Spartan Student

Tutorials

WAVEFUNCTION

Wavefunction, Inc.
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Wavefunction, Inc., Japan Branch Office
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[email protected] • www.wavefun.com/japan

Spartan Student is a collaboration with Q-Chem, Inc.

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A Quantum Leap Into the Future of Chemistr y

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Copyright © 2002-2009 by Wavefunction, Inc.

All rights reserved in all countries. No part of this

book may be reproduced in any form or by any
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storage and retrieval systems without permission in
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may quote brief passages in a review.
Table of Contents
1. Basic Operations.......................................................................1
2. Acrylonitrile: Building an Organic Molecule.........................13
3. Sulfur Tetrafluoride: Building an Inorganic Molecule............22
4. Infrared Spectrum of Acetone.................................................26
5. Benzene Chromium Tricarbonyl.............................................30
6. Proton NMR Spectrum of 2-Norbornene................................33
7. 13
C NMR Spectrum of Coumarin............................................38
8. Weak vs. Strong Acids............................................................42
9. Internal Rotation in n-Butane..................................................46
10. Ene Reaction...........................................................................49
11. SN2 Reaction of Bromide and Methyl Chloride......................53
12. Polypeptides and Polynucleotides...........................................57
13. Biomolecules...........................................................................62

Table of Contents iii

1
Basic Operations
This tutorial introduces a number of basic operations in Spartan
Student required for molecule manipulation, property query and
spectra and graphics display. It should be completed first. Specifically
it shows how to: i) open molecules, ii) view different models and
manipulate molecules on screen, iii) measure bond distances, angles
and dihedral angles, iv) display energies, dipole moments, atomic
charges and infrared and NMR spectra and v) display graphical
surfaces and property maps. Spreadsheet operations are not
illustrated, no molecules are built and no calculations are performed.
1. Start Spartan Student. Click (left mouse button) on File from
the menu bar that appears at the top of Spartan Student’s main
window. Click on Open... from the File menu that appears.
Alternatively, click on the icon at the top of the screen. A
file browser appears.
Move to the tutorials directory*, click on basic operations and
click on Open (or double click on basic operations). A single
file containing ethane, acetic acid dimer, propene, ammonia,
hydrogen peroxide, acetic acid, water, cyclohexanone,
ethylene, benzene, aniline and cyclohexenone will be opened.
A ball-and-spoke model for the first molecule (ethane) will be
displayed, and its name appears at the bottom right of the screen.
2. Practice rotating (move the mouse while holding down the left
button) and translating (move the mouse while holding down
the right button). Click on Model from the menu bar.

* For Windows, this is found in Program Files/Wavefunction/SpartanStudent. For

Macintosh, this is located on the disc image.

Tutorial 1 1

Wire Ball-and-Wire Tube Ball-and-Spoke

One after another, select Wire, Ball and Wire, Tube and finally
Ball and Spoke from the Model menu. All four models for
ethane show roughly the same information. The wire model
looks the most like a conventional line formula. It uses color to
distinguish different atoms, and one, two and three lines between
atoms to indicate single, double and triple bonds, respectively.
The ball-and-wire model is identical to the wire model, except
that atom positions are represented by small spheres, making
it easy to identify atom locations. The tube model is identical
to the wire model, except that bonds are represented by solid
cylinders. The tube model is better than the wire model in
conveying three-dimensional shape. The ball-and-spoke model
is a variation on the tube model; atom positions are represented
by colored spheres, making it easy to see atom locations.
Select Space Filling from the Model menu.

2 Tutorial 1
 Space-Filling

The space-filling model is different from the other models in that

bonds are not shown. Rather, each atom is displayed as a colored
sphere that represents its size. Thus, the space-filling model for
a molecule provides a measure of its size. While lines between
atoms are not drawn, the existence (or absence) of bonds can be
inferred from the extent to which spheres on neighboring atoms
overlap. If two spheres substantially overlap, then the atoms are
almost certainly bonded, and conversely, if two spheres barely
overlap, then the atoms are not bonded. Intermediate overlaps
suggest weak bonding, for example, hydrogen bonding.
3. Click once on the right arrow key at the bottom left of the
screen. This will move to the next molecule in the document,
acetic acid dimer. Its name will appear at the bottom of the
screen. If you make a mistake, use the backward or forward
step keys to get to acetic acid dimer in the document. Switch
to a space-filling model and look for overlap between the (OH)
hydrogen on one acetic acid molecule and the (carbonyl)
oxygen on the other. Return to a ball-and-spoke model and
select Hydrogen Bonds from the Model menu.

Ball-and-Spoke model for acetic acid dimer

with hydrogen bonds displayed

The two hydrogen bonds, that are responsible for holding the
acetic acid molecules together, will be drawn.

Tutorial 1 3
 Use the 3 key to toggle between stereo 3D and regular display.
To view in 3D you will need to wear the red/blue glasses.
4. Distances, angles, and dihedral angles can easily be measured
with Spartan Student using Measure Distance, Measure
Angle, and Measure Dihedral, respectively, from the
Geometry menu.

a) Measure Distance: This measures the distance between

two atoms. Click once on to move to the next molecule,
propene, and then select Measure Distance from the
Geometry menu (or click on the icon at the top of the
screen). Click on a bond or on two atoms (the atoms do not
need to be bonded). The distance (in Ångstroms) will be
displayed at the bottom of the screen. Repeat the process for
several atoms. When you are finished, select View from the
Build menu (or click on the icon at the top of the screen).

b) Measure Angle: This measures the angle around a central

atom. Click once on to move to the next molecule,
ammonia, and then select Measure Angle from the
Geometry menu (or click on the icon at the top of the
screen). Click first on H, then on N, then on another H.

4 Tutorial 1
 Alternatively, click on two NH bonds. The HNH angle (in
degrees) will be displayed at the bottom of the screen. Click
on when you are finished.
c) Measure Dihedral: This measures the angle formed by
two intersecting planes, one containing the first three
atoms selected and the other containing the last three atoms
selected. Click once on to move to the next molecule,
hydrogen peroxide, then select Measure Dihedral from
the Geometry menu (or click on the icon at the top of
the screen) and then click in turn on the four atoms (HOOH)
that make up hydrogen peroxide. The HOOH dihedral
angle will be displayed at the bottom of the screen. Click
on when you are finished.
5. Energies, dipole moments and atomic charges among other
calculated properties, are available from Properties under the
Display menu.

a) Energy: Click once on to move to the next molecule,

acetic acid, and then select Properties from the Display
menu. The Molecule Properties dialog appears.

This provides the energy for acetic acid in atomic units

Tutorial 1 5
 (Energy in au). Also provided is an estimate of the energy in
water (Energy(aq) in au).
b) Dipole Moment: The magnitude of the dipole moment
(Dipole Moment in debyes) is also provided in the Molecule
Properties dialog. A large dipole moment indicates large
separation of charge. You can attach the dipole moment
vector, where the + side refers to the positive end of the
dipole, to the model on the screen, by checking the box to the
left of Display Dipole Vector near the bottom of the dialog.
c) Atomic Charges: To display the charge on an atom, click on it
with the Molecule Properties dialog on the screen. The Atom
Properties dialog replaces the Molecule Properties dialog.

Electrostatic atomic charges are given in units of electrons.

A positive charge indicates a deficiency of electrons on an
atom and a negative charge, an excess of electrons. Repeat
for other atoms. Confirm that the positively-charged atom(s)
lie at the positive end of the dipole moment vector. When
you are finished, close the dialog by clicking on at the top
of the dialog.
d) Infrared Spectra: Molecules vibrate (stretch, bend, twist)
even if they are cooled to absolute zero. This is the basis
of infrared spectroscopy, where absorption of energy occurs
when the frequency of a particular molecular motion matches
the frequency of the light. Infrared spectroscopy is important
for identifying molecules as different functional groups
vibrate at noticeably different and characteristic frequencies.

6 Tutorial 1
 Click once on to move to the next molecule in the
document, water. To animate a vibration, select Spectra
from the Display menu and click on the IR tab. This leads
to the IR Spectra dialog.

This displays the three vibrational frequencies for the water

molecule, corresponding to bending and symmetric and
antisymmetric stretching motions. One after the other, click
on each frequency and examine the motion. Turn “off” the
animation when you are finished.
Click once on to move to the next molecule, cyclohexanone.
The Spectra dialog now lists its 45 vibrational frequencies.
Examine each in turn (click on the entry in the dialog) until
you locate the frequency corresponding to the CO (carbonyl)
stretch. Next, click on Draw Calculated at the top of the
dialog. The infrared spectrum of cyclohexanone appears.

Tutorial 1 7
 You can move the spectrum around the screen by first clicking
on it to select it (it will turn yellow) and then moving the
mouse while holding down the right button. You can size it
by moving the mouse up and down while holding down both
the Shift key and the right button.
Identify the line in the spectrum associated with the C=O
stretch (a small red circle moves from line to line as you step
through the frequencies in the Spectra dialog). Note that this
line is isolated and that it is very intense, making it easy to find.
If your computer is connected to the internet, you can draw
the experimental IR spectrum for cyclohexanone on top of the
calculated spectrum. Select Web Site under Experimental
Data From: at the bottom of the dialog and click on Draw
Experimental in the middle of the dialog.

Note that the two spectra are broadly similar, but that the
lines in the calculated spectrum are consistently of higher
frequency. To see this more clearly, click on the calculated
spectrum and move the slider bar to the right of Scale near
the top of the dialog. The calculated spectrum will be uniformly
scaled and it will be possible to bring it into close agreement
with the experimental spectrum. Calculated and experimental
spectra are automatically fit by selecting Experimental
under Calculated Fit at the center of the IR Spectra dialog.

