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-.     

Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid

An all-atom molecular dynamics simulation of rhodopsin in a membrane environment has been carried out with lipid composition similar to that of the retinal membrane. The initial conformation of the protein was taken from the X-ray crystallographic structure (1F88), while those of the lipids came from a previous molecular dynamics simulation. During the course of the 12.5 ns simulation, the initially randomly placed lipids adopt an anisotropic solvation structure around the protein. The lipids, having one saturated stearic acid chain and one polyunsaturated docosohexaenoic acid chain with a zwitterionic phosphatidylcholine headgroup, arrange themselves to maximize contact between the polyunsaturated chain and the protein surface. This organization is driven by energetically favorable interactions between the transmembrance helices and the docosohexaenoyl chains that are largely of the van der Waals type. These observations are consistent with various experimental studies on rhodopsin and other G-protein coupled receptors and with the picture of extreme flexibility in polyunsaturated fatty acid chains that has arisen from recent NMR and computational work.     

Intradiffusion coefficients in perchloric acid solutions: Water at 5°C; water and perchlorate ion at 25°C

Intradiffusion coefficients for tritiated water (³HHO) and perchlorate ion (³⁶ClO ₄ ^- ) were measured in perchloric acid solutions. At 5°C the diffusion coefficient measured for the tritiated species increases to a maximum near 1.3 mol-dm^–3. The data at 25°C have been used to calculate distinct diffusion coefficients, D _ij ^d . As a precursor for those calculations, new estimates were made of the Onsager phenomenological coefficients, l _ij . The l _ij and D _ij ^d are similar to the respective coefficients in hydrochloric acid solutions.     

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free-energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free-energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two-stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations.     

The heat of formation of sulphuryl fluoride and the stability of fluorosulphates

A standard enthalphy of -767.2 kJ mol^-1 was determined for sulphuryl fluoride from the heat of alkaline hydrolysis, and a standard free energy of -720.8 kJ mol^-1 derived. The thermodynamically preferred product of ionic fluorosulphate decompositions is always sulphuryl fluoride. Kinetic control must predominate when sulphur trioxide is the main product.     

Surface reconstructions and phase transitions on the GaAs(111)B surface

The (111)B surface of GaAs has been investigated using scanning tunneling microscopy (STM) and a number of different reconstructions have been found at different surface stoichiometries. In accordance with electron diffraction studies, we find the series (2 × 2), (1 × 1)_LT, ( ) and (1 × 1)_HT with increasing annealing temperature, corresponding to decreasing surface As concentration. The (1 × 1)_LT is of particular interest, since it only occurs in a narrow temperature window between the two more established reconstructions, the (2 × 2) and the ( ). We find the (1 × 1)_LT to take the form of a mixture of the local structures of both the (2 × 2) and ( ) phases, rather than having a distinct structure. This is behaviour consistent with a kinetically limited system, dominated by the supply of As adatoms to the surface, and may be an example of a continuous phase transition. Above the (1 × 1)_LT transition, atomic resolution images of the ( ) surface reveal only a three-fold symmetry of the hexagonal structural units, brought about by inequivalent surface bonding due to the 23.4° rotation of the surface unit cell relative to the substrate. This is responsible for the disorder found in the ( ) reconstruction, since the structure may form in one of two domains. At lower surface As concentration, the (1 × 1)_HT surface adopts a structure combining small domains of a 19.1° structure and random disorder. There is no apparent similarity between the (1 × 1)_LT and (1 × 1)_HT structures, which may be due to our measurements being conducted at room temperature and without an As flux to control the surface As concentration.     

Positive fluorine - misconception or reality?

Some of the evidence for positive fluorine is summarized. Evidence against positive fluorine based on the direction of addition to fluoroolefins, and polarity as judged by electronegativity values, is queried.     

Rationalizing structures of transition metal fluorides

Engel's theory of intermetallic bonding which differentiates transition metals into acid and bases about a Group VII dividing line is used to rationalize transition metal fluoride structures. Some chemical consequences are indicated