Wavefunction, Inc.

Simple. Software. Solutions.

INTRODUCING
SPARTAN 5.1
PC SPARTAN Pro
The Molecular Modeling Workbook for
ORGANIC CHEMISTRY
 What Wavefunction
is All About
Wavefunction is about providing chemists with state-of-
the-art molecular modeling tools. Our customers include
academic and industrial researchers who push modeling to
its limits, and educators who bring the power of modeling
to the next generation of chemists.
Whatever your chemistry needs, Wavefunction
is here to help. We’re not about just software,
we’re about creating real tools to solve real
problems.
The following pages describe what we do. If we
don’t do what you need, call us. Tell us what you
want. Chances are, we’ll have it sooner than you
thought possible.

—Dr. Warren J. Hehre, President & CEO

Quotables
“SPARTAN should be in every chemistry department in the world.”
—Prof. Richard Johnson, University of Hew Hampshire

“PC SPARTAN Plus allows me to truly express the visual nature of organic chemistry.”
—Prof. Thomas Poon, Randolph-Macon College

“I have found MacSPARTAN Plus to be an educational and research tool of constantly

increasing value and efficacy."
—Prof. Paul Lahti, University of Massachusetts, Amherst

“The Molecular Modeling Workbook (and CD-ROM) may be the most significant
advance in teaching organic chemistry in twenty years.”
—Prof. John Meisenheimer, Eastern Kentucky University

1
introducing the

software line
Simplicity is POWER

We chose the name “Spartan” as an

embodiment of this principle.
Then we turned this principle into
the most affordable and user-friendly
molecular modeling packages in the world
today: MacSPARTAN Plus, PC SPARTAN Plus,
PC SPARTAN Pro, and our flagship—
SPARTAN 5.1.

SPARTAN is Simplicity

All SPARTAN software is fully-integrated and offers a full range of modeling tools,
superior computational methods, and phenomenal graphics and animations. All this
through one, elegant graphical user interface. So . . .

You don’t have to be a theorist to use molecular

modeling.

You don’t have to be a computational chemist

to run powerful calculations.

And even if you are, your life just got easier.

This is “Chemistry at Your Fingertips!”

SPARTAN is POWER
2
 (UNIX) version 5.1
A Full Range of Computational Methods
No single computational method is ideal for all applications. The best approach to a
particular problem often involves a combination of different methods—taking
advantage of the strengths of each. This is why SPARTAN 5.1 offers a full suite of modern
computational methods.
Each of these methods—ranging from molecular mechanics and semi-empirical to ab
initio and density functional—can be quickly and easily applied using SPARTAN 5.1’s
graphical interface. And the results from one calculation may be used as a starting point
for another.

Molecular Mechanics—Featuring MMFF94

For molecules comprising hundreds or even thousands of atoms,
molecular mechanics is the only real option. SPARTAN 5.1 provides SYBYL,
available for the entire Periodic Table, and MMFF94 for organic molecules
and biopolymers.
MMFF94 typifies the new generation of molecular mechanics force fields,
specifically parameterized to reproduce both geometries and
conformational energy differences. MMFF94 is rapidly becoming the
method of choice for conformational searches on complex molecules, a
simple task using SPARTAN 5.1’s graphical interface.

Semi-Empirical Molecular Orbital—Including Transition Metals

Molecular mechanics is restricted to stable molecules. Molecular orbital models, in
contrast, can treat reactive species and transition states as easily as stable molecules.
The simplest semi-empirical methods are a melding of the quantum mechanical
framework with approximations and empirical data, or “parameters”. SPARTAN 5.1
includes MNDO, MNDO/d, AM1, and PM3, as well as semi-empirical solvent models
for both water and hexadecane.
And SPARTAN 5.1 features PM3 parameters for calculations on transition-metal
inorganic and organometallic compounds. Parameters for most important transition
metals already exist—and more are on the way.

3
 Computational Power
Ab Initio Molecular Orbital—the Archetypical Quantum Method
Ab initio molecular orbital models continue to be the mainstay for quantitative
investigations of molecular structure and energetics. SPARTAN 5.1
provides both Hartree-Fock and MP2 methods, with a wide
range of Gaussian basis sets—STO-3G, 3-21G, 6-31G* and
6-311G** to name a few. Hartree-Fock models may easily
be applied to molecules with more than 50 atoms,
while MP2 models—which are usually more
accurate—are restricted to smaller systems.

