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Gasevic T, Bamberg M, Wicke J, Bolte M, Virovets A, Lerner HW, Grimme S, Hansen A, Wagner M, Bursch M. Confined Lewis Pairs: Investigation of the X - →Si 20 Interaction in Halogen-Encapsulating Silafulleranes. Angew Chem Int Ed Engl 2024; 63:e202314238. [PMID: 38059423 DOI: 10.1002/anie.202314238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
A joint theoretical and experimental study on 32 endohedral silafullerane derivatives [X@Si20 Y20 ]- (X=F-I; Y=F-I, H, Me, Et) andT h ${T_h }$ -[Cl@Si20 H12 Y8 ]- (Y=F-I) is presented. First, we evaluated the structure-determining template effect of Cl- in a systematic series of concave silapolyquinane model systems. Second, we investigated the X- →Si20 interaction energy (E int ${E_{{\rm{int}}} }$ ) as a function of X- and Y and found the largestE int ${E_{{\rm{int}}} }$ values for electron-withdrawing exohedral substituents Y. Given that X- ions can be considered as Lewis bases and empty Si20 Y20 clusters as Lewis acids, we classify our inseparable host-guest complexes [X@Si20 Y20 ]- as "confined Lewis pairs". Third, 35 Cl NMR spectroscopy proved to be highly diagnostic for an experimental assessment of the Cl- →Si20 interaction as the paramagnetic shielding and, in turn, δ ${\delta }$ (35 Cl) of the endohedral Cl- ion correlate inversely withE int ${E_{{\rm{int}}} }$ . Finally, we disclose the synthesis of [PPN][Cl@Si20 Y20 ] (Y=Me, Et, Br) and provide a thorough characterization of these new silafulleranes.
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Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Marcel Bamberg
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Julius Wicke
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Alexander Virovets
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Hans-Wolfram Lerner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Matthias Wagner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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2
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Lafiosca P, Rossi F, Egidi F, Giovannini T, Cappelli C. Multiscale Frozen Density Embedding/Molecular Mechanics Approach for Simulating Magnetic Response Properties of Solvated Systems. J Chem Theory Comput 2024; 20:266-279. [PMID: 38109486 PMCID: PMC10782454 DOI: 10.1021/acs.jctc.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
We present a three-layer hybrid quantum mechanical/quantum embedding/molecular mechanics approach for calculating nuclear magnetic resonance (NMR) shieldings and J-couplings of molecular systems in solution. The model is based on the frozen density embedding (FDE) and polarizable fluctuating charges (FQ) and fluctuating dipoles (FQFμ) force fields and permits the accurate ab initio description of short-range nonelectrostatic interactions by means of the FDE shell and cost-effective treatment of long-range electrostatic interactions through the polarizable force field FQ(Fμ). Our approach's accuracy and potential are demonstrated by studying NMR spectra of Brooker's merocyanine in aqueous and nonaqueous solutions.
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Affiliation(s)
- Piero Lafiosca
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Rossi
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Software
for Chemistry and Materials BV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | - Chiara Cappelli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [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: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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4
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Fernández-Alarcón A, Autschbach J. Relativistic Density Functional NMR Tensors Analyzed with Spin-free Localized Molecular Orbitals. Chemphyschem 2023; 24:e202200667. [PMID: 36169984 DOI: 10.1002/cphc.202200667] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Indexed: 01/07/2023]
Abstract
The implementation of fast relativistic methods based on density functional theory, in conjunction with localized molecular orbital (LMO) based analysis, allows straightforward interpretations of NMR parameters in terms of contributions from core shells, lone pairs, and bonds, for compounds containing elements from across the periodic table. We present a conceptual review of a frequently used LMO analysis of NMR parameters calculated in the presence of spin-orbit interactions and other relativistic effects. An accompanying example focuses on the 15 N shielding in a heavy metal complex.
