Exercises 1 and 2

1. An Introduction to ChemDraw
Introduction
ChemDraw can be used to draw simple two-dimensional representations of organic
molecules. These structures must precisely describe the connectivity of atoms. Five different
representations of 2-propanol (isopropanol or "rubbing alcohol") are shown below. While
structure A shows all bonds and lone pairs of electrons, a number of short-cuts are often
used when drawing molecules. For example, -CH 3 is used to represent the methyl groups
in (B) and (C).
H
H
:O:
H
OH
OH
OH
H
C
H
C
H
C
H
H
CH 3 CH(OH)CH 3
H 3 C
A B C D E
Bond-line structures (D) are often the simplest representation of organic molecules. A
chain of carbon atoms is shown as a series of lines; each angle between lines and each line
end is a carbon atom. The carbon atoms are not labeled. All heteroatoms (i.e., N, O, S,
halogens) are labeled. Hydrogens on carbons are not shown, although it is assumed that
3
they are present to account for the tetravalency of carbon. Since sp carbon atoms are
tetrahedral it is often useful to show the structure of organic molecules using
wedge-and-dash structures (E). The wedge indicates a bond coming out of the page toward
you, the dashed bond is going into the page. In structure E the methyl groups are
abbreviated as “Me”. Other common abbreviations for substituents are Et (ethyl), i-Pr
(isopropyl), t-Bu (tert-butyl). ChemDraw can also be used to draw Newman and Fischer
projections of organic molecules (see your textbook).
Getting Started
The ChemDraw screen has a vertical palette of tools on the left, a series of pull-down
menus at the top of the screen, and a blank window on which to draw.
The following instructions illustrate how to draw molecules. Work through OH
the step-by-step instructions to draw the structure of 2-propanol shown on the
right.
i. Launch ChemDraw by clicking on the program icon (or use the start menu).
ii. First you will draw a bond: Click on the bond drawing tool in the palette on the
left-hand side of the screen. Move the cursor to the blank window, click-holddrag-and-release
the mouse to draw a bond.
C
H
CH 3
H
Me
Me
-1-

select bond
drawing tool
place cursor
on page click drag
Each end of the bond represents a carbon atom until you change it to another type
of atom (see below).
iii. You will now draw the other bonds: Place the cursor on one end of the bond; a
black square will appear. Click-and-drag the mouse to draw a second bond.
Click-and-drag from the middle atom to draw a third bond.
place cursor
on atom
click and
drag
place cursor
on atom
click and
drag
iv.
One of the carbon atoms should be changed to a hydroxyl group: Click on the text
tool; place the cursor on the atom you want to label, a black square will appear.
Click the mouse when the end of a bond is highlighted with a black square, a text
box will appear. Type OH using the keyboard, and then click the mouse elsewhere
on the window. Numbers entered in atom labels are automatically written as
subscripts.
select
text tool
A
place cursor
on atom
click
type
label
OH
click
elsewhere
on page
OH
Other Drawing Tools
A series of bond drawing tools are available to show the three-dimensional
arrangement of atoms.
Double bonds are made by clicking on an atom and dragging along an existing bond
to an adjacent atom. A number of ring structures can be drawn automatically. Work through
the following example.
i. Select the five-membered ring tool, click-and-drag on the drawing window and see
what happens.
ii. Now select the bond drawing tool, click on an atom in the five
membered ring (the structure of cyclopentane), drag to an adjacent
atom and release. A double bond will appear (to give the structure of
cyclopentene).
-2-

