Martin Brändle

Comparison of a combined quantum mechanics/interatomic potential function approach with its periodic quantum-mechanical limit: Proton siting and ammonia adsorption in zeolite chabazite

Comparison is made between a combined quantum mechanics/interatomic potential function approach (QM-Pot) and its fully quantum-mechanical limit, ab initio calculation applying periodic boundary conditions. The Hartree–Fock (HF) method is combined with ab initio-parametrized ion pair shell model potential functions. The CRYSTAL code is employed for the periodic Hartree–Fock calculations. The same double-/valence triple-zeta polarization basis sets are used in both the approaches. The proton siting and ammonia adsorption in a high-silica acidic zeolite catalyst, H-chabazite (Si/Al=11, space group P1, unit cell H–AlO2[SiO2]11) are examined. The combined QM-Pot relative stabilities and reaction energies deviate from the periodic full QM results by 4–9 kJ/mol only, which demonstrates the power of our combined approach. This conclusion is also supported by comparison of the electrostatic potential inside the zeolite pore, calculated from the periodic wave function and by the QM-Pot approach. Framework oxygen O1...

Citation analysis with microsoft academic

We explore if and how Microsoft Academic (MA) could be used for bibliometric analyses. First, we examine the Academic Knowledge API (AK API), an interface to access MA data, and compare it to Google Scholar (GS). Second, we perform a comparative citation analysis of researchers by normalizing data from MA and Scopus. We find that MA offers structured and rich metadata, which facilitates data retrieval, handling and processing. In addition, the AK API allows retrieving frequency distributions of citations. We consider these features to be a major advantage of MA over GS. However, we identify four main limitations regarding the available metadata. First, MA does not provide the document type of a publication. Second, the “fields of study” are dynamic, too specific and field hierarchies are incoherent. Third, some publications are assigned to incorrect years. Fourth, the metadata of some publications did not include all authors. Nevertheless, we show that an average-based indicator (i.e. the journal normalized citation score; JNCS) as well as a distribution-based indicator (i.e. percentile rank classes; PR classes) can be calculated with relative ease using MA. Hence, normalization of citation counts is feasible with MA. The citation analyses in MA and Scopus yield uniform results. The JNCS and the PR classes are similar in both databases, and, as a consequence, the evaluation of the researchers’ publication impact is congruent in MA and Scopus. Given the fast development in the last year, we postulate that MA has the potential to be used for full-fledged bibliometric analyses.

The coverage of Microsoft Academic: analyzing the publication output of a university

This is the first detailed study on the coverage of Microsoft Academic (MA). Based on the complete and verified publication list of a university, the coverage of MA was assessed and compared with two benchmark databases, Scopus and Web of Science (WoS), on the level of individual publications. Citation counts were analyzed, and issues related to data retrieval and data quality were examined. A Perl script was written to retrieve metadata from MA based on publication titles. The script is freely available on GitHub. We find that MA covers journal articles, working papers, and conference items to a substantial extent and indexes more document types than the benchmark databases (e.g., working papers, dissertations). MA clearly surpasses Scopus and WoS in covering book-related document types and conference items but falls slightly behind Scopus in journal articles. The coverage of MA is favorable for evaluative bibliometrics in most research fields, including economics/business, computer/information sciences, and mathematics. However, MA shows biases similar to Scopus and WoS with regard to the coverage of the humanities, non-English publications, and open-access publications. Rank correlations of citation counts are high between MA and the benchmark databases. We find that the publication year is correct for 89.5% of all publications and the number of authors is correct for 95.1% of the journal articles. Given the fast and ongoing development of MA, we conclude that MA is on the verge of becoming a bibliometric superpower. However, comprehensive studies on the quality of MA metadata are still lacking.