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Affiliation(s)
- Alberto Fernández-Alarcón
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
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5
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Abstract
A recently developed methodology for calculating, analyzing, and visualizing nuclear magnetic shielding densities is used for studying spatial contributions including ring-current contributions to 1H nuclear magnetic resonance (NMR) chemical shifts of aromatic and anti-aromatic free-base porphyrinoids. Our approach allows a visual inspection of the spatial origin of the positive (shielding) and negative (deshielding) contributions to the nuclear magnetic shielding constants. Diatropic and paratropic current-density fluxes yield both shielding and deshielding contributions implying that not merely the tropicity of the current density determines whether the contribution has a shielding or deshielding character. Instead the shielding or deshielding contribution is determined by the direction of the current-density flux with respect to the studied nucleus.
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6
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Bamberg M, Bursch M, Hansen A, Brandl M, Sentis G, Kunze L, Bolte M, Lerner HW, Grimme S, Wagner M. [Cl@Si 20H 20] -: Parent Siladodecahedrane with Endohedral Chloride Ion. J Am Chem Soc 2021; 143:10865-10871. [PMID: 34255517 DOI: 10.1021/jacs.1c05598] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fullerenes and diamondoids are at the core of nanoscience. Comparable monodisperse silicon analogues are scarce. Herein, we report the synthesis of the parent siladodecahedrane, which represents the largest Platonic solid. It shares its pattern of pentagonal faces with the smallest fullerene, C20, and its saturated, H-terminated skeleton with diamondoids. Similar to endofullerenes, the silicon cage encapsulates a chloride ion ([Cl@Si20H20]-); similar to diamondoids, its Si-H termini offer a wealth of opportunities for further functionalization. Mere treatment with chloromethanes leads to the perchlorinated cluster [Cl@Si20Cl20]-. Both compounds were characterized by mass spectrometry, X-ray crystallography, NMR spectroscopy, and quantum-chemical calculations. The experimentally determined 35Cl resonances of the endohedral chloride ions are particularly diagnostic to probe the Cl- → Si20 interaction strength as a function of the different surface substituents, as we have proven by high-level computational analyses.
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Affiliation(s)
- Marcel Bamberg
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Matthias Brandl
- Institut für Pharmazeutische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Gabriele Sentis
- Institut für Pharmazeutische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Lukas Kunze
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Hans-Wolfram Lerner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Matthias Wagner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
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8
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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9
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Jinger R, Fliegl H, Bast R, Dimitrova M, Lehtola S, Sundholm D. Spatial Contributions to Nuclear Magnetic Shieldings. J Phys Chem A 2021; 125:1778-1786. [PMID: 33605721 PMCID: PMC8023705 DOI: 10.1021/acs.jpca.0c10884] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/05/2021] [Indexed: 01/09/2023]
Abstract
We develop a methodology for calculating, analyzing, and visualizing nuclear magnetic shielding densities which are calculated from the current density via the Biot-Savart relation. Atomic contributions to nuclear magnetic shielding constants can be estimated within our framework with a Becke partitioning scheme. The new features have been implemented in the GIMIC program and are applied in this work to the study of the 1H and 13C nuclear magnetic shieldings in benzene (C6H6) and cyclobutadiene (C4H4). The new methodology allows a visual inspection of the spatial origins of the positive (shielding) and negative (deshielding) contributions to the nuclear magnetic shielding constant of a single nucleus, something which has not been hitherto easily accomplished. Analysis of the shielding densities shows that diatropic and paratropic current-density fluxes yield both shielding and deshielding contributions, as the shielding or deshielding is determined by the direction of the current-density flux with respect to the studied nucleus instead of the tropicity. Becke partitioning of the magnetic shieldings shows that the magnetic shielding contributions mainly originate from the studied atom and its nearest neighbors, confirming the localized character of nuclear magnetic shieldings.
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Affiliation(s)
- Rahul
Kumar Jinger
- Indian
Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Heike Fliegl
- Karlsruhe
Institute of Technology, Institute of Nanotechnology, Hermann-von-Helmholtz Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Radovan Bast
- Department
Information Technology, UiT Arctic University
Norway, Tromsø, Norway
| | - Maria Dimitrova
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Susi Lehtola
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
| | - Dage Sundholm
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
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10
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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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11
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Prokopiou G, Autschbach J, Kronik L. Assessment of the Performance of Optimally Tuned Range‐Separated Hybrid Functionals for Nuclear Magnetic Shielding Calculations. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Georgia Prokopiou
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
| | - Jochen Autschbach
- Department of ChemistryState University of New York at BuffaloBuffalo NY 14260‐3000 USA
| | - Leeor Kronik
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
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12
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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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13
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Roggatz CC, Lorch M, Benoit DM. Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules. J Chem Theory Comput 2018; 14:2684-2695. [PMID: 29566332 DOI: 10.1021/acs.jctc.7b01020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.
