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Chem & Bio Draw 12.0
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Chem & Bio Draw 12.0
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Chem & Bio Draw 12.0
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Chem & Bio Draw 12.0 15

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3

2. Object Object Settings
Object Settings
3. Captions Atom Labels
4. OK
5.
1.
2.
3. Color
4.
1.
2. Color
1.
2.
•
•
BackSpace Delete
Chem & Bio Draw 12.0
tert-
1.
2.
3. 3(tert- )
‘t-Bu’
4. ‘t-Bu’ Structure
Expand Label
n ( )O ( )I ( )
-2-
( A)
( B)
Chem & Bio Draw 12.0 17

1.
2. Shift
n
Shortcuts and HotKeys
NOTE: Automatically Rectify Hydrogens in Atom
Labels (19
)
3.
:
4. OK
1.
2.
MeEtPh
ChemDraw Items
GUI (
)
NOTE:
ChemDraw ProChemDraw Ultra ChemBioDraw
Ultra 12.0 107
4
“Ph”
1.
2. = ( )
NOTE:
“OTHP” “PHTO”
“THP”
“THPO” 145
/
(
)
18
3

3
Structure Contract
Label
(Name
DescriptionTypeOther Info)
NOTE: ChemBioDraw Ultra 12.0ChemDraw
Ultra 12.0 ChemDraw Pro 12.0
1.
2. Object Annotate
Annotate
3. Keyword
•
• Add New Keyword
4.
Content
5. OK
1. Annotate Keyword
2. Delete Keyword
3. OK
Chem & Bio Draw 12.0
File
Preferences Building/Display
Automatic Atom Label Alignment (
)
‘CH 3 ’ ‘H 3 C’
Automatically Rectify Hydrogens in Atom Labels
( )
‘CH3’ ‘CH2’
NOTE: Automatically Rectify Hydrogens in Atom
Labels ( )
File Document Settings
Atom Labels
Chem & Bio Draw 12.0 19

3.3 a)
b) c)
1. File Documents and Settings
2. Atoms Labels Show Labels on Terminal
Carbons
3. OK
1
1. (1 )
2. Object Settings
Object Settings
3. Atoms Labels Show Labels on Terminal
Carbons
Show Terminal Carbon Labels
/
CH 3 OH
Interpret Chemically
Analysis
( File
Document Settings Auto-update
)
Analysis
1.
2.
1. File Preferences
2. Building/Display Sprout Rings Instead of
Spiro When Clicking
20
3

1.
2. Ctrl (Windows) Command
(Macintosh)
2
NOTE:
Ctrl Command
3.4
NOTE: Ctrl+Alt
Command+Option
Shift
1.
2.
Ctrl
Command
X
X
15
1.
Chem & Bio Draw 12.0 21

2.
Add Chain
3.
4. Add
Alt (Windows) Option
(Macintosh)
(
)
Fixed Angles
15
Alt Option
Chem & Bio Draw 12.0
( )
3
2
•
•
3.5
22
3

NOTE:
Curves
(
)
NOTE: “left” ( )
“right” ( )
1.
2. Shift
3. Shift
3
Alt
Option
2
Object Group
29
Chem & Bio Draw 12.0 23

X
Info
1.
2.
1.
2.
3.
1.
2.
2
•
•
1.
2.
0 120
180 270
1.
• ChemDraw Standard
• Chem & Bio Draw 12.0
2.
1.
2.
3.
4.
X
Info
Info
Info
{ } [ ] ( )
1.
2.
1.
2.
3.
24
3

1.
2.
NOTE: Text
Settings
1.
2. Object Add Frame
(
View Other ToolbarsPen Tools
)
CurvesClosed
Curve Filled
FadedShaded
Color
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
3.6 A)
B) C) D)
E)
Alt Option
Chem & Bio Draw 12.0 25

Ctrl+Alt+Tab Command
+Option+tab
3
(
)
3.7 A)
B) C)
1.
2.
3.
1.
2.
1
1.
2.
3.
NOTE:
29
Shift
Edit
Select All
•
• Esc
•
• Shift
26
3

1
Shift
NOTE:
2.
Ctrl Command
NOTE: 1
3.8
•
•
X Y
• Shift
(X Y )
1.
1.
• Object Rotate
• Rotate
Objects
2. degrees
CW degrees CCW
3. ( )
Rotate Atom Labels
4. Rotate
1.
2. Edit Repeat Rotate
Chem & Bio Draw 12.0 27

1.
(+)
2. Alt
3.
1.
2.
Shift
1.
2.
1
NOTE:
Alt Option
10
NOTE:
15
1. 1
2. Ctrl Option
Ctrl Option
• Delete
• Edit Clear
2
1.
2. Shift 2
3. Object Join
2
1. 2
2. 2
28
3

3. Object Join
NOTE:
NOTE:
2
B:
“Integral ”
Integral
1
1.
2. Object Group
1
1.
2. Object Ungroup
GroupUngroup
Integral
1.
2. Object Group
3. GroupIntegral
Integral
1. Integral
2. GroupIntegral
1.
2.
• Object Scale
•
Scale Objects
3.
•
•
2
(
)
•
3
Chem & Bio Draw 12.0 29

100%
100%
4. Scale
( )
1.
2. Object Center on Page
1.
2. Structure Check Structure
NOTE:
2
1.
2. Object Align
NOTE:
3
1.
2. ObjectDistribute Vertically
Horizontally
3. Ignore
Ignore All
Stop
1. File Preferences
2. General Check Structure When Copying
to Clipboard or Exporting
Chem & Bio Draw 12.0
30
3

•
NOTE:
•
View
Show Chemical Warnings
Display Warnings
Display Warnings
•
• Check Structure
(Structure
Check Structure )
•
• Explain This Warning
• Structure Check
Structure
Preferences
1. File Preferences
2. Warnings
3. OK
Chem & Bio Draw 12.0 31

32
3

4
BioDraw
Chem & Bio Draw
Chem & Bio Draw 12.0
13
BioDraw
BioDraw
BioDraw View
Show BioDraw Toolbar
Chem & Bio Draw 12.0 Color
Curves
BioDraw
X Y
(DNA )
BioDraw
BioDraw ChemBioDraw Ultra
FileOpen TemplatesAdvanced
BioDraw
68
BioDraw
BioDraw
1 “ ”
G
( )
DNA
2
NOTE: BioDraw ChemBioDraw Ultra 12.0
BioDraw Ultra 12.0 BioDraw Pro 12.0
( )
(
)
Chem & Bio Draw 12.0 33

( )
( )
( )
/
4.1
2 G
( )
:
G
( )
( )
( ) ( )
( ) 3
•
•
•
( )
1. ( )
2. ( )
Fixed Angles
15
Alt
Option
1.
2.
Object Fixed Angles
15
Alt Option
34 BioDraw
4

4
4.3 DNA : A) B) C)
D)
4.2 : A)
B) C) D)
DNA
DNA
1. DNA
2.
Object Fixed Angles
DNA
15 Alt
Option
DNA 4
2
DNA
(ShadingFadingFilled)
1.
2. Color
3. Curves FilledShaded
Faded
tRNA
tRNA
1. tRNA
2. tRNA
tRNA
A B
BioDraw
A B
1. BioDraw
2.
Chem & Bio Draw 12.0 35

R
NOTE: tRNA
ChemBioDraw Ultra
BioDraw Ultra
1. BioDraw
2.
Insert Plasmid Map
3.
OK
1.
Regions
2. Regions Start
End
1 1000
11000
3. Start End
Add Markers At Region
Ends
4. Add
5. 2 4
6. OK
1.
Markers
2. Markers
Position
3. Label
4. Add
5. OK
1.
( )
2.
36 BioDraw
4

RNA RNA
2.
3. 1 3
NOTE: 39
IUPAC
( )
RNA
1.
(1 )
1
(3 ) 3
DNA
DNA
4. 3
5.
1. 1
( Shift
)
2. Structure Expand Label
( )
1.
2. Structure Contract Label
1.
2.
3. Delete
Chem & Bio Draw 12.0 37

1
1.
2.
3.
NOTE:
( ) 3’
(DNA/RNA )
1.
2. Object Object Settings
3. Object Settings Atom
Labels
4. Amino-acid Termini NH2/COOH H/OH
5. OK
/
1.
2. Object Object Settings
3. Object Settings Atom
Labels
4. Amino-acid Termini Show Sequence Termini
5. OK
Chem & Bio Draw
1.
2.
( ‘His’)
3. Enter
2
1.
Modify Nickname
2. Modify Nickname
3. OK
Modify Nickname
38 BioDraw
4

IUPAC
IUPAC
IUPAC
3
A A Ala
C C Cys
G D Asp
T ( U) ( ) E Glu
R A G F Phe
Y C T G Gly
S G C H His
W A T I Ile
K G T K Lys
M A C L Leu
B C G T M Met
D A G T N Asn
H A C T P Pro
V A C G Q Gln
N R Arg
. - S Ser
T Thr
V Val
W Trp
Y Tyr
Chem & Bio Draw 12.0 39

( )
2.
4.4
•
•
•
4.5
1. 2
2
1. 2
2.
40 BioDraw
4

5
1
4
Chem & Bio Draw 12.0
(
)
Display Warnings
1:
1. ObjectFixed LengthsFixed Angles
NOTE:
Document Settings
Drawing 15
2. View Show Main Toolbar
3.
4.
(+)
5. 2
5.1
2 120
NOTE:
Document Settings
Drawing Chain Angle
Chem & Bio Draw 12.0 41

.
6. 5
2:
5.2 3
6
5.3
1.
2. O
3. Esc
1.
2. 2-propanone
3. Esc
1. File New Document
2. File Save As
3. tut2.cdx
4.
5. Save
1.
2. Shift
NOTE:
Shift
3.
4. 1
5.4
42
5

5. 2 1
2 1
1
8. 1
2
5.5 1
9.
o
6. 2
2
7.
3
10.
Chem & Bio Draw 12.0 43

3:
4.
5. Save
1.
2.
3.
2
Show Chemical Warnings
4. 3 3 5
5.6
1. File Open Style Sheets
ACS Document 1996
Special Documents
NOTE: ACS
ACS
1 (Page Setting)0.2
(Drawing Setting)10 Arial
Helvetica (Text Setting)
2. File Save As
3. tut3.cdx
5.7
NOTE:
+
+
2
1. 1
44
5

2.
3. 1 2
2. B
()
5.10
5.8
1.
2. 1
CHO
3. 1 CH2OH
:
3.
O.oooo
4.
5.9
1. A H
5.11
1.
Chem & Bio Draw 12.0 45

