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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)
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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)
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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)
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skos:notation
| - RIV/00216224:14740/13:00067940!RIV14-MSM-14740___
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http://linked.open...avai/riv/aktivita
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http://linked.open...avai/riv/aktivity
| - I, P(ED1.1.00/02.0068), P(LC06030), Z(MSM0021622413)
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http://linked.open...iv/cisloPeriodika
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http://linked.open...vai/riv/dodaniDat
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http://linked.open...aciTvurceVysledku
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http://linked.open.../riv/druhVysledku
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http://linked.open...iv/duvernostUdaju
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http://linked.open...titaPredkladatele
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http://linked.open...dnocenehoVysledku
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http://linked.open...ai/riv/idVysledku
| - RIV/00216224:14740/13:00067940
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http://linked.open...riv/jazykVysledku
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http://linked.open.../riv/klicovaSlova
| - phosphorus chemical shift nucleic acids MD DFT (en)
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http://linked.open.../riv/klicoveSlovo
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http://linked.open...odStatuVydavatele
| - US - Spojené státy americké
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http://linked.open...ontrolniKodProRIV
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http://linked.open...i/riv/nazevZdroje
| - Journal of Chemical Theory and Computation
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http://linked.open...in/vavai/riv/obor
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http://linked.open...ichTvurcuVysledku
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http://linked.open...cetTvurcuVysledku
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http://linked.open...vavai/riv/projekt
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http://linked.open...UplatneniVysledku
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http://linked.open...v/svazekPeriodika
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http://linked.open...iv/tvurceVysledku
| - Dračínský, Martin
- Novotný, Jan
- Sklenář, Vladimír
- Munzarová, Markéta
- Přecechtělová, Jana
- Vaara, Juha
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http://linked.open...ain/vavai/riv/wos
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http://linked.open...n/vavai/riv/zamer
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issn
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number of pages
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http://bibframe.org/vocab/doi
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http://localhost/t...ganizacniJednotka
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