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14
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da Silva JAV, Modesto-Costa L, de Koning MC, Borges I, França TCC. Theoretical NMR and conformational analysis of solvated oximes for organophosphates-inhibited acetylcholinesterase reactivation. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.09.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Kalra A, Zhang M, Parkin S, Li T. Crystal packing and crystallization tendency from the melt of 2-((2-ethylphenyl)amino)nicotinic acid. Z KRIST-CRYST MATER 2017. [DOI: 10.1515/zkri-2017-2070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
2-((2-ethylphenyl)amino)nicotinic acid (2EPNA) was synthesized and its crystal structure was determined. It was observed that alkylation of the phenyl ring with ethyl group disrupts the planar conformation of the molecule by steric repulsion, resulting in formation of an acid-pyridine heterosynthon (instead of acid-acid homosynthon) in the crystal. Crystallization tendency from the melt state of the polymorph was studied by differential scanning calorimetry (DSC). It was revealed that this compound could form a very stable amorphous phase on melt quenching and not crystallize even on re-heating. The formation of acid-pyridine hydrogen bonding in the amorphous state is believed to be responsible for its good glass forming ability.
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Affiliation(s)
- Arjun Kalra
- Department of Industrial and Physical Pharmacy , College of Pharmacy, Purdue University , West Lafayette, IN 47907 , USA
| | - Mingtao Zhang
- Department of Industrial and Physical Pharmacy , College of Pharmacy, Purdue University , West Lafayette, IN 47907 , USA
| | - Sean Parkin
- Department of Chemistry , University of Kentucky , Lexington, KY 40536 , USA
| | - Tonglei Li
- Department of Industrial and Physical Pharmacy , College of Pharmacy, Purdue University , West Lafayette, IN 47907 , USA
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16
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Gupta R, Huang W, Francesconi LC, Polenova T. Effect of positional isomerism and vanadium substitution on 51V magic angle spinning NMR Spectra Of Wells-Dawson polyoxotungstates. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:28-33. [PMID: 27998683 PMCID: PMC5466850 DOI: 10.1016/j.ssnmr.2016.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
We examined the positional isomerism and vanadium substitution on the 51V magic angle spinning NMR spectra of potassium salts of vanadium-substituted polyoxotungstates of the Wells-Dawson series. NMR parameters of this class of catalytically active polyoxotungstates effect of are reported. Multiple species, indicative of differences in the local environment at the substitution sites, are observed in solid-state NMR spectra of the di- and tri- substituted complexes in contrast to solution NMR spectra, where single average chemical shift was observed. The quadrupolar and chemical shift anisotropy parameters depend strongly on the position and the degree of the vanadium substitution into the oxoanion core establishing 51V SATRAS NMR spectroscopy as a sensitive probe of the local electronic environment in these catalytically active solids.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Wenlin Huang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Lynn C Francesconi
- Department of Chemistry, City University of New York, Hunter College, 695 Park Avenue, New York 10021, USA; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York 10016, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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17
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Jose KVJ, Raghavachari K. Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment. J Chem Theory Comput 2017; 13:1147-1158. [DOI: 10.1021/acs.jctc.6b00922] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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18
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Navarro-Vázquez A. State of the art and perspectives in the application of quantum chemical prediction of 1 H and 13 C chemical shifts and scalar couplings for structural elucidation of organic compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:29-32. [PMID: 27531665 DOI: 10.1002/mrc.4502] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/13/2016] [Accepted: 08/14/2016] [Indexed: 06/06/2023]
Abstract
Quantum mechanical prediction of chemical shifts and scalar couplings involving 1 H and 13 C nuclei is now a popular tool in structural elucidation of organic compounds. Here, we summarize the current state of the art and present to the reader present limitations and problems, mostly related to treatment of conformational flexibility, as well as future perspectives and potential applications in the field.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil
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19
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Benassi E. Benchmarking of density functionals for a soft but accurate prediction and assignment of1H and13C NMR chemical shifts in organic and biological molecules. J Comput Chem 2016; 38:87-92. [DOI: 10.1002/jcc.24521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 09/27/2016] [Accepted: 10/06/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Enrico Benassi
- Tomsk Polytechnic University; Lenin Ave. 43А Tomsk 634034 Russian Federation
- Scuola Superiore Normale, Piazza dei Cavalieri 7; Pisa Italy 56126
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20
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Lomas JS. (1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:28-38. [PMID: 26256675 DOI: 10.1002/mrc.4312] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/17/2015] [Indexed: 06/04/2023]
Abstract
Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.
