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Liang J, Wang Z, Li J, Wong J, Liu X, Ganoe B, Head-Gordon T, Head-Gordon M. Efficient Calculation of NMR Shielding Constants Using Composite Method Approximations and Locally Dense Basis Sets. J Chem Theory Comput 2023. [PMID: 36594660 DOI: 10.1021/acs.jctc.2c00933] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This paper presents a systematic study of applying composite method approximations with locally dense basis sets (LDBS) to efficiently calculate NMR shielding constants in small and medium-sized molecules. The pcSseg-n series of basis sets are shown to have similar accuracy to the pcS-n series when n ≥ 1 and can slightly reduce computational costs. We identify two different LDBS partition schemes that perform very effectively for density functional calculations. We select a large subset of the recent NS372 database containing 290 H, C, N, and O shielding values evaluated by reference methods on 106 molecules to carefully assess methods of the high, medium, and low computational costs to make practical recommendations. Our assessment covers conventional electronic structure methods (density functional theory and wave function) with global basis calculations, as well as their use in one of the satisfactory LDBS approaches, and a range of composite approaches, also with and without LDBS. Altogether 99 methods are evaluated. On this basis, we recommend different methods to reach three different levels of accuracy and time requirements across the four nuclei considered.
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Affiliation(s)
- Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Zhe Wang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Jie Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Jonathan Wong
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Brad Ganoe
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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2
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Shi M, Jin X, Wan Z, He X. Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals. J Chem Phys 2021; 154:064502. [PMID: 33588539 DOI: 10.1063/5.0039115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the 13C and 1H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For 13C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the 1H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental 13C and 1H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for 13C chemical shift calculations, but not for the 1H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the 13C and 1H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.
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Affiliation(s)
- Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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3
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Chandy SK, Thapa B, Raghavachari K. Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method. Phys Chem Chem Phys 2020; 22:27781-27799. [PMID: 33244526 DOI: 10.1039/d0cp05064d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical shifts of large biomolecules. To investigate the performance of our fragmentation approach and demonstrate its applicability, MIM-NMR calculations are first calibrated on a test set of six proteins. The MIM2-NMR method yields a mean absolute deviation (MAD) from unfragmented full molecule calculations of 0.01 ppm for 1H and 0.06 ppm for 13C chemical shifts. Thus, the errors from fragmentation are only about 3% of our target accuracy of ∼0.3 ppm for 1H and 2-3 ppm for 13C chemical shifts. To compare with experimental chemical shifts, a standard protocol is first derived using two smaller proteins 2LHY (176 atoms) and 2LI1 (146 atoms) for obtaining an appropriate protein structure for NMR chemical shift calculations. The effect of the solvent environment on the calculated NMR chemical shifts is incorporated through implicit, explicit, or explicit-implicit solvation models. The expensive first solvation shell calculations are replaced by a micro-solvation model in which only the immediate interaction between the protein and the explicit solvation environment is considered. A single explicit water molecule for each amine and amide proton is found to be sufficient to yield accurate results for 1H chemical shifts. The 1H and 13C NMR chemical shifts calculated using our protocol give excellent agreement with experiments for two larger proteins, 2MC5 (the helical part with 265 atoms) and 3UMK (33 residue slice with 547 atoms). Overall, our target accuracy of ∼0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for the larger proteins. The proposed MIM-NMR method is accurate and computationally cost-effective and should be applicable to study a wide range of large proteins.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
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4
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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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5
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Holl MG, Struble MD, Singal P, Siegler MA, Lectka T. Positioning a Carbon–Fluorine Bond over the π Cloud of an Aromatic Ring: A Different Type of Arene Activation. Angew Chem Int Ed Engl 2016; 55:8266-9. [DOI: 10.1002/anie.201601989] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/14/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Maxwell Gargiulo Holl
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Mark D. Struble
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Prakhar Singal
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Maxime A. Siegler
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Thomas Lectka
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
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6
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Holl MG, Struble MD, Singal P, Siegler MA, Lectka T. Positioning a Carbon–Fluorine Bond over the π Cloud of an Aromatic Ring: A Different Type of Arene Activation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601989] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maxwell Gargiulo Holl
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Mark D. Struble
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Prakhar Singal
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Maxime A. Siegler
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
| | - Thomas Lectka
- Department of Chemistry Johns Hopkins University 3400 North Charles Street Baltimore MD 21218 USA
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7
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Gao Q, Yokojima S, Fedorov DG, Kitaura K, Sakurai M, Nakamura S. Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Shaghaghi H, Ebrahimi HP, Bahrami Panah N, Tafazzoli M. Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 51-52:31-36. [PMID: 23414630 DOI: 10.1016/j.ssnmr.2013.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/15/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Solid state (13)C and (15)N chemical shifts of uracil and imidazole have been calculated using a 2-layer ONIOM approach at 32 levels of theory. The effect of electron correlation between two layers has been investigated by choosing two different kinds of layer selection. Factorial design has been applied as a multivariate technique to analyze the effect of wave function and layer selection on solid state (13)C and (15)N chemical shifts calculations. PBEPBE/6-311+G(d,p) was recommended as an optimally selected level of theory for high layer in both models. It is illustrated that considering the electron correlation of two layers of ONIOM models is important factor to calculate solid state (15)N chemical shifts. The agreement between the calculated and experimental values of solid state (13)C and (15)N chemical shifts using ONIOM (PBEPBE/6-311+G(d,p):AM1) for both uracil and imidazole confirmed the reliability of the selected wave functions and layer selection.
