On partitioning the overlap charge density in self-consistent charge molecular-orbital calculations

Alternatives to the Mulliken method of partitioning the overlap charge density in self-consistent charge molecular-orbital calculations are examined. It is found that more realistic methods may lead to significantly different self-consistent charges, and different ordering of the electronic energy levels.     

Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods

The use of hybrid methods, involving both quantum mechanics and molecular mechanics, to model the mechanism of enzyme-catalysed reactions, is discussed. Two alternative approaches to treating the electrostatic interactions between the quantum mechanical and molecular mechanical regions are studied, involving either the inclusion of this term in the electronic Hamiltonian (QM/MM), or evaluating it purely classically (MO + MM). In the latter scheme, possible problems of using force fields that are standard for macromolecular modelling are identified. The use of QM/MM schemes to investigate the mechanism of the enzymes thymidine phosphorylase (ThdPase) and protein tyrosine phosphatase (PTP) is described. For both systems, transition states have been identified using a PM3 Hamiltonian. For ThdPase, concerted motion of the enzyme during the course of the reaction is suggested and, for PTP, a two-step dephosphorylation reaction is indicated, both with quite low barriers.     

Construction of a tethered poly(ethylene glycol) surface gradient for studies of cell adhesion kinetics

Surface gradients can be used to perform a wide range of functions and represent a novel experimental platform for combinatorial discovery and analysis. In this work, a gradient in the coverage of a surface-immobilized poly(ethylene glycol) (PEG) layer is constructed to interrogate cell adhesion on a solid surface. Variation of surface coverage is achieved by controlled transport of a reactive PEG precursor from a point source through a hydrated gel. Immobilization of PEG is achieved by covalent attachment of the PEG molecule via direct coupling chemistry to a cystamine self-assembled monolayer on gold. This represents a simple method for creating spatial gradients in surface chemistry that does not require special instrumentation or microfabrication procedures. The structure and spatial distribution of the PEG gradient are evaluated via ellipsometry and atomic force microscopy. A cell adhesion assay using bovine arteriole endothelium cells is used to study the influence of PEG thickness and chain density on biocompatibility. The kinetics of cell adhesion are quantified as a function of the thickness of the PEG layer. Results depict a surface in which the variation in layer thickness along the PEG gradient strongly modifies the biological response.     

An alternative to pseudopotentials: a core—valence approximation scheme for molecular calculations

A core—valence approximation scheme is described in which the integral-evaluation time varies as (N_valence)⁴ rather than (N_total)⁴. The scheme is based on expanding core—valence overlap distributions in terms of a mono-centric basis centred at the core. The method is illustrated with comparative calculations on NF₃ and PCl₃.     

Gun tunnel flow calibration: defining input conditions for hypersonic flow computations

The procedures used to calibrate a hypersonic gun tunnel nozzle flow are described. The values obtained using these methods are then used as input conditions for computations of hypersonic flow over a long slender test body. Only by completely specifying the flow field, including the effects of nozzle flow angularity, can the best agreement between experiment and computations be achieved. Received 18 February 2000 / Accepted 7 July 2000     

The origin of the conformational preference of N,N'-diaryl-N,N'-dimethyl ureas

Poly aromatic ureas and poly aromatic amides are important classes of foldamers-oligomers with well defined conformations. We have explored the origins of the conformational preference of some N,N'-diaryl-N,N'-dimethyl ureas by a combination of NMR spectroscopy and electronic structure calculations using both a recently developed density functional (M06-2X) and a DFT approach (DFT-D) having empirical corrections for dispersive interactions. We have validated the DFT-D approach for structures of this type using high level wavefunction calculations, (CCSD(T)), of the unsubstituted N,N'-diphenyl-N,N'-dimethyl urea. For the N,N'-diaryl-N,N'-dimethyl ureas we have identified a number of 'endo' conformers (i.e. having an E,E geometrical conformation about the two urea C-N bonds), both π- and tert-butyl-stacked, as well as 'exo' structures (having a Z geometrical conformation about at least one of the C-N bonds), and have computed the relative energies of these conformers as well as the barriers for their interconversion. We find that the relative energies of the 'endo' structures closely follow the relative values of the dispersive interactions. The calculations have allowed us to associate different conformers with the various peaks in the NMR spectra, which point to relatively small differences in energy between the conformers. Somewhat larger energy differences are predicted by the two computational approaches, with the M06-2X functional performing the better of the two. It is suggested that the continuum model employed may not be sufficiently accurate to reflect the solvation of the various conformers.     

The role of tetrahydrobiopterin in catalysis by nitric oxide synthase

Electronic structure calculations show that the cofactor H4B can be a key factor in a proton transfer relay in nitric oxide synthase, and that 4-amino-H4B cannot fulfill this role.     

Quantifying the reactivity of a remarkably long-lived difluorinated enol in acidic methanol via solution kinetics and electronic structure calculations

A simple enol acetal underwent rapid cleavage in acidic solution to generate a difluorinated enol, which was sufficiently long-lived to be characterized by 2D NMR in a protic solvent at ambient temperature. Density functional theory calculations on a model reaction suggest that there are significant differences in protonation transition state timing between the fluorinated and nonfluorinated enols.     

How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study

We have explored possible mechanisms for the formation of the catalytically active Ni(a)-S state of the enzyme, nickel iron hydrogenase, from the Ni*(r) (ready) or Ni*(u) (unready) state, by reaction with H(2), using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an -OH bridge, the rate determining step is the cleavage of H(2) at the Ni(3+) centre with a barrier of approximately 15 kcal mol(-1). We take the unready state to have a -OOH bridge, and find that reaction with H(2) to form the Ni(r)-S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of approximately 19 kcal mol(-1). The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.