Density Functional—MP2 Quality,

Faster than Hartree-Fock
Density functional models now provide a
viable alternative to traditional Hartree-Fock
and MP2 calculations. Featured in SPARTAN 5.1
is a complete implementation of the Becke-
Perdew non-local density functional model. This
yields reaction energies, including activation
energies, of the same quality as MP2 models at a
fraction of the cost (see graph, below). High quality calculations on large molecules are
now a reality.
As an added bonus, density
functional models provide very
good descriptions of transition-
metal inorganic and organometallic
compounds; something Hartree-
Fock methods cannot do.
Time

Method

Compound

4
 (UNIX) version 5.1
Combinatorial Processing
Combinatorial libraries are typically
based on a parent compound, to which
substituents are added in one or many
positions. SPARTAN 5.1 lets you generate
these libraries quickly and easily, and
even provides a starter library.
Plots and Graphs
Spreadsheet information can be used to
generate plots, histograms, and more.
Single or multiple molecular properties
can be graphed, and plots can be
animated along with associated graphics.
5
Spreadsheet Analysis Tools
SPARTAN 5.1 can display and analyze lists
of molecules and molecular properties in
Spreadsheet form. You can run a
conformational search or combinatorial
process, compare by linear regression or
other basic statistical processes, and then
export your results to other applications.
Conformational Searching
SPARTAN is state-of-the-art conformational
searching, for both cyclic and acyclic
molecules. Combine this with any level
of calculation, from simple molecular
mechanics to powerful density
functional methods, and then quickly
pass your results off for further analysis
at an even higher computational level.
 even
more “CHEMISTRY AT YOUR FINGERTIPS!”
Nucleotide Builder
In addition to builders for
organic, inorganic and
organometallic molecules
and polypeptides, SPARTAN
5.1 allows you to build
nucleotides—from a single
base pair to full strands of
RNA and DNA. You can
change RNA to DNA with
just a tap on your mouse.
Library/
Custom Fragments
All of SPARTAN’s builders
intercommunicate, and all
can now access a structure
library. You can define and
use your own custom
fragments, and even take
advantage of the large
library of transition states
included with SPARTAN 5.1.

Internet Graphics Formats Crystal Visualization

SPARTAN 5.1 allows you to export graphics

as SGI rgb files for easy conversion to gif or SPARTAN 5.1 can import FDAT files and
other formats, for publications and web generate and display unit cells and
pages. You can even export 3D graphics in extended structures. And new polyhedral
VRML format for interactive web display! displays make visualization crystal clear!

Try it for Yourself!

See SPARTAN 5.1 in action with a free, fully functional demonstration. The demo lasts
for thirty days and includes complete documentation and technical support. But be
careful . . . once you try SPARTAN, you won’t want to live without it!
6
 Graphics =
All SPARTAN software provides easy access to p
You can build molecules, set up calculations
graphical interface or even touching the keyb
graphics and as traditional numerical output. T

Molecule Builders—Simple
is Better. All SPARTAN This image tells me
software allows you to Volumes. SPARTAN 5.1
quickly build molecules and PC Pro allow
using a series of graphical you to see any of
model kits. To the right is the the properties of a
Expert model kit from molecule within an
SPARTAN 5.1. With just entire volume of
a few clicks on the mouse, space using “slices”
you can build anything and of various shapes.
everything from acetic acid
to zirconocene dichloride.

Computation dialogs—Let’s talk What’s your Style? All SPARTAN software allows
power! All SPARTAN software helps you you to view molecules in a variety of standard
set up single or repetitive calculations model styles. Below, you can see ball-and-wire,
in seconds. You can refine geometries, ball-and-spoke, and space-filling styles.
find energies, and calculate many other
molecular properties. Mechanics, semi-
empirical, ab initio, and density
functional methods are all available—
the choice is yours.

Information on everything from bond lengths

and angles, to areas and volumes, and even
charges and dipole moments, is just a click away.

Note. Images on this page may not be possible with all Wavefunction software. Tec
7
 Information
phenomenal graphics and computational power.
s, and view results without ever leaving the
board. Computational results shine as brilliant
This is truly “Chemistry at Your Fingertips!”

At left you can

see the electrostatic
potential for the
famous Buckyball
(C60) mapped in
texture bands to a
sphere-shaped
slice. Planar and
cylindrical slices are
also available.
Tables and Graphs. SPARTAN 5.1 and
PC SPARTAN Pro allow you to tabulate and
graph multiple properties for lists of
molecules using its new spreadsheets.
Spreadsheets also facilitate internal
statistical analysis and the export of data to
other analysis packages. Above is a graph
of bond distance versus both angle and
relative energy for an SN2 reaction.