Other tools allow you to draw brackets, arrows, orbitals and curves. To use these, clickand-hold
on the tool palette, move the mouse to select the particular type of object you want,
then release. Then click-and-drag on the drawing window.
Moving and Rotating Structures
Draw a molecule and then move, shrink or enlarge, and rotate it using the following
instructions.
i. Click on the Lasso tool. Click on the window close to a molecule you
want to move; hold down the mouse, circle around the molecule and
release. The circled molecule will be highlighted in a highlight box.
ii.
To move the molecule: Move the cursor into the middle of the box until
a hand appears. Click-and-drag to move the highlighted molecule.
iii. To shrink or enlarge the molecule: Move the cursor to the bottom right
corner of the highlight box (a double-headed arrow will appear). Clickand-drag
to shrink and enlarge the highlighted molecule.
iv.
To rotate the molecule: Put the cursor at the top right corner of the
highlight box (a curved arrow will appear). Click and drag to rotate the
highlighted molecule.
Text can be written anywhere on the window by choosing the Text tool and clicking
on the drawing window (NOT on an atom). Font, size and style (i.e., italics, underlining)
can be changed using the Text menu. The Object menu lets you further manipulate
highlighted items. ChemDraw can be used to prepare structures, reaction schemes and
mechanisms as answers to homework questions from your textbook, and to illustrate lab
reports. Some representative questions are provided below. A suggested style for answers
to these problems, using different examples, is shown on page 8.
Problem 1.1
Draw line bond structures of all of the constitutional isomers of C H 7 16.
Problem 1.2.
Draw line bond structures of all of the constitutional isomers of alcohols (molecules
with -OH groups) with the formula C H O. 4 10
Problem 1.3
Draw line bond structures of both carboxylic acids (molecules with a -CO2H group)
with formula C4H8O 2.
-3-

2. An Introduction to Chem3D
Introduction
Although ChemDraw allows us to represent the topology of complex organic molecules
(i.e., which atoms are bonded to one another), these drawings only hint at the threedimensional
arrangement of the atoms and bonds. We will use cylindrical bond models,
which are similar to ball-and-stick models, to clearly show the bond connectivity and
geometry of molecules in Chem3D. A cylindrical bond model of 2-propanol is shown below
(A). The volume occupied by atoms is better represented in space-filling models (B) but it
is often difficult to locate the bonds in these models.
A
The valence shell electron pair repulsion (VSEPR) model is a useful tool to predict the
shape of organic molecules. Pairs of bonding electrons and lone pairs are arranged to
minimize charge repulsion. Thus, methane with four bonding pairs adopts a tetrahedral
structure, whereas boron trifluoride with three bonds is trigonal planar. The shape of simple
molecules can be described in terms of bond lengths (d, in Å) between two adjacent atoms
and bond angles (, in degrees) between three adjacent atoms. In more complex molecules
we will also define the structure in terms of torsion angles (f , in degrees; also called dihedral
angles) between four adjacent atoms. See the diagrams below for pictorial definitions of d,
and f .
B
d
θ
φ
For well over a century, organic chemists have built simple models to provide insight
into molecular structure. Familiar ball-and-stick models are still useful learning tools. Today,
in addition to plastic model kits, we can build and examine three-dimensional models using
programs such as Chem3D. There are two ways to draw molecular structures in Chem3D,
either by importing the structure from ChemDraw, or by using the drawing tools in Chem3D
itself. We will concentrate on importing structures from ChemDraw.
-4-

Importing Structures from ChemDraw
The Chem3D screen has a vertical palette of tools on the left, a series of pull-down
menus at the top of the screen, and a blank window on which to draw.
Work through the following step-by-step instructions to draw the molecular models of
2-methylpentane shown below.
i. Launch both ChemDraw and Chem3D by double
clicking on the program icons (or use the start menu).
ii. Draw a molecule of 2-methylpentane in ChemDraw
(see Exercise 1). Select the molecule using the Lasso
tool and copy it using the Edit menu.
iii. Switch to Chem3D by clicking on the Chem3D
window (or Taskbar) and select Paste from the Edit
menu. The molecule copied from ChemDraw will
appear as a cylindrical bond model in the Chem3D
window.
iv. Convert the cylindrical bond model to a space-filling
model by selecting Model Display Settings from the
Preference line of the View menu and choosing Space
Filling.
Drawing and Modifying Structures in Chem3D
Although it is generally quite convenient to create three-dimensional models by drawing
structures in ChemDraw and then importing them into Chem3D, it is also useful to be able
to draw and modify molecules in Chem3D. The following instructions will allow you to
modify the model of 2-methylpentane drawn above to give 3-hexanol.
i. It is best to modify cylindrical bond models, NOT
space-filling models. If you have the space-filling
model of 2-methylpentane on the screen from the
previous set of instructions, you should revert back to
a cylindrical bond model: Select Model Display
Settings from the Preference line of the View menu
and choose Cylindrical Bond.
ii. To make a model of 3-hexanol you will need to add a
carbon to the chain: Select the bond drawing tool
then click on C(1), drag out to one of the attached
hydrogens and release. A new C-C bond is drawn to
a new methyl group.
-5-