8 Tutorial 1
 You can remove the plot by clicking on both Delete
Calculated and Delete Experimental in the Spectra dialog.
(These buttons have replaced Draw Calculated and Draw
Experimental, respectively.)
e) NMR Spectra: Along with mass spectrometry, NMR
spectroscopy is the most powerful tool available with which
to assign molecular structure. Many nuclei exhibit NMR
spectra, but proton and 13C are by far the most important.
We will use cyclohexanone to illustrate 13C NMR. This is
already selected so there is no need to move in the list of
molecules. With the Spectra dialog on screen, click on the
NMR tab to bring up the NMR Spectra dialog.

Click on Draw Calculated under 13C Spectrum to show the

calculated 13C spectrum.

This comprises four lines, corresponding to the four distinct

Tutorial 1 9
 carbons. If you are connected to the internet, select Web
Site under Experimental Data From: at the bottom right
of the dialog and click on Draw Experimental (under 13C
Spectrum) to superimpose the experimental spectrum onto
the calculated one.

Remove the spectra by clicking on Delete Calculated

and Delete Experimental in the NMR Spectra dialog.
(These buttons have replaced Draw Calculated and Draw
Experimental, respectively.)
6. Spartan Student permits display, manipulation and query of a
number of important graphical quantities resulting from quantum
chemical calculations. Most important are the electron density
(that may reveal both the chemical bonds and how much space
a molecule actually takes up), and key molecular orbitals (that
provide insight into both bonding and chemical reactivity). In
addition, the electrostatic potential map, an overlaying of the
electrostatic potential (the attraction or repulsion of a positive
charge for a molecule) onto the electron density, is valuable
for describing overall molecular charge distribution as well as
anticipating sites of electrophilic addition. Another indicator
of electrophilic addition is provided by the local ionization
potential map, an overlaying of the energy of electron removal
(ionization) onto the electron density. Finally, an indicator
of nucleophilic addition is provided by the LUMO map, an
overlaying of the lowest-unoccupied molecular orbital (the
LUMO) onto the electron density.
Click once on to move to the next molecule, ethylene, and
then select Surfaces from the Display menu. The Surfaces
dialog appears.

10 Tutorial 1
 Display ethylene’s highest-occupied molecular orbital (the
HOMO) as an opaque solid. Click inside the box to the left of the
line homo inside the dialog. What you see is a π orbital, equally
concentrated above and below the plane of the molecule. The
colors (red and blue) give the sign of the orbital. Changes in
sign correlate with bonding or antibonding character. You can
if you wish, turn “off” the graphic by deselecting HOMO.
Click once on to move to the next molecule, benzene,
and select density potential inside the Surfaces dialog. An
electrostatic potential map for benzene will appear. Click on
the map. The Style menu will appear at the bottom right of
the screen. Select Transparent from this menu. Making the
map transparent allows you to see the molecular skeleton
underneath. Go back to a Solid display (Style menu) in order to
clearly see color differences. The surface is colored red in the
π system (by convention, indicating negative potential and the
fact that this region is attracted to a positive charge), and blue
in the σ system (by convention, indicating positive potential
and the fact that this region is repelled by a positive charge).
Bring up the Properties dialog (Display menu) and click on
the surface. Click inside the box to the left of Bands in the
Surface Properties dialog to replace the continuous display
with a series of color bands. When you are finished, click on
at the top of the Surface Properties dialog to close it.
Click once on to move to the next molecule, aniline, and
select density ionization inside the Surfaces dialog. The
graphic that appears, a local ionization potential map. By

Tutorial 1 11
 convention, red regions on the density surface indicate areas
from which electron removal (ionization) is relatively easy,
meaning that they are subject to electrophilic attack. These are
easily distinguished from regions where ionization is relatively
difficult (by convention, colored blue). Note that the ortho and
para ring carbons are more red than the meta carbons, consistent
with the known directing ability of the amino substituent.
Click once on to move to the next molecule, cyclohexenone,
and select LUMO in the Surfaces dialog. The resulting graphic
portrays the lowest-energy empty molecular orbital (the LUMO)
of cyclohexenone. This orbital is delocalized onto several atoms
and it is difficult to tell where exactly a pair of electrons (a
nucleophile) will attack the molecule.
A clearer portrayal is provided by a LUMO map, that displays
the (absolute) value of the LUMO on the electron density
surface. By convention, the color blue is used to represent
maximum value of the LUMO and the color red, minimum
value. First, remove the LUMO from your structure (select
LUMO in the Surfaces dialog) and then turn on the LUMO
map (select density |LUMO| in the dialog). Note that there are
two blue regions, one directly over the carbonyl carbon and the
other over the β carbon. This is entirely consistent with known
chemistry. Enones may either undergo carbonyl addition or
conjugate (Michael) addition.
HO CH3 O O

CH3Li (CH3)2CuLi
carbonyl addition Michael addition
CH3

7. When you are finished, close the document by selecting Close

from the File menu or alternatively by clicking on the icon
at the top of the screen.

12 Tutorial 1
2
Acrylonitrile: Building an
Organic Molecule
This tutorial illustrates use of the organic model kit, as well as the
steps involved in examining and querying different molecular model
styles and in carrying out a quantum chemical calculation.
The simplest building blocks incorporated into Spartan Student’s
organic model kit are atomic fragments. These constitute specification
of atom type, for example, carbon, and local environment, for example,
tetrahedral. However, much of organic chemistry is organized around
functional groups, collections of atoms, the structure and properties of
which are roughly the same in every molecule. The organic model kit
also incorporates a small library of functional groups that can easily
be extended or modified. For example, the carboxylic acid group may
be modified to build a carboxylate anion (by deleting a free valence
from oxygen), or an ester (by adding tetrahedral carbon to the free
valence at oxygen).
C O O
C H C C CH3
R O R O– R O
carboxylic acid carboxylate anion ester

Acrylonitrile provides a good opportunity to illustrate the basics of

molecule building in Spartan Student, as well as the steps involved
in carrying out and analyzing a quantum chemical calculation.
N
H C
C C
H H

* Spartan Student includes a subset of approximately 5,000 molecules from the full Spartan
Molecular Database (SMD) which comprises more than 150,000 molecules along with their
structures, energies, spectra and properties calculated with up to 10 theoretical models.

Tutorial 2 13
1. Click with the left mouse button on File from the menu bar. Then
click on New from the menu that appears (or click on the icon
at the top of the screen). The organic model kit appears.

At the center of the kit is a library of atomic fragments. Click

on trigonal planar sp2 hybridized carbon from the fragment
library. A model of the fragment appears at the top of the model
kit. Bring the cursor anywhere on screen and click. Rotate the
carbon fragment (drag the mouse while holding down the left
button) so that you can clearly see both the double free valence
(=) and the two single free valences (–).

Spartan Student’s model kits connect atomic fragments (as well as

groups, rings and ligands) through free valences. Any free valences
that remain upon exiting a model kit are automatically converted
to hydrogen atoms; it is not necessary to explicitly add hydrogens
to open valences.

2. sp2 carbon is still selected. Click on the double free valence. The
two fragments are connected by a double bond, leaving you with
ethylene. The name “ethylene” will appear at the bottom right
of the screen. If you make a mistake and click instead on the
single free valence, select Undo from the Edit menu. You can
also start over by selecting Clear from the Edit menu.

14 Tutorial 2
 Spartan Student’s organic model kit allow only the same type of
free valences to be connected, for example, single to single, double
to double, etc.

3. Click on Groups in the model kit, and select Cyano from the
functional groups available from the menu.

Click on any of the four single free valences on ethylene (they

are equivalent). This bonds the cyano group to ethylene, leaving
you with acrylonitrile.* Its name will now appear at the bottom
right of the screen.
4. Select Minimize from the Build menu (or click on the icon
at the top of the screen). The final molecular mechanics energy
(36.2 kJ/mol) and symmetry point group (Cs) are provided at the
bottom right of the screen.
5. Select View from the Build menu (or click on the icon at
the top of the screen). The model kit disappears, leaving only a
ball-and-spoke model of acrylonitrile on screen.

* You could also have built acrylonitrile without using the Groups menu. Starting from scratch
(Clear from the Edit menu), first build ethylene as above, then select sp hybridized carbon
from the model kit and then click on one of the free valences on ethylene. Next, select
sp hybridized nitrogen from the model kit and click on the triple free valence on the sp
carbon. Alternatively, you could have built the molecule entirely from groups. Starting from
scratch, click on Groups, select Alkenyl from the menu and click anywhere on screen. Then
select Cyano from the menu of functional groups and click on one of the free valences on
ethylene. In general, molecules can be constructed in more than one way.

Tutorial 2 15
 ball-and-spoke model

This model can be rotated, translated and zoomed by using the

mouse in conjunction with keyboard functions. To rotate the
model, drag the mouse while holding down the left button; to
rotate in the plane of the screen also hold down the Shift key.
To translate the model, drag the mouse with the right button
depressed. To zoom the model (translation perpendicular to the
screen), use the center mouse wheel (scroll wheel) if available,
or hold down the Shift key in addition to the right button while
dragging the mouse up (zoom in) or down (zoom out).
6. Select Configure... from the Model menu, and click to select
Mass Number under Atom in the Configure dialog that appears.

Click on OK to remove the dialog. Mass numbers will appear

next to the individual atoms. Remove the atom labels by clicking
to deselect Labels from the Model menu.*

* Labels from the Model menu is automatically selected (turned “on”) following a change
in the Configure dialog by choosing OK or Apply.

