Force Fields For Use Research Articles

ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

26] Simple force field for study of peptide and protein conformational properties

Publisher Summary This chapter discusses the simple force field for use in the study of peptide and protein conformation. Both backbone and side chains have been examined and are shown to be in generally good agreement with properties derived from high-resolution protein structures. CRASS, a simple force field for use in the study of conformational properties of peptides and proteins is derived. CRASS explores the conformational properties of small peptides. To keep CRASS simple, the united atoms approximation is adopted: nonpolar hydrogens are not included explicitly; instead, the radii of the atoms to which they are attached are enlarged accordingly. A set of vander Waals radii, Ri, is determined from a survey of small molecule crystal structures. CRASS vander Waals radii and atom (and group) types are listed. The residue is simulated in the center of flexible blocked tripeptides using the CRASS force field at a temperature of 298 K. The simulated serine and threonine distributions do not agree with those observed in proteins, presumably because electrostatic interactions are ignored in CRASS. In particular, within CRASS it is possible for two atoms of like charge (for example, two oxygen) to interact favorably at short distances.

Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules

AbstractA new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross‐term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.

Comparative molecular mechanics study of the low-spin nickel(II) complexes of an extended series of tetraaza macrocycles

Molecular mechanics calculations of metal complex structures are often not straight forward because of uncertainties concerning the appropriate force-field parameters for structural elements involving the metal. A systematic study aimed at extending the Allinger MM2 force field for use with N 4 -macrocyclic complexes of low-spin Ni(II) is reported. The application of the extended force field to the re-examination of the configurational isomers of [Ni(cyclam)] 2+ and their N,N,N,N-tetramethylated derivatives is reported