D. S. Ermolat’ev · B. Savaliya · A. Shah ·
E. Van der Eycken
Received: 19 May 2010 / Accepted: 7 August 2010
© Springer Science+Business Media B.V. 2010
Abstract An efficient microwave-assisted one-pot two-step
protocol was developed for the construction of disubstituted
2-amino-1H-imidazoles. This process involves the sequential
formation of 2,3-dihydro-2-hydroxyimidazo[1,2-a]pyrimidinium
salts from readily available 2-aminopyrimidines
and α-bromoketones, followed by cleavage of the pyrimidine
ring with hydrazine.
Keywords Heterocycles · 2-Aminoimidazoles ·
Microwave-assisted synthesis · Ring opening ·
Rearrangement
Introduction
The class of 2-aminoimidazoles has recently attracted particular
interest due to various biological properties of these compounds.
2-Aminoimidazole alkaloids and their metabolites,
isolated from the marine sponges Hymeniacidon sp., have
been described as potent antagonists of serotonergic [1] and
histaminergic receptors [2]. Naamine and isonaamine alkaloids
from the marine sponges Leucetta sp. exhibit antiviral
and anticancer activity [3–10]. Because of these interesting
Electronic supplementary material The online version of this
article (doi:10.1007/s11030-010-9270-5) contains supplementary
material, which is available to authorized users.
D. S. Ermolat’ev · B. Savaliya · E. Van der Eycken (B)
Laboratory for Organic and Microwave-Assisted Chemistry
(LOMAC), Department of Chemistry, Katholieke Universiteit
Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
e-mail: erik.vandereycken@chem.kuleuven.be
B. Savaliya · A. Shah
Department of Chemistry, Saurashtra University,
Rajkot 360 005, Gujarat, India
N
2
N
N
R 2
R 2
A
R1HN N
B
R1 = H
N
H
1
N
Br
Scheme 1 Synthesis of substituted 2-amino-1H-imidazoles
3
N
N
OH
biological activities, numerous synthetic routes to 1-substituted
and 1-unsubstituted 2-aminoimidazoles have been
reported. Modern synthetic methods for accessing 1-unsubstituted
2-amino-1H-imidazoles can be roughly classified
as heterocyclization of substituted or protected guanidines
with 1,2-dielectrophiles [11,12], heteroaromatic nucleophilic
substitution, and recyclization of 2-aminooxazoles [13].
Although different substituted guanidines are readily available
and can be prepared in situ (e.g., from cyanamides [14]),
the high basicity of guanidines together with non-regioselectivity
often leads to multiple products. Protection by acetyl
[11] and Boc-groups [12] requires, in turn, acidic deprotection
conditions.
Recently, we have described two new approaches to the
synthesis of substituted 2-amino-1H-imidazoles 1. The first
approach is based on the cleavage of imidazo[1,2-a]pyrimidines
[15] 2 with hydrazine (Scheme 1, route A) [16]. In the
second approach, the hydrazinolysis of 2-hydroxy-2,
3-dihydroimidazo[1,2-a]pyrimidinium salts 3 followed
by Dimroth-type rearrangement afforded trisubstituted
2-amino-1H-imidazoles 1 (Scheme 1, route B) [17].
2-Hydroxy-2,3-dihydroimidazo[1,2-a]pyrimidinium salts
3 can be easily prepared from 2-aminopyrimidines 4 with
α-bromoketones 5 under microwave irradiation (Scheme 2).
We found that the outcome of this reaction strongly depends
on the temperature [18]. The microwave-assisted reaction
R 2
R 1
123

Scheme 2 Competitive
formation of 1-unsubstituted
and 1-substituted
2-amino-1H-imidazoles upon
microwave irradiation
Table 1 Investigation of the
condensation under
conventional heating and
microwave irradiation
All reactions were carried out on
a 1 mmol scale of
2-methylaminopyrimidine
(1, R1 = Me) with 1.35 equiv. of
α-phenacylbromide (2, R2 =Ph)
in MeCN (5 mL)
a Isolated yield after
recrystallization from MeCN
N
N
NHMe
N
Br
N
4
5
+
+ Br
NHR 1
O
R 2
MW
O
Ph
4 (R 1 = Me) 5 (R 2 = Ph)
between 2-aminopyrimidines 4 and α-bromoketones 5 performed
at 80–100 ◦ C gave 2-hydroxy-2,3-dihydroimidazo
[1,2-a]pyrimidinium salts 3, while irradiation of the
reaction mixture at temperatures above 100 ◦ C provided
aromatic 1-substituted imidazo[1,2-a ]pyrimidinium salts
6 (Scheme 2). The hydrazinolysis of the salts 3 and 6 leads to
the corresponding 1-unsubstituted and 1-substituted
2-amino-1H-imidazoles 1 and 7. Thus, by performing the
reaction at 130−150 ◦ C, we were able to prepare a library of
1,4,5-trisubstituted 2-aminoimidazoles 7 via a one-pot twostep
protocol [18].
