SYBYL Molecular Modelling System

Sybyl Molecular Modeling System (version 6.9.2) Tripos Inc. St. Louis MO. 

SYBYL molecular modeling system version 6.4, Tripos Associates Inc, 1699 South Hanley Road, St. Louis, MO... 

SYBYL Molecular Modeling System, software available from Tripos Inc., 1699 S. Hanley Rd., St. Louis, MO 63144. 

Anon., Manual to SYBYL Molecular Modeling Software. Tripos Associates, St. Louis, Missouri, 1989 N. Van Opdenbosch, R. Cramer III, and F. F. Giarrusso,/. Mol. Graphics, 3,110 (1985). SYBYL The Integrated Molecular Modeling System. 

SYBYL molecular mechanics is completely unsatisfactory for describing conformational energy differences in acyclic systems, and should not be employed for this purpose. On the other hand, the MMFF mechanics model provides a good account of all systems examined. In fact, the performance of MMFF is significantly better than any of the semi-empirical models, and in the same league as the best of the Hartree-Fock, local density, density functional and MP2 models (see discussion following). 

Similar comments apply to cyclic systems (Table 8-2). SYBYL molecular mechanics is completely unsatisfactory for establishing relative conformer stabilities, while MMFF appears to be quite well suited for this purpose. The only unsatisfactory case for the MMFF model is 2-chlorotetrahydropyran, where the noted preference for an axial chlorine (usually attributed to the anomeric effecF) is not reproduced. Caution should be exercised in the application of MMFF to carbohydrates where the anomeric effect may lead to significant conformational preferences. 

All of these programs are available for Unix operating system. Most of the Windows versions are incorporated into commercial molecular modeling packages such as MM in Chem3D of CambridgeSoft (http //www.camsoft.com), AMBER and CHARMm in HyperChem of HyperCube (http //www.hyper.com), and SYBYL... 

For those with an interest in true 3-D structures, we have also a number of user-friendly molecular modeling packages available on our system, among them SYBYL, from Tripos Associates, Inc., and Macromodel, from Prof. Clark Still, Columbia University. Both can be accessed via the Versaterm Pro emulation software on the Macintosh, as well as from intermediate and high-performance workstations like the NEC-APC and the Evans and Sutherland PS-300. These specialist packages are maintained by our Drug Design department, who help out users with the specifics of the software. 

A module of the SYBYL system (see entry under molecular modelling) which characterizes molecules by the calculation of interaction energies of probes at grid points in three-dimensional space. Analysis by PLS and factor analysis. 

Theoretical models include those based on classical (Newtonian) mechanical methods—force field methods known as molecular mechanical methods. These include MM2, MM3, Amber, Sybyl, UFF, and others described in the following paragraphs. These methods are based on Hook s law describing the parabolic potential for the stretching of a chemical bond, van der Waal s interactions, electrostatics, and other forces described more fully below. The combination assembled into the force field is parameterized based on fitting to experimental data. One can treat 1500-2500 atom systems by molecular mechanical methods. Only this method is treated in detail in this text. Other theoretical models are based on quantum mechanical methods. These include ... 

Molecular mechanics models differ both in the number and specific nature of the terms which they incorporate, as well as in the details of their parameterization. Taken together, functional form and parameterization, constitute what is termed a force field. Very simple force fields such as SYBYL, developed by Tripos, Inc., may easily be extended to diverse systems but would not be expected to yield quantitatively accurate results. On the other hand, a more complex force field such as MMFF94 (or more simply MMFF), developed at Merck Pharmaceuticals, while limited in scope to common organic systems and biopolymers, is better able to provide quantitative accounts of molecular geometry and conformation. Both SYBYL and MMFF are incorporated into Spartan. 

The MMFF molecular mechanics model provides an excellent account of C-N and C-0 bond distances. SYBYL also presents a credible account, although bond lengths for some systems are significantly in error. MMFF is clearly the better choice. 

---