2. View Show Analysis Window
3. Analysis Paste
1. FileOpen Style SheetsNew Document
NOTE: Chem & Bio Draw 12.0
ACS
1
New Document
5.12
1. File Save
2. File Close
4:
-
D-
2. File Save As
3. tut4.cdx
4.
5. Save
1.
2.
1. Edit Select All (
Ctrl A )
2. Object Rotate (
Ctrl R )
3. Rotate Objects
30 Rotate
5.13
1.
46
5

2. o
1.
2.
5.14
1. Edit Select All (
Ctrl A )
2.
200%
3. 1
4. 4
1. Edit Select All
( Ctrl A )
2.
150%
3. No
OH
4
o
1.
Chem & Bio Draw 12.0 47

2. OH
OH CH2
5.15 OH
3.
5.16 CH 2 OH
NOTE: Enter
(Windows) Return (Macintosh)
1.
2.
:
View Magnify
CH 2 OH
1. C5
2. Enter (Windows) Return
(Macintosh)
3.
4.
5.
6. 2
48
5

:
View Magnify
NOTE:
1. File New Document
2. File Save As
3. tut6.cdx
4.
5. Save
1.
2.
3. 2
4.
3
1. File Save
2. File Close
5:
5.17
1.
2. Ctrl (Windows) Option (Macintosh)
5.18
1.
Chem & Bio Draw 12.0 49

2.
:
NOTE:
1. s
2.
Document Settings
Drawing
2.
3
2
Shift
1
1. Rotate
Objects
2. Angle 180
Rotate
5.19
NOTE:
1
Object Group
1.
5.20
3. Object Bring to Front
(
)
1.
50
5

2.
3. tut7.cdx
4.
5. Save
NOTE:
1 “
”
3.
1.
2.
3. 2
4.
3
5.21
1. File Save
2. File Close
6:
flip
1. File New Document
2. File Save As
5.22
5. 9 (2
)
5.23
Chem & Bio Draw 12.0 51

1.
2. Object Show Stereochemistry
S
1.
NH2
Esc
2. (o )
O OH
3. Object Flip Horizontal
R
4. Object
Rotate 180× Vertical
(
5
)
2
(R) (S)
•
• w
(R)
1. File Save
2. File Close
7:
Chem & Bio Draw 12.0
52
5

2
2
1. FileOpen Style SheetsNew Document
2.
3. Aromatics
(4 3
)
4.
2 2
1.
2.
3.
4.
5. ( )
6. O
7. 1
Chem & Bio Draw 12.0 53

54
5

6
Chem & Bio Draw
3D
Chem & Bio Draw 12.0
•
•
•
•
•
•
• 3
•
•
•
•
NOTE: Clean Up Structure
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0
X Y
1.
2. Ctrl
Option
3. Object Flip
Horizontal Flip Vertical
Object
Rotate 180
s
1.
2.
• Color
• Color
• Object Object Settings
Drawing
OK
Chem & Bio Draw 12.0 55

Chem & Bio Draw
Integral Integral
:
:
6.24 A)
B) C) Integral
“Ph”
NOTE:
ChemBioDraw UltraChem & Bio Draw 12.0 Ultra
Chem & Bio Draw 12.0 Pro
2 H-Ala-
OH 1
(H) 2
(OH)
1.
2.
3. Structure Expand Label
56
6

1.
:
6.1
2. Structure Contract Label
Contract Label
3. OK
1.
2. CH2NHC3
3.
4. Expand Structure
Structure Expand Label
6.2
NOTE:
Ignore
Ignore All
Stop
:
6.3
Chem & Bio Draw 12.0 57

29
160
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
Clean Up Structure
• Document Settings
Drawing
•
•
• 15
• Clean Up Structure
Clean Up Structure :
1.
2. Structure Clean Up Structure
Shift+Ctrl+K
NOTE:
((Cp) 2 Fe)
6.5
6.4
58
6

2.
: Object Fixed Lengths
:
1.
2. Structure Add Multi-Center Attachment
59
1.
1.
2.
3. Structure Add Variable Attachment
4.
NOTE:
6.6
Chem & Bio Draw 12.0 59

• (123...)
• ( 1)
• Symbol
• (abc...)
:
60
1. 1
2.
• Control
Atom
Show Atom Number
• ‘( )
3. 1
•
Show Atom Number
• ‘( )
1.
2. Control
Atom Show Atom
Number
•
•
Backspace
Delete
1.
2.
NOTE:
2
3.
Text
Position Indicators
1.
Position
Position Indicators
60
6

2.
3
3
3
NOTE: 3
Flatten
3
1.
2. Object Flatten
z-
(
)
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw Pro
12.0
1
1. 3
2.
3. X Y
Shift+
6.7
Chem & Bio Draw 12.0 61

NOTE:
Alt (Windows) Option
(Macintosh)
Alt
Option
6.8
1
1
/
( )
Chem & BioDraw 12.0 2
Beyer
6.9
( )
2
2-
1.
2.
3. 3
4.
2-
5.
6.
62
6

7. OHEsc
NOTE: Show Chemical Warnings (
)
OH
1.
2.
Circle Minus
3. OH
O
4.
1.
2. Color
(
)
1.
2. Color
3. FilledFaded
Shaded
2- 4-
-4- -2-
1. 2-
2. Ctrl (Windows) Option (Macintosh)
+
3.
6.10
NOTE:
Shift
Chem & Bio Draw 12.0 63

1.
2.
( A)
3. A
4. 3
( )
NOTE:
6.11
5. A
6. OH
1.
2.
3.
Group
1.
2.
•
• Shift OH
Shift
NOTE: Shift
6.12
1.
4-hydroxy-
4-methyl-2-pentanoneEnter
Return 1 mole
2.
2 Mole
3. Object Group
NOTE:
64
6

1.
2. ObjectAlignT/B centers
• “+”
•
•
NOTE: ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. View Show Reaction Interpretation
2.
•
•
•
•
• 1
• 1
1. File New Document
2. File Save As
3. tut2.cdx
4.
5. Save
1.
2.
1
1.
Chem & Bio Draw 12.0 65

.
2. 6.13 A
2
6.16 B
6.16
6.13
NOTE: 1
6. A
o
1.
2. 6.14
3.
7. -( )
OH O -
6.14
2 3
4. 2 ( 6.15 )
2 2
OH 1
1. A
6.15 2
5. 6.16
2.
• o
•
OH
66
6

1.
2.
3.
2. O -
6.19
6.17
4.
5.
1.
2. ( )
3. ( )
6.18
1.
6.20
4. Curves
Full Arrow at End
Chem & Bio Draw 12.0 67

5. Esc
6.
Chem & Bio Draw 12.0
1. File Open
2.
3. View Templates>
1.
2.
:
Alt
Chem & Bio Draw 12.0
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. FileOpen Style SheetsNew Templates
2.
68
6

.
3.
4.
5.
File Save
NOTE: Chem & Bio Draw 12.0
Items
6.
1. File Open Templates
2.
1.
2. Edit
File Save
1.
2.
3. Edit Clear
4. File Save
NOTE: ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
Chem & Bio Draw 12.0
6.21
1
2
H-Leu-OH
Chem & Bio Draw 12.0 69

2
( 2
)
NOTE:
‘1’
Object Bring to Front
18
1.
2.
6.22
3. Structure Define Nickname
4.
5. OK
Ac
Check
Structure
Ac
Am
Np -
Pr
File
List Nicknames
Nicknames
1. File List Nicknames
2. Delete
Define Nicknames
•
• 3
•
70
6

a
b 1
a
3D
3D 3
1.
2. Edit Get 3D Model
3
Chem 3D
NOTE: 3D
137
Chem3D Preview
b
(
) 3
Chem3D Preview
( )
View Show Chem3D
Preview Window
NOTE: Chem3D Preview
“No preview available”
3D
3
Chem & Bio Draw 3
2
NOTE: 3
Chem 3D
Chem3D Preview ChemBioDraw
Ultra Chem & Bio Draw 12.0 Ultra
Chem3D Preview
Chem & Bio Draw 12.0 71

Chem 3D Chem 3D
&
3 (
ChemBio3D Preview )
Chem3D Preview
3 D
1. 3 Chem &
Bio 3D
2. Chem & Bio 3D
ChemDraw
ChemScript
ChemScript Software Development
Kit (SDK) CambridgeSoft
“ ”
ChemBioDraw
Ultra
ChemBioDraw Ultra
ChemScript
ChemBioOffice Desktop
ChemScript
1. File Run ChemScript
2. Open
Open
3. ( ) File
Re-run Previously Selected ChemScript
ChemBioDraw Ultra
File ChemScripts
72
6

7
Chem & Bio Draw 12.0
2 (Name>Struct Struct>Name)
2
2
Struct=Name
Struct>Name Cahn-
Ingold-Prelog (CIP)
Name>Struct
IUPAC ( )IUBMB (
) CAS
NOTE: Struct>Name Name>Struct
ChemBioDraw Ultra ChemDraw Ultra
Struct=Name
Struct=Name
Convert Structure to
Name Struct=Name
Struct=Name
NOTE: Struct=Name ChemBioDraw
Ultra ChemDraw Ultra
•
•
•
•
Struct=Name
•
•
•
•
•
•
•
•
•
•
•
•
•
Chem & Bio Draw 12.0 73

•
•
•
• SSeTe
• SSeTe
• SSeTe
• SSe Te
•
•
• (PBA )
•
•
•
•
•
•
•
•
•
•
•
•
•
•
• ( )
Struct>Name
•
•
•
•
•
•
•
•
•
2
von Baeyer
1
7.23 : 1,1':2',1''-
Struct>Name 2
7.24 : [ij] [2,1,6-
cde]
Chem & Bio Draw 12.0 (
) ()
2 (2 )
74
7

Name=Struct
Name=Struct
NOTE: Name=Struct
ChemBioDraw Ultra ChemDraw Ultra
7.25 : 9,10-
•
• SiGeSn Pb
•
•
Struct=Name CIP
Struct=Name
1.
2. Structure Convert Structure to Name
Auto-update
/
( )
NOTE: CPU
Name=Struct
•
•
•
• /
• : +-+/-+-Dl
dlendoexosynantirtc
Name=Struct
chemfinder.com
NOTE:
Name=Struct
1. Structure Convert Name to Structure
Insert Structure
Chem & Bio Draw 12.0 75

