Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization

To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, fourth-order Møller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+ 1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople’s basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C–H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree–Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed

Delta(1232) isobar excitations in nuclear many-body systems from varios NN interactions.

Delta isobar components in the nuclear many-body wave function are investigated for the deuteron, light nuclei (16O), and infinite nuclear matter within the framework of the coupled-cluster theory. The predictions derived for various realistic models of the baryon-baryon interaction are compared to each other. These include local (V28) and nonlocal meson exchange potentials (Bonn2000) but also a model recently derived by the Salamanca group accounting for quark degrees of freedom. The characteristic differences which are obtained for the NDelta and Delta Delta correlation functions are related to the approximation made in deriving the matrix elements for the baryon-baryon interaction.

Delta(1232) isobar excitations and the ground state of nuclei

The influence of Delta isobar components on the ground-state properties of nuclear systems is investigated for nuclear matter as well as finite nuclei. Many-body wave functions, including isobar configurations and binding energies, are evaluated employing the framework of the coupled-cluster theory. It is demonstrated that the effect of isobar configurations depends in a rather sensitive way on the model used for the baryon-baryon interaction. As examples for realistic baryon-baryon interactions with explicit inclusion of isobar channels we use the local (V28) and nonlocal meson-exchange potentials (Bonn2000) but also a model recently developed by the Salamanca group, which is based on a quark picture. The differences obtained for the nuclear observables are related to the treatment of the interaction, the pi-exchange contributions in particular, at high momentum transfers.

Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters

Background: Hox and ParaHox gene clusters are thought to have resulted from the duplication of a ProtoHox gene cluster early in metazoan evolution. However, the origin and evolution of the other genes belonging to the extended Hox group of homeobox-containing genes, that is, Mox and Evx, remains obscure. We constructed phylogenetic trees with mouse, amphioxus and Drosophila extended Hox and other related Antennapedia-type homeobox gene sequences and analyzed the linkage data available for such genes.Results: We claim that neither Mox nor Evx is a Hox or ParaHox gene. We propose a scenariothat reconciles phylogeny with linkage data, in which an Evx/Mox ancestor gene linked to aProtoHox cluster was involved in a segmental tandem duplication event that generated an arrayof all Hox-like genes, referred to as the `coupled¿ cluster. A chromosomal breakage within thiscluster explains the current composition of the extended Hox cluster (with Evx, Hox and Moxgenes) and the ParaHox cluster.Conclusions: Most studies dealing with the origin and evolution of Hox and ParaHox clustershave not included the Hox-related genes Mox and Evx. Our phylogenetic analyses and theavailable linkage data in mammalian genomes support an evolutionary scenario in which anancestor of Evx and Mox was linked to the ProtoHox cluster, and that a tandem duplication of alarge genomic region early in metazoan evolution generated the Hox and ParaHox clusters, plusthe cluster-neighbors Evx and Mox. The large `coupled¿ Hox-like cluster EvxHox/MoxParaHox wassubsequently broken, thus grouping the Mox and Evx genes to the Hox clusters, and isolating theParaHox cluster.

Creating and using a non-dedicated HPC cluster with ParallelKnoppix

This note describes ParallelKnoppix, a bootable CD that allows econometricians with average knowledge of computers to create and begin using a high performance computing cluster for parallel computing in very little time. The computers used may be heterogeneous machines, and clusters of up to 200 nodes are supported. When the cluster is shut down, all machines are in their original state, so their temporary use in the cluster does not interfere with their normal uses. An example shows how a Monte Carlo study of a bootstrap test procedure may be done in parallel. Using a cluster of 20 nodes, the example runs approximately 20 times faster than it does on a single computer.

ParallelKnoppix - Rapid deployment of a linux cluster for MPI parallel processing using non-dedicated computers

This note describes ParallelKnoppix, a bootable CD that allows creation of a Linux cluster in very little time. An experienced user can create a cluster ready to execute MPI programs in less than 10 minutes. The computers used may be heterogeneous machines, of the IA-32 architecture. When the cluster is shut down, all machines except one are in their original state, and the last can be returned to its original state by deleting a directory. The system thus provides a means of using non-dedicated computers to create a cluster. An example session is documented.

Regional decomposition of CO2 emissions in the world: a cluster analysis

The purpose of this paper is to study the possible differences among countries as CO2 emitters and to examine the underlying causes of these differences. The starting point of the analysis is the Kaya identity, which allows us to break down per capita emissions in four components: an index of carbon intensity, transformation efficiency, energy intensity and social wealth. Through a cluster analysis we have identified five groups of countries with different behavior according to these four factors. One significant finding is that these groups are stable for the period analyzed. This suggests that a study based on these components can characterize quite accurately the polluting behavior of individual countries, that is to say, the classification found in the analysis could be used in other studies which look to study the behavior of countries in terms of CO2 emissions in homogeneous groups. In this sense, it supposes an advance over the traditional regional or rich-poor countries classifications .