16 Tutorial 2
7. Select Calculations... from the Setup menu, and perform the
following operations in the Calculations dialog which appears.

Select Equilibrium Geometry from the leftmost menu to the

right of Calculate. This specifies optimization of equilibrium
geometry. Select Hartree-Fock and then 3-21G from the middle
and right menus to the right of Calculate. This specifies a
Hartree-Fock calculation using the 3-21G split-valence basis set.
This method generally provides a reliable account of geometries.
When you finish, click on OK to remove the dialog.
8. Select Submit from the Setup menu.* A file browser appears.

The name acrylonitrile will be presented to you in the box to

the right of File name. Either use it or type in whatever name

* You could also have clicked on Submit inside the Calculations dialog.

Tutorial 2 17
 you like and then click on Save.* You will be notified that the
calculation has been submitted.

Click on OK to remove the message from the screen.

After a molecule has been submitted, and until the calculation has
completed, you are not permitted to modify any dialogs or other
information associated with it.

9. You will be notified when the calculation has completed.

Click on OK to remove the message from the screen. Select

Output from the Display menu. A window containing text output
for the job appears.

* Proper names will automatically be provided for you to accept, modify or replace whenever
the molecule exists in the Spartan Molecular Database and where the document being
submitted contains only one molecule. Otherwise the names “spartan1”, “spartan2”, etc.,
will be provided.

18 Tutorial 2
 You can scan the output from the Hartree-Fock calculation by
using the scroll bar at the right of the window or by clicking (left
button) on or inside the output window and using the scroll wheel
on your mouse. The information at the top of the dialog includes
the task, basis set, number of electrons, charge and multiplicity,
as well as further details of the calculation. Below this is the
symmetry point group of the molecule that was maintained
during the optimization.
Eventually, a series of lines appear, under the heading
“Optimization”. These tell the history of the optimization
process. Each line (or “Step”) provides results for a particular
geometry. Ideally, the energy will monotonically approach a
minimum value for an optimized geometry. If the geometry
was not optimized satisfactorily an error message, such as:
“Optimization has exceeded N steps – Stop”, will be displayed
following the last optimization cycle. If this were the case, you
would have been notified that the job had failed, rather than
seeing the “completed” message dialog.
Near the end of the output is the final energy (-168.82040 atomic
units for acrylonitrile with the 3-21G basis set), and the computation
time. Click on at the top of the output dialog to close it.
You may examine the total energy and dipole moment among
other calculated properties without having to go through the
output. Select Properties from the Display menu to bring up
the Molecule Properties dialog.

To see the dipole moment vector (indicating the sign and

Tutorial 2 19
 direction of the dipole moment), check the box to the right of
Display Dipole Vector. (wire, ball-and-wire or tube models are
best for this display.)

Uncheck the box to remove the dipole moment vector.

Click on an atom. The (Molecule Properties) dialog will be
replaced by the Atom Properties dialog.

Among other things, this provides atomic charges. To obtain

the charge on another atom, simply click on it. Inspect all the
atomic charges on acrylonitrile (by clicking on the appropriate
atoms). When you are finished, click on at the top of the Atom
Properties dialog to close it.
10. Select Surfaces from either the Setup or Display menu. Click
on Add... (at the bottom of the Surfaces dialog that results) to
bring up the Add Surface dialog.

20 Tutorial 2
 Select density from the Surface menu and potential from the
Property menu. This requests an electrostatic potential map (an
electron density surface onto which the value of the electrostatic
potential will be mapped). Click on OK. A line density potential
appears at the top of the dialog. If you make a mistake, click on
this line (select density potential) and then click on Delete at
the bottom of the dialog.
11. The graphics calculation will run without needing to submit
the job following your request. When it has completed, select
density potential by clicking in the selection box in the Surfaces
dialog. The surface itself corresponds to the electron density and
provides a measure of the overall size and shape of acrylonitrile.
The colors indicate values of the electrostatic potential on this
surface; by convention, colors toward red correspond to negative
potential (stabilizing interaction between the molecule and a
positive charge), while colors toward blue correspond to positive
potential. The nitrogen (the most electronegative atom) is red and
the hydrogens (the most electropositive atoms) are blue.
12. Select Close from the File menu (or click on ) to remove
acrylonitrile from the screen.* Also, close any open dialogs.

* While Spartan permits as many molecules as desired on screen at a given time, it will be
less confusing for first-time users to keep only a single molecule open at a time.

Tutorial 2 21
3
Sulfur Tetrafluoride: Building
an Inorganic Molecule
This tutorial illustrates the use of the inorganic model kit for
molecule building. It also shows how molecular models may be used
to quantify concepts from more qualitative treatments.

Organic molecules are made up of a relatively few elements and

generally obey conventional valence rules. They may be easily built
using the organic model kit. However, many molecules incorporate
other elements, or do not conform to normal valence rules, or involve
ligands. They cannot be constructed using the organic model kit.
Sulfur tetrafluoride is a good example.
F
F
S
F
F
sulfur tetrafluoride

The unusual “see-saw” geometry observed for the molecule is

a consequence of the fact that the “best” (least crowded) way to
position five electron pairs around sulfur is in a trigonal bipyramidal
arrangement. The lone pair assumes an equatorial position so as to
least interact with the remaining electron pairs. The rationale behind
this is that a lone pair is “bigger” than a bonding electron pair.
Sulfur tetrafluoride provides the opportunity to look at the bonding and
charges in a molecule which “appears” to have an excess of electrons
around its central atom (ten instead of eight), as well as to look for
evidence of a lone pair.
1. Bring up the inorganic model kit by clicking on and then
clicking on the Inorganic tab at the top of the (organic) model kit.

22 Tutorial 3
 The inorganic model kit comprises an atom bar (clicking on
which bring up the Periodic Table*) followed by a selection of
atomic hybrids, then bond types, and finally Rings, Groups,
Ligands, More and Clipboard menus (all except for Ligands
are the same as found in the organic model kit).
2. Click on the atom bar to bring up the Periodic Table.

Select (click on) S in the Periodic Table and the five coordinate
trigonal bipyramid structure from the list of atomic hybrids.
Click on screen. A trigonal bipyramid sulfur will appear at the
top of the model kit.
3. Again, click on the atom bar, select F in the Periodic Table and

* Not all methods are available for all elements listed. Elements for which a specific method
(selected in the Calculations dialog) are available will be highlighted following selection of
a theoretical model from the Model menu that appears in the center of the Periodic Table.

Tutorial 3 23
 the one-coordinate entry from the list of atomic hybrids.
One after the other, click on both axial free valences of sulfur,
and two of the three equatorial free valences.
4. It is necessary to delete the remaining free valence (on an
equatorial position); otherwise it will become a hydrogen. Click
on and then click on the remaining equatorial free valence.
5. Click on . Click on to remove the model kit.
6. Select Calculations... from the Setup menu. Specify calculation
of Equilibrium Geometry using the Hartree-Fock 3-21G
model.
7. Select Surfaces from the Setup menu. Click on Add... at the
bottom of the Surfaces dialog and select HOMO from the
Surface menu in the (Add Surface) dialog which appears.

Click on OK. Leave the Surfaces dialog on screen.

8. Select Submit from the Setup menu, and supply the name
“sulfur tetrafluoride see-saw”.
9. After the calculations have completed, select Properties from
the Display menu to bring up the Molecule Properties dialog.
Next, click on sulfur to bring up the Atom Properties dialog. Is
sulfur neutral or negatively charged, indicating that more than
the normal complement of (eight) valence electron surrounds this
atom, or is it positively charged, indicating “ionic bonding”?
F
F
S
F
F

10. Click on the line “homo...” inside the Surfaces dialog to examine

24 Tutorial 3
 the highest-occupied molecular orbital. Does it “point” in the
expected direction? It is largely localized on sulfur or is there
significant concentration on the fluorines? If the latter, is the
orbital “bonding” or “antibonding”?
11. Build square planar SF4 as an alternative to the “see-saw”
structure. Bring up the inorganic model kit ( ), select S from the
Periodic Table and the four-coordinate square-planar structure
from the list of atomic hybrids. Click anywhere on screen.
Select F in the Periodic Table and the one-coordinate entry
from the list of atomic hybrids. Click on all four free valences
on sulfur. Click on and then on .
12. Enter the Calculations dialog (Setup menu) and specify
calculation of equilibrium geometry using the HF/3-21G model
(the same level of calculation as you used for the “see-saw”
structure*). Click on Submit at the bottom of the dialog, with the
name “sulfur tetrafluoride square planar”.
13. After the calculation has completed, bring up the Molecule
Properties dialog (Properties from the Display menu) and note
the energy. Is it actually higher (more positive) than that for the
“see-saw” structure?
14. Close both molecules as well as any remaining dialogs.

* You need to use exactly the same theoretical model in order to compare energies or other
properties for different molecules.

Tutorial 3 25
4
Infrared Spectrum of Acetone
This tutorial illustrates the steps required to calculate and display
the infrared spectrum of a molecule. It also illustrates retrieval of
the experimental spectrum from an on-line database and fitting the
calculated spectrum to the experimental spectrum.

Molecules vibrate in response to their absorbing infrared light.

