Molecular mechanics programs

Very recently, we have developed and incorporated into the CHARMM molecular mechanics program a version of LN that uses direct-force evaluation, rather than linearization, for the fast-force components [91]. The scheme can be used in combination with SHAKE (e.g., for freezing bond lengths) and with periodic boundary conditions. Results for solvated protein and nucleic-... 

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

The following are programs created specifically for force field based simulations. There are also molecular mechanics programs bundled with the Spartan, Gaussian, and Hyperchem products discussed previously in this appendix. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

Once requiring minicomputers and worksta tions many molecular mechanics programs are avail able for personal computers The information that strain energy calculations can provide is so helpful... 

The first widely used molecular mechanics program was developed by Professor N. L. Allinger of the University of Georgia and was known in its various versions as MM2, MM3, and so on. They have been refined to the extent that many structural features can be calculated more easily and more accurately than they can be measured experimentally. 

All the structural models in this book are computer-drawn. To make sure they accurately portray bond angles, bond iengtiis, torsional interactions, and steric interactions, the most stable geometry of each molecule has been calculated on a desktop computer using a commercially available molecular mechanics program based on work by N. L. Allinger of the University of Georgia. 

The intramolecular Diels-Alder reaction of 23-1 carried out under LiC104 catalysis is rather nonselective. Use a molecular mechanics program to assess the energies of the competing TSs and products. Are the results in agreement with the experimental outcome ... 

The course of stereospecific olefin polymerization was studied by using the molecular mechanics programs, MM-2 and Biograph, based on the optimized geometries of the ethylene complex and the transition state [13,203]. Interestingly, the steric interaction at the transition state mainly controls the stereochemistry in polymerization, which proceeds specifically isotactic or syndiotactic depending on the kind of catalyst. 

There are many different molecular mechanics force fields available. Many of them were originally developed in academic laboratories to solve specific problems. For example, some were designed to handle small molecules while others were developed to deal with protein structures. Today, the original demarcation between macromolcules and small molecules has become blurred, and they now are commercially available. Initially, many molecular mechanics programs were distributed at nominal costs, but due to the lack of federal funding for most molecular mechanics... 

For many purposes and for medium to large molecules, molecular mechanics is clearly the method of choice. Actually, the molecular mechanics programs are current best-sellers of QCPE, and a surprisingly larger number of applications have been published in every field of chemistry, especially in stereochemistry. 

The reference 4 authors discuss criteria that should be applied when describing molecules with these molecular mechanics programs. Some of these are as follows (1) Check the error file for interactions not in the parameter set, because some programs will assign a force constant of zero to unrecognized atom types (2) check all interactions generating >5 kJ/mol of strain to determine, for instance, whether that bond or angle really is that strained or whether there is a parameterization or molecular structure problem and (3) check the... 

The theoretician uses these programs to predict structure, either of single molecules or of assemblages of molecules, using X-ray or NMR data, when available, to test his predictions (13-15). It has been known for a long time that even the earlier molecular mechanics programs can predict the structures of certain types of molecules with excellent reliability. For the cyclic alkanes, an accuracy comparable to that of the best X-ray crystal structure analysis can be obtained. In fact, the method is more widely applicable since neither compound nor crystals are necessary (1 . 

Conformational Anafysis of a Disaccharide (Cellobiose) mth the Molecular Mechanics Program (MM2)... 

The basis for the determination of solution conformation from NMR data lies in the determination of cross relaxation rates between pairs of protons from cross peak intensities in two-dimensional nuclear Overhauser effect (NOE) experiments. In the event that pairs of protons may be assumed to be rigidly fixed in an isotopically tumbling sphere, a simple inverse sixth power relationship between interproton distances and cross relaxation rates permits the accurate determination of distances. Determination of a sufficient number of interproton distance constraints can lead to the unambiguous determination of solution conformation, as illustrated in the early work of Kuntz, et al. (25). While distance geometry algorithms remain the basis of much structural work done today (1-4), other approaches exist. For instance, those we intend to apply here represent NMR constraints as pseudoenergies for use in molecular dynamics or molecular mechanics programs (5-9). 

In order to incorporate distance constraints derived from two-dimensional crossrelaxation data in a molecular mechanics program, we have chosen to treat the constraints as a pseudoenergy function. This function should ideally reflect the distance dependence of cross relaxation rates. Previously, we had proposed a function of the form (40) ... 

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