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Affiliation(s)
- John S Lomas
- ITODYS, UMR 7086, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France
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21
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Ribeiro RF, Marenich AV, Cramer CJ, Truhlar DG. Solvent Dependence of (14)N Nuclear Magnetic Resonance Chemical Shielding Constants as a Test of the Accuracy of the Computed Polarization of Solute Electron Densities by the Solvent. J Chem Theory Comput 2015; 5:2284-300. [PMID: 26616615 DOI: 10.1021/ct900258f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although continuum solvation models have now been shown to provide good quantitative accuracy for calculating free energies of solvation, questions remain about the accuracy of the perturbed solute electron densities and properties computed from them. Here we examine those questions by applying the SM8, SM8AD, SMD, and IEF-PCM continuum solvation models in combination with the M06-L density functional to compute the (14)N magnetic resonance nuclear shieldings of CH3CN, CH3NO2, CH3NCS, and CH3ONO2 in multiple solvents, and we analyze the dependence of the chemical shifts on solvent dielectric constant. We examine the dependence of the computed chemical shifts on the definition of the molecular cavity (both united-atom models and models based on superposed individual atomic spheres) and three kinds of treatments of the electrostatics, namely the generalized Born approximation with the Coulomb field approximation, the generalized Born model with asymmetric descreening, and models based on approximate numerical solution schemes for the nonhomogeneous Poisson equation. Our most systematic analyses are based on the computation of relative (14)N chemical shifts in a series of solvents, and we compare calculated shielding constants relative to those in CCl4 for various solvation models and density functionals. While differences in the overall results are found to be reasonably small for different solvation models and functionals, the SMx models SM8, and SM8AD, using the same cavity definitions (which for these models means the same atomic radii) as those employed for the calculation of free energies of solvation, exhibit the best agreement with experiment for every functional tested. This suggests that in addition to predicting accurate free energies of solvation, the SM8 and SM8AD generalized Born models also describe the solute polarization in a manner reasonably consistent with experimental (14)N nuclear magnetic resonance spectroscopy. Models based on the nonhomogeneous Poisson equation show slightly reduced accuracy. Scaling the intrinsic Coulomb radii to larger values (as has sometimes been suggested in the past) does not uniformly improve the results for any kind of solvent model; furthermore it uniformly degrades the results for generalized Born models. Use of a basis set that increases the outlying charge diminishes the accuracy of continuum models that solve the nonhomogeneous Poisson equation, which we ascribe to the inability of the numerical schemes for approximately solving the nonhomogeneous Poisson equation to fully account for the effects of electronic charge outside the solute cavity.