In continuation of our ongoing studies, herein we report
a simple one-pot procedure for the synthesis of 1-unsubstituted
2-amino-1H-imidazoles 1 from 2-aminopyrimidines 4
and α-bromoketones 5 under microwave irradiation.
123
100 °C
N
Br
Conditions
N
N
3
6
N
N
OH
R 2
Br
N
Br
R 2
N
R 1
R 1
3
N
N 2H 4
MW
N 2H 4
MW
N Me
OH
Ph
+
R 1HN
H 2N
N
Mol Divers
N
N
H
N
N
R 1
1
7
Ph
R 2
R 2
N
Br
N Me
Entry Conditions Time (min) T ( ◦ C) 3 (Yield %) a 6 (Yield %) a
1 30 80 64 0
2 60 80 77 0
3 30 100 81 Traces
4 60 100 85 Traces
5 30 120 68 17
6 60 120 53 28
7 MW 30 80 88 0
8 60 80 85 0
9 30 100 48 33
10 60 100 45 35
11 30 120 12 79
12 60 120 Traces 84
Results and discussion
We carefully investigated the formation and dehydratation of
salt 3 resulting in the formation of salt 6 under conventional
heating conditions as well as upon microwave irradiation.
As a proof of concept, the condensation of 2-methylaminopyrimidine
(4,R1 = Me) and α-phenacylbromide (5,R2 = Ph)
was studied (Table 1). A sealed vial containing a solution of
the starting compounds in acetonitrile was conventionally
heated with an oil bath (Table 1, entries 1–6) or irradiated
with microwaves (Table 1, entries 7–12) at different temperatures
for 30–60 min. The formation of the 2-hydroxy
salt 3 was faster under microwave irradiation, and this compound
was obtained in 88% yield within 30 min. Further
increase of the temperature up to 120 ◦ C using conventional
6

Mol Divers
Table 2 Microwave-assisted
synthesis of substituted
2-amino-1H-imidazoles 1
N
Br
N
+
NHR 1
O
R 2
1. MW 80 °C
MeCN 30 min
heating or microwave irradiation led to a mixture of salts 3
and 6 (Table 1). Interestingly, using microwave irradiation at
120 ◦ C for 60 min, we were able to drive the reaction completely
to the formation of the imidazo[1,2-a]pyrimidinium
salt 6 (Table 1, entry 12).
As the transformation of salts 3 into salts 6 is relatively
rapid at the temperatures above 100 ◦ C, the synthesis of
salts 3 was conducted at 80 ◦ C. Treatment of substituted
4
5
N
Br
3
N
N R1 OH
R 2
2. N 2H 4, MW 90 °C
MeCN 10 min
R 1HN
entry 2-aminopyrymidine 4 α–bromoketone 5 product 1 yield
1
2
3
4
5
6
N
N
N
N
N
N
N
N
N
N
N
N
H
N
N
H
NH 2
NH 2
NH 2
Me
Piperonyl
N
H
Pr
Br
Br
Br
Br
Br
Br
O
O
O
O
O
O
OMe
Ph
F
Cl
OMe
Cl
Cl
H 2N
H 2N
H 2N
Me
HN
Piperonyl
Pr
HN
N
N
H
N
N
H
N
N
H
MeO
N
N
H
HN
N
N
H
N
N
H
1{1}
1{2}
1{3}
1{4}
1{5}
1{6}
Ph
F
Cl
OMe
N
N
H
1
R 2
(%) a
2-aminopyrimidines 4 with 15 mol% excess of α-bromoketones
5 in MeCN under microwave irradiation for 30 min
generated the intermediate salts 3 which, in most cases, precipitated
from the reaction mixture upon cooling (Table 2).
Reaction progress was monitored by mass-spectrometry.
