Jl Finney

Structure and hydrogen ordering in ices VI, VII, and VIII by neutron powder diffraction

The structures of deuterated ices VI, VII, and VIII have been studied under their conditions of stability by neutron powder diffraction. The mode of ordering of (tetragonal) ice VIII is clearly established, and no evidence is found of partial ordering as the temperature is raised. Ice VII is accurately cubic with D2O molecules disordered around their center of mass; there is no evidence of partial ordering at any temperature. The water molecule geometry is normal in both phases, and the hydrogen‐bonded first neighbor in ice VIII is confirmed to be more distant than the first nonbonded neighbor. The transition temperature between the two phases occurs at 263±2 K, some 11 K lower than expected. Hydrogen bond lengths in both phases are equal at the transition. Although the ice VI data are not as good, we can see no evidence of the antiferroelectric ordering proposed by Kamb from work on recovered samples. Our results are consistent with thermodynamic measurements indicating disorder in ice VI at 193 K. We co...

Neutron diffraction studies of ices III and IX on under‐pressure and recovered samples

Detailed structural studies using powder neutron diffraction have been carried out on ices III and IX on both under‐pressure and recovered samples. The incomplete hydrogen ordering in recovered ice IX first observed by La Placa et al. is confirmed, and our studies suggest similar orderings for the under‐pressure and recovered phases. Sample history was observed to influence the lattice constants of ice IX, an effect which could relate to hydrogen ordering. There is an indication that ice III is not fully disordered, a conclusion which would be consistent with independent thermodynamic measurements.

Two, three, and four body interactions in model water interactions

Dimer energy surfaces for three models of the water-water interaction are examined and compared with high level ab initio SCF calculations for two important sections. All three models studied (ST2, MCY, and PE(Q) show significant differences which would be expected to be important in full liquid state simulation; the inclusion of an additional dipole-octupole term in PE appears sufficient to reproduce the energy-angle variations shown in the SCF calculations. ST2 distinguishes too strongly between the lone pairs on the acceptor water molecule, while MCY shows little sign at all of lone pair separation. All three models disagree with the rotational barrier heights given by the SCF calculations; these differences we would expect to have structural consequences in a room temperature liquid ensemble. Although there are insufficient experimental and numerical data available to fully test the three-body (and higher) interactions of the PE model, good agreement is obtained with experimental enhanced dipole momen...

An SCF-CI study of the water dimer potential surface and the effects of including the correlation energy, the basis set superposition error and the Davidson correction

A study at SCF-CI level has been performed on the water dimer, with a [541|31] basis set. The effects of the correlation energy, basis set superposition error (BSSE) and Davidson correction were investigated. Maintaining the experimental water geometry, several sections of the energy surface were calculated. They show only one minimum energy structure, the linear trans dimer, in agreement with experiment. The linear cis and bifurcated forms are found to be unstable. The Davidson correction has a minimal effect on the energy surface. The correlation energy and BSSE are important, being ∼ 10 per cent or more of the total interaction energy, and are distance dependent. They also show a complex angular dependence. As the BSSE size is an indication of the basis set quality, only those surface features virtually unaffected by the BSSE correction can be regarded as reliable. Here, these features are the angular parameters of the minimum, the O-O stretching frequency and the general surface shape. Basis sets with...

Monte Carlo Computer Simulation of Water--Amino Acid Interactions

The sensitivity of computer simulated solvent structures to changes in both non-bonded (Lennard-Jones) coefficients and partial atomic charges has been investigated with use of amino acid hydrate crystals in which the water structure is well defined experimentally. The polarizable electropole (p. e.) model of water has been extended to describe water–protein interactions; thus, the cooperative nature of the hydrogen bond (i. e. non-pair additive effects) is allowed for through a polarizable dipole. By means of Monte Carlo calculations, the predicted water positions were found to be very sensitive to the input parameters used to define both the non-bonded and electrostatic interactions. Root mean square deviations between simulated and X-ray structures were not always adequate to describe these differences and so more detailed comparisons were made. Non-pair additive effects were shown to lead to large changes in water dipoles, the values of which depended specifically on the system under consideration.

Computer Simulation of Aqueous Biomolecular Systems

Computer simulation techniques are increasingly being used to predict structural and thermodynamic properties of large heterogeneous macromolecule and solvent assemblies. We discuss, with examples from our own studies, some problems we and others have experienced in using these techniques, which were originally devised for simple liquids. In particular, we consider the problems which arise from the large size and heterogeneity of macromolecule water systems, comparisons with experimental data and equilibrium and sampling procedures.

Solvent structure in vitamin B12 coenzyme crystals

Both the ordered and disordered solvent networks of vitamin B12 coenzyme crystal hydrate have been generated by Monte Carlo simulation techniques. Several different potential functions have been use to model both water-water and water-solute (i.e., water-coenzyme) interactions. The results have been analysed in terms of the structural properties of the water networks, such as mean water oxygen and hydrogen positions, coordination of each water molecule, and maxima of probability density maps in all four asymmetric units of this crystal.The following results were found: (I) Within each asymmetric unit only one hydrogen bonding network was predicted although there were several hydrogen atom positions for any one solvent molecule (defined as maxima in probability density). (II) Reasonable agreement was obtained between predicted and experimental positions in the ordered solvent region, independent of the potential function used. (III) The positions of the calculated probability density maxima for the disordered channel region were different in different asymmetric units; this led to different simulated hydrogen bond networks which were not always consistent with the experimentally determined alternative (lower occupancy) sites.The results suggest that it is advisable to simulate more than one asymmetric unit if one wishes to look at disorder in the solvent regions. Probability density maps were qualitatively very useful for picturing these disordered regions. However, there were no significant differences between quantitative results predicted using either average atomic positions or maxima of the probability density distributions.Problems in quantifying agreement between experimental and predicted disordered solvent networks are discussed. The potential which included hydrogen atoms explicitly (EMPWI) seemed to give the best overall agreement, mainly because it was successful in predicting the unusually short hydrogen bonds which are found in this crystal.