2. ( 2-bromobenzoic acid)
NOTE:
Crtl+V Command+V
3.
Paste name below structure
4. OK
1.
2. EditPaste SpecialName as Structure
1.
2. Structure Convert Name to Structure
Struct=Name
(PBA )
SSe Te
SSeTe
SSeTe
SSeTe
Si, Ge, Sn, Pb
76
7

8
Analysis
(
) m/z
View Show
Analysis Window
Decimals Exact MassMolecular Weight
m/z
Formula
Exact Mass
Molecular Weight (atomic mass units)
m/z / = 1
(
)
Elemental Analysis
1.
2. Paste
8.1
/
1.
2. Analysis /
ChemBioFinder
CambridgeSoft
ChemBioDraw 12.0
ChemDraw Ultra 12.0
Chem & Bio Draw 12.0 77

• CambridgeSoft ChemIndex
•
•
• CAS ChemACX ID
3. Drawing Atom Indicators Bond
Indicators Show Stereochemistry
ChemBioFinder
ChemBioFinder
1.
2. View Show ChemBioFinder HotLink
Window
Show Stereochemistry Cahn-Ingold-
Prelog (CIP)
CIP 169
Cahn-Ingold-Prelog
(R), (S)
(r), (s)
cis- myo-
(E), (Z)
1.
2. Object Settings
8.2
1.
2. Hide Indicator
Preferences
Building/Display
78
8

1.
2. Position
Position Indicator
3.
( )
( )
Structure
Enhanced
Stereochemistry
-
2 4
1
NOTE: ChemBioDraw UltraChem & Bio Draw 12.0
Ultra Chem & Bio Draw 12.0 Pro ISIS
(
)
( 1 )
8.3 -
8.3 2 &1
(R)
(S)
1. Shift
2. Structure Enhanced Stereochemistry
Chem & Bio Draw 12.0 79

3 &2
1
78
(CDXCDXMLMOL
V3000RXN V3000SKCTGF)
NOTE: Mol V3000SKC TGF
ChemBioDraw UltraChem & Bio
Draw 12.0 Ultra Chem & Bio Draw 12.0 Pro
SKC TGF
SGroup
SGroup SKC TGF
Enhanced Stereochemistry
Chem & Bio Draw 12.0
Color
Info
X
Object
Fixed Lengths Fixed Angles
NOTE:
Object Group
29
s-
s-
1.
s-
2.
-
1.
-
2.
1.
2.
p-
p-
1.
p-
2.
(‘sp3’)
1.
80
8

2.
d-
d- (‘dxy’)
1.
d-
2.
d z 2-
d z 2-
1.
d z
2-
2.
(H- H- )
H- H-
Z
H-
Z
H- H- H-
1.
2.
1.
2.
1.
2.
1.
2.
4
8.4
Chem & Bio Draw 12.0 81

(58 )
X Info
1.
2.
27
Chemical Properties
100
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
Log P CMR
Boiling Point1
Melting Point1
Critical Temperature
(T c )
Critical Pressure (P c )
Critical Volume
(V c )cm 3 /mol
Gibbs Energy
G1 298.15K kJ/mol
Henry’s Law [-log
(H)] ( )
Heat of Formation (H f )1
298.15K kJ/mol
tPSA PSA
CLogP/CMRCLogP n-octanol/
(log P ow )
LogP
CMR
MR
NOTE: CLogP CMR
ChemBioDraw Ultra ChemDraw Ultra
1.
2. View Show Chemical Properties
Window Chemical Properties
3.
Paste
4.
Report
NOTE:
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0
82
8

1.
2. Structure Analyze Stoichiometry
NOTE:
Interpret Chemically
3.
( )
Limiting
Sample Mass
1
: g
%Weight 100%
1.
Volume
Molarity
Density
: ml
: M
: g/ml
NOTE:
8.5
2.
Limiting
‘No’ Ctrl-
Set Limiting
Reactants
Formula
MW
Limiting
Equivalents
Sample Mass
%Weight
Molarity
Density
Volume
Reactant Moles
Reactant Mass
C 3 H 6 O 2 S
106.14
Yes
807.50g/l
100.00ml
760.76mmol
80.75g
C 2 H 4 O
44.05
No
788.00g/l
760.76mmol
33.51g
Products
Formula
MW
Equivalents
Expected Mass
Expected Moles
Measured Mass
Purity
Product Mass
Product Moles
%Yield
C 5 H 10 O 3 S
150.20
114.26g
760.76mmol
8.6
Chem & Bio Draw 12.0 83

TLC
TLC
R f
NOTE: TLC ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw Pro
12.0
TLC
1. TLC
2.
Ctrl-
TLC
Transparent
1.
(
)
2.
Ctrl-
3.
R f
Ctrl Option
R f
1.
Ctrl-
2. TLC Spots
R f
Ctrl- TLC
Spots Show
Rf
84
8

R f
1.
Ctrl-
2.
Ctrl-
TLC Spots
Shift
Shift
3
• (
)
•
( )
•
(
)
Show R f
2 R f
Ctrl-
Position Position Indicators
R f
R f
R f
Shift
4
3
TLC
Set Custom Spot
TLC
ChemNMR
ChemBioDraw Ultra ChemDraw Ultra
ChemNMR
ChemNMR
-13
NMR Shifts
1 H 13 C NMR
1.
2. Structure Predict 1H-NMR Shifts
Predict 13C-NMR Shifts
Chem & Bio Draw 12.0 85

ChemNMR
O
10
8
6
PPM
4
2
0
ChemBioDraw Ultra
1.
2. ( )
3.
4. ( ) Shift
5. Structure Make Spectrum-Structure
Assignment
1.
2.
8.7 -
86
8

1.
2.
3. Structure Clear Spectrum-Structure
ChemNMR
SDF
Chem & Bio Draw ChemNMR
ACD Labs MestreNova
SDF
(
)ChemBioFinder
SDF
NMR
SDF
>
,,
>
2,9.61,0.0
>
3,8.92,0.0
SDF
NMR
ChemNMR
SDF
ChemNMR
1. Chem & Bio Draw
2. Chem & Bio Draw ChemNMR
C:Documents and SettingsAll Users
Application DataCambridgeSoft
ChemOffice2010ChemDrawChemNMR
3. DOS
• Windows XP
cmd
OK
• Windows Vista
cmd
Enter
4. DOS 2 ChemNMR
5.
MakeChemNMRUserDB.exe
•
SDF
•
ChemNMR
6. Chem & Bio Draw
NMR
Chem & Bio Draw
1. Chem & Bio Draw
2. ChemNMR
3. Ushiftdb5H1.txt Usimilvecx.h1
4. Chem & Bio Draw
2 NMR SDF
(
)
Chem & Bio Draw 12.0 87

ACD/Labs07190711112D
14 14 0 0 0 0 0 0 0 0 15 V2000
5.7578 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7578 -3.3267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6062 -1.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6062 -3.9825 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.4547 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4547 -3.3267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9094 -1.3275 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
8.0609 -1.9992 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
6.9094 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.3031 -1.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3031 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1516 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1516 -3.3267 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.3275 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
1 7 1 0 0 0 0
2 4 2 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 2 0 0 0 0
12 14 1 0 0 0 0
M ZZC 1 5
M ZZC 2 6
M ZZC 3 4
M ZZC 4 1
M ZZC 5 3
M ZZC 6 2
M CHG 2 7 1 8 -1
M ZZC 7 9
M ZZC 8 13
M ZZC 9 10
M ZZC 10 7
M ZZC 11 8
M ZZC 12 11
M ZZC 13 12
M END
>
1
88
8

d6-DMSO
>
2,9.61,0.0
>
3,8.92,0.0
>
6,9.01,0.0
>
10,3.11,0.0
>
11,1.16,0.0
>
5
$$$$ TH
>
d6-DMSO
>
2,9.6,0.0
>
3,8.91,0.0
>
6,9.11,0.0
>
10,2.75,0.0
>
11,1.17,0.0
>
12,2.41,0.0
>
6
$$$$
Chem & Bio Draw 12.0 89

ACD/Labs07190711112D
15 15 0 0 0 0 0 0 0 0 16 V2000
7.1683 -1.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1683 -3.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0438 -1.2962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0438 -3.8887 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.9194 -1.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9194 -3.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2927 -1.2962 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
9.4171 -1.9521 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
8.2927 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7950 -1.2962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7950 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2489 -2.1708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1401 -1.5149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -2.1552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.1401 -0.2186 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
1 7 1 0 0 0 0
2 4 2 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
13 15 1 0 0 0 0
M ZZC 1 5
M ZZC 2 6
M ZZC 3 4
M ZZC 4 1
M ZZC 5 3
M ZZC 6 2
M CHG 2 7 1 8 -1
M ZZC 7 9
M ZZC 8 14
M ZZC 9 10
M ZZC 10 7
M ZZC 11 8
M ZZC 12 11
M ZZC 13 12
M ZZC 14 13
M END
>
2
90
8

d6-DMSO
>
2,9.6,0.0
>
3,8.91,0.0
>
6,9.11,0.0
>
10,2.75,0.0
>
11,1.17,0.0
>
12,2.41,0.0
>
6
$$$$
Chem & Bio Draw 12.0 91

92
8

9
ChemDraw/Excel
ChemDraw/Excel Microsoft © Excel © ( Windows
) ChemDraw/Excel
• Chem & Bio Draw 12.0 ChemFinder
Excel
• ChemFinder
•
Excel
ChemOffice
ChemDraw/Excel
ChemDraw Chem & Bio Draw
ChemDraw/Excel
ChemOffice ChemOffice
New ChemOffice Worksheet
ChemDraw/Excel Chem &
Bio Draw 12.0
ChemDraw/Excel
MDL SDFile
SD
MDL SDFile
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0
Chem & Bio Draw 12.0
ChemDraw/Excel
Structure
n
NOTE: CFW Excel
allow CAL/OLE
Automation access
ChemFinder
3
1
1. Excel
2. ChemOffice12 Import/Export
Import Table Import
Table
3.
Open
NOTE: ChemOffice
Excel ChemDraw/Excel
ChemOffice12
Convert Worksheet
Chem & Bio Draw 12.0 93