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Affiliation(s)
- Raphael F Ribeiro
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431
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22
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Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids. J Chem Theory Comput 2015; 11:5229-41. [DOI: 10.1021/acs.jctc.5b00752] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean T. Holmes
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Robbie J. Iuliucci
- Department
of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, United States
| | - Karl T. Mueller
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Cecil Dybowski
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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23
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Liu Y, Junk T, Liu Y, Tzeng N, Perkins R. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Density functional investigation of intermolecular effects on 13C NMR chemical-shielding tensors modeled with molecular clusters. J Chem Phys 2014; 141:164121. [DOI: 10.1063/1.4900158] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, USA
| | - Karl T. Mueller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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25
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Pierens GK. 1H and 13C NMR scaling factors for the calculation of chemical shifts in commonly used solvents using density functional theory. J Comput Chem 2014; 35:1388-94. [PMID: 24854878 DOI: 10.1002/jcc.23638] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 11/05/2022]
Abstract
Calculation of NMR chemical shifts and coupling constants using quantum mechanical calculations [density functional theory (DFT)], has become a very popular tool for the determination of conformation and the assignment of stereochemistry within a molecule. We present the scaling factors (linear regression parameters) from 10 DFT methods for 10 commonly used NMR solvents using the same set of reference compounds. The results were compared with the corresponding gas-phase calculations to assess the inclusion of the polarizable continuum model for solvent effects.
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Affiliation(s)
- Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland, 4072, Australia
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26
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Siskos MG, Kontogianni VG, Tsiafoulis CG, Tzakos AG, Gerothanassis IP. Investigation of solute-solvent interactions in phenol compounds: accurate ab initio calculations of solvent effects on 1H NMR chemical shifts. Org Biomol Chem 2014; 11:7400-11. [PMID: 24071830 DOI: 10.1039/c3ob41556b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate (1)H chemical shifts of the -OH groups of polyphenol compounds can be calculated, compared to experimental values, using a combination of DFT, polarizable continuum model (PCM) and discrete solute-solvent hydrogen bond interactions. The study focuses on three molecular solutes: phenol, 4-methylcatechol and the natural product genkwanin in DMSO, acetone, acetonitrile, and chloroform. Excellent linear correlation between experimental and computed chemical shifts (with the GIAO method at the DFT/B3LYP/6-311++G(2d,p) level) was obtained with minimization of the solvation complexes at the DFT/B3LYP/6-31+G(d) and DFT/B3LYP/6-311++G(d,p) level of theory with a correlation coefficient of 0.991. The use of the DFT/B3LYP/6-31+G(d) level of theory for minimization could provide an excellent means for the accurate prediction of the experimental OH chemical shift range of over 8 ppm due to: (i) strong intramolecular and solute-solvent intermolecular hydrogen bonds, (ii) flip-flop intramolecular hydrogen bonds, and (iii) conformational effects of substituents of genkwanin. The combined use of ab initio calculations and experimental (1)H chemical shifts of phenol -OH groups provides a method of primary interest in order to obtain detailed structural, conformation and electronic description of solute-solvent interactions at a molecular level.
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Affiliation(s)
- Michael G Siskos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina GR 45110, Greece.
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27
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Tsipis AC, Karapetsas IN. Accurate prediction of 195Pt NMR chemical shifts for a series of Pt(ii) and Pt(iv) antitumor agents by a non-relativistic DFT computational protocol. Dalton Trans 2014; 43:5409-26. [DOI: 10.1039/c3dt53594k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exhaustive benchmark DFT calculations reveal that the non-relativistic GIAO-PBE0/SARC-ZORA(Pt)∪6-31+G(d)(E) computational protocol predicts accurate 195Pt NMR chemical shifts for a wide range of square planar Pt(ii) and octahedral Pt(iv) anticancer agents.
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Affiliation(s)
- Athanassios C. Tsipis
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- , Greece
| | - Ioannis N. Karapetsas
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- , Greece
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28
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Andrews KG, Spivey AC. Improving the Accuracy of Computed 13C NMR Shift Predictions by Specific Environment Error Correction: Fragment Referencing. J Org Chem 2013; 78:11302-17. [DOI: 10.1021/jo401833b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keith G. Andrews
- Department
of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
| | - Alan C. Spivey
- Department
of Chemistry, Imperial College, London SW7 2AZ, United Kingdom
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29
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Srebro M, Autschbach J. Computational Analysis of47/49Ti NMR Shifts and Electric Field Gradient Tensors of Half-Titanocene Complexes: Structure-Bonding-Property Relationships. Chemistry 2013; 19:12018-33. [DOI: 10.1002/chem.201301301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Indexed: 11/08/2022]
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30
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Pandey MK, Ramamoorthy A. Quantum chemical calculations of amide-15N chemical shift anisotropy tensors for a membrane-bound cytochrome-b5. J Phys Chem B 2013; 117:859-67. [PMID: 23268659 PMCID: PMC3564578 DOI: 10.1021/jp311116p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is considerable interest in determining amide-(15)N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-(15)N CSA tensors have been determined using density functional theory for a 16.7 kDa membrane-bound paramagnetic heme containing protein, cytochrome-b(5) (cytb(5)). All the calculations were performed by taking residues within 5 Å distance from the backbone amide-(15)N nucleus of interest. The calculated amide-(15)N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance r(N-H) = 1.023 Å and a constant angle β = 18° that the least shielded component (δ(11)) makes with the N-H bond. The variation of amide-(15)N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein-protein complexes such as cytochromes-b5-P450.
