About: Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	A comprehensive quantum chemical analysis of the influence of backbone torsion angles on 31P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 +/- 0.3 and 1.6 +/- 0.3 ppm between the BI and BII chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative 31P chemical shift for a residue in pure BI conformation compared to residues in mixed BI/BII conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both BI and BII regions of DNA structures. 31P chemical shift ranges within 3.5 +/- 0.8 ppm in the BI region and within 4. A comprehensive quantum chemical analysis of the influence of backbone torsion angles on 31P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 +/- 0.3 and 1.6 +/- 0.3 ppm between the BI and BII chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative 31P chemical shift for a residue in pure BI conformation compared to residues in mixed BI/BII conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both BI and BII regions of DNA structures. 31P chemical shift ranges within 3.5 +/- 0.8 ppm in the BI region and within 4. (en)
Title	Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations (en)
skos:prefLabel	Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations (en)
skos:notation	RIV/00216224:14310/10:00040633!RIV11-MSM-14310___
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(IAA500040903), P(LC06030), S, Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	48
http://linked.open...vai/riv/dodaniDat	2011
http://linked.open...aciTvurceVysledku	Přecechtělová, Jana Novák, Petr Sklenář, Vladimír Munzarová, Markéta
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 / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	278787
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/10:00040633
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	MD DFT nucleic acids NMR phosphorus (en)
http://linked.open.../riv/klicoveSlovo	MD DFT nucleic acids NMR phosphorus
http://linked.open...odStatuVydavatele	CZ - Česká republika
http://linked.open...ontrolniKodProRIV	[1CC599EE0731]
http://linked.open...i/riv/nazevZdroje	The Journal of the American Chemical Society
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Biomolecular centre Biophysics and bioinformatics of genomic DNA fragments very rich in guanine and adenine
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	132
http://linked.open...iv/tvurceVysledku	Novák, Petr Sklenář, Vladimír Munzarová, Markéta Přecechtělová, Jana Kaupp, Martin
http://linked.open...n/vavai/riv/zamer	Proteiny v metabolismu a při interakci organismů s prostředím
issn	0002-7863
number of pages	10 (xsd:int)
http://localhost/t...ganizacniJednotka	14310

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