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

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

The fate of chemical and radioactive wastes in the environment is related to the ability of natural phases to attenuate and immobilize contaminants through chemical sorption and precipitation processes. Our understanding of these complex processes at the atomic level is provided by a few experimental and analytical methods such as X-ray absorption and NMR spectroscopies. However, due to complexities in the structure and composition of clay and other hydrated minerals, and the inherent uncertainties of the experimental methods, it is important to apply theoretical molecular models for a fundamental atomic-level understanding, interpretation, and prediction of these phenomena. In this effort, we have developed a general force field, CLAYFF, suitable for the simulation of hydrated and multicomponent mineral systems and their interfaces with aqueous solutions. Interatomic potentials were derived from parametrizations incorporating structural and spectroscopic data for a variety of simple hydrated compounds. A...

Molecular Models of Hydroxide, Oxyhydroxide, and Clay Phases and the Development of a General Force Field

The ability of simple potential functions to reproduce accurately the density of liquid water from −37 to 100 °C at 1 to 10 000 atm has been further explored. The result is the five-site TIP5P model, which yields significantly improved results; the average error in the density over the 100° temperature range from −37.5 to 62.5 °C at 1 atm is only 0.006 g cm−3. Classical Monte Carlo statistical mechanics calculations have been performed to optimize the parameters, especially the position of the negative charges along the lone-pair directions. Initial calculations with 216 molecules in the NPT ensemble at 1 atm focused on finding a model that reproduced the shape of the liquid density curve as a function of temperature. Calculations performed for 512 molecules with the final TIP5P model demonstrate that the density maximum near 4 °C at 1 atm is reproduced, while high-quality structural and thermodynamic results are maintained. Attainment of high precision for the low-temperature runs required sampling for more than 1 billion Monte Carlo configurations. In addition, the dielectric constant was computed from the response to an applied electric field; the result is 81.5±1.5 at 25 °C and the experimental curve is mirrored from 0–100 °C at 1 atm. The TIP5P model is also found to perform well as a function of pressure; the density of liquid water at 25 °C is reproduced with an average error of ∼2% over the range from 1 to 10 000 atm, and the shift of the temperature of maximum density to lower temperature with increasing pressure is also obtained.

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A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

Classical molecular dynamics computer simulations have been used to investigate the thermodynamics and kinetics of sodium chloride association in polarizable water. The simulations make use of the three‐site polarizable water model of Dang [J. Chem. Phys. 97, 2659 (1992)], which accurately reproduces many bulk water properties. The model’s static dielectric constant and relaxation behavior have been calculated and found to be in reasonable agreement with experimental results. The ion–water interaction potentials have been constructed through fitting to both experimental gas‐phase binding enthalpies for small ion–water clusters and to the measured structures and solvation enthalpies of ionic solutions. Structural properties and the potential of mean force for sodium chloride in water have been calculated. In addition, Grote–Hynes theory has been used to predict dynamical features of contact ion‐pair dissociation. All of the calculated ionic solution properties have been compared with results from simulatio...

Computer simulations of NaCl association in polarizable water

The molecular dynamics computer simulation technique is used to develop a rigid, four-site polarizable model for water. The suggested model reasonably describes the important properties of water clusters, the thermodynamic and structuralproperties of the liquid and the liquid/vapor interface of water. The minimum energy configurations and the binding energies for these clusters are in reasonable agreement with accurate electronic structure calculations. The model predicts that the water trimer, tetramer, and pentamer have cyclic planar minimum energy structures. A prismlike structure is predicted to be lowest in energy for the water hexamer, and a cagelike structure is the second lowest in energy, with an energy of about 0.2 kcal/mol higher than the prismlike structure. The results are consistent with recent quantum Monte Carlo simulations as well as electronic structure calculations. The computed thermodynamic properties for the model, at room temperature, including the liquid density, the enthalpy of vaporization, as well as the diffusion coefficient, are in excellent agreement with experimental values. Structuralproperties of liquidwater, such as the radial distribution functions, neutron, and x-ray scattering intensities, were calculated and critically evaluated against the experimental measurements. In all cases, we found the agreement between the observed data and the computed properties to be quite reasonable. The computed density profile of the water’s liquid/vapor interface shows that the interface is not sharp at a microscopic level and has a thickness of 3.2 A at 298 K. These results are consistent with those reported in earlier work on the same systems. The calculated surface tension at room temperature is in reasonable agreement with the corresponding experimental data. As expected, the computed average dipole moments of water molecules near the interface are close to their gas phase values, while water molecules far from the interface have dipole moments corresponding to their bulk values.

Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials

We have performed extensive classical molecular dynamics simulations to examine the mechanism and thermodynamics for ion selectivity of 18-crown-6 ether in aqueous solutions. We have computed the free energy profiles or potentials of mean force and the corresponding binding free energies for M{sup +}:18-crown-6 (M{sup +} = K{sup +}, Na{sup +}, Rb{sup +}, Cs{sup +}) complexation in water. To the best of our knowledge, the present work is the first to employ the potential of mean force approach to the evaluation of crown ether selectivity in an aqueous solution. The resultant potentials of mean force indicate that minima free energy surfaces for K{sup +} and Na{sup +} are located at the crown ether center-of-mass. A well-defined second minimum is also observed in the potential of mean force of the Na{sup +}:18-crown-6 complex in water. It appears that K{sup +} is selected over Na{sup +} because of the greater free energy penalty associated with displacing water molecules from Na{sup +} as it approaches the crown ether. This leads to a substantial increase in the activation free energy and a decrease in the corresponding binding free energy for Na{sup +}:18-crown-6 complexation as compared to K{sup +}:18-crown-6. The selection of K{sup +} overmore » Rb{sup +} and Cs{sup +} is due to the size of the cation relative to that of the crown ether cavity. 26 refs., 11 figs., 2 tabs.« less

Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study

Ion solvation in polarizable water: molecular dynamics simulations

Implementation of nonadditive intermolecular potentials by use of molecular dynamics: development of a water-water potential and water-ion cluster interactions

Liem X. Dang

Papers

Computer simulations of NaCl association in polarizable water

Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials

Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study

Ion solvation in polarizable water: molecular dynamics simulations

Implementation of nonadditive intermolecular potentials by use of molecular dynamics: development of a water-water potential and water-ion cluster interactions