Statistical Analysis of Quantum Chemical Data Using Generalized XML/CML Archives for the Derivation of Molecular Design Rules

Elsener, Andreas; Samson, Claire C. M.; Brändle, Martin; Bühlmann, Peter; Lüthi, Hans Peter

doi:10.2533/chimia.2007.165

Cited by 4 publications

(6 citation statements)

References 4 publications

(5 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, we did not want to parse the standard output and create XML code as in an earlier study [22], but rather have the programs write out XML code directly.…”

Section: Computational and Technical Details 21 The Turbomole-xml-ementioning

confidence: 99%

“…The extracted XML data can be post-processed and converted to any other format using XSL transformations [30]. After an evaluation of several XML native databases (Apache Xindice [31], used by us in earlier work [22], Oracle Berkeley DB XML [32], and eXist [21]), we chose the open source XML database eXist because this product showed fast performance for queries, offers efficient automatic indexing of XML elements and attributes, and is compliant with the W3C standards XPath, XQuery, and XUpdate. Since it is written in Java, it can be installed on any operating system as a stand-alone or embedded client-server system.…”

Section: Molecular Physics 2525mentioning

confidence: 99%

“…The data, generated with the TURBOMOLE program package [20] and expressed in an extended CML format, are imported in a searchable database (eXist [21]) for analysis and exchange. This study follows earlier work where a parser-based infrastructure was used to find structure-property relationships in over one thousand donor-acceptor substituted polyacetylenes [22].…”

Section: Introductionmentioning

confidence: 98%

See 2 more Smart Citations

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

et al. 2012

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…Furthermore, we did not want to parse the standard output and create XML code as in an earlier study [22], but rather have the programs write out XML code directly.…”

Section: Computational and Technical Details 21 The Turbomole-xml-ementioning

confidence: 99%

Section: Molecular Physics 2525mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

See 1 more Smart Citation

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

et al. 2012

Self Cite

View full text Add to dashboard Cite

show abstract

“…Figure 9 (HOPV15): Data-centric-and first-principle-based modeling interoperating in order to enrich (finding new lead prospects) and expedite (better descriptors) the screening process. UUID calculation identifier 2,3 Program-name 2,3 , -version 2,3 , -mode 2,3 (serial, parallel), OS 2,3 , host name 2,3 Start and end time of calculation (wall time) 2,3 Total energies and components (potential, kinetic) 3,4 , RI-MP2-[R12/F12] pair energies (single point) 3,4 , orbital energies and orbital occupation numbers 4 *, HOMO/LUMO energy difference 4 * charge 3,4 , dipole 3,4 , quadrupole 3,4 , quadrupole anisotropy 3,4 Mulliken 4 , Löwdin 4 and NPA atomic charges 4 * 1 CML element or attribute 2 used in CML element metadata 3 for details see [8] 4 used in CML element property Table 2: Exploring the computed information at greater detail: the result of a query on the number of hydrogen bonds formed as a result of the quantum chemical optimization process. Only OHO bonds were searched for in these two collections.…”

Section: Figure 3 (Xquery)mentioning

confidence: 99%

“…In an effort to optimize the non-linear optical properties of donor-acceptor functionalized linearly pi-conjugated polymers, some of the present authors (HPL, MPB) developed a "computing infrastructure", which allowed the processing of the results of a few thousand compounds using statistical analysis to establish relationships between molecular properties [2]. The output of the quantum chemical code (Gaussian03, [3]) was transformed to Chemical Markup Language format (CML, [4]), an Extensible Markup Language "dialect" (XML, [5]), using a parser (JumboMarker, [6]).…”

Section: Introductionmentioning

confidence: 99%

The quantum chemical search for novel materials and the issue of data processing: The InfoMol project

Lüthi

Heinen

Schneider

et al. 2016

Journal of Computational Science

Self Cite

View full text Add to dashboard Cite

In the search for novel materials, quantum chemical modeling and simulation has taken an important role. Molecular properties are computed on the basis of first-principles methods and screened against pre-defined criteria. Alternatively, the results of these computations are used as source data to enhance the predictions of data-centric models. Whichever modeling strategy is being applied, dataintense steps are involved in the process. One key bottleneck in this regard is the lack of availability of machine-readable output for virtually all quantum chemistry codes. The results of computations need to be extracted manually or using scripts and parsers, instead of directly being written out in machinereadable format to be imported into a database for archival, analysis and exchange. We present two solutions implemented in two selected examples, the TURBOMOLE and PSI4 program packages. Next to the standard output, both codes generate Extensible Markup Language (XML) output files, but in two different ways. The generation of machine-readable output in a structured format can easily be implemented, and, as long as the data can be transformed, the choice of data format is secondary. The concept is illustrated for two different use cases from method benchmarking and drug design. A third illustration addresses the definition of a data processing and exchange protocol for screening libraries of light-harvesting compounds.

show abstract

State-of-the-art and challenges in theoretical simulations of heterogeneous catalysis at the microscopic level

López

Almora‐Barrios

Carchini

et al. 2012

Catal. Sci. Technol.

View full text Add to dashboard Cite

Theoretical simulations of systems that represent heterogeneous catalysts constitute one of the main tools in the research for new catalytic materials. Theory plays a role in the three stages of the development ladder: characterisation, understanding and prediction. Due to the complexity of the computational methods, there is a strong need to integrate different models and cover the relevant scales in heterogeneous catalysis. This requirement constitutes an important drawback as scientists need training in several aspects of the problem including chemical, physical and engineering views of the modelling while keeping the experimental and industrial interests and needs in perspective. Here we present some of the latest developments in the field of theoretical simulations at the microscopic level while illustrating suitable examples that show how theory can shed light on several aspects of characterisation, activity, selectivity and long-term stability.

show abstract

Statistical Analysis of Quantum Chemical Data Using Generalized XML/CML Archives for the Derivation of Molecular Design Rules

Cited by 4 publications

References 4 publications

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

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

The quantum chemical search for novel materials and the issue of data processing: The InfoMol project

State-of-the-art and challenges in theoretical simulations of heterogeneous catalysis at the microscopic level

Contact Info

Product

Resources

About