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Affiliation(s)
- Hoora Shaghaghi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
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9
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Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J Chem Theory Comput 2013; 9:2104-14. [PMID: 26583557 DOI: 10.1021/ct300999w] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have performed a density functional theory (DFT) calculation of the amide proton NMR chemical shift in proteins using a recently developed automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. Systematic investigation was carried out to examine the influence of explicit solvent molecules, cooperative hydrogen bonding effects, density functionals, size of the basis sets, and the local geometry of proteins on calculated chemical shifts. Our result demonstrates that the predicted amide proton ((1)HN) NMR chemical shift in explicit solvent shows remarkable improvement over that calculated with the implicit solvation model. The cooperative hydrogen bonding effect is also shown to improve the accuracy of (1)HN chemical shifts. Furthermore, we found that the OPBE exchange-correlation functional is the best density functional for the prediction of protein (1)HN chemical shifts among a selective set of DFT methods (namely, B3LYP, B3PW91, M062X, M06L, mPW1PW91, OB98, OPBE), and the locally dense basis set of 6-311++G**/4-31G* is shown to be sufficient for (1)HN chemical shift calculation. By taking ensemble averaging into account, (1)HN chemical shifts calculated by the AF-QM/MM approach can be used to validate the performance of various force fields. Our study underscores that the electronic polarization of protein is of critical importance to stabilizing hydrogen bonding, and the AF-QM/MM method is able to describe the local chemical environment in proteins more accurately than most widely used empirical models.
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Affiliation(s)
- Tong Zhu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
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10
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Urbanova M, Brus J, Sedenkova I, Policianova O, Kobera L. Characterization of solid polymer dispersions of active pharmaceutical ingredients by 19F MAS NMR and factor analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 100:59-66. [PMID: 22421443 DOI: 10.1016/j.saa.2012.02.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/07/2012] [Accepted: 02/14/2012] [Indexed: 05/31/2023]
Abstract
In this contribution the ability of (19)F MAS NMR spectroscopy to probe structural variability of poorly water-soluble drugs formulated as solid dispersions in polymer matrices is discussed. The application potentiality of the proposed approach is demonstrated on a moderately sized active pharmaceutical ingredient (API, Atorvastatin) exhibiting extensive polymorphism. In this respect, a range of model systems with the API incorporated in the matrix of polvinylpyrrolidone (PVP) was prepared. The extent of mixing of both components was determined by T(1)((1)H) and T(1ρ)((1)H) relaxation experiments, and it was found that the API forms nanosized domains. Subsequently it was found out that the polymer matrix induces two kinds of changes in (19)F MAS NMR spectra. At first, this is a high-frequency shift reaching 2-3 ppm which is independent on molecular structure of the API and which results from the long-range polarization of the electron cloud around (19)F nucleus induced by electrostatic fields of the polymer matrix. At second, this is broadening of the signals and formation of shoulders reflecting changes in molecular arrangement of the API. To avoid misleading in the interpretation of the recorded (19)F MAS NMR spectra, because both the contributions act simultaneously, we applied chemometric approach based on multivariate analysis. It is demonstrated that factor analysis of the recorded spectra can separate both these spectral contributions, and the subtle structural differences in the molecular arrangement of the API in the nanosized domains can be traced. In this way (19)F MAS NMR spectra of both pure APIs and APIs in solid dispersions can be directly compared. The proposed strategy thus provides a powerful tool for the analysis of new formulations of fluorinated pharmaceutical substances in polymer matrices.
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Affiliation(s)
- Martina Urbanova
- Department of NMR Spectroscopy, Institute of Macromolecular Chemistry, Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic.
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11
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Bonhomme C, Gervais C, Babonneau F, Coelho C, Pourpoint F, Azaïs T, Ashbrook SE, Griffin JM, Yates JR, Mauri F, Pickard CJ. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: a chemist's point of view. Chem Rev 2012; 112:5733-79. [PMID: 23113537 DOI: 10.1021/cr300108a] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris, Université Pierre et Marie Curie, CNRS UMR, Collège de France, France.
