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

Glöß, Andreas; Brändle, Martin; Klopper, Wim; Lüthi, Hans Peter

doi:10.1080/00268976.2012.708793

Cited by 7 publications

(3 citation statements)

References 25 publications

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“…We calculated the binding energies of the transition states and sigma complexes using the explicitly correlated CCSD(T)-F12 method along with the same 6-311+G(2d,2p) basis set. The F12 methods essentially eliminate BSSE as has been demonstrated by Glob et al (2012). Zero point vibrational energies calculated using the B3LYP (ωB97X in the case of the weak interacting van der Wall complexes and TSs) were included in the single point CCSD(T) (or CCSD(T)-F12) energies.…”

Section: Electronic Structure Calculationsmentioning

confidence: 99%

LOW TEMPERATURE FORMATION OF NITROGEN-SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS (PANHs)—BARRIERLESS ROUTES TO DIHYDRO(iso)QUINOLINES

Parker

Yang

Dangi

et al. 2015

ApJ

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Meteorites contain bio-relevant molecules such as vitamins and nucleobases, which consist of aromatic structures with embedded nitrogen atoms. Questions remain over the chemical mechanisms responsible for the formation of nitrogen-substituted polycyclic aromatic hydrocarbons (PANHs) in extraterrestrial environments. By exploiting single collision conditions, we show that a radical mediated bimolecular collision between pyridyl radicals and 1,3-butadiene in the gas phase forms nitrogen-substituted polycyclic aromatic hydrocarbons (PANHs) 1,4-dihydroquinoline and to a minor amount 1,4-dihydroisoquinoline. The reaction proceeds through the formation of a van der Waals complex, which circumnavigates the entrance barrier implying it can operate at very low kinetic energy and therefore at low temperatures of 10 K as present in cold molecular clouds such as TMC-1. The discovery of facile de facto barrierless exoergic reaction mechanisms leading to PANH formation could play an important role in providing a population of aromatic structures upon which further photo-processing of ice condensates could occur to form nucleobases.

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Section: Electronic Structure Calculationsmentioning

confidence: 99%

LOW TEMPERATURE FORMATION OF NITROGEN-SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS (PANHs)—BARRIERLESS ROUTES TO DIHYDRO(iso)QUINOLINES

Parker

Yang

Dangi

et al. 2015

ApJ

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“…Interactions of aromatic molecules were often studied as models for interactions of π-systems [1,2,7,8,23]. In addition, interactions of ethene (ethylene) have been studied as systems for interactions of molecules with double bonds [11][12][13][14][15][16][17][18][19][20][21][22]. Differences in behavior between saturated molecules and unsaturated molecules with double bonds, as well as differences between unsaturated molecules with cis-and trans-double bonds are of great importance in various molecular systems and processes.…”

Section: Introductionmentioning

confidence: 99%

Best methods for calculating interaction energies in 2-butene and butane systems

Zaric

Bugarski

Kijevčanin

2017

Computational and Theoretical Chemistry

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311++G** and 6-31G**, for each method, have been performed, calculating interaction energies in (1) unsaturated/unsaturated systems (2-butene dimers), (2) unsaturated/saturated system (between butane and 2-butene) and (3) saturated/saturated (butane dimers). The calculated interaction energies are compared with accurate CCSD(T)/CBS energies. The data shows that most levels of theory have the highest errors for systems with butane dimers, and calculated interaction energies in these systems are overestimated. The best levels, overall for all systems, are BLYP-D3BJ/def2-QZVP and BLYP-D3BJ/cc-pVQZ with similar root mean square deviation (RMSD) values of 0.056 kcal mol −1 and 0.060 kcalmol −1 compared to CCSD(T) values. The best level for (1) 2-butene dimers is B3LYP-D3BJ/aug-cc-pVDZ; for (2) interactions between 2-butene and butane is BLYP-D3BJ/def2-SVP; while for (3) butane dimers is BLYP-D3BJ/def2-QZVP. The difference in calculated energies among several method are not high, however, it is important that most of the DFT methods overestimate interactions in butane dimers.

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“…FoX and its interfaceswere used to allow solid-state simulation codes such as SIESTA [39] and GULP [40] to directly output CML without introducing additional dependencies intothe applications’ compilation process. Very recently, developers of theTURBOMOLE package reported the use of CML and the interfaces in the FoX library tostore a subset of their output data needed to develop a database for computationaldata [41]. …”

Section: Introductionmentioning

confidence: 99%

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

2013

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BackgroundMultidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinformation. In this paper an end-to-end use of semantically rich data incomputational chemistry is demonstrated utilizing the Chemical MarkupLanguage (CML) framework. Semantically rich data is generated by the NWChemcomputational chemistry software with the FoX library and utilized by theAvogadro molecular editor for analysis and visualization.ResultsThe NWChem computational chemistry software has been modified and coupled tothe FoX library to write CML compliant XML data files. The FoX library wasexpanded to represent the lexical input files and molecular orbitals used bythe computational chemistry software. Draft dictionary entries and a formatfor molecular orbitals within CML CompChem were developed. The Avogadroapplication was extended to read in CML data, and display molecular geometryand electronic structure in the GUI allowing for an end-to-end solutionwhere Avogadro can create input structures, generate input files, NWChem canrun the calculation and Avogadro can then read in and analyse the CML outputproduced. The developments outlined in this paper will be made available infuture releases of NWChem, FoX, and Avogadro.ConclusionsThe production of CML compliant XML files for computational chemistrysoftware such as NWChem can be accomplished relatively easily using the FoXlibrary. The CML data can be read in by a newly developed reader in Avogadroand analysed or visualized in various ways. A community-based effort isneeded to further develop the CML CompChem convention and dictionary. Thiswill enable the long-term goal of allowing a researcher to run simple“Google-style” searches of chemistry and physics and have theresults of computational calculations returned in a comprehensible formalongside articles from the published literature.Electronic supplementary materialThe online version of this article (doi:10.1186/1758-2946-5-25) contains supplementary material, which is available to authorized users.

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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

Cited by 7 publications

References 25 publications

LOW TEMPERATURE FORMATION OF NITROGEN-SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS (PANHs)—BARRIERLESS ROUTES TO DIHYDRO(iso)QUINOLINES

LOW TEMPERATURE FORMATION OF NITROGEN-SUBSTITUTED POLYCYCLIC AROMATIC HYDROCARBONS (PANHs)—BARRIERLESS ROUTES TO DIHYDRO(iso)QUINOLINES

Best methods for calculating interaction energies in 2-butene and butane systems

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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