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Tichotová MC, Tučková L, Kocek H, Růžička A, Straka M, Procházková E. Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach. Phys Chem Chem Phys 2024; 26:2016-2024. [PMID: 38126374 DOI: 10.1039/d3cp04099b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.
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Affiliation(s)
- Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice 532 10, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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2
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Fukal J, Zgarbová M, Jurečka P, Šebera J, Sychrovský V. Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA. J Chem Theory Comput 2022; 18:6989-6999. [PMID: 36206364 DOI: 10.1021/acs.jctc.2c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interpretation of 3JP,H3' NMR scalar spin-spin coupling constants in DNA becomes more reliable by including distinct structural states such as BI and BII, using the weighted-static or, better still, the recently implemented adiabatic-MD (Ad-MD) method. The calculation method employs an adiabatic ("Ad") dependence of 3JP,H3' coupling on NMR-assigned torsion angle, ε, weighted by P(ε) probability distribution calculated by molecular dynamics (MD). Ad-MD calculations enable cross-validation of the bsc1, OL15, and OL21 force fields and various parametrizations of the Karplus equation describing the dependence of 3JP,H3' coupling on ε torsion (KE). The mean absolute deviation of Ad-MD 3JP,H3' couplings from the experimental values in Dickerson-Drew DNA is comparable to the scatter of 3JP,H3' couplings among four separate NMR experiments. A commonly accepted assumption of homogeneity of one kind of structure-dynamic state within DNA (BI or BII) is questionable because the principal characteristics of relevant P(ε) probabilities (shapes and positioning) vary with DNA sequence. The theory outlined in the present work sets limits to future reparameterization of MD force fields, as relevant to NMR data.
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Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marie Zgarbová
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Electrotechnology, Electrical Engineering, Czech Technical University, Technická 2, 166 27 Praha 6, Czech Republic
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3
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Tichotová M, Ešnerová A, Tučková L, Bednárová L, Císařová I, Baszczyňski O, Procházková E. 31P NMR parameters may facilitate the stereochemical analysis of phosphorus-containing compounds. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107149. [PMID: 35121491 DOI: 10.1016/j.jmr.2022.107149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Conventional Nuclear Magnetic Resonance (NMR) analysis relies on H-H/C-H interactions. However, these interactions are sometimes insufficient for an accurate and precise NMR analysis. In this study, we show that 31P NMR parameters can provide critical structural insights into the stereochemistry of phosphorus-containing compounds. For this purpose, we prepared a set of model phosphorus-based proline derivatives, separated diastereoisomers, and determined their absolute configuration by single-crystal X-ray diffraction. After supplementing these results by electronic circular dichroism (ECD) spectroscopy, we combined experimental data and DFT calculations from our model compounds to perform a detailed conformational analysis, thereby determining their relative configuration. Overall, our findings establish an experimental paradigm for combining 31P NMR spectroscopy with other optical methods to facilitate the stereochemical analysis of phosphorus-containing compounds.
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Affiliation(s)
- Markéta Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Aneta Ešnerová
- Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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4
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Fukal J, Buděšínský M, Páv O, Jurečka P, Zgarbová M, Šebera J, Sychrovský V. The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31 P NMR shift in DNA. J Comput Chem 2022; 43:132-143. [PMID: 34729803 DOI: 10.1002/jcc.26778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/11/2022]
Abstract
A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31 P NMR shift (δ31P ) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31 P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.
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Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Jurečka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marie Zgarbová
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.,Department of Electrotechnology, Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic
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5
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Krivdin LB. Recent advances in computational 31 P NMR: Part 2. Spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:500-511. [PMID: 31808570 DOI: 10.1002/mrc.4973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
This is the second part of two closely related reviews dealing with the computation of 31 P nuclear magnetic resonance (NMR) parameters in a wide range of phosphorous containing compounds. The first part of this review concentrated primarily on the computation of 31 P NMR chemical shifts, whereas the second part concerns the calculation of spin-spin coupling constants involving phosphorus nucleus, focusing primarily on their stereochemical dependencies and stereodynamic behavior in particular classes of organophosphorus compounds. This review is dedicated to the Full Member of the Russian Academy of Sciences Professor Boris A. Trofimov in view of his invaluable contribution to the field of synthesis, NMR, and computation studies of organophosphorus compounds.
