Force fields with molecular dynamics

Pool et al studied the adsorption of alkyl thiols on gold surfaces, both without and with a solvent. As solvent they considered w-hexane. For the simulations they used a force field with a so called united-atom model. This means that the thiol heads, the CH2 and CH3 groups, and the gold atoms are treated as individual united atoms . The interactions between these united pseudoatoms are described in terms of the force fields. Subsequently, molecular dynamics simulations were carried through for the different systems. 

Recently, semiempirical molecular-orbital methods have been combined with force-field-based molecular-dynamics techniques into hybrid schemes The interesting part of the system is described by quantum chemistry, while the surroundings are treated by a classical force field. These hybrid schemes allow calculation of the energy and gradients fast enough for molecular dynamics simulations of hundreds of picoseconds (10s time steps) duration to be feasible. This provides sufficient sampling for the calculation of many statistical-mechanical properties. A short synopsis is given of work carried out at ETH Zurich on conformational equilibria in solution, reactions in solution and enzyme reactions. 

Using the CHARMM force field for molecular dynamics, Lipkowitz simulations reproduced the correct retention order and separation factor from the chromatography experiments. Their simulation results also agreed with both intermolecular and intramolecular NOE observations from NMR experiments they carried out. 

The problem of choosing, creating or improving a force field for molecular dynamics calculations is obviously non trivial and requires a careful validation of the field with the existing experimental observables. There are even many different paradigms which one may choose from in order to build a force field for example the "atomistic" level and the... 

Dynamic NMR gives information on the number and symmetries of conformations present in solution and on the energy barriers separating these conformations. This is particularly true for systems with barriers between about 25 and 90 kJ mol-1, a situation which often occurs in the medium ring. The interpretation of the NMR data can be carried out by the examination of molecular models, but this is a relatively crude and sometimes misleading method. Empirical force field (or molecular mechanics) calculations are much superior, even though the parametrization of heteroatoms may be open to question. Quantum mechanical calculations are not very suitable the semiempirical type, e.g. MINDO, do not reproduce conformational properties of even cyclohexane satisfactorily, and the ab initio... 

A force field for solid state modeling of fluoropolymers predicted a suitable helical conformation but required further improvement in describing intermole-cular effects. Though victory cannot yet be declared, the derived force fields improve substantially on those previously available. Preliminary molecular dynamics simulations with the interim force field indicate that modeling of PTFE chain behavior can now be done in an all-inclusive manner instead of the piecemeal focus on isolated motions and defects required previously. Further refinement of the force field with a backbone dihedral term capable of reproducing the complex torsional profile of perfluorocarbons has provided a parameterization that promises both qualitative and quantitative modeling of fluoropolymer behavior in the near future. 

In the last decades, the modeling of both compacted particulates and flowing particle assemblies under loads and under flow conditions has been advanced by DEM, first developed by Cundall (46) for two-dimensional compacted-disk assemblies in 1971. The origins of DEM are in the field of molecular dynamics (MD), where the motions of individual molecules are tracked under the influence of an external force (e.g., electrostatic) field (47). Experimental results such as those with model photo-elastic assemblies just discussed have also assisted the development of the DEM simulation models. 

PCFF force fields, alternatively with molecular dynamics, in order to identify the global minimum of the energy value). The investigated single chain has a polymerization degree DP=25, similar to the results obtained by synthesis. 

Other recent microscopic approaches are based on the Langevin dipoles solvent model or on the all-atom solvent model, using a standard force field with van der Waals and electrostatic terms as well as intramolecular terms, and molecular dynamics simulations of the fluctuation of the solvent and the solute, incorporating the potential from the permanent and induced solvent dipoles in the solute Hamiltonian in a self-consistent way (Luzhkov and Warshel, 1991). 

---