Excel “ChemDraw for Excel”
ChemDraw/Excel
ChemOffice12 Upgrade
Workbook
ChemFinder Import ChemFinder
List
Excel ChemFinder
1. ChemOffice12 Import/Export
Import ChemFinder List
2. Yes
Excel
Import ChemFinder List
“ChemFinder is not running, would you like to
start it up” (ChemFinder
)
1. Yes “After loading your
desired database and performing your search, return
to Excel and redo the operation.”
2. OK ChemFinder
3.
4. Excel ChemOffice12 Import/
ExportImport ChemFinder List
“No database loaded in ChemFinder. Load a
database and perform your search. Then return to Excel
and redo the operation.” (ChemFinder
Excel
)
ChemFinder
1. OK ChemFinder
2.
3. Excel ChemOffice12
Import/ExportImport ChemFinder List
“Form has no database or hit list has no
records. Load a database and perform your search. Then
return to Excel and redo the operation.”(
Excel )
1. OK ChemFinder
2.
3. Excel ChemOffice12 Import/
ExportImport ChemFinder List
ChemDraw/Excel MDL SDFile
1
“Structure”
1
1. “Structure”
2. ChemOffice12 Import/Export
Export Table
3. Save Table To
Save
Chem & Bio Draw 12.0
Chem & Bio Draw
12 “Structure ”
n
94 ChemDraw/Excel
9

Chem & Bio
Draw 12.0
1. ChemDraw for
Excel
2. Yes Chem & Bio Draw
12.0
3.
4. Chem & Bio Draw 12.0 File Exit
and Return to New Molecule
1. Excel
2. ChemOffice12 MoleculeLoad
Choose Molecule to Load
3.
Open
SMILES
SMILES
NOTE: ChemBioDraw Ultra 12.0ChemDraw
Ultra 12.0 ChemDraw Pro 12.0
1. SMILES
2.
NOTE: ()
3. ChemOffice12 ConvertSMILES
to Molecule “Structure”
4. Show Pictures
SMILES
1.
2.
NOTE: ()
Excel
3. ChemOffice12 ConvertName To
Molecule
Name=Struct
4.
ChemOffice12 PictureShow
1.
2. ChemOffice12 MoleculeSave
Save To File
3.
Save
ChemDraw/Excel
3
•
•
• R-
1. Excel ChemOffice12 New
ChemOffice Worksheet
Chem & Bio Draw 12.0 95

2. ChemOffice12 Import/Export
Import Table Import ChemFinder
list
1. Structure
2. ChemOffice12 SearchNormal
3. ChemDraw for Excel
4. Search
5.
6. Normal
7. Search Type Full Structure Sub Structure
8. Filter Type
9.
10. Search
Match
TRUE
ChemFinder
1. Structure
2. ChemOffice12 SearchSimilarity
ChemDraw for Excel
3. Search
4.
5. Similarity
6. Search Type
7. Sort Results
8. Similarity Percent
9. Search
Similarity
TRUE
R-
R-
( p- o-
)
1
4
o-m-p-
4
R-
3
•
o-m- p-
• R-
R-
o-m- p-
96 ChemDraw/Excel
9

• R n
R-
R 1 R 2
R 3
ChemDraw/Excel
Excel
Excel
1.
2. ChemOffice12 MoleculeName All
Selected Name Molecule
3. OK
&
1.
2. ChemOffice12 MoleculeCut
1.
2. ChemOffice12 MoleculeCopy
1.
2. ChemOffice12 MoleculePaste
ChemDraw/Excel
1. /
2. ChemOffice12 Picture
Show Hide
Align All Pictures
ChemOffice
Align Pictures
1.
2. ChemOffice Resize Picture
3.
4.
NOTE:
Align Pictures
Align Pictures
Chem & Bio Draw 12.0 97

ChemDraw/Excel
ChemDraw/Excel
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
: =CFW_CHEMICAL_NAME(A2)
: 1-(2,3-dihydro-1H-inden-2-yl)propan-2-one
NOTE: CambridgeSoft
NOTE: Michael Connolly
(M.L. Connolly. The Molecular Surface Package. J.
Mol. Graphics 1993, 11)
ChemDraw/Excel
1.
2. Insert Function
Insert Functions
3. Category ChemDraw
Functions
4. OK
5.
Structure
6. 2 Element type
Element type
7. OK
“ ”
#N/A
ChemDraw/Excel
Cahn-Ingold-Prelog (CIP)
CFW_CHEMICAL_NAME( )
CHEM_COMPOSITION( )
CHEM_COMPOSITION( , )
: =CHEM_COMPOSITION(A2)
: C,82.72;H,8.10;O,9.18
: =CHEM_COMPOSITION(A2, "C")
: 0.827188133
CHEM_FORMULA( )
CHEMPROPSTD_MOL_FORMULA( )
: =CHEM_FORMULA(A2)
: C12H14O
: =CHEMPROPSTD_MOL_FORMULA(A2)
: C12H14O
98 ChemDraw/Excel
9

CHEM_MOLWEIGHT( )
CHEMPROPSTD_MOL_WEIGHT( )
CHEMPROPSTD_MASS( )
: =CHEM_MOLWEIGHT(A2)
: 174.23896
: =CHEMPROPSTD_MOL_WEIGHT(A2)
: 174.238960
: =CHEMPROPSTD_MASS(A2)
: 174.238960
g/mol
CHEMPROPSTD_EXACT_MASS( )
: =CHEMPROPSTD_EXACT_MASS(A2)
: 174.104465
CHEM_NUM_ATOMS( )
CHEM_NUM_ATOMS( , )
: =CHEM_NUM_ATOMS(A2)
: 27
: =CHEM_NUM_ATOMS(A2, "C")
: 12
CHEM_NUM_HBACCEPTORS( )
: =CHEM_NUM_HBACCEPTORS(A2)
: 1
CHEM_NUM_HBDONORS( )
: =CHEM_NUM_HBDONORS(A2)
: 0
SMILES
SMILES
CHEM_SMILES( )
: =CHEM_SMILES(A2)
: O=C(C)CC(C1)Cc2c1cccc2
CHEMPROPSTD_FORMAL_CHARGE( )
: =CHEMPROPSTD_FORMAL_CHARGE(A2)
: -1
Chem & Bio Draw 12.0 99

ChemOffice/Excel ( )
TRUE FALSE
ISSTRUCTURE( )
: =ISSTRUCTURE(A2)
: False
ChemOffice/Excel
TRUE FALSE
CHEMPROP_FREEZING( )
CHEMPROPPRO_MELTING_POINT( )
: =CHEMPROP_FREEZING(A2)
: 331.31
: =CHEMPROPPRO_MELTING_POINT(A2)
: 331.31
25
P a
ISREACTION( )
: =ISREACTION(A2)
: True
1
CHEMPROP_BOILING( )
CHEMPROPPRO_BOILING_POINT( )
: =CHEMPROP_BOILING(A2)
: 540.059
: =CHEMPROPPRO_BOILING_POINT(A2)
: 540.059
/
1 /
CHEMPROPPRO_VAPOR_PRESSURE( )
: =CHEMPROPPRO_VAPOR_PRESSURE(A2)
: 0
CHEMPROP_CRITICAL_PRESSURE( )
CHEMPROPPRO_CRITICAL_PRESSURE( )
: =CHEMPROP_CRITICAL_PRESSURE(A2)
: 49.8035
: =CHEMPROPPRO_CRITICAL_PRESSURE(A2)
: 49.804
100 ChemDraw/Excel
9

CHEMPROP_CRITICAL_TEMP( )
CHEMPROPPRO_CRITICAL_TEMPERATURE()
: =CHEMPROP_CRITICAL_TEMP(A2)
: 615.351
:=CHEMPROPPRO_CRITICAL_TEMPERATURE(A2)
: 615.351
cm 3 /mol
CHEMPROP_CRITICAL_VOLUME( )
CHEMPROPPRO_CRITICAL_VOLUME( )
: =CHEMPROP_CRITICAL_VOLUME(A2)
: 562.5
: =CHEMPROPPRO_CRITICAL_VOLUME(A2)
: 562.5
298.15 K 1
kJ/mol
CHEMPROP_GIBBS( )
CHEMPROPPRO_GIBBS_FREE_ENERGY()
: =CHEMPROP_GIBBS(A2)
: 84.77
: =CHEMPROPPRO_GIBBS_FREE_ENERGY(A2)
: 84.77
CHEMPROP_HENRY_LAW_CONSTANT( )
: =CHEMPROP_HENRY_LAW_CONSTANT(A2)
: 4.78182
298.15 K1
kcal/mol
CHEMPROP_HOF( )
CHEMPROPPRO_HEAT_OF_FORMATION( )
: =CHEMPROP_HOF(A2)
: ^-105.73
: =CHEMPROPPRO_HEAT_OF_FORMATION(A2)
: -105.73
298.15K (1 )
J/[mol K]
CHEMPROP_IDEAL_GAS( )
CHEMPROPPRO_IDEAL_GAS_THERMAL_CAPACITY
( )
: =CHEMPROP_IDEAL_GAS(A2)
: 201.036
:
=CHEMPROPPRO_IDEAL_GAS_THERMAL_CAPACIT
Y(A2)
: 201.036
Chem & Bio Draw 12.0 101

LogP
n- /
CHEMPROPPRO_LOGP( )
CLOGP_DRIVER_PARTITION_COEFFICIENT(
)
: =CHEMPROPPRO_LOGP(A2)
: 2.233
:
=CLOGP_DRIVER_PARTITION_COEFFICIENT(A2)
: 2.243
cm 3 /mol
CHEMPROPPRO_MOL_REFRACTIVITY( )
CLOGP_DRIVER_MOL_REFRACTIVITY( )
: =CHEMPROPPRO_MOL_REFRACTIVITY(A2)
: 53.305
: =CLOGP_DRIVER_MOL_REFRACTIVITY(A2)
: 5.3297
25
mg/L
CHEMPROPPRO_WATER_SOLUBILITY( )
: =CHEMPROPPRO_WATER_SOLUBILITY(A2)
: 0
( )
2
CHEMPROPSTD_CONNOLLY_ACCESSIBLE_AREA(
)
:
=CHEMPROPSTD_CONNOLLY_ACCESSIBLE_AREA(A2)
: 428.557
NOTE:
1.4
()
2
CHEMPROPSTD_CONNOLLY_MOLECULAR_AREA(
)
:
=CHEMPROPSTD_CONNOLLY_MOLECULAR_AREA(A2)
: 212.294
NOTE:
1.4
102 ChemDraw/Excel
9