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Affiliation(s)
- Leonid B Krivdin
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Irkutsk, Russia
- Department of Chemistry, Angarsk State Technical University, Angarsk, Russia
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6
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Rusakov YY, Rusakova IL, Fedorov SV, Gray GA, Krivdin LB. Stereochemical Dependences of 31P–13C Spin–Spin Coupling Constants of Heterocyclic Phosphines. J Phys Chem A 2019; 123:6298-6303. [DOI: 10.1021/acs.jpca.9b05385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yuriy Y. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Sergei V. Fedorov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - George A. Gray
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, California 95051, United States
| | - Leonid B. Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
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7
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Gholivand K, Maghsoud Y, Hosseini M, Kahnouji M. A theoretical study on 1H/13C/31P NMR chemical shifts, and the correlation between 2JP–H and the electronic structure of different phosphoryl benzamide derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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8
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Gholivand K, Maghsoud Y, Hosseini M, Kahnouji M. Toward the comprehensive calculations on the relationship between 1 H, 13 C, 31 P chemical shifts, 2 J PH , and the bonding structure of different phosphoryl benzamides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:S108-S116. [PMID: 30578739 DOI: 10.1002/mrc.4820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
A comprehensive investigation was performed on 1 H, 13 C, and 31 P nuclear magnetic resonance (NMR) chemical shifts (CSs) of phosphoryl benzamide derivatives (C6 H5 C(O)NHP(O)R1 R2 ), (R1 , R2 = aziridine [L1 ], azetidine [L2 ], pyrrolidine [L3 ], piperidine [L4 ], azepane [L5 ], 4-methylpiperidine [L6 ], propane-2-amine [L7 ], and 2-methylpropane-2-amine [L8 ]) by the gauge-independent atomic orbital method (GIAO) to find the most accordant level of theory with the experimental values. To achieve this goal, all the structures were optimized using the B3LYP, BP86, PBE1PBE, M06-2X, MPWB1K, and MP2 methods with 6-31+G* basis set. Computed structural parameters demonstrate that BP86 has the best agreement to the experimental values between the other methods. The def2-TZVP and aug-cc-pVDZ basis sets were also employed to inspect the effect of different types of basis sets with higher polarization and diffuse functions. The correlation between the empirical and computational values attests that 6-31+G* basis set is the optimum case regarding minimization of the costs and results. The comparison between calculated and experimental CSs at all mentioned combinations illustrated that in accordance with structural results, the best level of theory in CSs is also BP86/6-31+G*. Besides, 2 JPH values were computed with an acceptable agreement to experimental data at the optimum level of theory. The dependency between 2 JPH and the bonding structure of studied ligands was also scrutinized by the Natural Bond Orbital (NBO) analysis that interprets the relationship between the electronic properties and 2 JPH values.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Yazdan Maghsoud
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Mahdieh Hosseini
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Kahnouji
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran
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9
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Walder B, Berk C, Liao WC, Rossini AJ, Schwarzwälder M, Pradere U, Hall J, Lesage A, Copéret C, Emsley L. One- and Two-Dimensional High-Resolution NMR from Flat Surfaces. ACS CENTRAL SCIENCE 2019; 5:515-523. [PMID: 30937379 PMCID: PMC6439530 DOI: 10.1021/acscentsci.8b00916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Determining atomic-level characteristics of molecules on two-dimensional surfaces is one of the fundamental challenges in chemistry. High-resolution nuclear magnetic resonance (NMR) could deliver rich structural information, but its application to two-dimensional materials has been prevented by intrinsically low sensitivity. Here we obtain high-resolution one- and two-dimensional 31P NMR spectra from as little as 160 picomoles of oligonucleotide functionalities deposited onto silicate glass and sapphire wafers. This is enabled by a factor >105 improvement in sensitivity compared to typical NMR approaches from combining dynamic nuclear polarization methods, multiple-echo acquisition, and optimized sample formulation. We demonstrate that, with this ultrahigh NMR sensitivity, 31P NMR can be used to observe DNA bound to miRNA, to sense conformational changes due to ion binding, and to follow photochemical degradation reactions.