Feeling more Animated? SPARTAN and PC Pro let you construct and animate real-time
sequences of images corresponding to chemical reactions, normal modes of
vibration, and even conformational changes. Above are bond densities for stages of
a Claisen rearrangement.

Beauty may be Surface deep. All SPARTAN software allows you to

map molecular properties to surfaces in continuous colors or
(in SPARTAN) as texture maps. The crown ether complex at
right shows a continuous electrostatic potential mapped
onto an electron density surface. The SN2 animation at the
top of the page shows the same properties as a texture
map (banded colors). Surfaces can be solid, transparent,
and even mesh (upper left, facing page).

chnical overviews on the following pages detail the features of each software package.
8
 Macintosh and PC Software? Yes!

The SPARTAN Desktop Series—Powerful Tools for Powerful Machines

Today’s Macs and PCs are not toys.
PowerPC™, Pentium™, and Pentium II
chips give you workstation-level speed
and graphics right on your desktop. This
means real computational power on the
same computer that you use everyday for
word processing and structure drawing.
Wavefunction’s desktop packages
provide this power in the form of a
variety of molecular mechanics and
quantum chemical methods. Add this to
a perspicuous (that means easy!)
graphical interface, and molecular
modeling is simplicity itself.

MacSPARTAN Plus and PC SPARTAN Plus—Affordable Desktop Modeling!

Mac and PC SPARTAN Plus are designed
for organic and inorganic chemists.
Using the entry, expert, or peptide model
kits (right), you can rapidly construct
complex molecules. You can then
perform calculations, display graphics,
and even copy graphics into your Word™
documents or web pages—all without
leaving the desktop environment.
As for methods, Plus gives you SYBYL
molecular mechanics; AM1, AM1-SM2,
and PM3 semi-empirical; and 3-21G(*),
and 6-31G* ab initio. The performance
will leave you breathless.
And it’s all available for less than you
probably paid for your monitor.

9
 new!PC SPARTAN Pro
UNIX Power, Desktop Price!
PC SPARTAN Pro series is for chemists who want
nearly all the features of SPARTAN 5.1 on their
desktop computer. These powerful features
include everything in PC SPARTAN Plus and:
• MMFF94 molecular mechanics
• Extended Hartree-Fock basis sets
• MP2
• Local (SVWN) and non-local (BP86) DFT
• Spreadsheet based analysis and graphs
• Conformation searching, combinatorial
studies, reaction animation, and more!
In other words, PC SPARTAN Pro is the
modeling solution for chemists who want real
tools—without breaking the bank.

Putting it Together—Desktop Ease with Workstation Power

Modeling has never been easier.
First you run powerful calculations
at workstation speed, then you
copy the results into your
publications with desktop ease.
+ =
This is “Molecular Modeling for
the Desktop” at its best.

System Requirements
MACINTOSH PC
• Power Macintosh including iMac • Pentium, Pentium Pro, or Pentium II
• System 7.5 or Higher • Windows 95/98 or Windows NT
• 16 MB of RAM Minimum • 16 MB of RAM Min (32MB for Pro)
• CD-ROM Drive • 2 MB Super VGA Graphics Card
• CD-ROM Drive

Pricing
Mac or PC SPARTAN Plus PC SPARTAN Pro
$ 999 NAFTA ($749 Gov., $449 Acad.) $ 1,699 NAFTA ($1,199 Gov., $699 Acad.)
* *
$ 1,099 International ($849 Gov., $549 Acad.) $ 1,799 International ($1,299 Gov., $799 Acad.)
*
Does not apply in Japan.

Call for Your Free Demonstration CD-ROM Today!

