1. How to cite HyperChem?

Please cite HyperChem as:

HyperChem(TM), Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA

2. What platforms does HyperChem run on?

In general, HyperChem runs on Windows platforms, and we also have versions for the SGI and Dec Alpha platforms.

• HyperChem 5 runs on Windows 95 and Windows NT 4.0.

• HyperChem 4 and 4.5 run on Windows 3.1, 3.11, Windows for Workgroups, and Windows 95 and Windows NT 3.51 and 4.0.

• For Silicon Graphics platforms, HyperChem 4.5 is available; it runs on IRIX 5.x and 6.x systems.

• For the DEC Alpha platform, HyperChem 4 is available.

3. Do you have a Macintosh version of HyperChem?

No, for two reasons: the operating system is not the same-- which can be overcome by using SoftWindows-- and the LPT1 port onto which the dongle is attached is different from Apple ports. Unless you choose a no-dongle version of HyperChem such as HyperChem Lite or HyperChem release 5 with a soft-keyed license option, your computer would need a hardware modification.

4. Can I run HyperChem in networked mode?

Yes, if you purchase the network option. The supported network protocols are:

Note: HyperChem release 5 supports the TCP/IP transport protocol in addition to the above list.

5. How accurate are my HyperChem calculations?

The accuracy of results from HyperChem varies, depending upon the computational method (molecular mechanics, semi-empirical, ab-initio), the parameter set (MM+, Amber, etc.), the molecular system you are studying and the property you wish to compute. We suggest that users consult the literature - as well as the HyperChem Computational Chemistry manual - for guidelines based on published calculations of the same type.

Besides the usual library search for reports on related calculations, you might find the archives of the Computational Chemistry List (CCL) helpful. Their web site is http://ccl.osc.edu/chemistry.html.

6. Do you have a tutorial set for HyperChem?

All versions of HyperChem except HyperChem Lite come with the "Getting Started" manual. We encourage all HyperChem users to work through this book to increase their familiarity with this powerful software.

"Laboratory Exercises Using HyperChem" is a book of tutorials for use in the undergraduate curriculum. It provides exercises that integrate the use of HyperChem into the Chemisty curriculum.  

For the classroom setting, there are additional instructional materials available. Visit our Education page, accessible from the Hypercube home page, for more information.

7. What is the hardware lock or dongle?

The hardware lock, commonly known as a dongle, that comes with HyperChem is a small device which attaches to the printer port of the computer. Its purpose is to prevent unauthorized distribution of software. The dongle does not monopolize this port; a printer can be attached to the dongle and (unless the printer itself monopolizes the port) normal operation ensues.

The advantage of this means of software security (over a "software key") is the flexibility to the user; you can have HyperChem software installed on several different computers, and to access the software you need only move the dongle from one machine to another.

Like any physical device attached to your computer, the dongle needs software which will control, or "drive" its operation. HyperChem software arrives complete with the driver software. From time to time this is updated by Rainbow Technologies, the manufacturer of the dongle. Updates to the dongle driver software are available from our Support web page.

8. Do you have versions of HyperChem without a hardware lock?

Yes, we do. Our latest release of HyperChem 5 now permits a soft-keyed license option for stand-alone copies. This will overcome the need for a dongle, but will restrict the use of HyperChem software to one particular computer and one particular operating system.

HyperChem for the SGI has never required a hardware lock; instead it uses a software license which is obtained from license@support.com after the installation has been completed.

HyperChem Lite does not require a dongle, although you must always have the HyperChem Lite CD in a CD-ROM device during the running of HyperChem Lite to access certain files.

9. What are the file formats supported by HyperChem?

HyperChem releases 4, 4.5, and 5 allow the following I/O file types:

You might find the shareware Babel 1.6 to be helpful in converting between various file formats. The following files are on ftp://joplin.biosci.arizona.edu/pub/Babel:

ChemPlus, an add-on for HyperChem, will permit I/O with Cambridge Structural Data files in the "Crystal Builder" module.

HyperChem Lite permits only .HIN files for I/O.