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Affiliation(s)
- Manoj Kumar Pandey
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055
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31
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Babinský M, Bouzková K, Pipíška M, Novosadová L, Marek R. Interpretation of crystal effects on NMR chemical shift tensors: electron and shielding deformation densities. J Phys Chem A 2013; 117:497-503. [PMID: 23253123 DOI: 10.1021/jp310967b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The relationship between the NMR observables and the supramolecular structure of any system is not straightforward. In this work we examine the influence of the crystal packing for three purine derivatives (hypoxanthine, theobromine, and 6-(2-methoxy)benzylaminopurine) on the principal components of the NMR chemical shift tensors (CSTs). We employ density functional calculations to obtain various molecular properties (the ground-state electron density, the magnitudes and orientations of the components of NMR chemical shift tensor, and the spatial distribution of the isotropic magnetic shielding) for the isolated molecules and for the molecules embedded in supramolecular clusters modeling the crystal environment and evaluate their differences. The concept has enabled us to rationalize the effect of the crystal packing on the NMR CSTs in terms of the redistribution of the ground-state electron density induced by intermolecular interactions in the solid state.
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Affiliation(s)
- Martin Babinský
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic
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32
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Deng H. Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:153-82. [PMID: 24018325 PMCID: PMC5484042 DOI: 10.1016/b978-0-12-416596-0.00005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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33
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Computation of 3JHH coupling constants with a combination of density functional theory and semiempirical calculations. Application to complex molecules. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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34
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Halling MD, Unikela KS, Bodwell GJ, Grant DM, Pugmire RJ. Solid-State 13C NMR Investigations of Cyclophanes: [2.2]Paracyclophane and 1,8-Dioxa[8](2,7)pyrenophane. J Phys Chem A 2012; 116:5193-8. [DOI: 10.1021/jp210297c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Merrill D. Halling
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Kiran Sagar Unikela
- Department of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7
| | - Graham J. Bodwell
- Department of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7
| | - David M. Grant
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Ronald J. Pugmire
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
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35
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Abstract
AbstractTo investigate the influence of C-doping on the electrostatic structure properties in the frame work of density functional theory (DFT), we considered beryllium monoxide nanotubes (BeONTs), consisting of 60 Be and 60 O atoms. Full geometry optimizations are performed for all structures, i.e., all atoms are allowed to relax. Afterwards, the chemical shielding (CS) tensors are calculated for Be-9, O-17 and C-13 nuclei in the C-doped forms and also pristine models of the (10, 0) zigzag and (5, 5) armchair BeONTs. Formation energies indicate that C-doping of Be atom (CBe form) could be more favorable than C-doping of O atom (CO form) in both zigzag and armchair BeONTs. Gap energies and dipole moments detected the effects of dopant in the (5, 5) armchair models; however, those parameters did not indicate any significant changes in the C-doped (10, 0) zigzag BeONT models. The results show that the CS values for the Be and O atoms-contributed to the Be-C bonds or those atoms close to the C-doped region-in the CO form of BeONTs (zigzag and armchair) are changed. The same values only for the O atoms-contributed to the O-C bonds- in the CBe form of BeONTs (zigzag and armchair) are changed.
