Liquids, molecular mechanics

Nearly all liquid simulations have been done using molecular mechanics force fields to describe the interactions between molecules. A few rare simulations have been completed with orbital-based methods. It is expected that it will still be a long time before orbital-based simulations represent a majority of the studies done due to the incredibly large amount of computational resources necessary for these methods. 

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... 

This article reviews progress in the field of atomistic simulation of liquid crystal systems. The first part of the article provides an introduction to molecular force fields and the main simulation methods commonly used for liquid crystal systems molecular mechanics, Monte Carlo and molecular dynamics. The usefulness of these three techniques is highlighted and some of the problems associated with the use of these methods for modelling liquid crystals are discussed. The main section of the article reviews some of the recent science that has arisen out of the use of these modelling techniques. The importance of the nematic mean field and its influence on molecular structure is discussed. The preferred ordering of liquid crystal molecules at surfaces is examined, along with the results from simulation studies of bilayers and bulk liquid crystal phases. The article also discusses some of the limitations of current work and points to likely developments over the next few years. 

Molecular mechanics force fields have largely been parameterised using the best available data from the gas phase and (in some cases) from liquid phase or solution data. The question therefore arises as to how applicable molecular mechanics force fields are to predicting structures of molecules in the liquid crystal phase. There is now good evidence from NMR measurements that the structure of liquid crystal molecules change depending on the nature of their... 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

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... 

Note that the dried rhizome of Cimicifuga racemosa (British Pharmaceutical Codex, 1934 black cohosh) has been used as a bitter and mild expectorant in the form of a liquid alcoholic extract (1 in 1 dose 0.3-2 mL) and is sold as alternative remedy for the treatment of menopausal syndrome at dose of 40-80 mg/day. The active constituents of black cohosh, and, therefore, the precise molecular mechanism of action involved in the climacteric property of Cimicifuga racemosa, are still unknown. The most recent data suggest that the plant is not estrogenic sensu stricto (126). 

Tunon, I., M. T. C. Martins-Costa, C. Millot, M. F. Ruiz-Lopez, and J. L. Rivail. 1996. A Coupled Density Functional-Molecular Mechanics MonteCarlo Simulation Method The Water Molecule in Liquid Water. J. Comp. Chem. 17, 19. 

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. 

Dorsey, J.G and DiU, K.A., The molecular mechanism of retention in reversed-phase liquid-chromatography, Chem. Rev., 89, 331, 1989. 

Proton conductivities of 0.1 S cm at high excess water contents in current PEMs stem from the concerted effect of a high concentration of free protons, high liquid-like proton mobility, and a well-connected cluster network of hydrated pathways. i i i i Correspondingly, the detrimental effects of membrane dehydration are multifold. It triggers morphological transitions that have been studied recently in experiment and theory.2 .i29.i ,i62 water contents below the percolation threshold, the well-hydrated pathways cease to span the complete sample, and poorly hydrated channels control the overall transports ll Moreover, the structure of water and the molecular mechanisms of proton transport change at low water contents. 

The remaining problem of the molecular mechanisms of this action was judged to be related to the conformation of the dicarboxylic acid at the interface. This conformation is usually determined directly with the use of a Langmuir trough (16-18). The disadvantage of such a method for the present problem lies with the restrictions of the environment of the molecule to be Investigated. The basic requirement is that the molecule must be virtually insoluble in the liquid substrate on which the monolayer is supported. For the dicarboxylic acid in question, this meant a pH value as low as 2 and also a high electrolyte content in the aqueous substrate. 

The development of other methods with less computing requirements and free of such limitations seems to be necessary in order to understand better the processes that take place in the liquid phase, understand their molecular mechanism, predict the influence of various factors on their equilibria and kinetics, and evaluate correctly the thermodynamic functions for the whole process and its particular steps. 

New glycolipids have to be synthesized to get further insights into liquid crystal properties (mainly lyotropic liquid crystals), surfactant properties (useful in the extraction of membrane proteins), and factors that govern vesicle formation, stability and tightness. New techniques have to be perfected in order to allow to make precise measurements of thermodynamic and kinetic parameters of binding in 3D-systems and to refine those already avalaible with 2D-arrays. Furthermore, molecular mechanics calculations should also be improved to afford a better modeling of the conformations of carbohydrates at interfaces, in relation with physical measurements such as NMR. 

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