Molecular mechanics simulation

Weiner, S.J. Kollman, P.A. Case, D.A. Singh, U.C., Ohio, C. Alagona, G. Profeta Jr., S. Weiner, P. Anew force field for molecular mechanical simulation of nucleic acids and proteins 7 Am. Chem. Soc. 106 765-784, 1984. 

Combined Quantum and Molecular Mechanical Simulations. A recentiy developed technique is one wherein a molecular dynamics simulation includes the treatment of some part of the system with a quantum mechanical technique. This approach, QM/MM, is similar to the coupled quantum and molecular mechanical methods introduced by Warshel and Karplus (45) and at the heart of the MMI, MMP2, and MM3 programs by AUinger (60). These latter programs use quantum mechanical methods to treat the TT-systems of the stmctures in question separately from the sigma framework. 

Molecular mechanics simulations can be readily mapped onto such kinds of machine architecture by using the spatial locaUty of the atoms to determine their allocation to processors. Short-range van der Waals forces can usually be accurately modeled with a cut-off distance of less than one nm, so interprocessor communication requirements can also be localized. 

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

A New Force Field for Molecular Mechanics Simulation of Nucleic Acids and Proteins... 

Tab. 12.2 Combined ab initio quantum and molecular mechanical simulations of solvation of acetate and methylammonium ions in aqueous solution.

Ren PY, Ponder JW (2003) Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B 107(24) 5933-5947... 

Dixit, S. B. Chipot, C., Can absolute free energies of association be estimated from molecular mechanical simulations The biotin-streptavidin system revisited, J. Phys. Chem. A 2001,105, 9795-9799. 

Since the complete GVFF is rarely available for compounds of unknown structure, exact molecular mechanics simulation of small distortions is not... 

Quantitative XPS, 24 92-94 Quantum and molecular mechanical simulations, combined, 76 750-751 Quantum condition equation, 23 803 Quantum cellular automata (QCA),... 

CNT can markedly reinforce polystyrene rod and epoxy thin film by forming CNT/polystyrene (PS) and CNT/epoxy composites (Wong et al., 2003). Molecular mechanics simulations and elasticity calculations clearly showed that, in the absence of chemical bonding between CNT and the matrix, the non-covalent bond interactions including electrostatic and van der Waals forces result in CNT-polymer interfacial shear stress (at OK) of about 138 and 186MPa, respectively, for CNT/ epoxy and CNT/PS, which are about an order of magnitude higher than microfiber-reinforced composites, the reason should attribute to intimate contact between the two solid phases at the molecular scale. Local non-uniformity of CNTs and mismatch of the coefficients of thermal expansions between CNT and polymer matrix may also promote the stress transfer between CNTs and polymer matrix. 

Fig. 9.12 Results of molecular mechanics simulations (a) A Stone-Wales defect (A mode) in a zigzag SWCNT, (b) a Stone-Wales defect (B mode) in a zigzag SWCNT, the bonds with highest potential energy are indicated by arrows. Propagating cracks in (c) A defect-fiee zigzag tube, and (d) defect-lfee armchair tube. Fracture mode of armchair tube with (e) Stone-Wales defect (A mode), and (f) Stone-Wales defect (B mode). Fracture mode of zigzag tube with (g) Stone-Wales defect (A mode), and (h) Stone-Wales defect (B mode) (Huynh et al., 2002. With permission from Wiley)...

It is difficult to evaluate the shape of such dendritic particles experimentally. However, some insight can be gained by atomic force microscopy (AFM) and transmission electron microscopy experiments (TEM). AFM experiments can give information about the overall size of the dendrimers, as shown by De Schryver [43], by spincoating very dilute solutions of dendrimers like 30 on mica, then visualizing single dendrimers. Their height measured in this manner corresponds very well to the diameters calculated by molecular mechanics simulations. First results from TEM measurements also confirm the expected dimensions [44]. Unfortunately, due to resolution limits, up to now direct visual information could not be obtained about the shape of the dendrimers. 

Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 2003, 24, 1999-2012. 

Specific solute-solvent interactions, such as hydrogen bonding or protonation, may be included in the calculation of the shielding of solute nuclei by a supermolecule approach. The appropriate structure of the solute-solvent supermolecule may be obtained by the use of molecular mechanics simulations. At the semi-empirical MO level this approach has been successfully used to describe the effects of hydrogen bonding on the nuclear shielding of small molecules. 

Unfortunately specific solvation effects are very difficult to understand, although molecular mechanics simulations have recently gone some way towards modelling complexation phenomena... 

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