Conformational Dependence of 31P Chemical Shift Tensors

PŘECECHTĚLOVÁ, Jana, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ. Conformational Dependence of 31P Chemical Shift Tensors. In 42nd Symposium on Theoretical Chemistry CONFERENCE BOOK. Nemecko: Humboldt Universtaet Berlin, 2006, p. 137.

Basic information

• Original name: Conformational Dependence of 31P Chemical Shift Tensors
• Name in Czech: Konformacni zavislost tenzoru 31P chenickeho posunu.
• Authors: PŘECECHTĚLOVÁ, Jana, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ.
• Edition: Nemecko, 42nd Symposium on Theoretical Chemistry CONFERENCE BOOK, p. 137-137, 2006.
• Publisher: Humboldt Universtaet Berlin

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10403 Physical chemistry
• Country of publisher: Germany
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• Keywords in English: NMR DFT B-DNA 31P
• Tags: NMR DFT B-DNA 31P
• Tags: International impact

Abstract

NMR is a powerful tool to probe the conformation of the sugar phosphate backbone in nucleic acids. For instance, the large chemical shift anisotropy (CSA) of phosphorus nuclei can be used for constraining the orientation of phosphate groups relative to the molecular alignment tensor, provided that the P-31 chemical shift tensor and its orientation is known. Unfortunately, this is not the case for nucleic acids. Therefore, an assumption of a uniform CSA tensor for all backbone phosphates in oligonucleotides has been employed. In order to provide the necessary background for proving the relevance of such an assumption, we have carried out a study of the realtionships between the P-31 chemical shift tensors and the torsion angles in a nucleic acid backbone. Density functional theory has been applied to assess the influences of alpha (O3'--P--O5'--C5'), zeta (C3'--O3'--P--O5'), beta (P--O5'--C5'-C4'), and epsilon (C4'--C3'--O3'--P) on the principal tensor components. Two molecular models have been used for this purpose: a minimum model dimethylphosphate (dmp) and a dinucleside-3',5'-monophosphate with bases replaced by protons. Solvent effect has been treated by six water molecules hydrogen-bonded to the charged phosphate oxygens. The density functional calculations were carried out with Perdew and Wang's generalized gradient approximation (GGA) for exchange, Perdew's GGA for correlation (PWP86), and the IGLO-III orbital basis set. 31P chemical shift tensors have been obtained with the modified version of the deMon-KS program along with the deMon-NMR code. The trends in the torsion angle dependence of 31P chemical shift tensor components are very well reproduced with the minimum model dmp. These trends do change quantitatively but not qualitatively in explicit solvent compared to vacuo. The principal components delta_11 and delta_22 decrease while delta_33 increases upon solvation, which leads to the reduction of the chemical shift anisotropy. Furthermore, our calculations revealed a marked dependence of the 31P chemical shift tensor components on the backbone torsion angles. Although delta_11 varies only within 5--10 ppm, delta_22 and delta_33 vary within as much as 30 ppm due to changes in alpha or zeta up to 60 degs. In order to include the solvent and conformational dynamics, a combined MD/DFT study of 31P chemical shift tensors is currently in progress.

Abstract (in Czech)

NMR is a powerful tool to probe the conformation of the sugar phosphate backbone in nucleic acids. For instance, the large chemical shift anisotropy (CSA) of phosphorus nuclei can be used for constraining the orientation of phosphate groups relative to the molecular alignment tensor, provided that the P-31 chemical shift tensor and its orientation is known. Unfortunately, this is not the case for nucleic acids. Therefore, an assumption of a uniform CSA tensor for all backbone phosphates in oligonucleotides has been employed. In order to provide the necessary background for proving the relevance of such an assumption, we have carried out a study of the realtionships between the P-31 chemical shift tensors and the torsion angles in a nucleic acid backbone. Density functional theory has been applied to assess the influences of alpha (O3'--P--O5'--C5'), zeta (C3'--O3'--P--O5'), beta (P--O5'--C5'-C4'), and epsilon (C4'--C3'--O3'--P) on the principal tensor components. Two molecular models have been used for this purpose: a minimum model dimethylphosphate (dmp) and a dinucleside-3',5'-monophosphate with bases replaced by protons. Solvent effect has been treated by six water molecules hydrogen-bonded to the charged phosphate oxygens. The density functional calculations were carried out with Perdew and Wang's generalized gradient approximation (GGA) for exchange, Perdew's GGA for correlation (PWP86), and the IGLO-III orbital basis set. 31P chemical shift tensors have been obtained with the modified version of the deMon-KS program along with the deMon-NMR code. The trends in the torsion angle dependence of 31P chemical shift tensor components are very well reproduced with the minimum model dmp. These trends do change quantitatively but not qualitatively in explicit solvent compared to vacuo. The principal components delta_11 and delta_22 decrease while delta_33 increases upon solvation, which leads to the reduction of the chemical shift anisotropy. Furthermore, our calculations revealed a marked dependence of the 31P chemical shift tensor components on the backbone torsion angles. Although delta_11 varies only within 5--10 ppm, delta_22 and delta_33 vary within as much as 30 ppm due to changes in alpha or zeta up to 60 degs. In order to include the solvent and conformational dynamics, a combined MD/DFT study of 31P chemical shift tensors is currently in progress.

Links

• LC06030, research and development project: Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment