The effect of water on NMR spin-spin couplings in DNA:
Improvement of calculated values by application of two solvent
models

J 2003

The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models

SYCHROVSKÝ, Vladimír, Bohdan SCHNEIDER, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ et. al.

Basic information

Original name

The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models

Authors

SYCHROVSKÝ, Vladimír (203 Czech Republic), Bohdan SCHNEIDER (203 Czech Republic), Pavel HOBZA (203 Czech Republic), Lukáš ŽÍDEK (203 Czech Republic) and Vladimír SKLENÁŘ (203 Czech Republic, guarantor)

Edition

Physical Chemistry Chemical Physics, Great Britain, ROYAL SOC CHEMISTRY, 2003, 1463-9076

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 1.959

RIV identification code

RIV/00216224:14310/03:00007956

Organization unit

Faculty of Science

UT WoS

000181278300011

Keywords in English

NMR; coupling constants; DNA hairpin DFT

Abstract

V originále

A water solvent effects on isotropic one-bond 1J(X,H), 1J(C,X) and two-bond 2J(X,H), (X=C,N) indirect NMR spin-spin coupling constants measured previously in 13C, 15N-labeled DNA hairpin molecule d(GCGAAGC) were investigated theoretically at ab initio level by application of explicit and PCM models of solvent. Sensitivity of the Fermi contact contribution to the total J coupling towards the solvent inclusion calculated using coupled perturbed density functional theory with B3LYP hybrid functional is dominating, while the solvent shifts of the other three J contributions are negligible. Consideration of the solvent leads to the noticeable shift of especially 1J(C,H) couplings. The largest shift of 6.1 Hz was found for 1J(C8,H8) coupling in guanine. Further inclusion of solvent decreases mean absolute deviation between calculated and experimental J constants from 1.7 to 1.1 Hz for guanine, from 2.4 to 0.6 Hz for cytosine, and from 2.3 to 1.6 Hz for adenine. In the case of explicit solvent, the 1J(C8,H8) solvent shift seems to be sensitive to the magnitude of charge transfer from water sigma bonding O-H and Oxygen lone pair orbitals to the sigma* antibonding C8-H8, C8-N7, and C8-N9 orbitals of guanine. Both explicit and PCM solvent models provide similar improvement of calculated couplings.

Links

GA203/96/1513, research and development project

Name: Moderní metody magnetické rezonance a jejich využití pro studium struktury a dynamiky biologicky zajímavých molekul

Investor: Czech Science Foundation, Modern techniques of nuclear magnetic resonance and their applications to study structure and dynamics of biologically relevant macromolecules

MSM 143100005, plan (intention)

Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism

Citovat

SYCHROVSKÝ, Vladimír, Bohdan SCHNEIDER, Pavel HOBZA, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models. Physical Chemistry Chemical Physics. Great Britain: ROYAL SOC CHEMISTRY, 2003, vol. 5, No 4, p. 734-739. ISSN 1463-9076.

@article{484671,
   author = {Sychrovský, Vladimír and Schneider, Bohdan and Hobza, Pavel and Žídek, Lukáš and Sklenář, Vladimír},
   article_location = {Great Britain},
   article_number = {4},
   keywords = {NMR; coupling constants; DNA hairpin DFT},
   language = {eng},
   issn = {1463-9076},
   journal = {Physical Chemistry Chemical Physics},
   title = {The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models},
   volume = {5},
   year = {2003}
}

TY  - JOUR
ID  - 484671
AU  - Sychrovský, Vladimír - Schneider, Bohdan - Hobza, Pavel - Žídek, Lukáš - Sklenář, Vladimír
PY  - 2003
TI  - The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models
JF  - Physical Chemistry Chemical Physics
VL  - 5
IS  - 4
SP  - 734-739
EP  - 734-739
PB  - ROYAL SOC CHEMISTRY
SN  - 14639076
KW  - NMR
KW  - coupling constants
KW  - DNA hairpin DFT
N2  - A water solvent effects on isotropic one-bond 1J(X,H), 1J(C,X) and two-bond 2J(X,H), (X=C,N) indirect NMR spin-spin coupling constants measured previously in 13C, 15N-labeled DNA hairpin molecule d(GCGAAGC) were investigated theoretically at ab initio level by application of explicit and PCM models of solvent. Sensitivity of the Fermi contact contribution to the total J coupling towards the solvent inclusion calculated using coupled perturbed density functional theory with B3LYP hybrid functional is dominating, while the solvent shifts of the other three J contributions are negligible. Consideration of the solvent leads to the noticeable shift of especially 1J(C,H) couplings. The largest shift of 6.1 Hz was found for 1J(C8,H8) coupling in guanine. Further inclusion of solvent decreases mean absolute deviation between calculated and experimental J constants from 1.7 to 1.1 Hz for guanine, from 2.4 to 0.6 Hz for cytosine, and from 2.3 to 1.6 Hz for adenine. In the case of explicit solvent, the 1J(C8,H8) solvent shift seems to be sensitive to the magnitude of charge transfer from water sigma bonding O-H and Oxygen lone pair orbitals to the sigma* antibonding C8-H8, C8-N7, and C8-N9 orbitals of guanine. Both explicit and PCM solvent models provide similar improvement of calculated couplings.
ER  -

SYCHROVSKÝ, Vladimír, Bohdan SCHNEIDER, Pavel HOBZA, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models. \textit{Physical Chemistry Chemical Physics}. Great Britain: ROYAL SOC CHEMISTRY, 2003, vol.~5, No~4, p.~734-739. ISSN~1463-9076.

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