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Affiliation(s)
- Brennan
J. Walder
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Berk
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Wei-Chih Liao
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Aaron J. Rossini
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011-3020, United States
| | - Martin Schwarzwälder
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Ugo Pradere
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Jonathan Hall
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Anne Lesage
- Institut
de Sciences Analytiques, Centre de RMN à Très Hauts
Champs, Université de Lyon (CNRS/ENS
Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Christophe Copéret
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- E-mail:
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10
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Fukal J, Páv O, Buděšínský M, Rosenberg I, Šebera J, Sychrovský V. Structural interpretation of the 31P NMR chemical shifts in thiophosphate and phosphate: key effects due to spin–orbit and explicit solvent. Phys Chem Chem Phys 2019; 21:9924-9934. [DOI: 10.1039/c9cp01460h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural interpretation of the 31P NMR shifts measured in different molecules including thiophosphate or phosphate group was obtained by means of theoretical calculations including the effects of geometry, molecular dynamics, solvent, relativistic effects and the effect of NMR reference.
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Affiliation(s)
- J. Fukal
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - O. Páv
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - M. Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - I. Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - J. Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - V. Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Department of Electrotechnology
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11
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Viger-Gravel J, Schantz A, Pinon AC, Rossini AJ, Schantz S, Emsley L. Structure of Lipid Nanoparticles Containing siRNA or mRNA by Dynamic Nuclear Polarization-Enhanced NMR Spectroscopy. J Phys Chem B 2018; 122:2073-2081. [DOI: 10.1021/acs.jpcb.7b10795] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jasmine Viger-Gravel
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | - Arthur C. Pinon
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Aaron J. Rossini
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | | | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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12
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Fukal J, Páv O, Buděšínský M, Šebera J, Sychrovský V. The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate. Phys Chem Chem Phys 2017; 19:31830-31841. [DOI: 10.1039/c7cp06969c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A benchmark for structural interpretation of the 31P NMR shift and the 2JP,C spin–spin coupling in the phosphate group was obtained by means of theoretical calculations and measurements in diethylphosphate and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide.
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Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Department of Electrotechnology
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13
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Latypov SK, Polyancev FM, Yakhvarov DG, Sinyashin OG. Quantum chemical calculations of31P NMR chemical shifts: scopes and limitations. Phys Chem Chem Phys 2015; 17:6976-87. [DOI: 10.1039/c5cp00240k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High level of theory is not necessarily needed to obtain rather accurate predictions of31P chemical shifts by GIAO method. For example, the PBE1PBE/6-311G(2d,2p)//PBE1PBE/6-31+G(d) combination allowed to obtain good results for variety of middle-size organophosphorus compounds (M= 200–700 Da).
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Affiliation(s)
- Shamil K. Latypov
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Fedor M. Polyancev
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Dmitry G. Yakhvarov
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
| | - Oleg G. Sinyashin
- A.E. Arbuzov Institute of Organic and Physical Chemistry
- Kazan Scientific Center
- Russian Academy of Sciences
- Kazan
- Russian Federation
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14
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Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput 2013; 9:2339-2354. [PMID: 24058302 PMCID: PMC3775469 DOI: 10.1021/ct400154j] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultad de Farmacia, Universidad de Barcelona, Campus Torribera, Prat de la Riba 171, Edifici Verdaguer, 080921 Santa Coloma de Gramanet, Spain
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT 84112, USA
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
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Přecechtělová J, Munzarová ML, Vaara J, Novotný J, Dračínský M, Sklenář V. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations. J Chem Theory Comput 2013; 9:1641-56. [DOI: 10.1021/ct300488y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | - Juha Vaara
- NMR Research Group, Department of Physics,
University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
| | | | - Martin Dračínský
- NMR Laboratory, Institute of
Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nám.
2, CZ-16610 Prague 6, Czech Republic
- Department of Chemistry, Durham University, Durham, DH13LE, United Kingdom
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Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput 2012; 9:707-721. [PMID: 23976886 DOI: 10.1021/ct300671y] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Dickerson-Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic ; Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
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