Resource description framework technologies in chemistry

EditorialThe Resource Description Framework (RDF) is provid-ing the life sciences with new standards around dataand knowledge management. The uptake in the lifesciences is significantly higher than the uptake of theeXtensible Markup Language (XML) and even relationaldatabases, as was recently shown by Splendiani et al. [1]Chemistry is adopting these methods too. For example,Murray-Rust and co-workers used RDF already in 2004to distribute news items where chemical structures wereembedded using RDF Site Summary 1.0 [2]. Frey imple-mented a system which would now be referred to as anelectronic lab notebook (ELN) [3]. The use of theSPARQL query language goes back to 2007 where itwas used in a system to annotate crystal structures [4].The American Chemical Society (ACS) Division ofChemical Information (CINF) invited scientists fromaround the world to present their use of RDF technolo-gies in chemistry on 22nd-23rd August 2010 at the240th ACS National Meeting in Boston, USA. Duringthree half-day sessions, the speakers demonstrated a mixof smaller and larger initiatives where RDF and relatedtechnologies are used in cheminformatics and bioinfor-matics as Open Standards for data exchange, commonlanguages (ontologies), and problem solving. The fifteenpresentations were grouped in the themes computation,ontologies, and chemical applications. Figures 1, 2 and 3display the most important keywords reflecting theabstracts of the talks in each session as word clouds [5].The goal of the meeting was to make more chemistsaware of what the RDF Open Standard has to offer tochemistry. We are delighted to continue this effort withthis Thematic Series, for which the speakers (andothers) were invited to present their work in more detailto a wider chemistry community. The choice of anOpen Access journal follows this goal. At this place, wewould like to thank Pfizer, Inc., who had partiallyfunded the article processing charges for this ThematicSeries. Pfizer, Inc. has had no input into the content ofthe publication or the articles themselves. All articles inthe series were independently prepared by the authorsand were subjected to the journal’s standard peer reviewprocess.In the remainder of this editorial, we will briefly out-line the various RDF technologies and how they havebeen used in chemistry so far.1 ConceptsThe core RDF specification was introduced by theWorld Wide Web Consortium (W3C) in 1999 [6] anddefines the foundation of the RDF technologies. It hasevolved into a set of recommendations by the W3Cpublished in 2004 (See Table 1). RDF specifies a verysimple data structure linking a subject to an object or avalue (literal) using a predicate. Cheminformaticians willrecognize this data structure as an edge from graph the-ory. This structure allowsus to represent facts like“vanillin dissolves in methyl alcohol” [7]. RDF uses Uni-form Resource Identifiers (URIs) to identify things.Therefore, the RDF equivalent of the solution statementcould be like this so-called triple:http://dbpedia.org/resource/Vanillinhttp://example.com/dissolvesInhttp://dbpedia.org/resource/Methanol.Since URIs may be used to reference resources on anyserver worldwide, RDF triples allow to span a globalgraph data structure. This is not surprising, since RDFis the core technology behind the proposed SemanticWeb [8]. In fact, the Web nature is clear here, as onecan follow both the URIs for vanillin and methanol toobtain further information on those two chemicals.These molecules’ URIs are said to be dereferencable,allowing agents to spider the Web for information fol-lowing the hyperlinks, quite like how you follow hyper-links on websites. Hence, the term Semantic Web.Recent projects such as Bio2RDF [9], Chem2Bio2RDF[10], and OpenTox [11] have brought genomic, chemical

The MP2 binding energy of the ethene dimer and its dependence on the auxiliary basis sets: a benchmark study using a newly developed infrastructure for the processing of quantum chemical data

Data intense processes such as the establishment of quantitative structure–property relationships, the design of novel compounds and also the validation of new quantum chemical methods call for a structured approach for the processing of the results. Whereas in quantum chemistry there are established de facto standards for the computational methods, community standards for [exchange-] data formats are still under development. In this article we present a benchmark study of the (auxiliary-) basis set dependence of the binding energies of an array of conformers of the ethene dimer using the RI-MP2-F12 method. The study was performed using a version of the TURBOMOLE program package modified to provide output in an extended CML format to be imported in an eXist database. This infrastructure for the generation, archival, analysis, and exchange of quantum chemical data is briefly introduced in this article.

