ChemNews.Com VOL 9 NO 4

Reflect on how the computer has evolved into an integral part of the scientist. s life over the past 15 years. I would expect that most scientists did not have a personal computer and had very limited access to a network terminal before 1984. And yet today, the computer has become so critical to the scientific process that if the worst possible Y2K scenario came to pass, most ongoing research projects would be seriously crippled and set back months, if not years. Fortunately, that event is not about to happen, but I would like to discuss some software programs which do the tasks that chemists used to perform manually, if at all, just a few years ago.

Chemistry Software

As I. ve written in several earlier modeling review articles, the advances in computer technology have made it possible for the average chemist to model molecules and perform simulations on the desktop, that 15 years ago would have required mainframe supercomputers. These programs have sped up processes that would have taken weeks and months to perform.

ChemOffice

ChemOffice by CambridgeSoft has added significant new features with every release. The latest release, ChemOffice 2000 contains Chem3D 5.0 which has the ability to compute and map several properties (e.g. electrostatic potential, charge density, etc.) onto 3D surfaces using colors and color intensity to visually depict the property being examined. Chem3D can also compute and map partial atomic charges. ChemDraw 5.0 has added AutoNom 2.1 and Name=Struct features for naming structures and converting a name to a structure. ChemDraw can also depict proton and 13C NMR line spectra. ChemFinder 5.0 houses the rapidly expanding ChemInfo databases including ChemACX, the Available Chemical Xchange with over 200 chemical catalogs. Available for both Windows and Macintosh.

WinMOPAC

WinMOPAC from Fujitsu has expanded its capabilities to d-orbitals for column V, VI, and VII elements. Localized molecular orbital calculations provide analysis of large molecules and proteins. MOPAC continues to be the industry standard for semi-empirical calculations.

Gaussian 98

Gaussian 98 from Gaussian, Inc. is the mostly widely used ab initio program. Some of the newer features allow the user to optimize large molecules by a layered approach of analysis. It can also predict Raman and IR spectral intensities and NMR shifts. Gaussian 98 is available for workstations and Windows machines. Chem3D can create job files for either platform and visualize the results.

Conformer

Conformer from Princeton Simulations brings conformational analysis to its most elegant level as an add-on for Chem3D. The conformational search can now be extended to complex ring structures via the . ring-fold method.. Post-search analysis is one of the strongest points of the program. Available for both Windows and Macintosh. A free demo can be obtained from ChemStore.Com.

CAChe

CAChe from Oxford Molecular provides computational insight into structure, properties, and reactivities. The newest release has enhanced ZINDO capabilities, a crystal structure builder for the Windows version, RMS calculations of superimposed molecules, and a copy and paste interface with ChemDraw. The semi-empirical method, ZINDO, provides spectral prediction. It is probably the most capable program for the desktop for handling inorganics and organometallics. Available for both Windows and Macintosh.

Alchemy 2000

Alchemy 2000 by Tripos is a fairly comprehensive modeling package. This self-contained program allows you to sketch the molecule, view it in 3D, optimize its structure through molecular mechanics or semi-empirical methods, and perform further analysis. The program allows the user to perform molecular dynamics, conformational searching, vibrational motion viewing, and more. Available for Windows platforms only.

SciQSAR and SciLogP

SciQSAR and SciLogP from SciVision use powerful 2D and 3D molecular descriptors to create regression equations that allow the user to do accurate QSAR analyses and property predictions. The user has complete control over which descriptors and structures are used to create the QSAR study. Both programs interface directly with Chem3D and Alchemy 2000 for Windows machines.

Advanced Chemistry Development

Advanced Chemistry Development has several programs for predictions of properties. These include programs for NMR prediction, spectral prediction of UV, IR and Mass Spec. They also have a systematic chemical naming program. All programs are for Windows machines.

Chemical Inventory Systems

Index cards and logbook record keeping have become passe with the advent of chemical and equipment inventory tracking software. Coupled with this can be an automated ordering system for chemical supplies and equipment. Such systems have had major impact on the role of purchasing agents and laboratory managers.

CIS Pro

CIS Pro from ChemSW supports both network and stand alone systems. The system can track chemicals and supplies, shipments, formulations, locations, MSDS information and user-defined properties of the chemicals. There is a bar code reader system that can be added to the software to speed the data entry process.

ChIM

ChIM from Vertere is a full-featured chemical inventory management system. It provides total control by interfacing with purchasing, accounting, regulatory and research departments. Included with the package are bar-coding with scanners, MSDS database organization, a multi-level security system and report generation.

Mathematics and Statistics

There are a huge number of math-related programs; too many to mention here. These programs have taken away the slide rule and calculator from the chemist and replaced them with the mouse and keyboard. Creation of presentation quality figures and tables are no longer restricted to audio-visual departments and graphics companies.

SigmaPlot, SigmaStat, TableCurve

SPSS. s product line includes SigmaPlot, SigmaStat, SigmaScan and TableCurve 2D and 3D. This is probably the most comprehensive set of Windows based mathematical/statistics packages available. If you can. t find what you are looking for among their programs it probably doesn. t exist.

MathType

MathType from Design Science is a very affordable . math-word processing. program for both Windows and Macintosh. It is an advanced version of the standard equation editors found in most word processing packages.

CardPro from S-Matrix

CardPro from S-Matrix specializes in experimental design and sampling analysis techniques, which should be useful for scientists working with multiple factored experiments and production processes.

Summary

I have only scratched the surface of the many scientific software packages available to the chemist to facilitate the process of planning experiments, storing and analyzing results and reporting the findings in presentation quality fashion. You can find most of these programs and many, many more at ChemStore.Com with more detailed descriptions of their features.