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

Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

The pronounced glass-forming tendencies of alloys of S and Se with Ge and/or As are discussed topologically. An atomic model is introduced which for predominantly covalent forces constitutes the first microscopic realization of Kauzmann's description of the glass transition as an entropy (not enthalpy or volume) crisis. The model contains no adjustable parameters and predicts the glass-forming tendency as a function of composition in excellent agreement with experiment. Several related properties, including phase diagrams, radial distribution functions and crystal structures are discussed in the context of chemical bonding and short-range order in the non-crystalline covalent networks of these materials.

Topology of covalent non-crystalline solids I: Short-range order in chalcogenide alloys

A 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 I1 force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each

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

A vibrational and attendant conformational analysis of the liquid n‐paraffins and molten polyethylene is presented. For the purposes of the analysis a valence force field was derived which is applicable to both planar and nonplanar chains. The force field was evaluated from observed frequencies of trans (T) and gauche (G) n‐C4H10; TT and GT n‐C5H12; TTT, GTT, and TGT n‐C6H14; and (T)∞ polyethylene, all of whose infrared spectra were assigned in detail. Infrared spectra of the liquid‐n‐paraffins n‐C4H10 through n‐C17H36 were measured at room temperature and n‐C4H10 through n‐C12H26 also at a temperature just above their melting point. Frequencies and normal coordinates were calculated for the extended forms and for forms having one gauche bond of n‐C4H10 through n‐C8H18. These quantities were also calculated for the conformations of n‐C5H12 through n‐C7H16 having two gauche bonds and for the nonplanar but regular conformations (TG)∞ and (G)∞ of polyethylene. Some bands attributable to forms of n‐C5H12 and ...

R.G. Snyder

Papers

Vibrational analysis of the n-paraffins—II