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Statements

Subject Item
n2:RIV%2F00216224%3A14740%2F13%3A00067940%21RIV14-MSM-14740___
rdf:type
skos:Concept n14:Vysledek
rdfs:seeAlso
http://pubs.acs.org/doi/abs/10.1021/ct300488y?prevSearch=%255BContrib%253A%2BMunzarova%255D&searchHistoryKey=
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14740/13:00067940!RIV14-MSM-14740___
n14:predkladatel
n19:orjk%3A14740
n4:aktivita
n8:P n8:I n8:Z
n4:aktivity
I, P(ED1.1.00/02.0068), P(LC06030), Z(MSM0021622413)
n4:cisloPeriodika
3
n4:dodaniDat
n18:2014
n4:domaciTvurceVysledku
n6:1962604 n6:2066475 n6:2462354 n6:3906884
n4:druhVysledku
n9:J
n4:duvernostUdaju
n11:S
n4:entitaPredkladatele
n21:predkladatel
n4:idSjednocenehoVysledku
111331
n4:idVysledku
RIV/00216224:14740/13:00067940
n4:jazykVysledku
n22:eng
n4:klicovaSlova
phosphorus chemical shift nucleic acids MD DFT
n4:klicoveSlovo
n7:phosphorus%20chemical%20shift%20nucleic%20acids%20MD%20DFT
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[316537887562]
n4:nazevZdroje
Journal of Chemical Theory and Computation
n4:obor
n15:CF
n4:pocetDomacichTvurcuVysledku
4
n4:pocetTvurcuVysledku
6
n4:projekt
n20:ED1.1.00%2F02.0068 n20:LC06030
n4:rokUplatneniVysledku
n18:2013
n4:svazekPeriodika
9
n4:tvurceVysledku
Přecechtělová, Jana Novotný, Jan Sklenář, Vladimír Dračínský, Martin Munzarová, Markéta Vaara, Juha
n4:wos
000316168700035
n4:zamer
n12:MSM0021622413
s:issn
1549-9618
s:numberOfPages
16
n17:doi
10.1021/ct300488y
n5:organizacniJednotka
14740