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Calcagno F, Maryasin B, Garavelli M, Avagliano D, Rivalta I. Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM. J Comput Chem 2024; 45:1562-1575. [PMID: 38514234 DOI: 10.1002/jcc.27338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.
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Affiliation(s)
- Francesco Calcagno
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
- Center for Chemical Catalysis - C3, University of Bologna, Bologna, Italy
| | - Boris Maryasin
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Marco Garavelli
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
| | - Davide Avagliano
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
| | - Ivan Rivalta
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, Bologna, Italy
- Center for Chemical Catalysis - C3, University of Bologna, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
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2
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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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3
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Rusakov YY, Rusakova IL. New efficient pecS- n ( n = 1, 2) basis sets for quantum chemical calculations of 31P NMR chemical shifts. Phys Chem Chem Phys 2023. [PMID: 37409722 DOI: 10.1039/d3cp02664g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The basis sets that are used in the quantum chemical calculations of 31P NMR chemical shifts have always been one of the most important factors of accuracy. Regardless of what high-quality approach is employed, using basis sets of insufficient flexibility in the important angular regions may give poor results and lead to misassignments of the signals in the 31P NMR spectra. In this work, it was found that the existing nonrelativistic basis sets for phosphorus atom of double- and triple-ζ quality, specialized for the 31P NMR chemical shifts calculations, are essentially undersaturated in the d-angular space that occurred to play a significant role in the overall accuracy of these calculations. This problem has been thoroughly investigated, and new pecS-n (n = 1, 2) basis sets for phosphorus chemical shifts calculations were proposed. The exponents and contraction coefficients for the pecS-n basis sets were generated with the property-energy consistent method that has been introduced in our earlier paper, and has been proven useful in the creation of efficient property-oriented basis sets. New basis sets were optimized using the GIAO-DFT method with the B97-2 functional. Extensive benchmark calculations showed that the pecS-1 and pecS-2 basis sets provide very good accuracy, characterized by the corrected mean absolute percentage errors against the experiment of about 7.03 and 4.42 ppm, respectively. In particular, the accuracy of 31P NMR chemical shifts calculations achieved with the pecS-2 basis set is one of the most favorable accuracies for today. We believe that our new pecS-n (n = 1, 2) basis sets for phosphorus atom will prove useful in modern large-scale quantum chemical calculations of 31P NMR chemical shifts.
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Affiliation(s)
- Yuriy Yu 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.
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4
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Hersh WH, Chan TY. Improving the accuracy of 31P NMR chemical shift calculations by use of scaling methods. Beilstein J Org Chem 2023; 19:36-56. [PMID: 36726479 PMCID: PMC9843238 DOI: 10.3762/bjoc.19.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Calculation of 31P NMR chemical shifts for a series of tri- and tetracoordinate phosphorus compounds using several basis sets and density functional theory (DFT) functionals gave a modest fit to experimental chemical shifts, but an excellent linear fit when plotted against the experimental values. The resultant scaling methods were then applied to a variety of "large" compounds previously selected by Latypov et al. and a set of stereoisomeric and unusual compounds selected here. No one method was best for all structural types. For compounds that contain P-P bonds and P-C multiple bonds, the Latypov et al. method using the PBE0 functional was best (mean absolute deviation/root mean square deviation (MAD/RMSD) = 6.9/8.5 ppm and 6.6/8.2 ppm, respectively), but for the full set of compounds gave higher deviations (MAD/RMSD = 8.2/12.3 ppm), and failed by over 60 ppm for a three-membered phosphorus heterocycle. Use of the M06-2X functional for both the structural optimization and NMR chemical shift calculation was best overall for the compounds without P-C multiple bonds (MAD/RMSD = 5.4/7.1 ppm), but failed by 30-49 ppm for compounds having any P-C multiple-bond character. Failures of these magnitudes have not been reported previously for these widely used functionals. These failures were then used to screen a variety of recommended functionals, leading to better overall methods for calculation of these chemical shifts: optimization with the M06-2X functional and NMR calculation with the PBE0 or ωB97x-D functionals gave values for MAD/RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of -181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures.
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Affiliation(s)
- William H Hersh
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367-1597, USA,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Tsz-Yeung Chan
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367-1597, USA,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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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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6
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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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7
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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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Casabianca LB. Calculating nuclear magnetic resonance chemical shifts in solvated systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:611-624. [PMID: 31916612 DOI: 10.1002/mrc.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The nuclear magnetic resonance (NMR) chemical shift is extremely sensitive to molecular geometry, hydrogen bonding, solvent, temperature, pH, and concentration. Calculated magnetic shielding constants, converted to chemical shifts, can be valuable aids in NMR peak assignment and can also give detailed information about molecular geometry and intermolecular effects. Calculating chemical shifts in solution is complicated by the need to include solvent effects and conformational averaging. Here, we review the current state of NMR chemical shift calculations in solution, beginning with an introduction to the theory of calculating magnetic shielding in general, then covering methods for inclusion of solvent effects and conformational averaging, and finally discussing examples of applications using calculated chemical shifts to gain detailed structural information.
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Affiliation(s)
- Leah B Casabianca
- Department of Chemistry, Clemson University, Clemson, South Carolina
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Krivdin LB. Recent advances in computational 31 P NMR: Part 1. Chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:478-499. [PMID: 31703153 DOI: 10.1002/mrc.4965] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
This is the first part of two closely related reviews dealing with the computation of phosphorus-31 nuclear magnetic resonance chemical shifts in a wide series of organophosphorus compounds including complexes, clusters, and bioorganic phosphorus compounds. In particular, the analysis of the accuracy factors, such as substitution effects, solvent effects, vibrational corrections, and relativistic effects, is presented. 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, nuclear magnetic resonance, and computation studies of organophosphorus compounds.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Angarsk State Technical University, Irkutsk Region, Russia
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