In all the cases examined, the reaction appeared to be complete
after 30 min. The cleavage step was performed under
microwave irradiation at 90 ◦ C, using seven equivalents of
Cl
Cl
75
79
88
48
72
70
123

Table 2 continued
9
10
11
12 N
hydrazine hydrate. Based on the data given in Table 2, the
reaction appears to be compatible with both aryl and alkyl
substitutions. All the reactions were clean, smooth, and provided
the products 1{1–18} in good and high yields. The
compounds were purified by column chromatography using
5–10% MeOH in CH2Cl2 as the eluent. All the final 2-amino-
1H-imidazoles 1{1–18} were characterized by 1 H and 13 C
NMR spectroscopy. Their compositions were also confirmed
by HRMS.
123
7
8
13
14
N
N
N
N
N
N
N
N
N
N
N
N
N
N
H
N
H
N
H
N
H
N
N
H
N
Octyl
N
H
Pentyl
Hexyl
PMB
Br
Br
Cyclooctyl Br
N
H
N
H
Bu
PMB
Br
Br
Br
Br
Br
O
O
O
O
O
O
O
O
SO 2Me
Br
Cl
Cl
F
SO 2Me
NO 2
Mol Divers
Cl
Pentyl
HN
N
61
N
H 1{9}
Hexyl
HN
HN
N
N
H
N
N
H
1{7}
SO 2Me
1{10}
Cl
PMB N
Br
HN
N
H 1{11}
F
SO 2Me
69
44
Cyclooctyl
HN
N
66
N
H 1{12}
Bu
HN
N
83
N
H
1{13}
NO 2
73
Octyl
HN
N
79
N
H
1{8}
PMB
HN
N
89
N
H
1{14}
In conclusion, we have developed a simple and practical
microwave-assisted procedure for the preparation of substituted
2-amino-1H-imidazoles. We have investigated a onepot
synthesis and cleavage of 2-hydroxy-2,3-dihydroimidazo
[1,2-a]pyrimidinyl-4-ium bromides by hydrazine hydrate and
found microwave irradiation to be very effective in this regard.
A small library of 2-amino-1H-imidazoles was synthesized
for screening for potential antiviral and antibacterial
activities.

Mol Divers
Table 2 continued
All the reactions were carried
out on a 4 mmol scale of
2-alkylaminopyrimidine 4 with
1.15 equiv of α-bromoketone 5
in MeCN (3 mL)
a Isolated yield after column
chromatography
Experimental section
Microwave irradiation experiments
15
16
17 N
A monomode CEM-Discover microwave reactor (CEM Corporation,
P.O. Box 200, Matthews, NC 28106) was used
in the standard configuration as delivered, including proprietary
software. All the experiments were carried out in sealed
microwave process vials (10 mL) at the maximum power and
temperature, as indicated in the tables. After completion of
the reaction, the vial was cooled to 50 ◦ C via air-jet cooling
before it was opened.
General procedure for the one-pot two-step microwaveassisted
synthesis of 2-amino-1H-imidazoles 1{1–18}
In a microwave, vial (10 mL) was successively dissolved
in dry MeCN (3 mL), the corresponding 2-aminopyrimidine
(4 mmol) and α-bromoketone (4.6 mmol). The reaction tube
was sealed and irradiated in a microwave reactor at a ceiling
temperature of 80 ◦ C and a maximum power of 50 W for
30 min. After the reaction mixture was cooled with an air
flow for 15 min, hydrazine hydrate (0.9 mL, 28 mmol of a
64% solution, 7 equiv.) was added, and the mixture was irradiated
at a ceiling temperature of 90 ◦ C and a maximum
power of 50 W for another 10 min. After the reaction mixture
was cooled, hydrazine hydrate was removed by distillation
with toluene (3 × 20 mL). The resulting residue was purified
by column chromatography (silica gel; MeOH-DCM 1:9 v/v
with 0.5% of 6 N ammonia in MeOH) to afford 1 as amorphous
solid.
18
N
N
N
N
N
H
N
N
N
N
H
N
H
N
H
Bu
OMe
Br
Br
Br
Br
O
O
O
O
SMe
NO 2
OMe
Bu
HN
HN
OMe
HN
HN
N
N
H
N
N
H
N
N
H
N
N
H
1{15}
1{16}
1{17}
1{18}
SMe
NO 2
OMe
Acknowledgments The support for this project was provided by the
Research Fund of the University of Leuven and by the F.W.O. (Fund
for Scientific Research—Flanders (Belgium)). E.D.S. is grateful to the
University of Leuven for obtaining a postdoctoral fellowship, and S.B.
to Erasmus Mundus External Cooperation Window Lot 15 India
(EMECW15) for obtaining a scholarship. The authors thank Ir.
B. Demarsin for HRMS measurements.
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