3
CHEMPROPSTD_CONNOLLY_SOLVENT_EXCLUDED_
VOLUME( )
:
=CHEMPROPSTD_CONNOLLY_SOLVENT_EXCLUDED
_VOLUME(A2)
: 170.277
Connolly Molecular Surface Area
Solvent-Excluded Volume
CHEMPROPSTD_OVALITY( )
: =CHEMPROPSTD_OVALITY(A2)
: 1.428947
(X, Y, Z)
g/mol 2
CHEMPROPSTD_PRINCIPAL_MOMENT( )
: =CHEMPROPSTD_PRINCIPAL_MOMENT(A2)
: 249.546 1409.279 1658.824
Balaban
MOLECULAR_TOPOLOGY_BALABAN_INDEX()
:
=MOLECULAR_TOPOLOGY_BALABAN_INDEX(A2)
: 29909
MOLECULAR_TOPOLOGY_CLUSTER_COUNT()
:
=MOLECULAR_TOPOLOGY_CLUSTER_COUNT(A2)
: 13
MOLECULAR_TOPOLOGY_MOLECULAR_TOPOLOGIC
AL_INDEX( )
:
=MOLECULAR_TOPOLOGY_MOLECULAR_TOPOLOGI
CAL_INDEX(A2)
: 1998
MOLECULAR_TOPOLOGY_NUM_ROTATABLE_BONDS
( )
:
=MOLECULAR_TOPOLOGY_NUM_ROTATABLE_BOND
S(A2)
: 2
Chem & Bio Draw 12.0 103

MOLECULAR_TOPOLOGY_POLAR_SURFACE_AREA(
)
:
=MOLECULAR_TOPOLOGY_POLAR_SURFACE_AREA
(A2)
: 17.07
MOLECULAR_TOPOLOGY_RADIUS( )
: =MOLECULAR_TOPOLOGY_RADIUS(A2)
: 4
MOLECULAR_TOPOLOGY_SHAPE_ATTRIBUTE(
)
:
=MOLECULAR_TOPOLOGY_SHAPE_ATTRIBUTE(A2)
: 11.076923
MOLECULAR_TOPOLOGY_SHAPE_COEFFICIENT(
)
:
=MOLECULAR_TOPOLOGY_SHAPE_COEFFICIENT(A2)
: 0
MOLECULAR_TOPOLOGY_SUM_OF_DEGREES(
)
:
=MOLECULAR_TOPOLOGY_SUM_OF_DEGREES(A2)
: 28
MOLECULAR_TOPOLOGY_SUM_OF_VALENCE_DEGR
EES( )
:
=MOLECULAR_TOPOLOGY_SUM_OF_VALENCE_DEG
REES(A2)
: 40
MOLECULAR_TOPOLOGY_TOPOLOGICAL_DIAMETE
R( )
:
=MOLECULAR_TOPOLOGY_TOPOLOGICAL_DIAMET
ER(A2)
: 7
MOLECULAR_TOPOLOGY_TOTAL_CONNECTIVITY(
)
:
=MOLECULAR_TOPOLOGY_TOTAL_CONNECTIVITY
(A2)
: 0.009821
104 ChemDraw/Excel
9

MOLECULAR_TOPOLOGY_TOTAL_VALENCE_CONNE
CTIVITY( )
:
=MOLECULAR_TOPOLOGY_TOTAL_VALENCE_CONN
ECTIVITY(A2)
: 0.001157
Wiener
MOLECULAR_TOPOLOGY_WIENER_INDEX( )
:
=MOLECULAR_TOPOLOGY_WIENER_INDEX(A2)
: 249
Chem & Bio Draw 12.0 105

106 ChemDraw/Excel
9

10
Web
Web
(
)
2
10.1 2 A) ‘R’
B)
‘S/D’
Chem & Bio Draw
ChemBioFinder 12.0
1
NOTE: ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
‘Q’
Chem & Bio Draw 12.0 107

ChemDraw Items Generic
Nicknames
Generic
Nicknames
Chem &
Bio Office 12.0
(
)
• A: 1
• M:
• Q:
• X:
• R: 0
•
•
Insert Generic Label
148
()
“
”
NOTE:
2
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. 1
2. Atom Properties
• Atom Properties
• Structure Atom Properties
• /
3. Atom Properties
4. OK
108
10

10.1
109
* Substituents:Free Sites (
)
U Substituents:Up to ( )
X Substituents:Exactly ( )
H Implicit Hydrogens
R Ring Bond Count
S Unsaturation
C Reaction Change
T Reaction Stereo
L Translation
( ) Abnormal Valence
1.
2.
•
• Structure Properties
Atom Properties
1.
2. Atom
Bond Show Query Indicator
1.
2. Show Query Indicator
Indicator Position
1.
2. Position Position
Indicator
3. Position
( )
( )
1.
2. Hide Indicator
Chem & Bio Draw 12.0 109

1
1.
2. Structure Atom Properties
3. Use Defaults
•
Atom Properties
• Structure Atom Properties
•
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
Substituents
Substituents
(B)
2 (A)
(
) 1
Substituents
Unspecified
(DARC )
Free Sites
0
Free Sites
Up to
Exactly 15
Implicit Hydrogens
10.3 A) B)
Implicit Hydrogens
10.2
110
10

NOTE: Implicit Hydrogens ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
Fusion
Spiro or higher
(
3 )
(
4
)
Allowed
Unsaturation
Unsaturation
Not allowed
Ring Bond Count
Ring Bond Count
Unspecified
Must be absent
Any
No ring bonds
As drawn
Simple ring
1
(
2 )
Must be present
Reaction Change
1
(
)
Reaction Change
ChemFinder
NOTE: Reaction Change ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
Chem & Bio Draw 12.0 111

May be anything
Must be
as specified
Atom Properties
2.
3.
4.
Alt
Option
Atom Properties
108
Reaction Stereo
Reaction Stereo
10.4 Reaction Change
Free Sites
Free Sites
10.5 Reaction Stereo
NOTE: Free Sites ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. ViewOther
ToolbarsQuery Tools
Any
Inversion
Retention
112
10

Translation
Translation
Markush DARC
Unspecified
Equal
Definition
Any
ChemFinder
Broad
Natural
Narrow
Enriched
Any
Markush DARC
Isotopic Abundance
Isotopic Abundance
NOTE: Isotopic Abundance ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
Deficient
Nonnatural
Abnormal Valence
Abnormal Valence
“ ” Chem & Bio Draw 12.0 Items
Isotopes Table
NOTE: Abnormal Valence
Chem & Bio Draw 12.0 113

.
.
Not allowed
Allowed
Check Structure When
Copying to Clipboard or Exporting
OK
• /
Bond Properties
Bond Properties
OK
109
NOTE: Abnormal Valence Allowed
Check Structure
Invalid Valence
Any
S/D
D/A
S/A
Rng
Chn
R/C
Bond Types: Any
Bond Types: Single/Double
Bond Types: Double/Aromatic
Bond Types: Single/Aromatic
Tpoplogy: Ring
Tpoplogy: Chain
Tpoplogy: Ring Chain
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. 1
2.
• Bond
• Structure Properties
Bond Properties
Rxn
Reaction Center
Reaction Center
1.
2.
• Bond Properties
• Structure Bond Properties
114
10

1
1.
2. Structure Bond Properties
3. Use Defaults
1.
2.
•
• Structure Bond Properties
Bond Types
( )
Triple
Quadruple
Any
S/D
D/A
S/A
NOTE:
Single (all)
Dative
Topology
Topology
Double
Double Bold
Double Either
Aromatic
Tautomeric
Unspecified
Ring
Chain
(
)
Chem & Bio Draw 12.0 115

Ring Chain
Reaction Center
Reaction Center
NOTE: D (
) T ( )
Unspecified
Center
1.
2. [
(Cl, Br, I)]
3.
Make/Break
Change
Make&
Change
Not Center
10.6
Not Modified
Unmapped
1
(A)
(B)
S/D
(C)
116
10

1
NOT
NOT
10.7
NOTE: D
( ) T ( )
1.
2. [NOT
([NOT)
(Cl, Br, I)]
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. ViewOther
ToolbarsBracket
2. 1
3.
SRU
Bracket Properties
Bracket Properties
1.
2. Structure Bracket Properties
Bracket Properties
Flip Type
120 Flip Type
• Component (c#) Component Order
“c” (
“c” )
• Multiple Group (#) Repeat Count
• SRU (n) SRU
Bracket Usage
Bracket Usage
Chem & Bio Draw 12.0 117

1
“ ”
SRU (n)
“n”
IUPAC ( )
( )
“Mer (mer)”
“Component (co)”
“Copolymer, alternating (alt)”
“Copolymer, random (ran)” “Copolymer, block
(blk)”
“Mixture, unordered (mix)”
“Component (c)”
Bracket Usage “Crosslink (xl)”“Graft (grf)”
“Modification (mod)”
“Monomer (mon)”
( )
10.8
“Mixture, ordered (f)”
(
)
Unordered Mixtures
“Component (c)”
Unordered Mixtures Ordered
Mixtures
118
10

“c”
(“c1”“c2” )
“Multiple Group (#)”
Multiple Group
(
)
10.10 A
B C A B
10.9
Multiple Group (
)
( )
Analysis
(
)
NOTE: ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
2
• 1
• -
• [ ] ( ) { }
• ( : O 1-3 )
1.
Chem & Bio Draw 12.0 119

2.
[CH 2 ] 3-7
R- G- ( )
Flip Type
( 2
)
Flip Type
2
No Flip
Flip Type
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
(RG )
1. ViewOther ToolbarsQuery Tools
2.
120
10

3. Alternative Group Title (R 1
) Alternative Group
10.11
1.
•
(ViewOther ToolbarsChemical
Symbols )
•
.(
)
2.
10.13 R-
R-
R-
10.12
Chem & Bio Draw 12.0 121

A 2
B 2
10.14
1.
10.15 R-
2. “R1”
3.
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
1. File Preferences
2. Preferences Building/
Display
3. Show Attachment Rank Indicators
122
10

“R1”
1
10.16
•
•
Object Bring to Front Send
To Back
NOTE: ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
10.17
1.
2. [
]
Expand Labels
“”
500
CambridgeSoft CombiChem for Excel
NOTE: ChemBioDraw Ultra 12.0ChemDraw
Ultra 12.0 ChemDraw Pro 12.0
Chem & Bio Draw 12.0 123

4
R-
1. 1
NOTE: /R-
2. Structure Expand Generic Structure
R-
R-
R-
R- R-
R-Structure
R-Logic Query R-Logic Query
R- 1
R-
(
) R-
124
10

