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, vol. 5, No 4, p. 734-739. ISSN 1463-9076. 2003.
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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
Original language English
Type of outcome Article in a journal
Field of Study 10403 Physical chemistry
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
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
Tags coupling constants, DNA hairpin DFT, NMR
Changed by Changed by: prof. RNDr. Vladimír Sklenář, DrSc., učo 2611. Changed: 20/6/2008 12:55.
Abstract
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 projectName: 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
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