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36
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Lucero PL, Peláez WJ, Riedl Z, Hajós G, Moyano EL, Yranzo GI. Flash vacuum pyrolysis of azolylacroleins and azolylbutadienes. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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37
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Lodewyk MW, Siebert MR, Tantillo DJ. Computational prediction of 1H and 13C chemical shifts: a useful tool for natural product, mechanistic, and synthetic organic chemistry. Chem Rev 2011; 112:1839-62. [PMID: 22091891 DOI: 10.1021/cr200106v] [Citation(s) in RCA: 892] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael W Lodewyk
- Department of Chemistry, University of California-Davis, Davis, California 95616, USA
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38
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Frank A, Onila I, Möller HM, Exner TE. Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins. Proteins 2011; 79:2189-202. [PMID: 21557322 DOI: 10.1002/prot.23041] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/01/2011] [Accepted: 03/13/2011] [Indexed: 11/09/2022]
Abstract
Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in crystallography. Therefore, there is still the need for new, independent, and unbiased evaluation tools to identify problematic parts and in the best case also to give guidelines that how to fix them. We present here, quantum chemical calculations of NMR chemical shifts for many proteins based on our fragment-based quantum chemical method: the adjustable density matrix assembler (ADMA). These results show that (13)C chemical shifts of reasonable accuracy can be obtained that can already provide a powerful measure for the structure validation. (1)H and even more (15)N chemical shifts deviate more strongly from experiment due to the insufficient treatment of solvent effects and conformational averaging.
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Affiliation(s)
- Andrea Frank
- Department of Chemistry and Zukunftskolleg, University of Konstanz, Konstanz D-78457, Germany
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39
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40
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Maliňáková K, Novosadová L, Pipíška M, Marek R. Chemical Shift Tensors in Isomers of Adenine: Relation to Aromaticity of Purine Rings? Chemphyschem 2010; 12:379-88. [DOI: 10.1002/cphc.201000657] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/18/2010] [Indexed: 11/11/2022]
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41
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Abbandonato G, Catalano D, Marini A. Aggregation of perfluoroctanoate salts studied by 19F NMR and DFT calculations: counterion complexation, poly(ethylene glycol) addition, and conformational effects. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:16762-16770. [PMID: 20883045 DOI: 10.1021/la102578k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The aggregation of perfluoroctanoate salts in H(2)O is studied by (19)F NMR on solutions of LiPFO, NaPFO, and CsPFO, without and with the addition of two poly(ethylene glycol) (PEG) oligomers of molecular weight 1500 and 3400 Da, respectively, and with the addition of suitable crown ethers. The (19)F chemical shift (cs) trends are monitored, at 25 °C, in a concentration range including the critical micellar concentration (cmc) or, in the presence of PEG, the critical aggregation concentration (cac). The cac values in the samples with PEG are lower than the cmc values of the corresponding samples without PEG; moreover, the (19)F cs trends above the cac and above the polymer saturation concentration reveal and help to explain some peculiarities of the aggregation process of PEG on PFO micelles, which, in the first step, seems to occur while the surfactant concentration in water is still increasing. Also in LiPFO/H(2)O or NaPFO/H(2)O solutions containing 12-crown-4 or 15-crown-5 ethers, suitable to complex Li(+) or Na(+) ions, respectively, the cmc decreases. On the other hand, the micellization process in the presence of crown ethers does not show other peculiarities. The prevailing conformations of the PFO chain are discussed on the basis of quantum-mechanical calculations. The theoretical chemical shifts were computed at the DFT level of theory, taking into account the effects of the environment by means of the IEF-PCM method. The helical structure is the most stable one, but anti conformations are easily accessible, in both the aqueous and fluorinated environment. The comparison between computed and experimental chemical shifts indicates that anti conformations are more important in the micelles than in water and in CsPFO micelles than in LiPFO or NaPFO ones.
