Turning Structures Into Gold

A lchemy 2000 (version 2.05) is a comprehensive molecular modeling program with several advanced tools for real-time graphics visualization and computation of small molecules, material polymers, and biopolymers. It can create molecular structures for export into various formats, making it easy to transfer molecular structures between modeling programs. Alchemy 2000 also has five optional application modules: SciQSAR (quantitative structure-activity or structure-property relationships of small molecules), SciProtein [builds and views proteins in three-dimensional (3D) and effectively predicts secondary structure for a wide variety of biological proteins], SciPolymer (for de novo design and prediction of material polymer properties), SciLogP (predicts small molecules' logP values—a measure of hydrophobicity), and ChemPrint Pro (2D chemical drawings). Alchemy 2000 can download molecules for display directly from the Internet; build, modify, analyze, and convert 2D chemical drawings of molecules into their accurate 3D representations; minimize energy and optimizing geometry; predict molecular dynamics under controlled temperatures; and calculate molecular properties such as dipole moment, van der Waals volume, and surface area. Quantitative Structure Activity Relationship (QSAR) is an important computational analysis tool for medicinal chemists who design small molecules. The SciQSAR module of Alchemy 2000 designs and predicts the activities and properties of new compounds. It uses several expandable descriptors (e.g., logP, dipole moment, and volume) and can perform automated analysis of hundreds of compounds. SciProtein provides easy tools for building protein and peptide primary and secondary structures that can be displayed with Alchemy 2000. This module allows sequence similarity searching and motif identification from 3D structures in a database. Hydropathy, antigenicity, and mutability are generated by the module and are useful tools for researchers to investigate protein structure and function. The SciPolymer module can be used to design polymers based on monomeric units and to predict their properties (e.g., cohesive, electrical, optical, and thermal). It has an extensive polymer-property database of 659 polymers, which can be used for the development of the next generation of polymers. Of all the optional modules for Alchemy 2000, SciPolymer has the most thoroughly designed interactive database. SciLogP has five built-in regression equations for the prediction of logP values (octanol-water partition coefficients) that can be used with the internal regression analyzer. Overall, Alchemy 2000 is useful for building and visualization of small and large molecules (e.g., proteins and polymers) and could be used effectively to teach chemistry in classrooms. Serious drawbacks include the fixed setting of force fields and the absence of graphic display of molecular orbitals, but the integration of the optional application modules (SciQSAR, SciProtein, SciPolymer, and SciLogP) is a strength. Alchemy 2000 and the application modules run under Windows 95, 98, or NT. Alchemy 2000 SciVision200 Burlington, MA $995 (commercial) $695 (academic) SciQSAR $650 SciProtein $595 SciPolymer $995 SciLogP $495 ChemPrint Pro $150 800-861-6274