Absorption occurs only at specific wavelengths, which gives rise to
the use of infrared spectroscopy as a tool for identifying chemical
structures. The vibrational frequency is proportional to the square root
of a quantity called a “force constant” divided by a quantity called the
“reduced mass”.

force constant
frequency α
reduced mass

The force constant reflects the “flatness” or “steepness” of the energy

surface in the vicinity of the energy minimum. The steeper the energy
surface, the larger the force constant and the larger the frequency.
The reduced mass reflects the masses of the atoms involved in the
vibration. The smaller the reduced mass, the larger the frequency.
This tutorial shows you how to calculate and display the infrared
spectrum of acetone, and explore relationships between frequency
and both force constant and reduced mass. It shows why the carbonyl
stretching frequency is of particular value in infrared spectroscopy.
1. Click on to bring up the organic model kit. Select sp2 carbon
( ) and click anywhere on screen. Select sp2 oxygen ( ) and
click on the double free valence on carbon to make the carbonyl
group. Select sp3 carbon ( ) and, one after the other, click on the
two single free valences on carbon. Click on and then on .
2. Enter the Calculations dialog (from the Setup menu). Select

26 Tutorial 4
 Equilibrium Geometry from the left-hand menu to the
right of Calculate and Hartree-Fock and 3-21G from the
right-hand menu. Check Infrared Spectra in the center of
the dialog. You have requested that an infrared spectrum be
computed following optimization of geometry. Click on Submit
and accept the name acetone supplied to you.
3. Select Spectra from the Display menu. Click on the IR tab in
the dialog that results to bring up the IR Spectra dialog.

This contains a list of vibrational frequencies for acetone. First

click on the top entry (the smallest frequency) and, when you
are done examining the vibrational motion, click on the bottom
entry (the largest frequency).

The smallest frequency is associated with torsional motion of the

methyl rotors. The largest frequency is associated with stretching
motion of CH bonds. Methyl torsion is characterized by a flat
potential energy surface (small force constant), while CH stretching is
characterized by a steep potential energy surface (large force constant).

Locate the frequency corresponding to the CO stretch. The

experimental frequency is around 1740 cm-1, but the calculations
will yield a higher value (around 1940 cm-1).

Tutorial 4 27
 The CO stretching frequency is a good “chemical identifier” because
it “stands alone” in the infrared spectrum and because it is “intense”.

4. Click on Draw Calculated to display the calculated infrared

spectrum.

If you are on-line, click on Draw Experimental to also bring

up the experimental spectrum (superimposed on top of the
calculated spectrum).

You will note that the two are qualitatively similar, but are shifted
relative to each other. To provide a best fit, click on Experimental
below Fit at the top right of the IR Spectra dialog.

Note that the calculated spectrum now closely matches the

experimental spectrum. When you are done, click on Delete
Calculated (which has replaced Draw Calculated) and Delete
Experimental (which has replaced Draw Experimental) inside
the IR Spectra dialog to remove the two spectra.

28 Tutorial 4
5. Change all the hydrogens in acetone to deuteriums to see the
effect which increased mass has on vibrational frequencies. First
make a copy of “acetone” (Save As... from the File menu or click
on the icon at the top of the screen). Name the copy “acetone
d6” Select Properties from the Display menu and click on one
of the hydrogens. Select 2 deuterium from the Mass Number
menu. Repeat for the remaining five hydrogens.
6. Submit for calculation. When completed, examine the vibrational
frequencies. Note that the frequencies of those motions which
involve the hydrogens (in particular, the six vibrational motions
corresponding to “CH stretching”) are significantly reduced over
those in the non-deuterated system.
7. Close all molecules on screen in addition to any remaining
dialogs.

Tutorial 4 29
5
Benzene Chromium
Tricarbonyl
This tutorial illustrates structure calculation for a simple
organometallic compound. It also shows how an electrostatic
potential map may be employed to assess the effect of a chromium
tricarbonyl “substituent” on the charge distribution at benzene.

Organic chemists know that an amino group attached to benzene

adds electrons to the ring and leads to an increase in electrophilic
reactivity, whereas a nitro group has the opposite effect. Knowledge
of complexed substituents, for example, chromium tricarbonyl
complexed to one face of benzene, is more restricted. In this tutorial,
you will compare electrostatic potential maps for benzene, aniline,
nitrobenzene and chromium tricarbonyl in order to classify the
substituent effect of the Cr(CO)3 group and to rank it alongside of
NH2 and NO2 groups.

Cr CO
OC CO
benzene chromium tricarbonyl

1. Build benzene chromium tricarbonyl. Click on and bring

up the inorganic model kit. Click on the atom bar and select Cr
from the Periodic Table. Select the four-coordinate tetrahedral
structure from the list of atomic hybrids. Click anywhere on
screen.
2. Click on Ligands in the model kit, select Benzene from the
menu of available ligands.

30 Tutorial 5
 Click on one of the free valences on the four-coordinate chromium
center.
3. Select Carbon Monoxide from the Ligands menu, and click
on the remaining (three) free valences on chromium. Click on
to produce a refined structure.
4. Select New Molecule (not New) from the File menu. The screen
will blank. Build benzene (Benzene from the Rings menu).
Click on . Again, select New Molecule from the File menu
and build aniline (Benzene from the Rings menu and from
the fragment panel) and click on . Select New Molecule one
last time and build nitrobenzene (Benzene from the Rings menu
and Nitro from the Groups menu) and click on . Click on .
The document now contains four molecules, benzene chromium
tricarbonyl, benzene, aniline and nitrobenzene.
5. Select Calculations... (Setup menu). Specify calculation of
Equilibrium Geometry with the Semi-Empirical PM3 model.
Make certain that Global Calculations (at the bottom of the
dialog) is checked. You want the calculations to apply to all four
molecules. Click on OK.
6. Select Surfaces (Setup or Display menu). Click on Add....
Specify density from the Surface menu, and potential from
the Property menu, and click on OK. Make certain that Global
Surfaces is checked.
7. Submit the job. Name it benzene chromium tricarbonyl. When
completed bring up the spreadsheet (Spreadsheet from the
Display menu), and check the box to the left of the label for all
four entries. This allows them to be displayed simultaneously
on screen. If Coupled (Model menu) is checked, remove the
checkmark by selecting it. The two molecules may now be
Tutorial 5 31
 moved independently. Orient each molecule so that you can
clearly see the benzene face (exposed face in the case of the
organometallic).
8. Select density potential from the Surfaces dialog. In order to
better visualize and interpret the electrostatic potential map,
select Properties from the Display menu and click on one of the
surface maps to display the Surface Properties dialog. Adjust
the property range to -150 kJ/mol to 150 kJ/mol, and make sure
the Global Surfaces box is selected. Compare electrostatic
potential maps for both free and complexed benzene, with
attention to the exposed benzene face.* Does the Cr(CO)3 group
donate or withdraw electrons from the ring? Would you expect
the aromatic ring in benzene chromium tricarbonyl to be more or
less susceptible to electrophilic attack than free benzene? More
or less susceptible to nucleophilic attack? If the Cr(CO)3 is an
electron donor, how does it rank relative to an amino group?
If it is an electron acceptor, how does it rank relative to a nitro
group?
9 optional
9. Repeat the calculations using a more sophisticated theoretical
model, specifically the B3LYP density functional model.
Make a copy of benzene chromium tricarbonyl ( ); name it
benzene chromium tricarbonyl density functional. Inside the
Calculations dialog, specify an Energy calculation using the
B3LYP model with the 6-31G* basis set. Submit. This will require
significantly more computer time than the PM3 calculation.
When completed, examine the electrostatic potential maps. Are
they qualitatively similar to those from the PM3 calculations?
10. Remove all molecules and dialogs from the screen.

* Electrostatic potential maps (as well as other maps) for molecules in a group will be put onto
the same (color) scale. This allows comparisons to be made among different members.

32 Tutorial 5
6
Proton NMR Spectrum of
2-Norbornene
This tutorial illustrates the calculation of the proton NMR spectrum
for a simple organic molecule. Chemical shifts are directly evaluated
but coupling constants are obtained from an empirical relationship.

Proton NMR spectroscopy was the first tool available to chemists to

allow definitive assignment of the molecular structures of complex
organic molecules. While it has been supplanted to some extent
by 13C NMR spectroscopy and more recently by routine X-ray
crystallography, it remains indispensible.
NMR is based on the fact that nuclei possess spins that can either
align parallel or antiparallel to an applied magnetic field, giving rise
to different nuclear spin states. The relative energy of these states
(ΔE) depends on the nucleus and on the strength of the applied
magnetic field, by way of a simple relationship:
∆E = γh/2πB0

γ is the gyromagnetic ratio (a constant for a given type of nucleus),

h/2π is Planck’s constant divided by 2π and B0 is the strength of the
magnetic field at the nucleus. While the two nuclear spin states are
normally in equilibrium, this equilibrium can be upset by applying a
second magnetic field. The absorption of energy as a function of field
strength (a resonance) between the states can then be detected.
The key to the utility of the magnetic resonance experiment is that
the energy at which a nucleus “resonates” depends on its location in
the molecule, and is different for each (chemically) distinct nucleus.
The reason for this is that the applied magnetic field is weakened
by electrons around the nucleus. Nuclei that are well shielded by
the electron cloud will feel a lesser magnetic field than those that

Tutorial 6 33
are poorly shielded, and will show a smaller energy splitting. The
difference, given relative to a standard, is termed a chemical shift. By
convention, both proton and 13C chemical shifts (treated later in this
chapter) are reported relative to tetramethylsilane (TMS) as a standard.
While each unique proton in a molecule gives rise to a single line
(resonance) in the spectrum, the spins on nearby nuclei add and
subtract to the external magnetic field. This leads to a “splitting” of
lines, the splitting pattern depending on the number of neighboring
protons and their geometry. Discounting splitting, the intensity of
the lines is approximately proportional to the number of equivalent
protons that contribute. For example, the proton NMR spectrum of
2-norbornene shows six lines, two with unit intensity corresponding
to the two different protons on the methylene bridge (C7), and four
with twice the intensity corresponding to protons at C1 (C4), C2 (C3)
and the two different protons on C5 (C6).
7

4
5 3

1 2
6

In this tutorial, you will calculate the proton NMR spectrum of

2-norbornene and compare it with that contained in the Spectral
Database of Organic Compounds (SDBS), freely-accessible on the
web from the National Institute of Advanced Industrial Science and
Technology (AIST) in Japan.*
1. Build 2-norbornene. Start from cyclohexane (Rings menu), add
an sp3 carbon ( ) to an axial ring position and bond to ( ) to
a free valence on the opposite side of the ring. Make a double
bond between the appropriate ring carbons ( ). Minimize ( )
and click on ( ).
2. The name 2-norbornene will appear at the bottom right of the
screen. Click on ( ) to the left of the name, select B3LYP/6-31G*

* Web address: http://riodb1.ibase.aist.go.jp/sbds.cgi-bin/cre_index.cgi. Unfortunately,

electronic access to SDBS is prohibited by AIST, severely restricting the utility of this
significant resource.