10
 Software Feature Comparison
● SPARTAN
✱ PC SPARTAN Pro
◆ Mac & PC SPARTAN Plus
Graphical User Interface ▲ Mac & PC SPARTAN
Builders Entry (organic) ▲ ◆ ✱ ●
Expert (organic, inorganic, and organometallic) ◆ ✱ ●
Peptide ▲ ◆ ✱ ●
Nucleotide ✕ ●
Solids (crystals) ✕ ●
Transition states ▲ ◆ ✱ ●
Library ✕ ●

Utilities/Spreadsheets Spreadsheet-based graphs and tables ✱ ●

Combinatorial processor ✕ ●
Vibration animation ▲ ◆ ✱ ●
Reaction animation ✱ ●
Coordinate driving ✱ ●
Bond lengths and angles ▲ ◆ ✱ ●
Surface areas and volumes ✱ ●
Interface to Gaussian’s G92/G94/G98 ●
Import and export of SYBYL MOL2, PDB, and SPARTAN files ▲ ◆ ✱ ●
Import and export of MACROMODEL files ✱ ●
Import of FDAT (crystal data) files ✕ ●
Import of SPARTANView files ✕ ●
Export of SPARTANView files ◆ ✱ ●

Display/Animation Multiple model styles ▲ ◆ ✱ ●

Surface displays of molecular orbitals, electron and spin densities, and
electrostatic potentials ▲ ◆ ✱ ●
Surface displays of polarization potentials ●
Property maps on surfaces ▲ ◆ ✱ ●
Contour (slice) displays ✱ ●
Texture mapping ●
Export of graphics as PICT, jpeg (Mac), or rgb (SPARTAN) files ▲ ◆ ✱ ●
Export of VRML files for 3D Internet graphics ✕ ●

Tasks

Calculate energies (heats of formation or strain energies) ▲ ◆ ✱ ●

Determine equilibrium geometries ▲ ◆ ✱ ●
Determine transition-state geometries ▲ ◆ ✱ ●
Calculate normal-mode vibrational frequencies ▲ ◆ ✱ ●
Conformation search (systematic and stochastic) ✱ ●
Molecular alignment ✱ ●

11
 ● SPARTAN
✱ PC SPARTAN Pro
◆ Mac & PC SPARTAN Plus
Methods ▲ Mac & PC SPARTAN
Molecular SYBYL ▲ ◆ ✱ ●
Mechanics
MMFF94 ✱ ●

Semi-Empirical MNDO, MNDO/d ✱ ●

AM1 ▲ ◆ ✱ ●
PM3 and PM3(tm) ◆ ✱ ●
SM2 (for aqueous solvation) ▲ ◆ ●
SM5.4 (for aqueous solvation) ✱ ●

Ab Initio Hartree-Fock (RHF and UHF) ▲ ◆ ✱ ●

MP2 (RMP2 and UMP2) (energies only in Pro) ✱ ●
STO-3G ✱ ●
3-21G, 3-21G * , and 6-31G* basis sets
( )
▲ ◆ ✱ ●
6-31G**, 6-31+G*, 6-311G*, and 6-311+G** basis sets ✱ ●
6-31G (md, np) and 6-311G (md, np) basis sets ●
Custom; any basis sets comprising s-, p-, and d-type functions ●

Density Functional Local density (SVWN) models ✱ ●

Non-local (BP86 and pBP86) models ✱ ●
Numerical polarization basis sets ✱ ●

Properties
Mulliken and electrostatic-fit charges ▲ ◆ ✱ ●
Natural bond orbital charges ✱ ●
Dipole moments ▲ ◆ ✱ ●
Enthalpies, entropies, and free energies ▲ ◆ ✱ ●

Additional Features
Automatic processing of groups of molecules ✱ ●
Cartesian optimization subject to constraints and/or fixed atoms ▲ ◆ ✱ ●
Full and automatic use of molecular symmetry ▲ ◆ ✱ ●
Network support for distributed computing ●
Automatic job queuing including support for NQS ●
X-windows support for remote access from Macs, PCs, or workstations ●
Multiprocessor versions of key computing modules ●

“✕” These items may not be in the first release.

12
 Educational Projects
The Commitment
Wavefunction is committed to providing the best and most affordable educational
modeling tools available today. This includes both software and information on how
to best use this software in today’s classrooms . . .

The Molecular Modeling Workbook for Organic Chemistry

Wavefunction is proud to announce this new Workbook,
designed to be used in conjuction with any contemporary
organic chemistry textbook. Interactive, visual, and priced for
student budgets, the Workbook provides an ideal introduction to
the use of molecular modeling in learning and understanding
the fundamental concepts of organic chemistry. Included with
the 300-page, full-color workbook is a CD-ROM containing an
interactive viewer for Mac and PC and 1,000+ molecular models
keyed to each of the 200+ Workbook problems. Desk copies may
be available—please call for more information.