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12
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Zhu T, He X, Zhang JZH. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys Chem Chem Phys 2012; 14:7837-45. [PMID: 22314755 DOI: 10.1039/c2cp23746f] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson-Boltzmann) model. Our calculated chemical shifts of (1)H and (13)C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of (15)N, the results do not agree with experimental values as well as (1)H and (13)C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for (13)C(α) atoms in proteins, and using the (1)H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.
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Affiliation(s)
- Tong Zhu
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China 200062
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13
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Borkowski EJ, Suvire FD, Enriz RD. Advances in correlation between experimental and DFT/GIAO computed 13C NMR chemical shifts: A theoretical study on pentacyclic terpenoids (fernenes). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Gerothanassis IP. Oxygen-17 NMR spectroscopy: basic principles and applications (part I). PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:95-197. [PMID: 20633350 DOI: 10.1016/j.pnmrs.2009.09.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/24/2009] [Indexed: 05/29/2023]
Affiliation(s)
- Ioannis P Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina GR-451 10, Greece.
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15
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He X, Wang B, Merz KM. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. J Phys Chem B 2009; 113:10380-8. [PMID: 19575540 DOI: 10.1021/jp901992p] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach has been developed to routinely calculate ab initio protein NMR chemical shielding constants. The AF-QM/MM method is linear-scaling and trivially parallel. A general fragmentation scheme is employed to generate each residue-centric region which is treated by quantum mechanics, and the environmental electrostatic field is described with molecular mechanics. The AF-QM/MM method shows good agreement with standard self-consistent field (SCF) calculations of the NMR chemical shieldings for the mini-protein Trp cage. The root-mean-square errors (RMSEs) for 1H, 13C, and 15N NMR chemical shieldings are equal to or less than 0.09, 0.32, and 0.78 ppm, respectively, for all Hartree-Fock (HF) and density functional theory (DFT) calculations reported in this work. The environmental electrostatic potential is necessary to accurately reproduce the NMR chemical shieldings using the AF-QM/MM approach. The point-charge models provided by AMBER, AM1/CM2, PM3/CM1, and PM3/CM2 all effectively model the electrostatic field. The latter three point-charge models are generated via semiempirical linear-scaling SCF calculations of the entire protein system. The correlations between experimental 1H NMR chemical shifts and theoretical predictions are >0.95 for AF-QM/MM calculations using B3LYP with the 6-31G**, 6-311G**, and 6-311++G** basis sets. Our study, not unexpectedly, finds that conformational changes within a protein structure play an important role in the accurate prediction of experimental NMR chemical shifts from theory.
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Affiliation(s)
- Xiao He
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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16
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Cai L, Fushman D, Kosov DS. Density functional calculations of chemical shielding of backbone 15N in helical residues of protein G. JOURNAL OF BIOMOLECULAR NMR 2009; 45:245-253. [PMID: 19644655 PMCID: PMC2884268 DOI: 10.1007/s10858-009-9358-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 07/09/2009] [Indexed: 05/28/2023]
Abstract
We performed density functional calculations of backbone (15)N chemical shielding tensors in selected helical residues of protein G. Here we describe a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone (15)N. We analyzed the role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field. Our results show that the dipole moment of the alpha-helix can cause significant deshielding of (15)N; therefore, it needs to be considered when calculating (15)N chemical shielding. We found that it is important to include interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. Chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data.
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Affiliation(s)
- Ling Cai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Daniel S. Kosov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
- Department of Physics and Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Campus Plaine, CP 231, Blvd du Triomphe, B-1050 Brussels, Belgium
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17
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Williams DE, Peters MB, Wang B, Roitberg AE, Merz KM. AM1 Parameters for the Prediction of 1H and 13C NMR Chemical Shifts in Proteins. J Phys Chem A 2009; 113:11550-9. [DOI: 10.1021/jp9028722] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Duane E. Williams
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Martin B. Peters
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Bing Wang
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Adrian E. Roitberg
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Kenneth M. Merz
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435
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18
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Ling Y, Zhang Y. Deciphering the NMR fingerprints of the disordered system with quantum chemical studies. J Phys Chem A 2009; 113:5993-7. [PMID: 19331332 DOI: 10.1021/jp9001324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent developments in solid-state NMR techniques helped acquire high-resolution NMR spectra for solid systems with structural disorder. But the structural origin of the observed chemical shift nonequivalence in these systems has not been revealed. We report a quantum chemical investigation of the solid-state NMR spectrum in N,N-bis(diphenylphosphino)-N-((S)-alpha-methylbenzyl)amine, where eight nonequivalent (31)P NMR chemical shifts were resolved with a range of 13.0 ppm. Results from using different quantum chemical methods, computational algorithms, intermolecular effects, and structures indicate that for the disordered system, geometry optimization gives the best accord with experimental NMR chemical shifts, which has a theory-versus-experiment correlation R(2) = 0.949 and SD = 1.1 ppm, or R(2) = 0.994 and SD = 0.4 ppm when the average of two unassigned NMR shifts for each molecule is used. In addition, these calculations indicate that the experimental chemical shift nonequivalence in this system is mainly a consequence of the different geometries around the phosphorus atoms due to disordered environments. The experimental (31)P NMR chemical shifts are well correlated (R(2) = 0.981) with two conformation angles and one bond length, each associated with one of the three bonding interactions around the phosphorus atoms. These results will facilitate the use of quantum chemical techniques in structural characterization of disordered solids and elucidation of NMR properties.
