About: Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/ct300488y?prevSearch=%255BContrib%253A%2BMunzarova%255D&searchHistoryKey=
Description	This work addresses the question of the ability of the MD/DFT approach to reproduce sequence trend in 31P chemical shifts (delta_P) in the backbone of nucleic acids. delta_P for [d(CGCGAATTCGCG)]2 have been computed using DFT calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of 31P chemical shifts for two distinct B-DNA subfamilies BI and BII, delta_P/BI and delta_P/BII, have been determined as averages over the BI and BII subparts of the MD trajectory. This has been done for various samplings of MD trajectory and for two sizes of both the model and the solvent embedding. For all of the combinations of trajectory sampling, model size, and embedding size, sequence dependence of delta_P/BI in the order of 0.4–0.5 ppm has been obtained. This work addresses the question of the ability of the MD/DFT approach to reproduce sequence trend in 31P chemical shifts (delta_P) in the backbone of nucleic acids. delta_P for [d(CGCGAATTCGCG)]2 have been computed using DFT calculations on model compounds with geometries cut out of snapshots of classical molecular dynamics (MD) simulations. The values of 31P chemical shifts for two distinct B-DNA subfamilies BI and BII, delta_P/BI and delta_P/BII, have been determined as averages over the BI and BII subparts of the MD trajectory. This has been done for various samplings of MD trajectory and for two sizes of both the model and the solvent embedding. For all of the combinations of trajectory sampling, model size, and embedding size, sequence dependence of delta_P/BI in the order of 0.4–0.5 ppm has been obtained. (en)
Title	Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations (en)
skos:prefLabel	Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations (en)
skos:notation	RIV/00216224:14740/13:00067940!RIV14-MSM-14740___
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(LC06030), Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	3
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Přecechtělová, Jana Sklenář, Vladimír Munzarová, Markéta Novotný, Jan
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	111331
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00067940
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	phosphorus chemical shift nucleic acids MD DFT (en)
http://linked.open.../riv/klicoveSlovo	phosphorus chemical shift nucleic acids MD DFT
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[316537887562]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Biomolecular centre
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Dračínský, Martin Novotný, Jan Sklenář, Vladimír Munzarová, Markéta Přecechtělová, Jana Vaara, Juha
http://linked.open...ain/vavai/riv/wos	000316168700035
http://linked.open...n/vavai/riv/zamer	Proteiny v metabolismu a při interakci organismů s prostředím
issn	1549-9618
number of pages	16 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct300488y
http://localhost/t...ganizacniJednotka	14740

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