Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.     

Diffusion in organic solvents: Interdiffusion coefficient of 1,1,2,2-tetrabromoethane

Interdiffusion coefficient have been measured for 1,1,2,2-tetrabromoethane in 21 organic solvents in order to ascertain the influence of shape, size, viscosity, nature and degree of branching, of the solvent molecules on transport properties. None of the existing correlations for diffusion in binary liquid systems appear to fit all the experimental data. Steric effects due to the solvent molecules are shown to be very important in the interpretation of the diffusion process.     

OXYGEN QUENCHING IN MICELLAR SOLUTION AND ITS EFFECT ON THE PHOTOCYCLIZATION OF N-METHYLDIPHENYLAMINE

Abstract— Oxygen effects on the photocyclization of N-methyldiphenylamine to N-methylcarbazole were investigated in n-hexane, water, and aqueous surfactant solutions by steady state irradiations and flash photolysis measurements. The reaction sequence in micelles was found to involve the same intermediate steps as in homogeneous solutions. In aerated micellar solutions, the quantum yield of N-methylcarbazole is significantly higher than in n-hexane, while the rate constants of the unimolecular reaction steps show no solvent dependence. The bimolecular dehydrogenation of the intermediate 4a, 4b-dihydro-N-methylcarbazole by oxygen is enhanced in aqueous and micellar solutions, whereas the quenching rate of triplet intermediates by oxygen was not affected. The lesuhs are interpreted using a dispersed phase model of micellar solutions. Special 'micellar effects' need not be invoked since the dependence of the quantum yield on the solvent is shown to be due to the difference in the overall oxygen concentration.