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Affiliation(s)
- Yan Ling
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive No. 5043, Hattiesburg, Mississippi 39406, USA
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19
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Johnson ER, DiLabio GA. Convergence of calculated nuclear magnetic resonance chemical shifts in a protein with respect to quantum mechanical model size. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Harris RK, Hodgkinson P, Pickard CJ, Yates JR, Zorin V. Chemical shift computations on a crystallographic basis: some reflections and comments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S174-S186. [PMID: 18157842 DOI: 10.1002/mrc.2132] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Computations for chemical shifts of molecular organic compounds using the gauge-including projector augmented wave method and the NMR-CASTEP code are reviewed. The methods are briefly introduced, and some general aspects involving the sources of uncertainty in the results are explored. The limitations are outlined. Successful applications of the computations to problems of interpretation of NMR results are discussed and the range of areas in which useful information is obtained is illustrated by examples. The particular value of the computations for comparing shifts between resonances where the same chemical site is involved is emphasised. Such cases arise for shifts between different crystallographically independent molecules of the same chemical species, between polymorphs and for shift anisotropies and asymmetries.
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Affiliation(s)
- Robin K Harris
- Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK.
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21
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Heider EM, Harper JK, Grant DM. Structural characterization of an anhydrous polymorph of paclitaxel by solid-state NMR. Phys Chem Chem Phys 2007; 9:6083-97. [PMID: 18167583 DOI: 10.1039/b711027h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The three-dimensional structure of a unique polymorph of the anticancer drug paclitaxel (Taxol) is established using solid state NMR (SSNMR) tensor ((13)C & (15)N) and heteronuclear correlation ((1)H-(13)C) data. The polymorph has two molecules per asymmetric unit (Z' = 2) and is thus the first conformational characterization with Z' > 1 established solely by SSNMR. Experimental data are correlated with structure through a series of computational models that extensively sample all conformations. For each computational model, corresponding tensor values are computed to supply comparisons with experimental information which, in turn, establishes paclitaxel's structure. Heteronuclear correlation data at thirteen key positions provide shift assignments to the asymmetric unit for each comparison. The two distinct molecules of the asymmetric unit possess nearly identical baccatin III moieties with matching conformations of the C10 acetyl moiety and, specifically, the torsion angle formed by C30-O-C10-C9. Additionally, both are found to exhibit an extended conformation of the phenylisoserine sidechain at C13 with notable differences in the dihedral angles centered around the rotation axes of O-C13, C2'-C1' and C3'-C2'.
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Affiliation(s)
- Elizabeth M Heider
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA
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22
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Mukkamala D, Zhang Y, Oldfield E. A Solid State 13C NMR, Crystallographic, and Quantum Chemical Investigation of Phenylalanine and Tyrosine Residues in Dipeptides and Proteins. J Am Chem Soc 2007; 129:7385-92. [PMID: 17506558 DOI: 10.1021/ja071227y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of a solid-state NMR and quantum chemical investigation of the 13C gamma NMR chemical shifts in phenylalanine and tyrosine in dipeptides and proteins. Accurate computation of the experimental shifts is shown to require a good description of local electrostatic field effects, and we find the best results (R2=0.94, rmsd=1.6 ppm, range = 17.1 ppm, N=14) by using a self-consistent reaction field continuum model. There are no obvious correlations with phi, psi, chi 1, or chi2 torsion angles, unlike the results seen with other amino acids. There is, however, a linear relation between computed C gamma atomic charges and shifts for the 14 peptide as well as 18 protein residues investigated. This result is similar to the correlation reported in the 1960s between pi-electron density and 13C shifts for classical 4n + 2 (n=0, 1, 2) pi-electron aromatic species, such as cyclopentadienide and the tropylium cation, and in fact, we found that the shielding/atomic charge correlation seen in the peptides and proteins is virtually identical to that seen with a broad range of aromatic carbocations/carbanions. These results suggest the dominance of an electrostatic field polarization model in which increasing pi electron density results in an increase in C gamma atomic charge and increased shielding (of sigma 11 and sigma 22, perpendicular to the pi orbital) in Phe and Tyr, as well as in the other aromatic species. These results are of general interest since they demonstrate the importance of electrostatic field effects on Phe and Tyr C gamma chemical shifts in peptides and proteins and imply that inclusion of these effects will be necessary in order to interpret the shifts of other aromatic species, such as drug molecules, bound to proteins.