34 Tutorial 6
 from the models listed in the dialog that appears and click on
Replace. Your model will be replaced by the entry from the
Spartan Molecular Database.
3. Enter the Calculations dialog (Calculations from the Setup
menu), and specify an Energy calculation using the B3LYP
model with the 6-31G* basis set. Check NMR Spectra to
the right of Compute. Click on Submit. Accept the name
2-norbornene.
4. Calculation will require a few minutes. When it has completed,
proton shifts can be found in Atom Properties dialog. Select
Properties from the Display menu and one after the other click
on the hydrogens. Propose assignments for the six resonances
observed in the experimental spectrum: 5.99, 2.84, 1.61, 1.31,
1.08 and 0.95 ppm.
5. Select Spectra from the Display menu and click on the NMR
tab. The NMR Spectra dialog appears.

Click on Draw Calculated With HH Splittings (under 1H

Spectrum) at the top left of the dialog. The following proton
spectrum appears.

Tutorial 6 35
 Compare the calculated proton spectrum with that in SDBS (see
below or examine it on-line).

6. You may have a difficult time seeing that the lines are split
(in both calculated and observed spectra). This is because the
splittings are very small relative to differences in the magnitudes
of the chemical shifts themselves. Spartan Student provides a
magnifier tool to assist. With the Properties dialog on screen,
click on the horizontal axis of the spectra plot. Click on the
Magnifier button at the bottom right of the Plot Properties
dialog that results. Click on the border of the green magnifier
box that results to select it. Move it (as you would any graphical
object) to a position directly above the resonance around 6 ppm.
The single line (due to protons on the double bond) will be split
in two due to interaction (coupling) with the magnetic spins of
the protons on the bridgehead carbons.

36 Tutorial 6
7. Close 2-norbornene and any remaining dialogs when you are
finished.

Tutorial 6 37
7
13
C NMR Spectrum of
Coumarin
This tutorial illustrates calculation of a 13C NMR spectrum, matching
it to the corresponding experimental spectrum accessed via an on-
line database. It illustrates correction of the calculated spectrum for
the effect of the local environment.

There are several reasons why NMR spectroscopy, in particular

13
C NMR, is one of the most important analytical techniques for
characterizing organic molecules. The experiment is straightforward
and can be carried out rapidly. It requires relatively small samples
and is non-destructive. The resulting (proton decoupled) spectrum
is simple, comprising a single line (resonance) for each and every
unique carbon. However, assigning 13C spectra can be problematic
and prone to error, in particular, where several carbons in a molecule
may be in similar environments.
Directly calculated 13C chemical shifts may not in all cases be
sufficiently accurate to enable definitive assignments to be made.
Spartan Student allows calculated 13C chemical shifts to be corrected
for the effects of local chemical environment. The variables in the
correction formula are the numbers of the different kinds of directly-
bonded atoms, for example, the number of sp3 carbons. In this tutorial,
you will compare measured 13C chemical shifts for coumarin both with
those obtained directly from B3LYP/6-31G* calculations and then
with corrected values. Coumarin is a good example both because it is
simple enough for the experimental assignments to be unambiguous,
and because several of the carbons are closely related and therefore
difficult to assign.

38 Tutorial 7
 116.7
131.8
O O
154.0 160.6
118.8
124.4
116.6
128.0 143.5

1. Build coumarin. Click on to the left of its name at the bottom

of the screen, check B3LYP/6-31G* in the dialog that appears
and click on Replace. The structure of coumarin from a B3LYP/
6-31G* calculation will replace the one that you have built.
You will still need to calculate its NMR spectrum as this is not
available in the database.
2. Bring up the Calculations dialog (Setup menu) and select
Energy from the left-most menu to the right of Calculate and
B3LYP and 6-31G* from the two right-most menus. Check
NMR Spectra to the right of Compute. Click on Submit and
accept the name coumarin.
3. The calculation will require several minutes to complete. When
it has completed, select Spectra from the Display menu and
click on the NMR tab. The NMR Spectra dialog results.

The experimental 13C spectrum is available online.* Make certain

that Web site under Experimental Data From at the bottom right
* Skip this and the next two steps if you are not connected to the internet.

Tutorial 7 39
 of the dialog is checked, and click on Draw Experimental under
13
C Spectrum at the right near the top of the dialog. In a few
seconds, the experimental spectrum will appear. Make certain that
the box to the left of Use Corrected Shifts is not checked (click
inside of it if it is checked). Then, click on Draw Calculated
at the top right of the dialog. A second spectrum in a different
color will be superimposed onto the experimental spectrum.

4. Change the scale of the plot to make comparison of calculated

and experimental 13C spectra easier (the scale in the above plot
has already been changed). Select Properties from the Display
menu and click on the horizontal plot axes. Both axes will turn
gold to indicate that they are highlighted and then click on the
X-Scale tab of the Plot Properties dialog that results (not shown)
to pull up a dialog that allows you to change the scale.

Change the range from 225 to 0 ppm to 170 to 100 ppm. Type
over each entry and press the Enter key (return key on Mac).
You will notice that it is very difficult to visually associate the
lines in the two spectra.

40 Tutorial 7
5. Click on Delete Calculated inside the NMR Spectra dialog.
Check the box to the left of Use Corrected Shifts and click on
Draw Calculated. The calculated chemical shifts have now been
empirically corrected for local environment.

You will notice that it is now much easier to visually associate

lines in the two spectra.
Click on Delete Calculated and Delete Experimental to delete
both calcualted and experimental spectra when you are done.
Remove the NMR Spectra dialog.
6. Select Configure from the Model menu to bring up the Configure
Labels dialog. (If the Labels tab is not selected, click on it.)
Select Chem Shift and click on OK. Calculated (uncorrected)
chemical shifts are now attached to your model. Simplify the
display by removing hydrogens (and chemical shifts attached
to them). Select Hydrogens from the Model menu. (To revert
to the original model with hydrogens, simply select Hydrogens
again.)
7. Associate each of the calculated shifts with the corresponding
experimental and compute a signed error. Repeat for the corrected
shifts (select Chem Shift (Cor)) in place of Chem Shift inside
the Configure Labels dialog.
8. Close coumarin when you are done.

Tutorial 7 41
8
Weak vs. Strong Acids
This shows how electrostatic potential maps may be used to
distinguish between weak and strong acids, and quantify subtle
differences in the strengths of closely-related acids. It also shows
how information can be retrieved from Spartan’s database.
Nitric and sulfuric acids are strong acids, acetic acid is a weak acid, and
ethanol is a very weak acid. What these compounds have in common
is their ability to undergo heterolytic bond fracture, leading to a stable
anion and a “proton”. What distinguishes a strong acid from a weak
acid is the stability of the anion. NO3– and HOSO3– are very stable
anions, CH3CO2– is somewhat less stable and CH3CH2O– is even less so.
One way to reveal differences in acidity is to calculate the energy of
deprotonation for different acids, e.g., for nitric acid.
HONO2 H+ + NO3–

This involves calculations on both the neutral acid and on the

resulting anion (the energy of a proton is zero). An alternative
approach, illustrated in this tutorial, involves comparison of
electrostatic potential maps for different acids, with particular focus
on the potential in the vicinity of the “acidic hydrogen”. The more
positive the potential, the more likely dissociation will occur, and
the stronger the acid.
1. Build nitric acid. Click on to bring up the organic model
kit. Select Nitro from the Groups menu and click anywhere on
screen. Add sp3 oxygen to the free valence on nitrogen. Click
on . Build sulfuric acid. Select New Molecule (not New)
from the File menu. Select Sulfone from the Groups menu and
click anywhere on screen. Add sp3 oxygen to both free valences
on sulfur. Click on . Build acetic acid. Again select New
Molecule. Select Carboxylic Acid from the Groups menu
and click anywhere on screen. Add sp3 carbon to the free

42 Tutorial 8
 valence at carbon. Click on . Finally, build ethanol. Select
New Molecule and construct from two sp3 carbons and an sp3
oxygen. Click on , and then on .
2. Bring up the Calculations dialog and specify calculation of
equilibrium geometry using the HF/6-31G* model. Click on
OK. Bring up the Surfaces dialog and click on Add... (at the
bottom of the dialog). Select density from the Surface menu
and potential from the Property menu in the Add Surface
dialog which appears. Click on OK. Leave the Surfaces dialog
on screen. Submit for calculation with the name acids.
3. When completed, bring up the spreadsheet and check the box
immediately to the left of the molecule label for all four entries.
The four molecules will now be displayed simultaneously on
screen. Select (uncheck) Coupled from the Model menu so
that they may be independently manipulated, and arrange on
screen such that the “acidic” hydrogens are visible.

