Chemistry

Optimization of quantum monte carlo wave functions by energy minimization

J.Toulouse , C.J.


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We study three wave function optimization methods based on energy minimization in a variational Monte Carlo framework: the Newton, linear, and perturbative methods. In the Newton method, the parameter variations are calculated from the energy gradient and Hessian, using a reduced variance statistical estimator for the latter. In the linear method, the parameter variations are found by diagonalizing a nonsymmetric estimator of the Hamiltonian matrix in the space spanned by the wave function and its derivatives with respect to the parameters, making use of a strong zero-variance principle. In the less computationally expensive perturbative method, the parameter variations are calculated by approximately solving the generalized eigenvalue equation of the linear method by a nonorthogonal perturbation theory. These general methods are illustrated here by the optimization of wave functions consisting of a Jastrow factor multiplied by an expansion in configuration state functions CSFs for the C2 molecule, including both valence and core electrons in the calculation. The Newton and linear methods are very efficient for the optimization of the Jastrow, CSF, and orbital parameters. The perturbative method is a good alternative for the optimization of just the CSF and orbital parameters. Although the optimization is performed at the variational Monte Carlo level, we observe for the C2 molecule studied here, and for other systems we have studied, that as more parameters in the trial wave functions are optimized, the diffusion Monte Carlo total energy improves monotonically, implying that the nodal hypersurface also improves monotonically.

Addition and elimination reactions of \h2\ in ruthenaborane clusters: a computational study

J.Halet , J.Saillard , H.Rabaa , S.Ghosh , D.Sundholm


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Ruthenaborane clusters have been modelled by performing density functional theory calculations using the \B3LYP\ functional. The calculations gain insights into hydrogen storage and the H-H bond activation by ruthenaboranes. To study the nature of the chemical bond of \H2\ molecules attached to ruthenaboranes, we carried out structural optimizations for different ruthenaborane clusters and determined transition state structures for their hydrogenation addition/elimination reactions. Calculations of the reaction pathways yielded different transition-state structures involving molecular hydrogen bonded to the cluster or formation of metal hydrides. The H-H bond of \H2\ seems to be activated by the ruthenaborane clusters as activation energies of 24-42kcal/mol were calculated for the \H2\ addition reaction. The calculated Gibbs free energy for the \H2\ addition reaction is 14-27kcal/mol. The calculated activation energies and the molecular structures of the , and clusters with different degree of hydrogenation are compared. The mechanisms of the \H2\ addition and elimination reactions of the studied clusters suggest that they might be useful as hydrogen storage materials due to their ability to activate the H-H bond. They also serve as an example of the ability of hypoelectronic metallaboranes to reversibly or irreversibly bind hydrogen.

Genetic Structure and Origin of Peopling in the Azores Islands (Portugal): the View From Mtdna

S.C. , L.M. , P.L. , A.A. , M.R. , A.N. , A.Ma.


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The Azores islands (Portugal), uninhabited when discovered by Portuguese navigators in the fifteenth century, are located in the Atlantic Ocean 1500 km from the European mainland. The archipelago is formed by nine islands of volcanic origin that define three geographical groups: Eastern (S. Miguel and Sta. Maria), Central (Terceira, Faial, Pico, Graciosa and S. Jorge) and Western (Flores and Corvo). To improve the genetic characterisation of the Azorean population, and to clarify some aspects related to the history of settlement, a study of mtDNA was conducted in the population of the archipelago. The HVRI region was sequenced and specific RFLPs were screened in 146 samples obtained from unrelated individuals with Azorean ancestry (50 from the Eastern group, 60 from the Central group, and 37 from the Western group). Samples were classified into haplogroups based on the information obtained from both sequencing and RFLP analysis. All the analyses performed support the idea that, in the whole group of islands, the majority of mtDNA lineages originated from the Iberian Peninsula, mainly from Portugal (mainland). However contributions from other European populations, especially from Northern Europe, cannot be disregarded. The values obtained for the various diversity parameters in the Azores archipelago indicate that the Azorean population, as a whole, does not exhibit the typical characteristics of an isolated population. The analysis of genetic data by groups of islands showed that the Western group exhibited particular features. The distribution of haplogroups in the Western group is very atypical, being significantly different from what is observed in the Eastern and Central groups. Furthermore, the diversity values are, in general, lower than those observed in other populations used for comparison. African haplogroups were found in all the groups of islands. Therefore the presence of Moorish and African slaves on the islands, as reported in historical sources, is supported by the mtDNA genetic data, especially in the Eastern group. The presence of Jews in the Central group is also supported by the mtDNA data. Neither historical nor genetic data (phylogeography of mtDNA) supports the idea of a differential settlement history for the Western group; however, it is represented in the phylogenies as an isolated branch. The effect of genetic drift, induced by the reduced population size since peopling occurred, has led to a very atypical distribution of haplogroups/haplotypes in this group of islands. We cannot ignore the influence of biodemographic and genetic processes, namely founder effect, genetic drift, migration, and even recent mutational events in the mtDNA lineages of the Azorean populations. Nevertheless, a great part of the variation in the Azorean mtDNA can be explained by the settlement history.http://dx.doi.org/10.1046/j.1469-1809.2003.00031.

Spectroscopic characterisation of hydroxyapatite and nanocrystalline apatite with grafted aminopropyltriethoxysilane: nature of silanesurface interaction

C.Rey , S.Sarda , E.Manoury , R.Poli , A.Michelot , C.Audin , E.Deydier


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Heterogenised homogeneous catalysis is commonly performed with molecular catalysts grafted on solids via adsorption or via a covalent molecular link. Covalent grafting of organic groups on solid supports is usually carried out by silylation, using functionalised trialkoxysilanes. Among these solids supports, very few studies have been published on apatites. In the present work,aminopropyltriethoxysilane grafting was performed in toluene on different apatitic supports: crystallised stoichiometric hydroxyapatites differing by the drying method, freeze-dried and dried at 100 C , and a nanocrystalline apatite. All materials were fully characterised, before and after grafting, for better understanding of the nature of the alkoxysilane/surface interaction. The data show a clear competition between the covalent grafting of APTES and its polycondensation reaction, depending on the nature of the solid support surface. Silylation is accompanied by APTES covalent grafting to oxygen atom of the hydroxyl groups of the apatitic structure and/or of the OH species that are present on the surface hydrated layer. This work clarifies the nature of silane grafting onto selected apatitic surfaces and especially the influence of the composition and properties of the apatitic surfaces on the process of silylation.
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