A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relationship between bond distance and bond order on one hand and between bond order and bond energy on the other hand that leads to proper dissociation of bonds to separated atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become constant as Rij → 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chemical calculations on bond dissociation and reactions of small molecules plus heat of formation and geometry data for...

http://www.wag.caltech.edu/publications/sup/pdf/471.pdf

ReaxFF: A Reactive Force Field for Hydrocarbons

This article introduces MMFF94, the initial published version of the Merck molecular force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodology employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and experimental data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in molecular-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small molecules in a combined “organic/protein” force field that is equally applicable to proteins and other systems of biological significance. A second distinguishing feature is that the core portion of MMFF94 has primarily been derived from high-quality computational data—ca. 500 molecular structures optimized at the HF/6-31G* level, 475 structures optimized at the MP2/6-31G* level, 380 MP2/6-31G* structures evaluated at a defined approximation to the MP4SDQ/TZP level, and 1450 structures partly derived from MP2/6-31G* geometries and evaluated at the MP2/TZP level. A third distinguishing feature is that MMFF94 has been parameterized for a wide variety of chemical systems of interest to organic and medicial chemists, including many that feature frequently occurring combinations of functional groups for which little, if any, useful experimental data are available. The methodology used in parameterizing MMFF94 represents a fourth distinguishing feature. Rather than using the common “functional group” approach, nearly all MMFF parameters have been determined in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addition, MMFF94 reproduces experimental bond lengths (0.014 A root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm−1 rms), conformational energies (0.38 kcal/mol/rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermolecular interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field. © 1996 John Wiley & Sons, Inc.

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

Automatic atom type and bond type perception in molecular mechanical calculations.

In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges. This approach uses the simple "generic" force field model (Parm94), and attempts to add a minimal number of extra Fourier components to the torsional energies, but doing so only when there is a physical justification. The results are quite encouraging, not only for the 34-molecule set that has been studied by both the highest level ab initio model (GVB/LMP2) and experiment, but also for the 55-molecule set for which high-quality experimental data are available. Considering the 55 molecules studied by all the force field models for which there are experimental data, the average absolute errors (AAEs) are 0.28 (this model), 0.52 (MM3), 0.57 (CHARMm (MSI)), and 0.43 kcal/mol (MMFF). For the 34-molecule set, the AAEs of this model versus experiment and ab initio are 0.28 and 0.27 kcal/mol, respectively. This is a lower error than found with MM3 and CHARMm, and is comparable to that found with MMFF (0.31 and 0.22 kcal/mol). We also present two examples of how well the torsional parameters are transferred from the training set to the test set. The absolute errors of molecules in the test set are only slightly larger than in the training set (differences of <0.1 kcal/mol). Therefore, it can be concluded that a simple "generic" force field with a limited number of specific torsional parameters can describe intra- and intermolecular interactions, although all comparison molecules were selected from our 82-compound training set. We also show how this effective two-body

/pdf/how-well-does-a-restrained-electrostatic-potential-resp-5fgytd7p7h.pdf

How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules

Molecular mechanics. The MM3 force field for hydrocarbons. 1

The van der Waals' potentials used for interactions between carbon and hydrogen in both aliphatic and aromatic systems have been improved from those available in MM2, and the new values are used in MM3. The atoms are slightly larger and somewhat softer than they were with MM2. These values were optimized by fitting to the crystal parameters (six cell constants) and the heats of sublimation for the normal alkanes from C6 to C,,, plus C,2, and also diamond, graphite, benzene, biphenyl, and hexamethylbenzene, in addition to fitting structural and energy data on congested molecules as reported earlier. The parameters developed give good crystal structures and heats of sublimation for these molecules. Biphenyl is calculated to be twisted about 40' in the gas phase, but lattice forces cause it to flatten into a planar conformation in the crystal.

Jenn Huei Lii

Papers

Molecular mechanics. The MM3 force field for hydrocarbons. 1

Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons

Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics

A molecular mechanics force field (MM3) for alcohols and ethers

Finite Td symmetry models for diamond: from adamantane to super-adamantane (C35H36)