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Affiliation(s)
- Dushyant Mukkamala
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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23
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TheAb InitioComputation of Nuclear Magnetic Resonance Chemical Shielding. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125854.ch5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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24
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Orendt AM. Revisiting the calculation of (13)C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:385-9. [PMID: 16477671 DOI: 10.1002/mrc.1753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The chemical shift tensors of the acetate anions in cadmium acetate dihydrate are calculated using a cluster approach, the embedded ion method (EIM), and a combination of the two in the EIM/cluster method. The results of these calculations are compared with those completed on the isolated acetate anion and show the need for the inclusion of intermolecular interactions. The RMS difference between experiment and theory improves from over 60 ppm when the calculation is completed on an isolated anion, to below 10 ppm when interactions to nearby atoms are included. The best cluster model includes three cadmium acetate dihydrate and gives an RMS result of 4.4 ppm. The EIM method, which uses point charges to account for the intermolecular effects, achieves an RMS of 7.7 ppm on individual anions alone. A combination of the two, the EIM/cluster method, shows that the only necessary atom to explicitly add is the nearest cadmium; this addition results in an RMS of 4.1 ppm. These results are also discussed in terms of the computational cost of the different calculations.
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Affiliation(s)
- Anita M Orendt
- Center for High Performance Computing, University of Utah, 155 S 1452 E, Salt Lake City, UT 84112-0190, USA.
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25
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Zhang Y, Oldfield E. 31P NMR Chemical Shifts in Hypervalent Oxyphosphoranes and Polymeric Orthophosphates. J Phys Chem B 2005; 110:579-86. [PMID: 16471570 DOI: 10.1021/jp054022p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first quantum chemical investigation of the solid- and solution-state 31P NMR chemical shifts in models for phosphoryl transfer enzyme reaction intermediates and in polymeric inorganic phosphates. The 31P NMR chemical shifts of five- and six-coordinate oxyphosphoranes containing a variety of substitutions at phosphorus, as well as four-coordinate polymeric orthophosphates and four-coordinate phosphonates, are predicted with a slope of 1.00 and an R2= 0.993 (N = 34), corresponding to a 3.8 ppm (or 2.1%) error over the entire 178.3 ppm experimental chemical shift range, using Hartree-Fock methods. For the oxyphosphoranes, we used either experimental crystallographic structures or, when these were not available, fully geometry optimized molecular structures. For the four-coordinate phosphonates we used X-ray structures together with charge field perturbation, to represent lattice interactions. For the three-dimensional orthophosphates (BPO4, AlPO4, GaPO4 we again used X-ray structures, but for these inorganic systems we employed a self-consistent charge field perturbation approach on large clusters, to deduce peripheral atom charges. For pentaoxyphosphoranes, the solvent effect on 31P NMR chemical shieldings was found to be very small (<0.5 ppm). The 31P NMR chemical shielding tensors in the pentaoxyphosphoranes were in most cases found to be close to axially symmetric and were dominated by changes in the shielding tensor components in the equatorial plane (sigma22 and sigma33). The isotropic shifts were highly correlated (R2= 0.923) with phosphorus natural bonding orbital charges, with the larger charges being associated with shorter axial P-O bond lengths and, hence, more shielding. Overall, these results should facilitate the use of 31P NMR techniques in investigating the structures of more complex systems, such as phosphoryl transfer enzymes, as well as in investigating other, complex oxide structures.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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26
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Oldfield E. Quantum chemical studies of protein structure. Philos Trans R Soc Lond B Biol Sci 2005; 360:1347-61. [PMID: 16147526 PMCID: PMC1569496 DOI: 10.1098/rstb.2003.1421] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 09/24/2003] [Indexed: 11/12/2022] Open
Abstract
Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801, USA.
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Zhang Y, Oldfield E. Solid-State 31P NMR Chemical Shielding Tensors in Phosphonates and Bisphosphonates: A Quantum Chemical Investigation. J Phys Chem B 2004. [DOI: 10.1021/jp040281n] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong Zhang
- Departments of Chemistry and Biophysics, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Eric Oldfield
- Departments of Chemistry and Biophysics, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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29
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Moon S, Christiansen PA, DiLabio GA. Quantum capping potentials with point charges: A simple QM/MM approach for the calculation of large-molecule NMR shielding tensors. J Chem Phys 2004; 120:9080-6. [PMID: 15267843 DOI: 10.1063/1.1689633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A simple quantum-mechanics/molecular-mechanics (QM/MM) approach for calculating NMR shielding tensors (sigma) is presented. The method involves capping the QM region with quantum capping potentials (QCPs) and representing the MM region with point charges. Test calculations on simple systems without MM charges show that calculated sigma values improve relative to the full QM results with increasing distance between the capped bond and chromophore. Calculations on the histidine amino acid and cytosine monophosphate (CMP) nucleic acid show that the use of QCPs with point charges result in mean errors in the isotropic component of sigma that are less than 1.6 ppm. The results also reveal that, contrary to previous work, the explicit effect of point charges on sigma through coupling with gauge factors, as in the gauge including atomic orbital approach, is minimal for the CMP molecule. The present QM/MM approach for calculating sigma is easy to apply and requires no code modification.