Mouse operations normally refer only to the selected molecule. To

rotate/translate molecules together, hold down the Ctrl (Control)
key in addition to the left/right buttons, while moving the mouse.

4. Click on density potential... inside the Surfaces dialog.

Electrostatic potential maps for all four acids will be displayed.
Examine the potential in the vicinity of the acidic hydrogen (one
of the two equivalent acidic hydrogens for sulfuric acid). Change
the scale (color) to highlight differences in this region. Select
Properties (Display menu) and click on one of the maps. Type
0 and 90 inside the boxes underneath Property Range in the
Surface Properties dialog. Press the Enter key (return key for
Macintosh) following each data entry. “Blue” regions identify
acidic sites, the more blue the greater the acidity. On this basis,
rank the acid strength of the four compounds.
5. Remove acids and any open dialogs from the screen.
6. One after the other, build trichloroacetic, dichloroacetic,
chloroacetic, formic, benzoic, acetic and pivalic acids. Put all into

Tutorial 8 43
 the same document (New Molecule instead of New following
the first molecule). Click on when you are finished.

acid pKa acid pKa

trichloroacetic (Cl3CCO2H) 0.7 benzoic (C6H5CO2H) 4.19
dichloroacetic (Cl2CHCO2H) 1.48 acetic (CH3CO2H) 4.75
chloroacetic (ClCH2CO2H) 2.85 pivalic ((CH3)3CCO2H) 5.03
formic (HCO2H) 3.75

7. Note that the name of the presently selected molecule in the

document appears at the bottom of the screen. This indicates that
a calculated structure is available in Spartan’s database. Click
on to the left of the name, select 3-21G from the entries and
then click on Replace All in the dialog which results. Structures
obtained from Hartree-Fock 3-21G calculations will replace
those you have built.
8. Enter the Calculations dialog and specify an Energy calculation
using the Hartree-Fock 3-21G model. Click on OK. Enter the
Surfaces dialog (Surfaces under the Setup menu). Click on
Add..., select density from the Surface menu and potential
from the Property menu in the Add Surface dialog which
appears and then click on OK. Leave the Surfaces dialog on
screen. Submit for calculation. Name it carboxylic acids.
9. Bring up the spreadsheet. Expand it so that you can see all
seven molecules, and that three data columns are available.
Click inside the header cell for a blank column. Click on Add...
at the bottom of the spreadsheet, select Name from the list
of entries and click on OK. The name of each molecule will
appear. Next, double click inside the header cell of an available
data column, type “pKa” and press the Enter key (return key
for Macintosh). Enter the experimental pKa’s. Press the Enter
key (return key for Macintosh) following each entry.
10. After all calculations have completed, arrange the molecules
such that the “acidic hydrogen” is visible. Check the box to the
left of the Label column in the spreadsheet for each entry, and

44 Tutorial 8
 select (uncheck) Coupled from the Model menu.
11. Click on density potential... inside the Surfaces dialog to turn
on the electrostatic potential map for each molecule. Click on
a surface and click on the button next to Max. under the
property range to post the maximum value for electrostatic
potential in each molecule into the spreadsheet. Double click
the resulting header cell in the spreadsheet and replace the
contents with the word potential.
12. Plot experimental pKa vs. potential. Bring up the Plots dialog
(Plots under the Display menu), select pKa under the X Axis
menu and potential from the Y Axes list, and click on OK.
The data points are connected by a cubic spline. For a least
squares fit, select Properties from the Display menu, click on
the curve, and select Linear LSQ from the Fit menu in the
Curve Properties dialog.

13. Close carboxylic acids and any dialogs from the screen.

Tutorial 8 45
9
Internal Rotation in n-Butane
This tutorial illustrates the steps required to calculate the energy of
a molecule as a function of the torsion angle about one of its bonds,
and to produce a conformational energy diagram.

Rotation by 1800 about the central carbon-carbon bond in n-butane

gives rise to distinct anti and gauche staggered structures. Both
of these should be energy minima (conformers), and the correct
description of the properties of n-butane is in terms of a Boltzmann
average of the properties of both conformers.
CH3 CH3
H H H CH3

H H H H
CH3 H
anti gauche

This tutorial shows you how to calculate the change in energy as

a function of the torsion angle in n-butane, place your data in a
spreadsheet and make a conformational energy diagram.
1. Click on to bring up the organic model kit. Make n-butane
from four sp carbons. Click on
3
to dismiss the model kit.
2. Set the CCCC dihedral angle to 00 (syn conformer). Click on
. Click on the four carbon atoms in sequence. Type 0 (00)
into the box to the right of dihedral... at the bottom right of the
screen and press the Enter key (return key on Macintosh).
3. Select Constrain Dihedral (Geometry menu). Click again on
the four carbons, and then click on at the bottom right of
the screen. The icon will change to indicating a dihedral
constraint. Select Properties (Display menu) and click on the
constraint marker on the model. This leads to the Constraint
Properties dialog.
46 Tutorial 9
4. Check Dynamic inside the dialog. An extended form of the
Constraint Properties dialog allows the constraint value to be
replaced by a range of constraint values.

Leave the value of 0 (0°) in the box to the right of Value as

it is, but change the contents of the box to the right of to to
180 (1800). Be sure to press the Enter key (return key on
Macintosh) after you type in the value. The box to the right of
Steps should contain the value 10. (If it does not, type 10 in this
box and press the Enter key.) What you have specified is that
the dihedral angle will be constrained first to 0°, then to 20°*,
etc. and finally to 180°. Click on to dismiss the dialog.
5. Bring up the Calculations dialog and select Energy Profile
from the leftmost menu to the right of Calculate, and Semi-
Empirical and PM3 from the two rightmost menus. Click on
Submit and accept the name n-butane.
6. When the calculations on all conformers have completed, they

* The difference between constraint values is given by: (final-initial)/(steps-1).

Tutorial 9 47
 will go into a document named n-butane.prof.M0001. Choose
Yes when prompted to open the new file. (You might wish to
close n-butane to avoid confusion.) Align the conformers to get
a clearer view of the rotation. Select Align Molecules from the
Geometry menu and, one after the other, click on either the first
three carbons or the last three carbons. Then click on the Align
button at the bottom right of the screen, and finally click on
. Bring up the spreadsheet (Display menu), and enter both the
energies relative to the 180° or anti conformer, and the CCCC
dihedral angles. First, click on the label (“M0010”) for the bottom
entry in the spreadsheet (this should be the anti conformer),
then click on the header cell for the left most blank column, and
finally, click on Add... at the bottom of the spreadsheet. Select
rel. E from among the selections in the dialog which results,
kJ/mol from the Energy menu and click on OK. To enter the
dihedral angle constraints, select Constrain Dihedral from the
Geometry menu, click on the constraint marker and click on
at the bottom of the screen (to the right of the value of the
dihedral angle constraint). Finally, click on .
7. Select Plots... (Display menu). Select Constraint (Con1) from
the items in the X Axis menu and rel. E(kJ/mol) from the Y
Axes list. Click on OK to dismiss the dialog and display a plot
which, as expected, contains two energy minima.

8. Remove all molecules and dialogs from the screen.

48 Tutorial 9
10
Ene Reaction
This tutorial illustrates the steps involved in first guessing and then
obtaining a transition state for a simple chemical reaction. Following
this, it shows how to produce a “reaction energy diagram”.

The ene reaction involves addition of an allylic hydrogen to an

electrophilic double bond. The hydrogen is transferred and a new
carbon-carbon bond is formed, for example, in 1-pentene.
3
4 2
5 1
H H

The ene reaction belongs to the class of so-called pericyclic reactions

which also includes such important processes as the Diels-Alder
reaction and the Cope and Claisen rearrangements.
In this tutorial, you will locate the transition-state for the ene reaction
of ethylene and propene and show the detailed motions which the
atoms undergo during the course of reaction. It is easier to start from
1-pentene (the product), rather than from the reactants.
1. Bring up the organic model kit and build 1-pentene in a
conformation in which one of the terminal hydrogens on the
ethyl group is poised to transfer to the terminal methylene
group. Click on .
2. First, save 1-pentene as 1-pentene density functional for
optional use later ( ). Also save a copy for immediate use;
name it ene reaction 1-pentene. In both cases you will need to
replace the suggested name (1-pentene).
3. Select Transition States from the Search menu (or click on the
icon at the top of the screen). Click on bond a in the figure
on the following page and then click on bond b. A curved arrow

Tutorial 10 49
 from bond a to bond b will be drawn.
H
H e H H H
C C
d a
H C C
c C b H
H
HH

Next, click on bond c and then on bond d. A second curved

arrow from bonds c to d will be drawn. Finally, click on bond
e and, while holding down the Shift key, click on the (methyl)
hydrogen to be transferred and on the terminal (methylene)
carbon to receive this hydrogen. A third curved arrow from bond
e to the center of a dotted line that has been drawn between the
hydrogen and oxygen will appear.