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Affiliation(s)
- Gerardo Abbandonato
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
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Nicholas MP, Eryilmaz E, Ferrage F, Cowburn D, Ghose R. Nuclear spin relaxation in isotropic and anisotropic media. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:111-158. [PMID: 20633361 PMCID: PMC4015737 DOI: 10.1016/j.pnmrs.2010.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/13/2010] [Indexed: 05/28/2023]
Affiliation(s)
- Matthew P. Nicholas
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
| | - Ertan Eryilmaz
- Department of Chemistry, City College of the City University
of New York, New York 10031, U.S.A
- Graduate Center of the City University of New York, New York
10016, U.S.A
| | - Fabien Ferrage
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
- Département de Chimie, Ecole Normale
Supérieure, and CNRS, UMR 7203; 24 rue Lhomond, 75231 Paris cedex 05,
France
| | - David Cowburn
- New York Structural Biology Center, 89 Convent Avenue, Park
Building at 133rd St., New York, New York, 10027, USA
| | - Ranajeet Ghose
- Department of Chemistry, City College of the City University
of New York, New York 10031, U.S.A
- Graduate Center of the City University of New York, New York
10016, U.S.A
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Halling MD, Bell JD, Pugmire RJ, Grant DM, Miller JS. Solid-State NMR Spectra and Long, Intra-Dimer Bonding in the π-[TTF]22+ (TTF = Tetrathiafulvalene) Dication. J Phys Chem A 2010; 114:6622-9. [DOI: 10.1021/jp910509f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Merrill D. Halling
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2124, Salt Lake City, Utah 84112-0850
| | - Joshua D. Bell
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2124, Salt Lake City, Utah 84112-0850
| | - Ronald J. Pugmire
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2124, Salt Lake City, Utah 84112-0850
| | - David M. Grant
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2124, Salt Lake City, Utah 84112-0850
| | - Joel S. Miller
- Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2124, Salt Lake City, Utah 84112-0850
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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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Truflandier LA, Autschbach J. Probing the Solvent Shell with 195Pt Chemical Shifts: Density Functional Theory Molecular Dynamics Study of PtII and PtIV Anionic Complexes in Aqueous Solution. J Am Chem Soc 2010; 132:3472-83. [DOI: 10.1021/ja9096863] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
| | - Jochen Autschbach
- Department of Chemistry, 312 Natural Sciences Complex, State University of New York, Buffalo, New York 14260-3000
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Maliňáková K, Novosadová L, Lahtinen M, Kolehmainen E, Brus J, Marek R. 13C Chemical Shift Tensors in Hypoxanthine and 6-Mercaptopurine: Effects of Substitution, Tautomerism, and Intermolecular Interactions. J Phys Chem A 2010; 114:1985-95. [DOI: 10.1021/jp9100619] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kateřina Maliňáková
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
| | - Lucie Novosadová
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
| | - Manu Lahtinen
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
| | - Erkki Kolehmainen
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
| | - Jiří Brus
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
| | - Radek Marek
- National Center for Biomolecular Research, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic, Department of Chemistry, University of Jyväskylä, P. O. Box 35, FIN-40014, Finland, and Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, CZ-16206 Prague, Czech Republic
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Traer JW, Goward GR. The proton dynamics of imidazole methylphosphonate: an example of cooperative ionic conductivity. Phys Chem Chem Phys 2010; 12:263-72. [DOI: 10.1039/b917360a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Halling MD, Orendt AM, Strohmeier M, Solum MS, Tsefrikas VM, Hirao T, Scott LT, Pugmire RJ, Grant DM. Solid-state 13C NMR investigations of 4,7-dihydro-1H-tricyclopenta[def,jkl,pqr]triphenylene (sumanene) and indeno[1,2,3-cd]fluoranthene: Buckminsterfullerene moieties. Phys Chem Chem Phys 2010; 12:7934-41. [DOI: 10.1039/c001903h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Infante-Castillo R, Hernández-Rivera SP. On the choice of optimal protocol for calculation of 13C and 15N NMR isotropic chemical shifts in nitramine systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Johnston JC, Iuliucci RJ, Facelli JC, Fitzgerald G, Mueller KT. Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves. J Chem Phys 2009; 131:144503. [PMID: 19831448 PMCID: PMC2771050 DOI: 10.1063/1.3225270] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2009] [Accepted: 08/17/2009] [Indexed: 11/14/2022] Open
Abstract
In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all (13)C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.
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Affiliation(s)
- Jessica C Johnston
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, USA
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