Molecular modeling packages computational application

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

Currently, a large variety of flavors of the GB model are available in many molecular simulation packages. The vast majority, if not all, of these models share the same foundation—Eq. (3)— but may differ substantially in the way the effective radii are computed. The algorithmic simplicity and reasonable accuracy of the GB approximation, combined with its availability in popular modeling packages, have made it the current "workhorse" in many practical applications of the implicit solvent methodology. 

The information gleaned by these techniques for a wide range of atomic and molecular interactions is contained in computer modeling packages, such as MSI which are now widely used in dmg design and in many other applications. Much information can be gathered on web sites such as that at the Royal Institution in London. This information can then be used to put together... 

Computer programs dedicated to QSAR analyses or with a QSAR component have also been used to assist in the development of suitable QSARs for various applications. Using one such package, Samuel et al. were able to generate comparative molecular field analysis (CoMFA) models to predict the cytotoxicity of a series of dibenzyltin(IV) derivatives against two human cancer cell lines, MCF-7, a mammary carcinoma, and WiDr, a colon carcinoma. 

There are many different pieces of code available for molecular mechanics, ranging from the simple, such as MM2, to the elaborate, such as Cerius S YBYL, Spartan, and HyperChem. The code chosen for a particular model of catalytic processes depends on two factors (1) the complexity of the system that is to be studied, and (2) the amount of computer expertise available. Complicated structures, such as surfaces and zeolites, generally require specialized software packages for their visualization typically workers use commercial code with perhaps minor modifications. Simpler systems, such as modeling vanadium oxo species, are amenable to study using simpler codes, such as MM2, that are customized to suit the specific needs of the research group. It should be noted that the various available packages employ different force assumptions and some force fields are more suitable to one kind of application than to another (see Chapter 2). 

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