Undergraduate Curriculum Workshops

Wavefunction is currently presenting a
series of one-day workshops entitled
“Molecular Modeling in the
Undergraduate Curriculum”.
Each workshop provides a
brief introduction to
computational chemistry and
illustrates how molecular
modeling can be successfully
integrated into the undergraduate
chemistry curriculum. No prior
experience with molecular
modeling is required. Workshops are
generally presented by Dr. Hehre, and
include the use of desktop and UNIX
software. Call for schedule information.

13
 Intensive Workshops
One of the best ways to learn about molecular modeling is through our intensive
three-day workshops in Irvine, California. These workshops focus on the application
of modern electronic structure methods to real chemistry questions.
Lectures cover both molecular modeling theory and
its practical applications. Specifically, they assess the
performance of modern electronic structure methods,
outline practical strategies for doing calculations, and
illustrate the results of applications to diverse
chemical problems. A variety of graphical modeling
techniques are introduced and illustrated.
Workshops are taught by Dr. Warren J. Hehre and lab
instruction is provided by Dr. Wayne Huang. As with
our educational seminars, these intensive workshops
are hands-on and provide ample time to explore
your own chemistry.
Enrollment is strictly limited to seven people. This
small class size ensures participants their own
workstation and plenty of individual attention.

Can’t Make It to Wavefunction?

Maybe Wavefunction can come to you. Dr. Hehre makes frequent visits to give
seminars, discuss chemistry problems and solutions, and give extensive
demonstrations of all SPARTAN software. Call for more information.

In the Works
Someone once said that “The future is now,” but at Wavefunction the future is, well,
tomorrow. We’re practical that way. On tomorrow’s horizon you can expect to see a
broad array of new products from the company that brought you SPARTAN.
Biomolecular and solids modeling products. A new semi-empirical method to
accurately describe reaction energies. Textbooks for graduate and undergraduate
education. Internet plug-ins, and much more.
As you can see, Wavefunction is here to serve you. The chemist. So if we don’t have
what you want today, let us know. Tomorrow is what Wavefunction is all about.

14
 Wavefunction Publications
The Molecular Modeling Workbook for Organic Chemistry $ 29.95
(full color workbook+CD-ROM)
W.J. Hehre, A.J. Shusterman, J.E. Nelson, 1998
(ISBN 1-890661-06-6)

Practical Strategies for Electronic Structure Calculations $ 25.00

W.J. Hehre, 1995
(ISBN 0-9643495-1-5)

A Laboratory Book of Computational Organic Chemistry $ 25.00

W.J. Hehre, A.J. Shusterman, W.W. Huang, 1996
(ISBN 0-9643495-5-8)

A Short Course in Modern Electronic Structure Methods $ 150.00

(spiral bound lecture notes), W.J. Hehre, 1993-1997

An Even Shorter Course in Modern Electronic Structure Methods $ 50.00

(spiral bound lecture notes), W.J. Hehre, 1996-1998

Molecular Modeling in Undergraduate Chemistry Education $ 25.00

(spiral bound lecture notes), W.J. Hehre, W.W. Huang,
A.J. Shusterman, 1996-1998

A Brief Guide to Molecular Mechanics and Quantum

Chemical Calculations $ 25.00
W.J. Hehre, J. Yu, P.E. Klunzinger, L. Lou, 1998
(ISBN 1-890661-05-8)

A SPARTAN Tutorial $ 20.00

W.J. Hehre, W.W. Huang, P.E. Klunzinger, B.J. Deppmeier,
A.J. Driessen, 1997
(ISBN 1-890661-00-7)

SPARTAN User’s Guide $ 35.00

(ISBN 1-890661-02-3)

MacSPARTAN User’s Guide and Tutorial $ 35.00

(ISBN 0-9643495-4-X)

MacSPARTAN Plus Tutorial and User’s Guide $ 35.00

(ISBN 0-9643495-7-4)

PC SPARTAN Tutorial and User’s Guide $ 35.00

(ISBN 0-9643495-6-6)

PC SPARTAN Plus Tutorial and User’s Guide $ 35.00

(ISBN 1-890661-03-1)

A PC SPARTAN Pro Tutorial $ 20.00

W.J. Hehre, W.W. Huang, P.E. Klunzinger, B.J. Deppmeier, 1998
(ISBN 1-890661-08-2)

PC SPARTAN Pro User’s Guide $ 35.00

(ISBN 1-890661-09-0)

Wavefunction, Inc.
18401 Von Karman Ave., Ste. 370, Irvine, CA 92612 USA
Phone: (949) 955-2120 • Fax: (949) 955-2118
e-mail: sales@wavefun.com • http://www.wavefun.com