If you make a mistake, you can remove an arrow by selecting

Delete from the Build menu (click on ) and then clicking on
the arrow. (You will need to select to continue.) Alternatively,
hold down the Delete key as you click on an arrow. With all three
arrows in place, click on at the bottom right of the screen.
Your structure will be replaced by a guess at the ene transition
state. If the resulting structure is unreasonable, then you have
probably made an error in the placement of the arrows. In this
case, select Undo from the Edit menu to return to the model
with the arrows and modify accordingly.
4. Enter the Calculations dialog (Setup menu), and specify
calculation of transition-state geometry using the 3-21G Hartree-
Fock model. Select Transition State Geometry from the leftmost
menu to the right of Calculate, and choose Hartree-Fock and
3-21G from the two rightmost menus. Finally, check IR under
Calculate. This will allow you to confirm that you have found
a transition state, and that it smoothly connects reactant and
product. Click on Submit.
50 Tutorial 10
5. When the job completes, animate the motion of atoms along
the reaction coordinate. Select Spectra from the Display menu
and click on the IR tab. Click on the top entry in the list in the
IR dialog that results. It corresponds to an imaginary frequency,
and will be designated with an i in front of the number.

A vibrational frequency is proportional to the square root of a

quantity that reflects the curvature of the potential surface along a
particular (normal) coordinate corrected for the masses of atoms
involved in motion along that coordinate. At a transition state (the
“top of a hill”), the curvature is negative (it “points down”). Since
mass is positive, the quantity inside the square root is negative and
the frequency is an imaginary number.

Is the vibrational motion consistent with an ene reaction of

interest and not with some other process?
6. Controls at the bottom of the IR dialog allow for changing both
the amplitude of vibration (Amp) and the number of steps that
make up the motion (Steps). The latter serves as a speed control.
Change the amplitude to 0.3. Type 0.3 in the box to the right of
Amp and press the Enter key (return key on Macintosh). Click
on Make List at the bottom of the dialog. This will give rise to
a group of structures that follow the reaction coordinate from
the transition state toward both reactant and product. Remove
the original transition state: click on ene reaction 1-pentene (the
vibrating molecule) and close it, along with the IR dialog.
7. Enter the Calculations dialog and specify calculation of Energy
using the 3-21G Hartree-Fock model. Make certain that Global
Calculations is checked. Next, enter the Surfaces dialog and
specify evaluation of two surfaces: a density surface and a density
surface onto which the electrostatic potential has been mapped
(an electrostatic potential map). Click on Add . . ., select density
for Surface and none for Property and click on Apply. Select
density for surface and potential for Property and click on
OK. Make certain that Global Surfaces is checked before you
request the surfaces.

Tutorial 10 51
8. Submit for calculation. Name it ene reaction 1-pentene
sequence. Once the job has completed, enter the Surfaces
dialog and examine the surfaces that you have calculated. Select
Properties from the Display menu and click on the density
surface to bring up the Surface Properties dialog. Change the
Isovalue to include 75% of the electron density. Repeat this
procedure for the electrostatic potential map surface. For each,
step through the sequence of structures ( and ) keys at the
bottom of the screen) or animate the reaction ( ). Note, in
particular, the changes in bonding revealed by the bond density
surface. Also pay attention to the value of the potential on the
migrating atom. This reflects its charge. Is it best described as a
proton (blue), hydrogen atom (green) or hydride anion (red)?
9. Close ene reaction 1-pentene sequence and any open dialogs.
10 to 14 optional
Methods that account for electron correlation are generally needed
to furnish accurate estimates of absolute activation energies. Perform
B3LYP/6-31G* density functional energy calculations on both
1-pentene and on the ene reaction transition state (using 3-21G
geometries).
10. Open ene reaction 1-pentene ( ) and make a copy ( ). Name
it ene reaction 1-pentene density functional.
11. Enter the Calculations dialog, and specify calculation of Energy
with the B3LYP/6-31G* model. Remove the checkmark from
IR. Submit the job.
12. Open 1-pentene density functional ( ). Minimize the structure
and click on . Specify calculation of Equilibrium Geometry
using the B3LYP 6-31G* model. Submit the job.
13. Obtain the activation energy (difference in total energies between
1-pentene and the ene reaction transition state).
14. Remove any molecules and dialogs from the screen.

52 Tutorial 10
11
SN2 Reaction of Bromide
and Methyl Chloride
This tutorial illustrates construction of an energy profile for a
simple SN2 reaction. This starts from the reactants, passes through
the transition state and ends up with the products.

The SN2 reaction passes through a transition state in which carbon is

in a trigonal bipyramid geometry and the entering and leaving groups
are colinear.
H H H
Br– + C Cl Br C Cl Br C + Cl–
H H
H H
H H

1. First, construct methyl chloride. Then select bromine from the

palette of icons in the model kit, click on the Insert button at
the bottom right of the screen or hold down the Insert key (alt
key on Macintosh) and click anywhere on screen. Alternatively,
double click in a blank area of the screen following selection
of bromine. Two detached fragments, methyl chloride and
hydrogen bromide, appear on screen. Click on and then click
on the free valence on bromine. Click on . Alternatively, hold
down the Delete key and click on the free valence on bromine.
You are left with methyl chloride and bromine atom (bromide).
Manipulate the two such that bromide is poised to attack methyl
chloride from the backside (as in the transition state above).
(Recall that translations and rotations normally refer to both
fragments, but can be made to refer to a single fragment by first
clicking on the fragment and then holding down on the Ctrl
key while carrying out the manipulations.) Do not minimize (If
you do so by accident, select Undo from the Edit menu). Click
on .

Tutorial 11 53
2. Click on . Click on bromide and, while holding down the
Shift key, click again on bromide and then on carbon. A dotted
line will be drawn from bromine to carbon, together with an
arrow from bromine to the center of this line. Next, click on the
CCl bond and then click on the chlorine. A second arrow from
the carbon-chlorine bond to the chlorine will be drawn.

Br C Cl

Click on at the bottom right of the screen. Your structure will

be replaced by a guess at the transition state.
3. Click on and then on the CBr bond. Replace the current CBr
distance in the box at the bottom right of the screen by 3.8 (3.8Å)
and press the Enter key (return key on Macintosh). You have
now made a complex representing the reactant.
4. Select Constrain Distance from the Geometry menu. Click
on the CBr bond, and then click on at the bottom right of the
screen. The icon will change to indicating a constraint is to be
applied to this distance. Next, bring up the Properties dialog and
click on the constraint marker. The Constraint Properties dialog
appears. Click on Dynamic. Leave the value 3.8 (3.8Å) in the
box to the right of Value alone, but change the number in the box
to the right of to to 1.9 (1.9Å) and press the Enter (return) key.
Change the number in the box to the right of Steps from 10 (the
default) to 20. 20 Calculations with CBr bond lengths constrained
from 3.8Å (the starting point) to 1.9Å (the ending point) will be
performed. The transition state should have a CBr distance in
between these values. Dismiss the Constraint Properties dialog.
5. Enter the Calculations dialog, and select Energy Profile,
Hartree-Fock and 3-21G from the menus to the right of
Calculate. You need to change Total Charge to Anion.
6. Submit the job. Name it bromide+methyl chloride. When
completed, it will give rise to a sequence of calculations placed
in bromide+methyl chloride.Prof.M0001. You will be prompted

54 Tutorial 11
 as to whether you want to open this file. Click on Yes.
7. Bring up the Spreadsheet (Spreadsheet from the Display menu)
and click on Add.... Select E from among the quantities listed
at the top of the dialog, kJ/mol from the Energy menu, and
click on OK. Next, enter the (constrained) CBr distances and
bromine charges in the spreadsheet. Select Constrain Distance
from the Geometry menu, click on the constraint marker and
click on at the bottom right of the screen. Click on . Bring
up the Properties dialog. Click on bromine and click on to the
left of Electrostatic under Charges in the Properties dialog.
Finally, bring up the Plots dialog, and select Constraint (Con1)
(the distance at which the CBr bond has been constrained) from
the X Axis menu, and both E (kJ/mol) and Electrostatic (Br1)
from the Y Axes list. Click on OK.
One plot gives the energy as the reaction proceeds and the other
gives charge on bromine. Are the two related? Explain.

8. SN2 reactions involving charged species normally need to be

carried out in highly-polar media, for example, water. Add
aqueous phase data (based on the empirical SM5.4 model) to the
spreadsheet. Click on an empty column header, click on Add...,
select Eaq from the list of available quantities (kJ/mol from the
Energy menu), and click on OK. Bring up the Plots dialog and
select Constraint (Con1) from the X Axis and Eaq(kJ/mol)
from the Y Axes list. Click on OK.

Tutorial 11 55
9 to 12 optional
9. With bromide+methyl chloride.Prof.M0001 selected, enter the
Calculations dialog. Specify an Energy calculation using the
Hartree-Fock 3-21G model, and click on OK.
10. Enter the Surfaces dialog. Click on Add.... Select density from
the Surface menu and none from the Property menu and click
on Apply. Select density from the Surface menu, but this time
potential from the Property menu. Click on OK.
11. Submit the job. When completed, select density inside the
Surfaces dialog. Select Properties from the Display menu and
click on the surface to bring up the Surface Properties dialog.
Change the Isovalue to include 75% of the electron density.
Click on at the bottom left of the screen to animate the display.
Note, that bonds are smoothly broken and formed during the
course of reaction. Click on at the bottom of the screen when
you are done.
12. Reenter the Surfaces dialog. Turn “off” display of the bond
density (select density), and turn “on” display of the electrostatic
potential mapped onto the density (select density potential).
Reset the isovalue as before. Click on . Relate the migration
of negative charge during reaction as indicated by colors in the
electrostatic potential map to the plot you constructed earlier in
step 7. Recall, that colors near red indicate maximum negative
potential.
13. Remove all molecules and any remaining dialogs from the
screen.

