Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density

The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 A crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.     

An evaluation of the radial part of numerical integration commonly used in DFT

Recently, Gill and Chien introduced a new radial quadrature for multiexponential integrands (MultiExp grid) to deal with the radial part of the numerical integration. In this article, the MultiExp grid is studied and used to integrate the charge density. The MultiExp grid, along with an optimal pruning scheme, performed very well both in terms of accuracy and efficiency compared to other radial mappings commonly used in Density Functional Theory.     

A low-temperature electron diffraction study of structural disorder and its relationship to the Kondo effect in ThAsSe

A low-temperature electron diffraction study has been carried out on ThAsSe to search for evidence of structural disorder associated with the low-temperature non-magnetic Kondo effect. A highly structured and extremely complex characteristic diffuse intensity distribution has been observed at low temperature and interpreted in terms of a gradual charge density wave type phase transition upon lowering of temperature involving disordered As-As dimerization within (001) planes. Plausible models of the proposed As-As dimerization have been obtained using a group theoretical approach.     

Integrated Density of States For Random Metrics on Manifolds

We study ergodic random Schrödinger operators on a coveringmanifold, where the randomness enters both via the potentialand the metric. We prove measurability of the random operators,almost sure constancy of their spectral properties, the existenceof a self-averaging integrated density of states and a Pastur–ubintype trace formula. 2000 Mathematics Subjects Classification35J10, 58J35, 82B44.     

Estimation of heavy-tailed probability density function with application to Web data

Summary  Common non-parametric estimators of a probability density function (PDF) show bad performance for heavy-tailed PDFs. Using a parametric approximation of the true cumulative distribution function (CDF), the transformation-retransformation of the data is explored here as a useful tool for the reliable PDF prediction. The PDF estimators are compared by their capacity to solve a classification problem. Simulation results and an application to Web data analysis are presented, too.     

External Fields, Density Functionals, and the Gibbs Inequality

By combining the upper and lower bounds to the free energy as given by the Gibbs inequality for two systems with the same intermolecular interactions but with external fields differing from each other only in a finite region of space , we show that the corresponding equilibrium densities must also differ from each other somewhere in . We note that the basic equations of density functional theory arise naturally from a simple rearrangement and reinterpretation of the terms in the upper bound Gibbs inequality for such systems and briefly discuss some of the complications that occur when the intermolecular interactions of the two systems also differ.     

End-to-end correlation for a C-12 hydrocarbon chain

The 19F nuclear spin-lattice relaxation rate constants were measured as a function of magnetic field strength for 1,12-diaminododecane labeled at one end with a nitroxide radical and at the other with a trifluoromethyl group. The magnetic relaxation dispersion profile (MRD) reports the spectral density function appropriate to the end-to-end correlation function for the doubly labeled molecule. After extrapolation to zero concentration to eliminate the intermolecular relaxation contribution to relaxation, the resulting intramolecular MRD profile was compared with several model approaches. The rotational model for the spectral density functions as included in the Solomon-Bloembergen-Morgan equations does not describe the data well. The earlier model of Freed for nuclear spin relaxation induced by a freely diffusing paramagnetic co-solute is not rigorous for this case because the paramagnet is tethered to the observed nuclear spin and only a restricted space in the immediate vicinity of the nuclear spin is accessible for pseudo-translational diffusion of one end of the molecule with respect to the other. A generalization of the Torrey model for magnetic relaxation by translational diffusion developed by Nevzorov and Freed, which includes the effect of restrictions imposed by the finite length of the chain, describes the experiment within experimental errors. A simple modification of the Hwang-Freed model that does not specifically include the dynamical effects of the finite tether also provides a good approximation to the data when the tether chain is sufficiently long.     

An environmental pseudopotential approach to molecular interactions: Implementation in MOLPRO

We present the implementation into the MOLPRO package of a model for the interaction of a central system with its surrounding environment. The properties of a target system enclosed by a noncovalently bound environment or solvent are modeled as those of a system embedded into the effective pseudopotential arising from the exact electrostatic Coulomb potential and the approximated exchange-repulsion potential. For the latter we use the charge-density overlap model, which relates the exchange-repulsion interaction energy between two species with the overlap of their ground-state electron charge densities. The solutions of the modified Hartree-Fock equations for the target system are obtained self-consistently. This way the exchange-induction effects arising from the converged electron-charge density of the embedded system are implicitly included. Inclusion of the correlation effects is provided by the use of post-Hartree-Fock and density-functional techniques available in the MOLPRO package. The computational and conceptual advantages provided by this approach are shown in the calculation of the dipole polarizabilities of halide and chalcogenide anions in different environments.     

Electron density investigation of a push-pull ethylene (C14H24N2O2.H2O) by X-ray diffraction at T = 21 K

The electron charge distribution in a strongly twisted push-pull ethylene [PPE, 3-(1,3-diisopropyl-2-imidazolidinylidene)-2,4-pentanedione] has been determined by low temperature (T = 21 K) single-crystal X-ray diffraction analysis. The derived electronic properties are consistent with a zwitterionic molecule, as indicated by a charge transfer of 0.82(16) e from the push to the pull moieties and a charge polarization of 0.29(7) e on the olefinic bond. A dipole moment of 12(3) D has been determined, which compares well with ab initio theoretical results in terms of both modulus and orientation. The second moments, which have also been obtained with good precision, characterize PPE as a highly quadrupolar molecule. The special electronic features of the molecule confer particular topological properties to the electron density distribution, as evidenced by comparison with "standard" organic molecules. The crystallographic asymmetric unit of the present system includes one water molecule, which is hydrogen bonded to PPE. Its topological properties have also been investigated, together with an analysis of the hydrogen bonds involved.     

Theoretical study of rhodium(I) carbene complexes: the structural versatility of phosphino- compared with aminocarbenes

Density functional calculations are reported for complexes of general formula [(carbene)RhClL(2)] featuring model phosphino- and aminocarbenes. Both the cis and trans isomers of the rhodium(I) eta(1)-complexes (1-9) were investigated, and the influence of the rhodium co-ligands (L=ethylene, phosphine, or carbon monoxide) was evaluated. In the case of phosphinocarbenes and carbon monoxide as a ligand, a somewhat unusual coordination mode was observed, in which a significant intramolecular Cl-->C(carbene) interaction is present. The propensity of phosphino- and aminocarbenes to behave as four electron donors was also investigated both structurally and energetically on the related eta(2)-complexes 10-18. These results as a whole emphasize the structural versatility of phosphino- compared with aminocarbene complexes.