Liquids, molecular mechanics potentials

Tunon I, Martins-Costa MTC, Millot C, Ruiz-Lopez MF. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potential I. Proton transfer in strongly H-bonded complexes. J Chem Phys 1997 106 3633-3642. 

Combined Quantum Mechanical and Molecular Mechanical Potentials Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Continuum Solvation Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field MNDO Monte Carlo Simulations for Liquids Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mechanics/Molecular Mechanics (QM/MM) Self-consistent Reaction Field Methods Self-consistent Reaction Field Methods Cavities Solvation Modeling TURBOMOLE. 

Molecular mechanics methods have been used particularly for simulating surface-liquid interactions. Molecular mechanics calculations are called effective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force held is parameterized correctly. 

OPES (optimized potentials for liquid simulation) a molecular mechanics force field... 

The purpose of this chapter is to describe these experimental approaches for understanding the molecular mechanism of the membrane potentials for ionophore-incorpo-rated liquid membrane ion-selective electrodes. 

Wu Y, Yang ZZ (2004) Atom-bond electronegativity equalization method fused into molecular mechanics. II. A seven-site fluctuating charge and flexible body water potential function for liquid water. J Phys Chem A 108(37) 7563-7576... 

Here we present and discuss an example calculation to make some of the concepts discussed above more definite. We treat a model for methane (CH4) solute at infinite dilution in liquid under conventional conditions. This model would be of interest to conceptual issues of hydrophobic effects, and general hydration effects in molecular biosciences [1,9], but the specific calculation here serves only as an illustration of these methods. An important element of this method is that nothing depends restric-tively on the representation of the mechanical potential energy function. In contrast, the problem of methane dissolved in liquid water would typically be treated from the perspective of the van der Waals model of liquids, adopting a reference system characterized by the pairwise-additive repulsive forces between the methane and water molecules, and then correcting for methane-water molecule attractive interactions. In the present circumstance this should be satisfactory in fact. Nevertheless, the question frequently arises whether the attractive interactions substantially affect the statistical problems [60-62], and the present methods avoid such a limitation. 

The non-collective motions include the rotational and translational self-diffusion of molecules as in normal liquids. Molecular reorientations under the influence of a potential of mean torque set up by the neighbours have been described by the small step rotational diffusion model.118 124 The roto-translational diffusion of molecules in uniaxial smectic phases has also been theoretically treated.125,126 This theory has only been tested by a spin relaxation study of a solute in a smectic phase.127 Translational self-diffusion (TD)29 is an intermolecular relaxation mechanism, and is important when proton is used to probe spin relaxation in LC. TD also enters indirectly in the treatment of spin relaxation by DF. Theories for TD in isotropic liquids and cubic solids128 130 have been extended to LC in the nematic (N),131 smectic A (SmA),132 and smectic B (SmB)133 phases. In addition to the overall motion of the molecule, internal bond rotations within the flexible chain(s) of a meso-genic molecule can also cause spin relaxation. The conformational transitions in the side chain are usually much faster than the rotational diffusive motion of the molecular core. 

One of the important electrochemical interfaces is that between water and liquid mercury. The potential energy functions for modeling liquid metals are, in general, more complex than those suitable for modeling sohds or simple molecular liquids, because the electronic structure of the metal plays an important role in the determination of its structure." However, based on the X-ray structure of liquid mercury, which shows a similarity with the solid a-mercury structure, Heinzinger and co-workers presented a water/Hg potential that is similar in form to the water/Pt potential described earlier. This potential was based on quantum mechanical calculations of the adsorption of a water molecule on a cluster of mercury atoms. ... 

The approach with the partitioning of the system into a QM and a classical molecular mechanical (MM) part, thus usually termed hybrid QM/MM procedure, provides a reasonable reduction of the computational effort by restricting the time-consuming QM calculation of forces to the most relevant part of the liquid system. The main error sources in this approach are a too small choice of the QM region, an inadequate level of theory for the QM calculation, the choice of suitable potentials for the MM part of the system, and smooth transitions of particles between QM and MM region. In conventional QM/MM procedures, the whole system is first evaluated at MM level and then corrected by the QM data. This means that classical potential functions (with all their problems and difficulty of construction) are needed for all components of the system. A recently developed methodology can reduce the need for such potentials to the solvent only, as will be outlined below. 

Empirical or molecular mechanics (MM) potentials or force fields are traditionally the ones used for MC and MD simulations of large condensed phase systems, such as liquids or proteins. A typical force field is a sum of... 

Molecular quantum potential and non-local interaction depend on molecular size and the nature of intramolecular cohesion. Macromolecular assemblies such as polymers, biopolymers, liquids, glasses, crystals and quasicrystals are different forms of condensed matter with characteristic quanmm potentials. The one property they have in common is non-local long-range interaction, albeit of different intensity. Without enquiring into the mechanism of their formation, various forms of condensed matter are considered to have well-defined electronic potential energies that depend on the nuclear framework. A regular array of nuclei in a structure such as diamond maximizes cohesive interaction between nuclei and electrons, precisely balanced by the quantum potential, almost as in an atom. 

Lii J-H and N L Allinger 1989. Molecular Mechanics. The MM3 Force Field for Hydrocarbons 2 Vibrational Frequencies and Thermod5mamics Journal of the American Chemical Society 111-8566-8582 London F 1930 Zur Theori und Systematik der Molekularkrafte Zeiischrift fur Physik 63 245-279 Luckhurst G R, R A Stephens and R W Phippen 1990 Computer Simulation Studies of Anisotropic Systems XIX Mesophases Formed by the Gay-Beme Model Mesogen Liquid Crystals 8-451-464 Luque F J, F lias and M Orozco 1990 Comparabve Study of the Molecular Electrostatic Potential Obtained from Different Wavefunctions - Reliability of the Semi-Empirical MNDO Wavefunction Journal of Computational Chemistry 11-416-430. 

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