56 Tutorial 11
12
Polypeptides and
Polynucleotides
This tutorial illustrates use of the peptide and nucleotide model kits.
It shows how hydrogen bonds influence both the secondary structure
of polypeptides (proteins) and the double helix of DNA. No quantum
chemical calculations are performed.

Proteins perform a variety of vital roles in all living organisms: reaction

catalysis, transport and storage, structural support, immune protection,
and mediation of nerve impulses, to name a few. Despite the variety,
all proteins consist of the same basic building blocks (a set of 20 amino
acids), and are dominated by two main structural motifs (the a helix
and the b pleated sheet).

a Helix
1. Select New from the File menu and click on the Peptide builder
from the Model Kit. This contains a library of the 20 natural
amino acids, each identified by a 3-letter “code”.
2. Click on gly- (glycine). Toggle “on” and “off” the check-box
to the left of Sequence. The display window at the top of the
model kit will shift between a text field showing gly (with
the Sequence button checked) and a 2D rendering of non-
terminated glycine (with the Sequence button un-checked).
3. Make sure the Sequence box is checked, and randomly select
an additional 9 amino acid residues. Below the pallet of amino
acids are a series of buttons: a Helix, b Sheet and Other. These
allow specification of the secondary structure of constructed
polypeptide sequences. Select a Helix and click on screen.
4. A ball-and-spoke model of a 10-residue polypeptide is displayed.

Tutorial 12 57
 There are two open valences (indicated by their yellow color)
at either end of this non-terminated polypeptide molecule.
From the lower right side of the Peptide builder, click on the
Terminate button. The dialog that results provides the option
of terminating the amino acid in a an uncharged form (CO2H
and NH2) or a zwitterionic form (CO2– and NH3+).

Choose CO2– and NH3+ (the zwitterionic form) and click on the
OK button to terminate.
5. To simplify the model, display the molecule as a Tube model and
deselect Hydrogens from the Model menu. Select Hydrogen
Bonds from the Model menu. Dotted lines depicting hydrogen
bonds will appear on screen between the oxygens of carbonyl
groups and the nitrogens of amine groups (recall that display
of hydrogens has been turned off). In the a helix structure,
hydrogen bonds are formed between the C=O of one amino
acid and NH group of another amino acid, separated by a space
of 4 residues. It is this network of internal hydrogen bonding
that holds together the a helix.

O R2 O R4 O
H H
H2N N N
N N OH
H H
R1 O R3 O R5

6. To better see the a helix, select Ribbons from the Model menu.
You may also, if you choose, turn off the molecular structure
display of the peptide all together, by selecting Hide from the
Model menu. Rotate the model on screen to get an idea of its
3D structure. Note that the hydrogen bonds are still visible.
Close the document.

58 Tutorial 12
b Pleated Sheet
7. Select New from the File menu and click on the Peptide builder
from the Model Kit. The ten-residue sequence you previously
constructed will remain in the viewer window at the top of the
builder (if not, make sure the Sequence box is checked and
randomly choose another 10 amino acids). Select b Sheet and
click on screen.
8. Again, a model of a 10-residue polypeptide is displayed. This
time, the secondary structure is in the b sheet configuration.
Terminate the structure in either the uncharged or zwitterionic
form.
9. Click on to remove the model kit. Note that the same
10-residue sequence is significantly longer in the b sheet
arrangement. As you did for the a helix, switch to a tube model,
turn “off” hydrogens and turn “on” display of hydrogen bonds.
No hydrogen bonds appear. Close the document.
10. Hydrogen bonds play a role in connecting b strands to make
a b sheet. Open 1JIC* from the tutorials directory. Turn on
hydrogen bonds (Model menu). Hydrogen bonds appear
between different b strands. Note that hydrogen bonds may also
exist between residues on the same strand, in this example in
a “hairpin turn” resulting the same b sheet running adjacent to
itself but in the opposite (or anti-parallel) direction. Close 1JIC.

B-DNA
11. Select New from the File menu and click on the Nucleotide
model kit. This model kit includes options for building a
variety of nucleic acid sequences (based on nucleotide residues)
included both single and double stranded DNA and RNA, as
well as hybrid DNA-RNA sequences. Choose DNA from the
menu in the middle of the Nucleotide model kit.

* PDB designation 1JIC. Torres, A.M., Kini, R.M., Selvanayagam, N., Kuchel, P.W.; J.
Biochem. 360: 539-548 (2001).

Tutorial 12 59
12. Just below the viewer window (inside the model kit) are four
buttons designating the nucleotide bases. Click on A (adenine).
Toggle “on” and “off” the check-box to the left of Sequence.
The display window at the top of the model kit will shift between
a text field showing A- (with the Sequence button checked)
and a 2D rendering of adenine (with the Sequence button un-
checked). Note that even though the 2D rendering displays
only the nucleotide base, when building, the entire nucleotide,
include the organic base (purine or pyrimidine), sugar (ribose),
and phosphate group, will be inserted on screen. In the case of
double-stranded sequences, the complementary base will also
be inserted.
13. Click on screen to insert an adenosine nucleotide, and its
complementary base thymine nucleotide. Select Hydrogen
Bonds from the Model menu to display hydrogen bonding
between the AT base pair. Note that adenosine-thymine pairings
in double stranded DNA will always form two hydrogen bonds,
where as guanine-cytosine pairings result in the formation of
three hydrogen bonds. When you are finished examining the
A-T base pair, select Clear from the Edit menu.
14. Make sure the Sequence box is checked, and randomly select
an additional 15-20 nucleotide bases. Below the pallet of
nucleotide bases is a series of buttons (marked A, B, and Other)
that provide for specification of the nucleotide sequence Helix.
Select B for the helix type and click on screen. (DNA exists in
three forms, A, B, and Z. Almost all DNA in living organisms
is in the B-DNA configuration.)
15. Select Tube and Ribbon from the Model menu. Display of
hydrogen bonds has already been specified. If you turned this
off, hydrogen bonds can be accessed from the Model menu.
Also select Configure from the Model menu and click on the
Ribbons tab. Select By Strand from the Coloring options and
click OK. The ribbon tracing the backbone of the sequence you
constructed from the builder is colored red; the complementary
sequence is colored blue.

60 Tutorial 12
16. Because the glycosidic bonds of the base pairs (bonds connecting
the base pairs to their sugar molecules) are not exactly opposite
one another, B-DNA has two clearly visible grooves (called the
major groove and the minor groove). The major groove is ~ 12
Å wide and the minor groove is roughly half that size. Select
Space-Filling from the Model menu and locate the major
and minor grooves in your B-DNA sequence. When you have
finished examining the DNA sequence, close the document.

Tutorial 12 61
13
Biomolecules
This tutorial illustrates models appropriate to large biomolecules
(proteins and nucleotides), in particular, ribbon displays of secondary
structure and display of hydrogen bonds. Biomolecule building is
not illustrated, nor are any calculations performed.

Treatment of very large molecules, proteins and nucleotides

(“biopolymers”) most important among them, requires models which
are simpler than those appropriate for small organic and inorganic
molecules. This refers both to structural models for display and
manipulation (where a simplified ribbon display of the biomolecule’s
“backbone” is used) and to theoretical models used for calculation of
structure and properties (where molecular mechanics replaces quantum
chemical models).
This tutorial uses an enzyme (phospholipase A2) extracted from the
venom of the common cobra (Naja naja) to illustrate a variety of
models for the display of biomolecules, including ribbon displays to
elucidate the backbone and hydrogen-bond displays to disclose some
of the forces holding the structure together.
1. From the File menu, click on Access PDB Online... then type
1A3F* in the PDB Id code: field and click Open**.

Note that a simple ribbon display, demarking the protein

backbone (secondary structure) has replaced the usual structural
* PDB designation 1A3F. Segelke, B.W., Nguyen, D., Chee, R., Xuong, N.H., Dennis, E.A.;
J.Mol. Bio., 279, 223-232 (1998).
** If you do not have an internet connection, the file 1A3F is available from the tutorials
directory. See Basic Operations tutorial for tutorials location.

62 Tutorial 13
 models (ball-and-spoke, tube, etc.). To see why this is preferable,
turn “on” (select) one of these models from the Model menu.
The model styles that provide detail of the enzyme’s primary
structure have completely obliterated a significant structural
detail (namely that this enzyme is comprised of three identical
sub-units). Note, however, that a space-filling model (Space-
Filling from the Model menu) does provide indication of the
overall size and shape of the enzyme.
2. To better visualize the three sub-units, turn “off” (choose
Hide from the Model menu) the selected model style, and
select Configure from the Model menu, click on the Ribbons
tab, and finally select By Strand. Note that each oligomer is
colored differently. Explore the remaining options for coloring
(click Apply after each selection). Monochrome provides a
single colored model useful for tracing the backbone of the
biomolecule. By Secondary Structure gives information about
how the backbone is organized (alpha-helices are colored red,
beta-sheets are colored blue, while any remaining segments are
colored green). By Residue provides a multi-colored display
where each unique color represents a specific amino acid
residue. To further explore, click on the OK button to dismiss
the Configure dialogue, and then click on the individual colored
segments of the ribbon. The specific peptide or amino acid
residue (in the case of peptide chains, proteins, or enzymes)
or nucleotide base (in the case of nucleotide chains, DNA, or
RNA) will be specified in the lower right of the workspace.
Hydrogen bonding is known to be a decisive factor in determining
the three-dimensional structures of biopolymers. The base
pairs in complementary strands which make up DNA are held
together by hydrogen bonds. Helical structures in proteins are
also maintained by hydrogen bonds as are neighboring strands
in so-called b sheets.
3. Close 1A3F.

Tutorial 13 63