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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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2
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Thureau P, Carvin I, Ziarelli F, Viel S, Mollica G. A Karplus Equation for the Conformational Analysis of Organic Molecular Crystals. Angew Chem Int Ed Engl 2019; 58:16047-16051. [PMID: 31397043 DOI: 10.1002/anie.201906359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/08/2019] [Indexed: 01/01/2023]
Abstract
Vicinal scalar couplings (3 J) are extensively used for the conformational analysis of organic compounds in the liquid state through empirical Karplus equations. In contrast, there are no examples of such use for the structural investigation of solids. With the support of first principles calculations, we demonstrate here that 13 C-13 C 3 J coupling constants (3 JCC ) measured on a series of isotopically enriched solid amino acids and sugars can be related to dihedral angles by a simple Karplus-like relationship, and we provide a parameterized Karplus function for the conformational analysis of organic molecular crystals. Under the experimental conditions discussed, torsional angles can be estimated from the experimental 3 JCC values with an accuracy of 10° using this function. These results open new perspectives towards the use of 3 JCC as a new analytical tool that could considerably simplify structure determination of functional organic solids.
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Affiliation(s)
- Pierre Thureau
- Aix Marseille Univ, CNRS, ICR UMR 7273, Marseille, France
| | - Isaure Carvin
- Aix Marseille Univ, CNRS, ICR UMR 7273, Marseille, France
| | - Fabio Ziarelli
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM, FR1739, Marseille, France
| | - Stéphane Viel
- Aix Marseille Univ, CNRS, ICR UMR 7273, Marseille, France.,Institut Universitaire de France, Paris, France
| | - Giulia Mollica
- Aix Marseille Univ, CNRS, ICR UMR 7273, Marseille, France
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3
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Thureau P, Carvin I, Ziarelli F, Viel S, Mollica G. A Karplus Equation for the Conformational Analysis of Organic Molecular Crystals. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Isaure Carvin
- Aix Marseille UnivCNRS, ICR UMR 7273 Marseille France
| | - Fabio Ziarelli
- Aix Marseille UnivCNRSCentrale Marseille, FSCM, FR1739 Marseille France
| | - Stéphane Viel
- Aix Marseille UnivCNRS, ICR UMR 7273 Marseille France
- Institut Universitaire de France Paris France
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Perić B, Gautier R, Pickard CJ, Bosiočić M, Grbić MS, Požek M. Solid-state NMR/NQR and first-principles study of two niobium halide cluster compounds. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2014; 59-60:20-30. [PMID: 24581866 DOI: 10.1016/j.ssnmr.2014.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/31/2014] [Accepted: 02/05/2014] [Indexed: 06/03/2023]
Abstract
Two hexanuclear niobium halide cluster compounds with a [Nb6X12](2+) (X=Cl, Br) diamagnetic cluster core, have been studied by a combination of experimental solid-state NMR/NQR techniques and PAW/GIPAW calculations. For niobium sites the NMR parameters were determined by using variable Bo field static broadband NMR measurements and additional NQR measurements. It was found that they possess large positive chemical shifts, contrary to majority of niobium compounds studied so far by solid-state NMR, but in accordance with chemical shifts of (95)Mo nuclei in structurally related compounds containing [Mo6Br8](4+) cluster cores. Experimentally determined δiso((93)Nb) values are in the range from 2,400 to 3,000 ppm. A detailed analysis of geometrical relations between computed electric field gradient (EFG) and chemical shift (CS) tensors with respect to structural features of cluster units was carried out. These tensors on niobium sites are almost axially symmetric with parallel orientation of the largest EFG and the smallest CS principal axes (Vzz and δ33) coinciding with the molecular four-fold axis of the [Nb6X12](2+) unit. Bridging halogen sites are characterized by large asymmetry of EFG and CS tensors, the largest EFG principal axis (Vzz) is perpendicular to the X-Nb bonds, while intermediate EFG principal axis (Vyy) and the largest CS principal axis (δ11) are oriented in the radial direction with respect to the center of the cluster unit. For more symmetrical bromide compound the PAW predictions for EFG parameters are in better correspondence with the NMR/NQR measurements than in the less symmetrical chlorine compound. Theoretically predicted NMR parameters of bridging halogen sites were checked by (79/81)Br NQR and (35)Cl solid-state NMR measurements.
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Affiliation(s)
- Berislav Perić
- Laboratory for Solid-State and Complex Compounds Chemistry, Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000-HR, Zagreb, Croatia.
| | - Régis Gautier
- Institut des Sciences Chimiques de Rennes, UMR 6226, CNRS-Ecole Nationale Supérieure de Chimie de Rennes, CS 50837, 35708 Rennes Cedex 7, France
| | - Chris J Pickard
- Department of Physics and Astronomy, University College London, Gower Street, London, WC1E6BT, UK
| | - Marko Bosiočić
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, HR-10000 Zagreb, Croatia
| | - Mihael S Grbić
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, HR-10000 Zagreb, Croatia
| | - Miroslav Požek
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, HR-10000 Zagreb, Croatia
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Santos-Carballal D, Suardíaz R, Crespo-Otero R, González L, Pérez CS. Conformational and NMR study of some furan derivatives by DFT methods. J Mol Model 2013; 19:4591-601. [PMID: 23975160 DOI: 10.1007/s00894-013-1964-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/25/2013] [Indexed: 11/27/2022]
Abstract
4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative conformation were calculated by DFT methods. The trend and shape of the rotational barrier are rationalized within natural bond orbitals as well as atoms-in-molecules approach. For the corresponding equilibrium geometries, (1)H and (13)C substituent induced shifts (SIS) were calculated and compared with experimental values. Calculated shielding constants are shown to be sensitive to the substituent effect through a linear fit with substituent's Hammett constants. An alternative approach was followed for assessing the effect of substituents over SIS through comparing the differences in isotropic shielding constants with NBO charges as well as with (1)H and (13)C experimental chemical shifts.