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Affiliation(s)
- Seongho Moon
- Department de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québéc, H3C 3J7, Canada
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30
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CSGT-DFT calculation of 13C and 15N NMR shielding of the backbone amide group, 13Cα, and 13Cβ in ω-Conotoxin GVIA. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Sun H, Oldfield E. Tryptophan Chemical Shift in Peptides and Proteins: A Solid State Carbon-13 Nuclear Magnetic Resonance Spectroscopic and Quantum Chemical Investigation. J Am Chem Soc 2004; 126:4726-34. [PMID: 15070392 DOI: 10.1021/ja030612u] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have obtained the carbon-13 nuclear magnetic resonance spectra of a series of tryptophan-containing peptides and model systems, together with their X-ray crystallographic structures, and used quantum chemical methods to predict the (13)C NMR shifts (or shieldings) of all nonprotonated aromatic carbons (C(gamma), C(delta 2) and C(epsilon 2). Overall, there is generally good accord between theory and experiment. The chemical shifts of Trp C(gamma) in several proteins, hen egg white lysozyme, horse myoglobin, horse heart cytochrome c, and four carbonmonoxyhemoglobins, are also well predicted. The overall Trp C(gamma) shift range seen in the peptides and proteins is 11.4 ppm, and individual shifts (or shieldings) are predicted with an rms error of approximately 1.4 ppm (R value = 0.86). Unlike C(alpha) and N(H) chemical shifts, which are primarily a function of the backbone phi,psi torsion angles, the Trp C(gamma) shifts are shown to be correlated with the side-chain torsion angles chi(1) and chi(2) and appear to arise, at least in part, from gamma-gauche interactions with the backbone C' and N(H) atoms. This work helps solve the problem of the chemical shift nonequivalences of nonprotonated aromatic carbons in proteins first identified over 30 years ago and opens up the possibility of using aromatic carbon chemical shift information in structure determination.
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Affiliation(s)
- Haihong Sun
- Department of Biophysics, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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32
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Clawson JS, Anderson KL, Pugmire RJ, Grant DM. 15N NMR Chemical Shift Tensors of Substituted Hexaazaisowurtzitanes: The Intermediates in the Synthesis of CL-20. J Phys Chem A 2004. [DOI: 10.1021/jp0373999] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jacalyn S. Clawson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, and ATK Thiokol Propulsion, P.O. Box 707, Brigham City, Utah 84302
| | - Karen L. Anderson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, and ATK Thiokol Propulsion, P.O. Box 707, Brigham City, Utah 84302
| | - Ronald J. Pugmire
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, and ATK Thiokol Propulsion, P.O. Box 707, Brigham City, Utah 84302
| | - David M. Grant
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, and ATK Thiokol Propulsion, P.O. Box 707, Brigham City, Utah 84302
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33
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Strohmeier M, Stueber D, Grant DM. Accurate 13C and 15N Chemical Shift and 14N Quadrupolar Coupling Constant Calculations in Amino Acid Crystals: Zwitterionic, Hydrogen-Bonded Systems. J Phys Chem A 2003; 107:7629-42. [DOI: 10.1021/jp0350114] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark Strohmeier
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
| | - Dirk Stueber
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
| | - David M. Grant
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
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Potrzebowski MJ, Assfeld X, Ganicz K, Olejniczak S, Cartier A, Gardiennet C, Tekely P. An experimental and theoretical study of the 13C and 31P chemical shielding tensors in solid O-phosphorylated amino acids. J Am Chem Soc 2003; 125:4223-32. [PMID: 12670244 DOI: 10.1021/ja029840z] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of l and dl forms of O-phosphorylated amino acids (serine, threonine, tyrosine) have been studied by using solid-state multinuclear NMR spectroscopy and ab initio calculations. Principal elements of the (13)C and (31)P chemical shielding tensors have been measured and discussed in relation to zwitterionic structures and intermolecular contacts. DFT calculations have been compared with experimental data showing their ability to reproduce experimentally obtained tensor values in this challenging class of compounds. The changes of orientation of (31)P chemical shielding tensor with respect to the molecular frame in the presence of hydrogen bonds have been revealed and discussed on the ground of theoretical calculations. The measurements of internuclear P...P distances, based on Zeeman magnetization exchange between (31)P spins with differing chemical shielding tensor orientations, were exploited for a clear distinction between enantiomers and racemates.