R 1
R 2
R 1 F Cl R 2
Br I
1. Structure R-Logic Query
2. R-Group R 1
3. Occurrencee range 2
R 1 2
4. If R(i) R 2 R 2
Br I
5. Add
6. OK
Rest H
R- 2 1
1
R-
Logic Query Rest H
1
NOTE: ChemBioDraw
Ultra 12.0ChemDraw Ultra 12.0 ChemDraw
Pro 12.0
2
• (Structure Map Reaction
Atoms )
•
1. File Preferences
2. Preferences Building/
Display
3. Always Display and Print Reaction Mapping
4. OK
Always Display and Print Atom Mapping
1.
:
2. Structure Map Reaction Atoms
Rxn
Reaction Center
Chem & Bio Draw 12.0 125

114
2.
3.
10.18
10.20
10.19
1. File Preferences
2. General Automatic Reaction Mapping
3. OK
1.
1.
2. Structure Clear Reaction Map
(*.cdx) Chem
& Bio Draw 12.0 ChemFinder
126
10

3
Chem & Bio Draw 12.0 79
1.
NOTE: 3
Shift
2. Structure Add 3D Property
NOTE: ‘ ’
‘ ’
NOTE: ChemBioDraw Ultra
12.0ChemDraw Ultra 12.0 ChemDraw Pro 12.0
1. ViewOther Toolbars
Query Tools
2.
3.
3
3D
3D
3D
( ) (
)
2 4 5
2 80 100
NOTE: 3 ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
3
Angle
Dihedral
Distance
Line
Plane
Exclusion
Sphere
Normal
Point
3
( )
4 ( )2
2 2 ( )
2 1 1
1 1
0
2
( )
Chem & Bio Draw 12.0 127

.
Centroid
ISIS Mol Rxn
Unspecified X X X
2
2
CDXMOLSKC TGF
(
)
TIFF
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0 SKCTGF
CDX
• Free Sites
• Up to
• Exactly
Implicit Hydrogens
• Not allowed
• Allowed
Ring Bond Count
• Any
• No ring bonds
• As drawn
• Simple ring
• Fusion
• Spiro or higher
Unsaturation
• Unspecified
• Must be absent
• Must be present
b b b
a a a
Xc Xc Xc
X X X
X X X
X X X
X X X
X X X
X X X
X X X
X X X
X X X
X X X
Atom Properties
Substituents
ISIS Mol Rxn
Reaction Change
• May be anything
• Must be
as specified
X
X
X
X
128
10

ISIS Mol Rxn
ISIS Mol Rxn
Reaction Stereo
• Dative
f f f
• Any
X
X
• Double
Xg X X
• Inversion
X
X
• Double Either
X X X
• Retention
X
X
• Double Bold
h h h
Translation
• Aromatic
X X X
• Equal
• Tautomeric
i i i
• Broad
• Triple
X X X
• Any
• Quadruple
l l l
• Narrow
• Any
X X X
Abnormal Valence
• S/D
X X X
• Not Allowed
X X X
• D/A
X X X
• Allowed
X X X
• S/A
X X X
Bond Properties
Topology
Bond Type
• Unspecified
X X X
• Single
X X X
• Ring
X X X
• Dashed
X d X
• Chain
X X X
• Hashed
d d d
Reaction Center
• Wedged Hashed
X X X
• Unspecified
X
X
• Bold
X e e
• Center
X
X
• Wedged
X X X
• Make/Break
X
X
• Wavy
X X X
• Change
X
X
• Hollow Wedged
e e e
• Make&Change
X
X
Chem & Bio Draw 12.0 129

• Not Center
• Xj Xj Xj
X
• Xko Xko Xko
• Xk Xk Xk
• X Xm
• n n
• p p p
• X X X
•
•
3D
ISIS Mol Rxn
X
X
X
a
b “
”
c 5 “6 ”
d
e
f
g ISIS /
h
I S/D
j MXQA
k 5
l
m RG
n
o 5
p 1
130
10

11
Chem & Bio Draw 12.0
Chem &
Bio Draw 12.0
•
• &
•
Chem & Bio Draw 12.0 &
& &
Chem & Bio
Draw 12.0
Copy As
SMILES SLN InChI
Chem &
Bio Draw 12.0
133
PostScript
Chem & Bio Draw 12.0
134 PostScript
(Macintosh )
1
SMILES 1
SMILES
NOTE:
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0
SMIRKS
Copy As SMILES
SMIRKS
SMIRKS
Paste Special SMILES
SMILES
SMILES
1.
2. EditCopy AsSMILES
Chem & Bio Draw 12.0 131

SMILES
11.1 SMILES
SMILES
SMILES
SMILES
SMILES
Chem & Bio Draw 12.0
SMILES
SMILES
Chem & Bio Draw
12.0 Atom Properties
Aromatic
SMILES
11.2 SMILES
SMILES
SMILES
SMILES
1. SMILES
SMILES Ctrl+C
2. Chem & Bio Draw 12.0 EditPaste Special
SMILES
SLN
SLN
TRIPOS
SLN
1.
2. EditCopy AsSLN
SLN
11.3 SLN
InChI
Chem & Bio Draw 12.0 IUPAC International
Chemical Identifier (InChI) *
InChI
Copy As
InChI
InChI
&
&
&
*. InChI International Union of Pure and
Applied Chemistry Chem & Bio
Draw 12.0 InChI © IUPAC
2005
132
11

Chem & Bio Draw 12.0
(Macintosh )
(Windows ) Chem
& Bio Draw 12.0
1.
2.
&
& 1
Chem & Bio Draw 12.0
( )
1.0 cm
200% 2.0 cm
1.7 cm
2
3.4 cm
16
1
2 8
8/16 0.5
14
0.5
7
Chem & Bio Draw 12.0
Settings
1.0 cm
2.0 cm
12
(2.0 cm/1.0 cm) x
12 = 24
Document Settings
( 20 )
Chem & Bio Draw 12.0
Change Settings
Change Settings
Chem & Bio Draw 12.0 133

Don’t Change Settings
NOTE: 3.0
ChemDraw
“Unknown”
(Macintosh )
Chem & Bio Draw 12.0 Edit Graphic Object (EGO)
Chem & Bio Draw 12.0
EGO
Chem & Bio Draw 12.0
(Windows )
Chem & Bio Draw 12.0 Windows Object Linking
and Embedding (OLE)
Chem &
Bio Draw 12.0 OLE OLE
OLE
&
Chem & Bio Draw 12.0 OLE
6.0 Microsoft Word
(Windows )
• Word Edit CS
ChemDraw Drawing Object
•
Word Chem & Bio
Draw 12.0
Word
Word
NOTE: Microsoft Word 5.0
EGO
PostScript (Macintosh )
Chem & Bio Draw 12.0 PostScript
PostScript
2
Include PostScript Include ChemDraw Laser
Prep ( )
PostScript PostScript
PostScript
1. File Preferences
2. Include PostScript Include ChemDraw
LaserPrep
Preferences Include
PostScript Include ChemDraw Laser Prep
PostScript
ChemDraw Laser Prep
Chem & Bio Draw 12.0
134
11

PostScript Include PostScript
Chem & Bio Draw 12.0 QuickDraw
150
NOTE:
PostScript Preferences
General Include
PostScript Include ChemDraw Laser Prep
Chem & Bio Draw 12.0
Chem & Bio
Draw 12.0
1. File Save As
2. Save As
a.
Go To ChemDraw Items
ChemDraw Items
b.
c. OK Save
Chem & Bio Draw 12.0
• Connection Table
• MSI MolFile
• SMD
NOTE: Chem & Bio Draw 12.0
Options
Text Options
• ChemDraw XML
• CML
• Connection Table
• ISIS/TGF
• ISIS/Reactions
• MDL MolFile
• Accelrys MolFile
• SMD
Chem & Bio Draw 12.0
OLE
Chem & Bio Draw 12.0
1. Edit Insert File
2. Open
3. Open
Chem & Bio Draw 12.0 135

1. Edit Insert Object
2. Insert Object Create
from File
3. OK
NOTE: All files Chem &
Bio Draw 12.0
(TXT )
1. Edit Insert Object
1. Create New
2. Object Type
3. OK
ISIS
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0 R-
ISIS/Sketch
Chem & Bio Draw 12.0 “ ”
MDL “ SGroup”
MDL
SGroup
•
• 1
1
2 SGroup
1.
2. Object Attach Data
Attach Data
3. OK
NOTE:
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0
MDL
Chem & Bio Draw 12.0
MDL
4.
Chem & Bio Draw 12.0
2
• Select Linked Objects
• Position ObjectTags
NOTE: MDL
WMF
PICTEPSTIFFGIFBMP PNG
2 (0.278 0.071
)
136
11

Chem & Bio Draw 12.0
Save As Chem & Bio
Draw 12.0
135
ChemDraw (CDX)
ChemDraw XML (CDXML)
ChemDraw 3.5 (CHM)
ChemDraw 2.0 and ChemDraw 2.1
(CHM)
ChemDraw Template (CTP) a
ChemDraw Template Style Sheet
(CTS) a
ChemDraw Stationary Pads/ Style
Sheets (CDS)
Connection Table (CT) a
Chemical Markup Language
(CML)a
Bitmap (BMP)
Encapsulated PostScript (Macintosh
)
PostScript (EPS) (Windows )
Graphic Image Format (GIF)
ISIS (SKC, TGF, RXN) a
JCAMP (JDX, DX) a
JPEG (JPG, JPEG)
MDL V3000 MolFile (MOL)
MDL MolFile (MOL) a
MDL RGFile (RGF) a
(Macintosh)Accelrys MolFile
(MSM)
PICT (Macintosh )
Portable Network Graphics (PNG)
Standard Molecular Data (SMD) a
Structure-Data file (SD) a
Galactic Industries (SPC) a
Windows Metafile (EMF, WMF)
TIFF file (TIF)
a ChemBioDraw Ultra 12.0
ChemDraw Ultra 12.0 ChemDraw Pro 12.0
Macintosh Windows
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0 137

Macintosh Windows
Macintosh Chem & Bio Draw 12.0
Windows
Windows Macintosh
Windows Chem & Bio Draw 12.0
Macintosh
Macintosh
Windows
Windows
Macintosh
4.0 4.0 ChemDraw
.cdx
4.0 3.x ChemDraw 3.x
.chm
4.0 4.0
ChemDraw
(.cdx)
3.5.x 4.0 ChemDraw 3.x
(.chm)
3.5.x = 3.x ChemDraw
.chm
138
11

