Atomistic methods force field

In addition to the MD method, a wealth of Monte Carlo methods is used also at the atomistic level [6]. They use essentially the same models, force fields, for polymers. Their main advantage, however, is that by introduction of clever moves one can beat the slow physical dynamics of the systems and can run through phase space much faster than by MD. These methods are still in their infancy, but will certainly become more important. 

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. 

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]. 

An alternative approach to the finite element approach is one, introduced as a concept by Courant as early as 1943 [197], in which the total energy functional, implicit in the finite element method, is directly minimized with respect to all nodal positions. The approach is conjugate to the finite element method and merely differs in its procedural approach. It parallels, however, methods often used in atomistic modeling schemes where the potential energy functional of a system (e. g., given by the force field ) is minimized with respect to the position of all (or at least many) atoms of the system. A simple example of this emerging technique is given below. 

Classical molecular simulation methods such as MC and MD represent atomistic/molecular-level modeling, which discards the electronic degrees of freedom while utilizing parameters transferred from quantum level simulation as force field information. A molecule in the simulation is composed of beads representing atoms, where the interactions are described by classical potential functions. Each bead has a dispersive pair-wise interaction as described by the Lennard-Jones (LJ) potential, ULj(Ly) ... 

The periodic approach is not the only one available for atomistic simulations of these materials and we should first mention that much progress has been made in the application of molecular quantum chemical methods using cluster representations of the local structure of oxide materials [1, 2], More recently, this has given way to mixed quantum mechanics/molecular mechanics (QM/MM) calculations. In QM/MM simulations the important region, the active site for catalysis, is represented at a quantum chemical level while the influence of its environment, the extended solid, is represented using the computationally less-demanding atomistic force field approach. This allows complex structures such as metal particles supported on oxides to be tackled [3]. 

The success of any molecular simulation method relies on the potential energy function for the system of interest, also known as force fields [27]. In case of proteins, several (semi)empirical atomistic force fields have been developed over the years, of which ENCAD [28,29], AMBER [30], CHARMM [31], GRO-MOS [32], and OPLSAA [33] are the most well known. In principle, the force field should include the electronic structure, but for most except the smallest systems the calculation of the electronic structure is prohibitively expensive, even when using approximations such as density functional theory. Instead, most potential energy functions are (semi)empirical classical approximations of the Born-Oppenheimer energy surface. 

In principle, detailed atomistic simulations could offer a straightforward approach for describing bio-mimetic membranes with chemical accuracy. Commonly, they employ Molecular Dynamics (MD) methods built around force-fields representing the interactions of chemically bonded and non-bonded atoms, to obtain... 

Just a few years ago, the limitations of solubility parameter calculations and measurements discussed above were serious impediments to modeling the phasic and interfacial behaviors of polymeric systems. The coming of age of atomistic simulation methods over the last few years has improved this situation dramatically. As discussed in Section 5.A.3, whenever accuracy is important in calculating the phasic or the interfacial behavior of a system, it is nowadays strongly preferable to use atomistic simulations employing modem force fields of the highest available quality instead of solubility parameters in order to estimate the Flory-Huggins interaction parameters (%) between the system components as input for further calculations. 

In addition to the classical force fields above, many other force fields have been developed for small drug molecules or macromolecules. The MM2, MM3, and MM4 force fields were developed by Norman L. Allinger for a broad range of chemicals, and CFF is a family of force fields adapted to a broad variety of organic compounds, polymers, metals, and so on. The MMFF force field was developed at Merck for a broad range of chemicals. ReaxFF is a reactive force field, developed by William Goddard and coworkers, is fast, transferable, and the computational method of choice for atomistic-scale dynamics simulations of chemical reactions. 

Markus Meuwly is professor of physical and computational chemistry at the Department of Chemistry of the University of Basel and adjunct research professor at Brown University, USA. He is interested in developing computational/theoretical methods for quantitative atomistic simulations, specifically multipolar force fields and reactive processes in complex systems. 

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