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Affiliation(s)
- Marek J Potrzebowski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, 90-363 Łódź, Poland
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35
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Barich DH, Clawson JS, Stueber D, Strohmeier M, Pugmire RJ, Grant DM. Determination of 13C Chemical Shift Tensors in the Presence of Hydrogen Bonding and 14N Quadrupolar Coupling: p-Aminosalicylic Acid, Isoniazid, and Pyrazinamide. J Phys Chem A 2002. [DOI: 10.1021/jp021604n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dewey H. Barich
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | | | - Dirk Stueber
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Mark Strohmeier
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Ronald J. Pugmire
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - David M. Grant
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112
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36
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Kidambi S, Ramamoorthy A. Quantum Chemical Calculations of Cadmium Chemical Shifts in Inorganic Complexes. J Phys Chem A 2002. [DOI: 10.1021/jp0265891] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Srikanth Kidambi
- Department of Chemistry, Biophysics Research Division, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - A. Ramamoorthy
- Department of Chemistry, Biophysics Research Division, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055
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Harper JK, Facelli JC, Barich DH, McGeorge G, Mulgrew AE, Grant DM. 13C NMR investigation of solid-state polymorphism in 10-deacetyl baccatin III. J Am Chem Soc 2002; 124:10589-95. [PMID: 12197761 DOI: 10.1021/ja020371a] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To investigate the origins of solid-state NMR shift differences in polymorphs, carbon NMR chemical shift tensors are measured for two forms of solid 10-deacetyl baccatin III: a dimethyl sulfoxide (DMSO) solvate and an unsolvated form. A comparison of ab initio computed tensors that includes and omits the DMSO molecules demonstrates that lattice interactions cannot fully account for the shift differences in the two forms. Instead, conformational differences in the cyclohexenyl, benzoyl, and acetyl moieties are postulated to create the differences observed. X-ray analysis of six baccatin III analogues supports the suggested changes in the cyclohexenyl and benzoyl systems. The close statistical match of the (13)C chemical shifts of both polymorphic forms with those calculated using the X-ray geometry of 10-deacetyl baccatin III supports the contention that the B, C, and D rings are fairly rigid. Therefore, the observed tensor differences appear to arise primarily from conformational variations in ring substituents and the cyclohexenyl ring.
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Affiliation(s)
- James K Harper
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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Abstract
This chapter discusses recent progress in the investigation and use of (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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Clawson JS, Strohmeier M, Stueber D, Orendt AM, Barich DH, Asay B, Hiskey MA, Pugmire RJ, Grant DM. 15N Chemical Shift Tensors of β-HMX. J Phys Chem A 2002. [DOI: 10.1021/jp013679h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jacalyn S. Clawson
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Mark Strohmeier
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Dirk Stueber
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Anita M. Orendt
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Dewey H. Barich
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Blaine Asay
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Michael A. Hiskey
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Ronald J. Pugmire
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - David M. Grant
- Department of Chemistry and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84112, and High Explosives Physics Team, High Explosives Science and Technology, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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D'Ordine RL, Pawlak J, Bahnson BJ, Anderson VE. Polarization of cinnamoyl-CoA substrates bound to enoyl-CoA hydratase: correlation of (13)C NMR with quantum mechanical calculations and calculation of electronic strain energy. Biochemistry 2002; 41:2630-40. [PMID: 11851410 DOI: 10.1021/bi015845h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
When alpha,beta-unsaturated substrates bind to the active site of enoyl-CoA hydratase, large spectral changes can be observed [D'Ordine, R. L., et al. (1994) Biochemistry 33, 12635-12643]. The differences in the isotropic magnetic shieldings of the free and active site-bound forms of the carbonyl, alpha-, and beta-carbons of the substrates, hexadienoyl-CoA, cinnamoyl-CoA, and (N,N-dimethyl-p-amino)cinnamoyl-CoA have been experimentally determined. The carbonyl and beta-carbons are all deshielded, while the alpha-carbons show increased shielding. These chemical shift perturbations are interpreted to suggest that the pi-electrons of the enoyl thiolester are polarized when bound at the active site. Using the crystal structure of (N,N-dimethyl-p-amino)cinnamoyl-CoA bound at the enzyme active site, the shielding tensors were calculated at three different levels of theory, up to a density functional theory model that included all of the contiguous active site residues. These calculations successfully reproduced the observed spectral changes and permitted the electronic polarization of the substrate to be quantified as an electron density difference map. The calculated electron density difference confirms the loss of electrons at the electrophilic beta-carbon and carbonyl carbon, while a slight increase in electron density at the alpha-carbon where proton donation occurs during the hydration reaction and a larger increase in electron density at the carbonyl oxygen are predicted. The energy required to polarize the electrons to the observed extent was calculated to be 3.2 kcal/mol. The force that provides the requisite energy for the polarization is the interaction of the electric field generated by the protein at the enzyme active site with the polarizable electrons of the substrate. Because the induced electronic polarization is along the predicted reaction pathway, the extent of substrate activation by the induced electronic strain is catalytically relevant.