A
Chem & Bio Draw 12.0 Preferences
Document Settings
Preferences Settings
Document
Settings
Chem & Bio Draw
(
)Chem & Bio Draw 12.0
12.0
Classic I/
Draw
1. File Preferences General
2. Theme
3. OK
4. (Macintosh ) Chem & Bio Draw 12.0
I/Draw
I/Draw
2
• (
)
• I/Draw Styles.cds
I/Draw File
PreferencesI/Draw
Preferences
Chem & Bio Draw 12.0
1. Preferences
File Preferences
2. Use Defaults
Open
1. File Preferences
Preferences
2. Directories
3. Use Documents Location
Open
1. File Preferences
Preferences
2. Open/Save
3. Opening Files Use Default File
Format
Chem & Bio Draw 12.0 139

1. File Preferences
Preferences
2. Open/Save
3. Opening Files
Chem & Bio Draw 12.0
1. File Preferences
Preferences
2. Open/Save
3. Autosave Every
( )
1. File Preferences
Preferences
2. Open/Save
3. Saving Files Use Default File
Format
Enter Return
Alt+Enter Option+Return
1. File Preferences
: Macintosh OS X ChemDraw
Preferences
2. Building/Display
3. OK
Alt+Enter Option+
Return
Alt+Enter Option+
Return
(Macintosh)
TrueType
1. File Preferences
2. Use Bitmap Fonts When Available
TrueType
Use Bitmap Fonts When Available
/
5
5
140
A

1. File Preferences
2. General
ChemDraw Items
ChemDraw Items
ChemOffice 2010
Windows XPC:Documents and SettingsAll Users
ApplicationDataCambridgeSoftChemOffice2010
ChemDraw
Windows VistaC:Program DataCambridgeSoft
ChemOffice2010ChemDraw
MacintoshChemDraw Items
Chem & Bio Draw 12.0
ChemDraw Items
1. File Preferences
Preferences
2. Directories
3. Add New OK
4. Move Up
Move Down
5. Remove
Default Paths
Chem & Bio Draw 12.0
ChemDraw Items
C:Documents and SettingsAll Users
Application DataCambridgeSoft
ChemOffice2010ChemDrawChemDraw Items
File Open
Templates
1 XML
XML
Toolbars Toolbars.xsd
(
)
XML
Toolbars xml
xml
xml
XML
xml
xml
Chem & BioDraw
Chem & Bio Draw 12.0 141

XML
“Erase ( )”
NOTE:
png
/
• Document Settings
•
•
Chem & Bio Draw 12.0
(Windows)
(Macintosh) Chem &
Bio Draw 12.0
1. File Preferences (Macintosh: ChemDraw)
2. Open/Save Browse
( )
3. Opening Any Style Sheet(Stationery Pad) Changes
Default
4. OK
File
New
Chem & Bio Draw 12.0
CDS
CDS ChemDraw Items
(File
) Open Templates
142
A

1. File Save As
2. (OS X
) CD Style Sheet (cds) ChemDraw
Stationery pad
3. ChemDraw Item
Go To ChemDraw Items
4. Save
File
Apply Document Settings from
NOTE:
File
Open Style Sheets
1. FileApply Document Settings fromOther
Select document
2.
/
3. Open
1.
2. Object Apply Object Settings from
3.
•
No
•
Yes
• File
Document Settings Drawing
• Object
Settings
File Apply Document
Settings from
Chain Angle
Clean Up Structure (1
179 )
21 57
Bond Spacing
• (1 100%)
•
Fixed Length
Clean Up Structure
Chem & Bio Draw 12.0 143

13 57
Bold Width
1.5
Line Width
Margin Width
16
Hash Spacing
UnitsObject Settings
Atom and Bond Indicators
60
78
1. File Document Settings
2. Drawing
3. OK
Chem & Bio Draw 12.0
1. File Document Settings
2. Atom Labels
3. Show Labels On Terminal Carbons
1.
2. Object Object Settings
3. OK
Analysis Chemical
Properties
“Molecular Weight”
“MW”
Analysis
Chemical Properties
1. File Document Settings
2. Auto-update
3. Analysis
4. Label
5. Chemical Properties
3 4
6.
Automatically update
upon chemistry changes
7. OK
144
A

• ( )
• ( )
• ( )
•
•
Document Settings
Object Settings
Text
1. File Document Settings
2. Document Settings
Captions Atom Labels
3.
4. OK
5.
Normal
Superscript 25%
Subscript 25%
Formula
1
1
Text Style
3
Automatic
Variable
( )
Fixed
Object
Settings
Object Settings
1.
2. Object Object Settings
Object Settings
Object Settings
Captions 1
4
Flush Left
Centered
Flush Right
Justified
Centered ( )Flush Left (
)Flush Right ( )Stacked Above
( ) Automatic ( )
Chem & Bio Draw 12.0 145

C5
NOTE: Stacked Above ( )
Alt+Enter Option+Return
1
CH 3
C5 NCH 3
H 3 CN
CH 3 N
CH 3
C1
2 3
C4 2 3
A.1 A) B)
C) D)
Chem &
Bio Draw 12.0
N-
NCH 3
NCH 3
3 C3
•
• Text
•
146
A

1. File Document Settings
2. Document Settings
Captions Atom Labels
3.
4. OK
(Windows)
(Macintosh)
142
1.
2.
• TextFontStyle Size
•
3.
1.
2. Text
1
• Text
•
•
Macintosh
PostScript
1. File Document Settings
2. Document Settings Hdr/
Ftr
3. Fractional Widths
1. File Document Settings
Document settings
2. Drawing
Chem & Bio Draw 12.0 147

3. Margin Width
4. OK
XML
ChemDraw
Items CS ChemDraw Hotkeys.xml
CSChemDraw Hotkeys.dtd
Enter
return
Delete
Backspace
NOTE:
35mm
1600
Chem & Bio Draw 12.0
:
:
1. File Document Settings
Colors
2. Background Color Foreground Color
3. OK
NOTE:
148
A

(Macintosh “
” )
1. Color Define Custom
Colors
20 142
NOTE:
Color
1. File Document Settings
Document settings
2. Colors
3. (Background Foreground)
Other Color
4. Basic Colors Custom Colors
5. OK
Color
A.2 A) Color refiner
B) Luminosity
2. Color Refiner 1
3. Luminosity
4.
RGB
5. Add to Custom Colors
6. OK
Macintosh
1. File Document Settings
Document settings
2. Colors
Chem & Bio Draw 12.0 149

3. New Color
A.3 Macintosh Color Picker
4. 1
Macintosh
5. OK Color
Color
1. Color New Color Set Other Color
Color Picker
2.
3.
RGB
4. OK Other Colors
Color
1.
2. Remove Color
(
)
133
Print Background Color
1. File Preferences
2. Print Background Color
3. OK
Macintosh
Chem & Bio Draw 12.0
QuickDraw
PostScript
Chem & Bio Draw 12.0
PostScript ChemDraw LaserPrep
Macintosh
/
150
A

PostScript Include
ChemDraw LaserPrep Include PostScript
PostScript
PostScript PostScript
Postcript
Chem &
Bio Draw 12.0 PostScript
PostScript ChemDraw Laser Prep 2
ChemDraw Laser Prep
Chem & Bio Draw 12.0
PostScript
Include PostScript
PostScript
ChemDraw
1. File Preferences
2. Include PostScript
3. OK
Include PostScript
PostScript
&
Include
PostScript
Include ChemDraw Laser Prep
Include ChemDraw Laser Prep Chem
& Bio Draw 12.0
Chem & Bio Draw 12.0
PostScript
Include ChemDraw Laser Prep
1. File Preferences
2. Include ChemDraw Laser Prep
3. OK
Include ChemDraw Laser Prep
Include PostScript
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0
NOTE: “ ” Macintosh
“”
1.
2. Page SetupDrawingText SettingsColor
Palette
3. File Save As
4. Save As
a. Chem & Bio Draw 12.0 Style Sheet
Stationery Pad
b.
c. ChemDraw Items
5. OK Save
Chem & Bio Draw 12.0 151

ACS Document 1996
• :14.4 pt
• :2 pt
• : 0.6 pt
• : 1.6 pt
• : 2.5 pt
• ( ): 120
• ( %): 18
• (Win/Mac): /
• : 10 pt
• (Win/Mac): /
• : 10 pt
• ( x ): 540 pt x 720 pt
• : US Letter
• (%): 100
Adv.Synth Catal.
• : 17 pt
• : 2 pt
• : 1 pt
• : 1.6 pt
• : 2.5 pt
• ( ): 120
• ( %): 18
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156
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158
A

B
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Chem & Bio Draw 12.0 161

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Chem & Bio Draw 12.0 163

164
B

C
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0
Chem & Bio
Draw 12.0
Chem & Bio Draw 12.0
AcOo-C 6 H 4 COOH
“ ” (
5 16
21 )
Chem & Bio Draw 12.0
“
”
CH3COO
Chem & Bio Draw
12.0
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0
18
4
C.5
Chem & Bio Draw 12.0 165

Chem & Bio Draw 12.0
2
“”
(
)
2
“”
(
)
“ ” “ ”
N-O
1
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/
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Chem & Bio Draw 12.0
(OCH 3
H 3 CO )
Isotopes Table
“ ”
166
C

1
(
) (
)
MeOH H 2 O
Chem & Bio Draw 12.0
CH 3 COCH 2 CH 3
MeOH
C 6 H 6
200
1 Chem & Bio Draw 12.0 C 6 H 6
(C 2 H 6
H 2 SO 4 ) (CH 3 CH 3
HOSO 2 OH)
Expand Label
Chem & Bio Draw 12.0
Chem & Bio Draw 12.0 167

.
“”
Analyze Structure
CRC
Press, Inc Isotopes Table
1
“ ”
1
2
Ph
Ph
Ph
C
H- H-
H- H-
C
O
168
C

Cp 2 TiCl 2 1 -
Cl
Cl
Ti
Atom Properties
Abnormal Valence
Allowed
Structure
Add Multi-Center Attachment
3 -
-C 5 H 5 Mn(CO)
OC
Mn
CO
CO
Cahn-Ingold-Prelog
Cahn-Ingold-Prelog (CIP)
*
CIP
4
4
2 3 4
5
M
-
Fe
*. R.S. CahnC.K. Ingold V. Prelog
Specification of Molecular ChiralityAngew.
Chem., Int. Ed. Engl. 1966, 5, 385-414 (errata:
1966, 5, 511); Angew. Chem. 1966, 78, 413-447.
V. Prelog G. Helmchen Basic
Principals of the CIP-System and Proposals for a
RevisionAngew. Chem. 1982, 94, 614-631;
Angew. Chem. Int. Ed. Engl. 1982, 21, 567-583.
P. MataA.M. LoboC. Marshall A.P.
Johnson The CIP Sequence Rules:
Analysis and Proposal for a Revision
Tetrahedron:Asymmetry. 1993, 4, 657-668.
Chem & Bio Draw 12.0 169