Size quantization and surface states of molybdenum sulphide clusters: a molecular orbital approach

Abstract A projection procedure is described, as a tool to separately analyze the electronic states of surface and bulk regions of nanometer-sized particles. It allows to discuss surface states in terms of specific atoms, coordination numbers, oxidation states, and connectivities and it gives insight into the size quantization of clusters. The procedure is general and can be used for studying clusters up to respectable size, of different composition and different structure. Molecular orbital calculations on D3h−(MoS2)3n2S2(H2S)6n, n = 1,2… clusters, cluster chains and the band structure of ∞2[MoS2] are reported. The HOMO and LUMO are separated by only about 0.1 eV in Mo12S38H24. Even this small splitting vanishes in the larger clusters. However, in the limiting infinite case, ∞2[MoS2], the expected semiconductor band gap evolves. Applying the projection procedure to the clusters we find that surface states, originating from the outermost molybdenum atoms and being of mainly 4dx2−y2, 4dxy and 4dz2 with some S(3p) contributions, fill up the band gap and that the bulk shows the expected quantum-size behaviour.

Silver clusters in the cages of zeolites: A quantum chemical study

The electronic structure of zeolite A is developed in a step by step procedure from the simple OhH8Si8O12 molecule, to the ∞1[(-O)2H4[Si8O12)] chain, to the ∞2[(-O4)(Si8O12)] layer, and finally to the silica zeolite A framework ∞3[Si24O48]. It is remarkable how well the calculated band structures of both, ∞2[(-O)4(Si8O12)] and ∞3[Si24O48] correspond to the experimentally determined band structure of α-quartz with a Fermi level of -10.55 eV. The HOMO region consists in each case of nonbonding 2p-oxygen bands which in a localized language can be denoted as oxygen lone pairs ( | O<). We observe in each case the typical behaviour of an insulator with saturated valencies whose electronic structure can be described as being localized and is already present in the starting Oh-H8Si8O12 molecule. The double-8-rings D8R of the ∞2[(-O)4(Si8O12)] layer have a pore diameter of 4.1 Å, the same as the pore opening of zeolite A. It is large enough to accept up to four Ag, forming ∞2[(-O)4(Si8O12)Agn], n = 1, 2, 3, 4, layers, suitable for modelling the electronic interactions between the zeolite cavity embedded silver clusters and between the clusters and the zeolite framework. With one Ag per D8R the band structure is simply a superposition of the 4d, 5s and 5p levels of a layer of nearly noninteracting Ag and the silicon dioxide layer. The Ag-d band lies below the oxygen lone pairs, the Ag-s band lies about 3 eV above the oxygen lone pairs, and the Ag-5p bands are in the antibonding silicon dioxide region. The first electronic transition is of oxygen lone pair to Ag-5s LMCT type. Increasing silver content results in progressive splitting of the 5σ Ag bands and shifts the first (Agm+n)• ← (| O<) charge transfer transition to lower energies. The filled Ag 4d-bands lie always significantly below the (| O<) HOCOs (highest occupied crystal orbitals) but their band width increases with increasing silver content. In all cases the zeolite environment separates the Ag clusters through antibonding Ag-(← O<) interactions so that the coupling remains weak and it makes sense to describe the Ag clusters in the D8R as quantum dots weakly interacting with each other.

The number of linked references of publications in Microsoft Academic in comparison with the Web of Science

In the context of a comprehensive Microsoft Academic (MA) study, we explored in an initial step the quality of linked references data in MA in comparison with Web of Science (WoS). Linked references are the backbone of bibliometrics, because they are the basis of the times cited information in citation indexes. We found that the concordance of linked references between MA and WoS ranges from weak to nonexistent for the full sample (publications of the University of Zurich with less than 50 linked references in MA). An analysis with a sample restricted to less than 50 linked references in WoS showed a strong agreement between linked references in MA and WoS.