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Affiliation(s)
- Robert L D'Ordine
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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41
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Solı́s D, Ferraro M, Facelli J. Modeling NMR chemical shifts: surface charge representation of the electrostatic embedding potential modeling of crystalline intermolecular effects in 19F solid state NMR chemical shifts. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(01)00713-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Harper JK, Mulgrew AE, Li JY, Barich DH, Strobel GA, Grant DM. Characterization of stereochemistry and molecular conformation using solid-state NMR tensors. J Am Chem Soc 2001; 123:9837-42. [PMID: 11583546 DOI: 10.1021/ja010997l] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A solid-state NMR technique is described for establishing stereochemistry using the natural product terrein as a model compound. This method involves comparison of experimental (13)C tensor principal values with ab initio computed values for all possible computer-generated stereoisomers. In terrein the relative stereochemistry is confirmed by NMR to be 2R*,3S with high statistical probability (>99.5%). The proposed approach also simultaneously verifies the molecular conformation of the two hydroxy groups in terrein established by X-ray data. It is sufficient to use only shift tensor values at carbons 2 and 3, the stereocenters, to characterize both the stereochemistry and molecular conformations. The solid-state NMR method appears to be especially useful for determining relative stereochemistry of compounds or their derivatives that are difficult to crystallize.
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Affiliation(s)
- J K Harper
- Department of Chemistry, University of Utah, Salt Lake City, 84112, USA
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43
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Sanders LK, Oldfield E. Theoretical Investigation of 19F NMR Chemical Shielding Tensors in Fluorobenzenes. J Phys Chem A 2001. [DOI: 10.1021/jp011114f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lori K. Sanders
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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44
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Czernek J. An ab Initio Study of Hydrogen Bonding Effects on the 15N and 1H Chemical Shielding Tensors in the Watson−Crick Base Pairs. J Phys Chem A 2001. [DOI: 10.1021/jp003471g] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 162 06 Praha 6, Czech Republic
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45
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Luman NR, King MP, Augspurger JD. Predicting15N amide chemical shifts in proteins. I. An additive model for the backbone contribution. J Comput Chem 2001. [DOI: 10.1002/1096-987x(200102)22:3<366::aid-jcc1008>3.0.co;2-f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Modeling NMR chemical shifts: crystal potential derived point charge (CPPCh) model to calculate solid state effects on 31P chemical shifts tensors. Int J Mol Sci 2000. [DOI: 10.3390/ijms1040075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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47
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DerHovanessian A, Rablen PR, Jain A. Ab Initio and Density Functional Calculations of 19F NMR Chemical Shifts for Models of Carbonic Anhydrase Inhibitors. J Phys Chem A 2000. [DOI: 10.1021/jp000785v] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Paul R. Rablen
- Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
| | - Ahamindra Jain
- Department of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
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48
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Cui Q, Karplus M. Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules. J Phys Chem B 2000. [DOI: 10.1021/jp994154g] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qiang Cui
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut Le Bel, Universitè Loius Pasteur, F-6700 Strasbourg, France
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut Le Bel, Universitè Loius Pasteur, F-6700 Strasbourg, France
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49
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Furó I, Iliopoulos I, Stilbs P. Structure and Dynamics of Associative Water-Soluble Polymer Aggregates As Seen by 19F NMR Spectroscopy. J Phys Chem B 1999. [DOI: 10.1021/jp9927404] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I. Furó
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden, and Laboratoire de Physico-chimie Macromoléculaire, UMR-7615, ESPCI-CNRS-UPMC, 10, rue Vauquelin, F-75231 Paris Cedex 05, France
| | - I. Iliopoulos
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden, and Laboratoire de Physico-chimie Macromoléculaire, UMR-7615, ESPCI-CNRS-UPMC, 10, rue Vauquelin, F-75231 Paris Cedex 05, France
| | - P. Stilbs
- Division of Physical Chemistry, Department of Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden, and Laboratoire de Physico-chimie Macromoléculaire, UMR-7615, ESPCI-CNRS-UPMC, 10, rue Vauquelin, F-75231 Paris Cedex 05, France
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50
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de Dios AC, Earle EM. Electric Field Effects on 13C and 17O Chemical Shifts and CO Stretching Frequency of Carbon Monoxide Bound to Fe2+. J Phys Chem A 1997. [DOI: 10.1021/jp972153n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angel C. de Dios
- Department of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, D.C. 20057
| | - Emily M. Earle
- Department of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, D.C. 20057
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