5
1
2
3
4
5R S
Chem & Bio Draw 12.0
15
Z
E
• 3
R
• 3
S
• r
s
C.6 Absolute
C.7 Relative
170
C

IUPAC
2
•
•
C.8 Racemic
117
NOTE:
ChemBioDraw Ultra 12.0ChemDraw Ultra 12.0
ChemDraw Pro 12.0
Graphic Representations (Chemical Formulae) of
Macromolecules (Recommendations 1994)Pure Appl.
Chem., 66, 2469-2482 (1994).
Source-Based Nomenclature for Copolymers
(Recommendations 1985) Pure Appl. Chem., 57,
1427-1440 (1985).
http://www.iupac.org/publications/books/pbook/
PurpleBook-C7.pdf
Basic Definitions of Terms Relating to Polymers
(1974)Pure Appl. Chem., 40, 479-491 (1974)
http://www.iupac.org/reports/1996/
6812jenkins/index.html
There are too many
bonds to this
unlabeled Carbon.
An atom in this label
has an invalid
valence.
ChemDraw can’t
interpret this label.
4
1.5
Substituents Free
SitesUp toExactly
2
Substituents: Up To
3Substituents: Exactly 3
Substituents: Free Sites 1
3
Isotopes Table
Chem & Bio Draw 12.0 171

Parentheses don’t
match.
This label has
conflicting or
unassignable
charges.
Formula cannot be
computed for
queries.
Text not in Formula
style won’t be
interpreted.
This named
alternative group
contains no
attachment point.
This named
alternative group
contains fragments
with inconsistent
valences.
This named
alternative group
contains no
fragment.
Part of a molecule is
outside of the
alternative group
definition.
This isolated bond is
probably not
intended to have
chemical
significance.
The atom is very
close to another
atom or bond.
The stereocenter has
no stereobonds
specified.
There is a valence
and charge error
somewhere in this
aromatic system.
C 2 H 6
Show Stereochemistry
1
( )
172
C

The stereocenter has
conflicting or
ambiguous
stereobonds
specified.
This label has an
unrecognized
isotopic mass.
(
)
4
Show
Stereochemistry
24 CH 3
Chem & Bio Draw 12.0 173

174
C

D
100
NOTE:
ChemBioDraw UltraChemDraw Ultra ChemDraw
Pro
LogP
LogP 3
• 1 830
94
0.47 logP
• 2 1
893 120
1
0.50 logP
• 3 1868
222
0.43 logP
logP
0.83 logP
2
• 1
59 15
345
0.30
0.45
• 2
2
• 1
504 93
1.27
cm 3 /mol
• 2 1
538
120
1
0.77 cm 3 /mol
CLogP CMR
Medicinal Chemistry Project BioByte
LogP
Chem & Bio Draw 12.0 175

LogP
NOTE: CLog P CMR ChemBioDraw
Ultra ChemDraw Ultra
TPSA ( )
PSA ( )
3D
Chem & Bio Draw 12.0
1
*
2
• Joback
• Stein Joback
1atm
Joback
*.
Ertl, P., Rohde, B., and Selzer, P., 2000. Fast
Calculation of Molecular Polar Surface Area as a
Sum of Fragment Based Contributions and Its
Application to the Prediction of Drug Transport
Properties.J.Med. Chem.43: 3714-3717.
176
D

E
ChemNMR
NOTE: ChemNMR ChemBioDraw Ultra
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ChemNMR
ChemNMR
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ChemNMR
ChemNMR
1H NMR Shift 700
2000
13C NMR Shift 4000
( /
) ( /
)
ChemNMR
HDHeLiBeBCNOFNeNaMg
AlSiPSClArKCaScTiVCrMn
FeCoNiCuZnGaGeAsSeBrKrRb
SrYZrNbMoTcRuRhPdAgCdIn
SnSbTeIXeCsBaLaCePrNdPm
SmEuGdTbDyHoErTmYbLuHf
TaWReOsIrPtAuHgTlPbBiPo
AtRnFrRaAcThPaUNepPuAmCm
BkCfEsFmMdNoLr
1H NMR 0.2 -0.3 ppm
CH x - 90%
13C NMR - 0.29 ppm
2.8 ppm 95
NMR
Chem & Bio Draw 12.0 NMR
Furst, A.; Pretsch, E. Anal. Chim. Acta 1990, 229, 17.
Pretsch, E.; Furst, A.; Badertscher M.; Burgin, R.; Munk,
M. E.J. Chem. Inf. Comp. Sci. 1992, 32, 291-295.
Burgin Schaller, R.; Pretsch, E. Anal. Chim. Acta 1994,
290, 295.
Burgin Schaller, R.; Arnold, C.; Pretsch, E. Anal. Chim.
Acta 1995, 312, 95-105.
Burgin Schaller, R.; Munk, M. E.; Pretsch, E. J. Chem.
Inf. Comput. Sci.1996, 36, 239-243.
Chem & Bio Draw 12.0 177

178 ChemNMR
E

F
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Chem & Bio Draw 12.0 179

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F

G
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182 CambridgeSoft Web
G

H
2
NOTE:
3
tert-
Q* q
Br
b
I
i
R
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n-Bu 1
K
k
S
s
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Me
m
Si
S
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N
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t
A
a
F
f
Ph P 4
Ac A 5
H
h
C
Na
X
Cl
O
COOCH3
c
N
x
C l
o
E
Chem & Bio Draw 12.0 183

D
d
H
OTs
T
CH2OH 6
Et
e
/ ( )
h
P
B
p
B
. ( )
‘ ( )
1
d
2
y
3
l
-
+
1 0
2 9
3 8
Atom Properties
/ ( )
4
c
Choose Nickname
= ( )
b
r
w
f
184
H

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Chem & Bio Draw 12.0 185

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186
H

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Chem & Bio Draw 12.0 187

Ac-Me
Ac Bz c-C7H13 cyclopropyl DPIPS i-C4H9
Ad BOM c-C8H15 Cys DPTBS i-C5H11
Ala Bs c-Hx Dan DTBMS i-Pr
Alloc Bt C10H20 DEAE DTBS Ile
Allyl Btm C10H21 DEIPS Et Im
Am Bu Cbz DMIPS Fmoc Leu
Arg Bzh cHx DMPM Gln Lys
Asn Bzl CoA DMPS Glu m-C6H4
Asp BzOM Cy DMTr Gly m-Phenylene
Benzoyl c-C3H5 cyclobutyl DNP His m-Tolyl
Benzyl c-C4H7 cycloheptyl Dnp i-Am MDIPS
Bn c-C5H9 cyclooctyl Dns i-Bu MDPS
Boc c-C6H11 cyclopentyl DNS i-C3H7 Me
MEM-Xyl
MEM n-Pr Phenyl s-Butyl TBDMS Thr
Mes N3 Pht s-C4H9 TBDPS TIPDS
Met neo-Am Piv s-C5H11 TBMPS TIPS
MMTr neo-C5H11 PMB SEM TBS TMS
MOM Np PMBM Ser TDS Tos
MPM o-C6H4 PNB SES Tf trans-Cinnamyl
Ms o-Phenylene Poc t-Am Tfa Troc
MTM o-Tolyl PPi t-BOC TFA Trp
n-Am p-C6H4 Pr t-Boc Thexyl Trt
188
H

MEM-Xyl
n-Bu p-Phenylene Pro t-Bu THF Ts
n-C3H7 p-Tolyl Pv t-Butyl Thf Tyr
n-C4H9 Ph s-Am t-C4H9 THP Val
n-C5H11 Phe s-Bu t-C5H11 Thp Xyl
Chem & Bio Draw 12.0 189

190
H

13 C 1 H 85
35 mm 161
3D 127
A
Abnormal Valence 113
ACX 182
Adv. Synth.Catal. 152
Analysis 77
Apply Document Settings 143
B
Balaban 103
BioDraw 9
DNA 35
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( ) 34
68
34
BioDraw
33
33
33
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C
Cahn-Ingold-Prelog 169
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ChemNMR
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ChemNMR 87
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CLogP 82, 175
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D
DOS 87
dz2- 81
d- 81
E
Elemental Analysis
Chem & Bio Draw 12.0 191

77
77
Exact Mass
77
77
F
FAQ
181
179
Flatten 61
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Formula
145
77
Free Sites
110
112
G
G 120
H
H- H-
168
I
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J
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L
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LogP 102, 175
M
m/z 77
MakeChemNMRUserDB.exe 87
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77
77
N
Name=Struct 75
75
75
NMRChemNMR 85
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OLE 134
Online
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P
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p- 80
Q
QuickDraw
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142
R
Reaction Center 116
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Rf 84, 85
192

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RS 170
R 120
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SLN 132
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SMILES 99
132
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SMIRKS 131
Struct=Name 5, 73, 75
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Structure
186
Subscript 145
Substituents 110
Superscript 145
SVG 1
Synthesis/Synlett 156
s- 80
T
Text
186
TLC 84
TLC
Rf 85
Rf 84
85
85
84
85
85
85
85
Topology 115
TPSA ( ) 176
Translation ( ) 113
tRNA 3, 35
U
Ungroup 29
Unsaturation 111
Unspecified 110
Up to 110
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Verlag Helvetica Chimica Acta 157
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Wiener 105
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159
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163
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148
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PostScript 134
160
PostScript 142
150
150
23
Chem & Bio Draw 12.0 193

109
109
60
78, 170
79
(CambridgeSoft Web ) 182
ChemDraw/Excel 93
135
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Check Structure 30
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171
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Include ChemDraw LaserPrep 134
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ChemDraw 165
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ChemDraw 139
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Chem & Bio Draw 12.0 195

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Abnormal Valence 113
Implicit Hydrogens 110
Reaction Stereo 112
Ring Bond Count 111
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PostScript 142
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Implicit Hydrogens 110
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Ring Bond Count 111
198

Substituents 110
Unsaturation 111
108
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Chem & Bio Draw 12.0 199

131
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139
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Adv. Synth.Catal. 152
J. Mol. Mod. 153
Phytomedicine 155
RSC 155
Science of Synthesis 156
Synthesis/Synlett 156
Verlag Helvetica Chimica Acta 157
Wiley Document 157
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154
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175
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Chem & Bio Draw 12.0 203

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