Do creative industries cluster? mapping creative local production systems in Italy

An important debate on the role of creativity and culture as factors of local economic development is distinctly emerging. Despite the emphasis put on the theoretical definition of these concepts, it is necessary to strengthen comparative research for the identification and analysis of the kind of creativity embedded in the territory as well as its determinants. Creative local production systems are identified in Italy and Spain departing from local labour markets as territorial units, and focusing on two different kinds of creative

Cluster algebras, quiver representations and triangulated categories

This is an introduction to some aspects of Fomin-Zelevinsky’s cluster algebras and their links with the representation theory of quivers and with Calabi-Yau triangulated categories. It is based on lectures given by the author at summer schools held in 2006 (Bavaria)and 2008 (Jerusalem). In addition to by now classical material, we present the outline of a proof of the periodicity conjecture for pairs of Dynkin diagrams (details will appear elsewhere) and recent results on the interpretation of mutations as derived equivalences.

Why do creative industries cluster? An analysis of the determinants of clustering of creative industries

Creative industries tend to concentrate mainly around large- and medium-sized cities, forming creative local production systems. The text analyses the forces behind clustering of creative industries to provide the first empirical explanation of the determinants of creative employment clustering following a multidisciplinary approach based on cultural and creative economics, evolutionary geography and urban economics. A comparative analysis has been performed for Italy and Spain. The results show different patterns of creative employment clustering in both countries. The small role of historical and cultural endowments, the size of the place, the average size of creative industries, the productive diversity and the concentration of human capital and creative class have been found as common factors of clustering in both countries.

The Role of the European Union in the Processes to Ban Cluster Munitions

At the end of 2008 the Convention on Cluster Munitions (CCM) that outlawed almost all types of cluster munitions was signed. It was the product of the so-called Oslo process, which had been set up two years earlier as a reaction to the failure to add a new protocol banning cluster munitions to the Convention on Certain Conventional Weapons (CCW). The position of the EU in these two processes was ambivalent: on the one hand it belonged to the strongest proponents for a new protocol within the CCW, but on the other hand the member states were in general not able to act jointly in the Oslo Process. According to this working paper especially the aspect of national security and the related relationship to the United States influenced the stances of many member states and complicated the formation of a common European position. There were common normative values of the EU detected, which played a role in the CCW, but they were only secondary to other interests of the member states.

Assessing the Precision of Compositional Data in a Stratified Double Stage Cluster Sample: Application to the Swiss Earnings Structure Survey

Precision of released figures is not only an important quality feature of official statistics,it is also essential for a good understanding of the data. In this paper we show a casestudy of how precision could be conveyed if the multivariate nature of data has to betaken into account. In the official release of the Swiss earnings structure survey, the totalsalary is broken down into several wage components. We follow Aitchison's approachfor the analysis of compositional data, which is based on logratios of components. Wefirst present diferent multivariate analyses of the compositional data whereby the wagecomponents are broken down by economic activity classes. Then we propose a numberof ways to assess precision

Identificació de paisatges funcionals mitjançant anàlisi cluster

El terme paisatge i les seves aplicacions són cada dia més utilitzats per les administracions i altres entitats com a eina de gestió del territori. Aprofitant la gran quantitat de dades en bases compatibles amb SIG (Sistemes d’Informació Geogràfica) existents a Catalunya s’ha desenvolupat una síntesi cartogràfica on s’identifiquen els Paisatges Funcionals (PF) de Catalunya, concepte que fa referència al comportament fisico-ecològic del terreny a partir de variables topogràfiques i climàtiques convenientment transformades i agregades. S’ha utilitzat un mètode semiautomàtic i iteratiu de classificació no supervisada (clustering) que permet la creació d’una llegenda jeràrquica o nivells de generalització. S’ha obtingut com a resultat el Mapa de Paisatges Funcionals de Catalunya (MPFC) amb una llegenda de 26 categories de paisatges i 5 nivells de generalització amb una resolució espacial de 180 m. Paral·lelament, s’han realitzat validacions indirectes sobre el mapa obtingut a partir dels coneixements naturalistes i la cartografia existent, així com també d’un mapa d’incertesa (aplicant lògica difusa) que aporten informació de la fiabilitat de la classificació realitzada. Els Paisatges Funcionals obtinguts permeten relacionar zones de condicions topo-climàtiques homogènies i dividir el territori en zones caracteritzades ambientalment i no políticament amb la intenció que sigui d’utilitat a l’hora de millorar la gestió dels recursos naturals i la planificació d’actuacions humanes.

Ab initio absorption spectrum of NiO combining molecular dynamics with the embedded cluster approach in a discrete reaction field

We developed a procedure that combines three complementary computational methodologies to improve the theoretical description of the electronic structure of nickel oxide. The starting point is a Car-Parrinello molecular dynamics simulation to incorporate vibrorotational degrees of freedom into the material model. By means ofcomplete active space self-consistent field second-order perturbation theory (CASPT2) calculations on embedded clusters extracted from the resulting trajectory, we describe localized spectroscopic phenomena on NiO with an efficient treatment of electron correlation. The inclusion of thermal motion into the theoretical description allowsus to study electronic transitions that, otherwise, would be dipole forbidden in the ideal structure and results in a natural reproduction of the band broadening. Moreover, we improved the embedded cluster model by incorporating self-consistently at the complete active space self-consistent field (CASSCF) level a discrete (or direct) reaction field (DRF) in the cluster surroundings. The DRF approach offers an efficient treatment ofelectric response effects of the crystalline embedding to the electronic transitions localized in the cluster. We offer accurate theoretical estimates of the absorption spectrum and the density of states around the Fermi level of NiO, and a comprehensive explanation of the source of the broadening and the relaxation of the charge transferstates due to the adaptation of the environment