The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, a...

https://sakai.rutgers.edu/access/content/user/kparis/biomaps_513_references/02_B_01_JACS118_11225_OPLS.pdf

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

New materials capable of storing hydrogen at high gravimetric and volumetric densities are required if hydrogen is to be widely employed as a clean alternative to hydrocarbon fuels in cars and other mobile applications. With exceptionally high surface areas and chemically-tunable structures, microporous metal–organic frameworks have recently emerged as some of the most promising candidate materials. In this critical review we provide an overview of the current status of hydrogen storage within such compounds. Particular emphasis is given to the relationships between structural features and the enthalpy of hydrogen adsorption, spectroscopic methods for probing framework–H2 interactions, and strategies for improving storage capacity (188 references).

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Hydrogen storage in metal–organic frameworks

MNDO/AM1‐type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO‐PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.

Optimization of parameters for semiempirical methods II. Applications

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.

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A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

SUPCRT92: a software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000 ° C

A fundamental equation of state has been formulated for heavy water in the form Ψ = Ψ(p,T) in which Ψ = Helmholtz free energyp = density T = thermodynamic temperature. The complete range of single phase states in the range up to 100 MPa and 600 °C is covered by a single equation which is fitted both to P v T values, for saturated and unsaturated states, and to enthalpy values for saturation states only. The equation is constrained to fit the critical point conditions determined by Blank. It represents all thermodynamic properties of D2O, in the above range of states, within what is believed to be the accuracy of the experimental data.

A Fundamental Equation of State for Heavy Water

Virial equations for light and heavy water

A study has been made of the saturation properties of D2O from the triple point temperature to 325 °C, in the light of information on the saturation properties of H2O. Saturated liquid volumes have been determined by extrapolation to saturation pressure of relatively abundant liquid phase data (corrected to 100% D2O). Saturated liquid enthalpy has been determined by extrapolation of liquid phase specific heat data, and integration along the saturation line, allowing for the compressibility effect. Saturated vapor volumes have been determined by use of an extended virial equation formulated for H2O and corrected for D2O. Saturated vapor enthalpies have been determined by use of the Clapeyron equation, and compared to vapor enthalpies calculated from the extended virial equation. Saturated liquid and vapor volumes have been extrapolated to the critical temperature to allow an inference of the critical density.

R. D. Chris MacMillan

Papers

A Fundamental Equation of State for Heavy Water

Virial equations for light and heavy water

Saturation states of heavy water

Erratum: A Fundamental Equation of State for Heavy Water [J. Phys. Chem. Ref. Data 11, 1 (1982)]