10. Where can I find published papers that describe work done using HyperChem?

We maintain a list of such papers based on our survey of the literature, which is updated annually. The HyperChem e-mail Users' Group is an additional source of contacts and current information; visit our Support page to find out more.

11. Where can I learn more about computational chemistry?

On-line, the NIH Molecular Modeling web site is a good resource; it provides information on computational methods, references to the literature, and examples of the use of computational methods. The NIH Guide to Molecular Modeling features a "Getting Started with Molecular Modeling" page, which provides useful guidelines for planning a molecular modeling project.

For additional www resources, visit some of the links on our Related Sites page.

The HyperChem Computational Chemistry manual (available separately; contact us directly to order) contains an annotated bibliography of texts which supply additional background for understanding calculations in HyperChem.

Excerpts from the Annotated Bibliography :

Brooks III, C.L.; Karplus, M.; Pettitt, B.M. adn Thermodynamics, in: Advances in Chemical Physics, Vol. 71. John Wiley and Sons, New York, 1988.Proteins: A Theoretical Perspective of Dynamics, Structure,

Provides background for force-field based calculations. Includes numerous examples of computing the structure, dynamics, and thermodynamics of proteins. There is an interesting chapter on the complementary nature of molecular mechanics calculations and specific experimental techniques.

 

Burkert, U. and Allinger, N.L., Washington, D.C. 1982.Molecular Mechanics, American Chemical Society Monograph 177,

The classical introduction to molecular mechanics calculations. The authors describe common components of force fields, parameterization methods, and computational techniques for molecular mechanics calculations; structure, thermodynamic, and chemical reaction calculations; and the application of molecular mechanics to common organic and biochemical molecular systems.

 

Clark, T. A Handbook of Computational Chemistry, John Wiley and Sons, New York, 1985,

A practical introduction to molecular mechanics and semi-empirical quantum mechanics calculations, with extensive examples from the MINDO/3 and MNDO methods. One of the more accessible books for new computational chemists.

 

Dewar, M.J.S. The Molecular Orbital Theory of Organic Chemistry. McGraw-Hill, New York, 1969.

Provides a survey of quantum mechanics, semi-empirical computational methods, and the application of molecular orbital theory to organic chemistry. The concepts explored in this book should be easy for most readers to understand.

 

Lipkowitz, K.B.; Boyd, D.B., Eds., 1990 - (series).Reviews in Computational Chemistry , VCH Publishers, New York,

Volume 1 is particularly useful for beginning computational chemists. Some of the topics addressed: semi-empirical quantum mechanics methods, using the results of semi-empirical calculations to obtain molecular properties, and a brief review of empirical calculations ( including molecular dynamics methods). The chapter by D.B. Boyd, "Aspects of Molecular Modeling", contains an excellent basic review of quantum mechanics calculations and summaries of the accuracies of these methods.

 

Hehre, W.J., Radom, L., Schleyer, P.v.R., Pople, J.A., and Sons, New York, 1986.Ab Initio Molecular Orbital Theory, John Wiley

Covers theory and applications of ab initio quantum mechanics calculations. The discussion of applications includes comparisons between experiment and many types and levels of calculation. The material is helpful in determining strategies for, and the validity of, ab initio calculations.

 

Szabo, A.; Ostlund, N.S., Modern Quantum Chemistry, Dover Publications, New York, 1996.

A textbook describing the theory associated with calculations of the electronic structure of molecular systems. While the book focuses on ab initio calculations, much of the information is also relevant to semi-empirical methods. The sections on the Hartree-Fock and Configuration Interaction methods, in particular, apply to HyperChem. The self-paced exercises are useful for the beginning computational chemist.

 

Stewart, J.J.P. MOPAC: A Semiempirical Molecular Orbital Program,Design, 4: 1-105, 1990. J. Computer-Aided Molecular

A valuable review of the MOPAC program and the semi-empirical methods. MNDO, MINDO/3, AM1, and PM3. Of particular use are theoretical discussions of these semi-empirical methods and many tables validating the accuracy of the MOPAC program and its associated Hamiltonians

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