iii. Then replace the methyl substituent with a hydroxyl
group: Choose the Selection tool and click on the
carbon of the methyl substituent (it will become
highlighted). Click in the text replacement box at the
top of the screen. Type OH, hit return and click on
the drawing window. The methyl substituent will be
changed into a hydroxyl group.
HO
Making Measurements in Chem3D
The model in Chem3D contains information about bond lengths (d), bond angles () and
dihedral angles (f). Use the following instructions to obtain details about the molecule of 3-
hexanol you have drawn in this exercise.
i. To identify atoms: Place the cursor on an atom (do not click); a label will appear
which describes the type of atom and provides an atom number.
ii. To measure bond lengths: Place the cursor on a bond (do not click); a label will
provide the bond order (1 = single bond, 2 = double bond, 3 = triple bond), and
a bond length in Å.
iii. To measure the distance between non-bonded atoms: Click on one atom (it will
become highlighted), and place the cursor on a second atom (do not click); the
iv.
label will list the distance between the atoms in Å .
To measure bond angles: Identify the three adjacent atoms which define the angle
in which you are interested; click on one of the terminal atoms, and shift-click on
the central atom and place the cursor on a third atom (do not click); the label will
list the angle in degrees.
v. To measure dihedral angles: Identify the four atoms which define the dihedral
angle in which you are interested. Shift-click on three adjacent atoms in sequence
and then place the cursor on the fourth atom (do not click); the label will list the
dihedral angle in degrees.
You will learn more about how to rotate structures, twist around bonds, make
measurements and perform calculations in later exercises. Chem3D (and ChemDraw) can
be used to prepare structures, reaction schemes and mechanisms as answers to homework
questions from your textbook, and to illustrate lab reports. Some representative questions are
provided below. A suggested style for answers to these problems is shown on page 8.
-6-

Problem 2.1
Produce cylindrical bond and space-filling models of the two carboxylic acids with
formula C4H8 O 2 (see Problem 1.3). Measure and label the lengths of the C=O and C–O
bonds.
Draw one of the structures in Chem3D, and measure the bond lengths. Copy the
structures back into Chem Draw or a word processing program to prepare your
answer set. Label the bond lengths using ChemDraw or the word processor. Repeat
the process for the second structure.
Problem 2.2
Draw cylindrical bond and space filling models of the isomers of C5H 12 which have the
following types of carbons:
(a) primary, secondary and tertiary
(b) only primary and secondary
(c) only primary and quaternary
-7-

Sample Answer Page for Problems in Exercises 1 and 2
This page can be created in ChemDraw or a word processing program (e.g., Microsoft
Word, Word Perfect, etc.). If ChemDraw is used, the text is created using the text tool; the
Chem3D structures are imported using the Cut and Paste functions in the Edit menus of the
two programs.
Exercises 1 & 2
Name: Gabriella Mei
Student ID# 73
Molecular Structure
a. Line-bond structures and names of the constitutional isomers of C H 6 14
hexane
2-methylpentane
2,2-dimethylbutane
3-methylpentane
2,3-dimethylbutane
b. Cylindrical bond structures of some of the constitutional isomers of alcohols
with the formula C H O 4 10
OH
OH
H O
-8-