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Affiliation(s)
- David Santos-Carballal
- Departamento de Química Física, Facultad de Química, Universidad de La Habana, Ciudad de La Habana, Cuba
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Thureau P, Mollica G, Ziarelli F, Viel S. Selective measurements of long-range homonuclear J-couplings in solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 231:90-94. [PMID: 23608042 DOI: 10.1016/j.jmr.2013.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/17/2013] [Accepted: 03/23/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate here that the principle of frequency-selective spin-echoes can be extended to the measurements of long-range homonuclear scalar J-couplings in the solid-state. Singly or doubly frequency-selective pulses were used to generate either a J-modulated experiment (S) or a reference experiment (S0). The combination of these two distinct experiments provides experimental data that, in favorable cases, are insensitive to incoherent relaxation effects, and which can be used to estimate long-range homonuclear J-couplings in multiple spin-systems. The concept is illustrated in the case of a uniformly (13)C and (15)N labeled sample of L-histidine, where the absolute value of homonuclear J-couplings between two spins separated by one, two or three covalent bonds are measured. Moreover, we show that a (2)J((15)N-C-(15)N) coupling as small as 0.9 Hz can be precisely measured with the method presented here.
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Affiliation(s)
- Pierre Thureau
- Aix-Marseille Univ., CNRS, UMR 7273: Institut de Chimie Radicalaire, 13397 Marseille, France.
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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: 326] [Impact Index Per Article: 25.1] [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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Kiani A, Lakhkar NJ, Salih V, Smith ME, Hanna JV, Newport RJ, Pickup DM, Knowles JC. Titanium-containing bioactive phosphate glasses. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:1352-1375. [PMID: 22349246 DOI: 10.1098/rsta.2011.0276] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The use of biomaterials has revolutionized the biomedical field and has received substantial attention in the last two decades. Among the various types of biomaterials, phosphate glasses have generated great interest on account of their remarkable bioactivity and favourable physical properties for various biomedical applications relating to both hard and soft tissue regeneration. This review paper focuses mainly on the development of titanium-containing phosphate-based glasses and presents an overview of the structural and physical properties. The effect of titanium incorporation on the glassy network is to introduce favourable properties. The biocompatibility of these glasses is described along with recent developments in processing methodologies, and the potential of Ti-containing phosphate-based glasses as a bone substitute material is explored.
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Affiliation(s)
- A Kiani
- Division of Biomaterials and Tissue Engineering, University College London Eastman Dental Institute, 256 Gray's Inn Road, London WC1X 8LD, UK
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Charpentier T. The PAW/GIPAW approach for computing NMR parameters: a new dimension added to NMR study of solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2011; 40:1-20. [PMID: 21612895 DOI: 10.1016/j.ssnmr.2011.04.006] [Citation(s) in RCA: 235] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 05/18/2023]
Abstract
In 2001, Mauri and Pickard introduced the gauge including projected augmented wave (GIPAW) method that enabled for the first time the calculation of all-electron NMR parameters in solids, i.e. accounting for periodic boundary conditions. The GIPAW method roots in the plane wave pseudopotential formalism of the density functional theory (DFT), and avoids the use of the cluster approximation. This method has undoubtedly revitalized the interest in quantum chemical calculations in the solid-state NMR community. It has quickly evolved and improved so that the calculation of the key components of NMR interactions, namely the shielding and electric field gradient tensors, has now become a routine for most of the common nuclei studied in NMR. Availability of reliable implementations in several software packages (CASTEP, Quantum Espresso, PARATEC) make its usage more and more increasingly popular, maybe indispensable in near future for all material NMR studies. The majority of nuclei of the periodic table have already been investigated by GIPAW, and because of its high accuracy it is quickly becoming an essential tool for interpreting and understanding experimental NMR spectra, providing reliable assignments of the observed resonances to crystallographic sites or enabling a priori prediction of NMR data. The continuous increase of computing power makes ever larger (and thus more realistic) systems amenable to first-principles analysis. In the near future perspectives, as the incorporation of dynamical effects and/or disorder are still at their early developments, these areas will certainly be the prime target.
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Affiliation(s)
- Thibault Charpentier
- CEA, IRAMIS, SIS2M, Laboratoire de Structure et Dynamique par Résonance Magnétique, UMR CEA-CNRS 3299, F-91191 Gif-sur-Yvette cedex, France.
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Barrow NS, Yates JR, Feller SA, Holland D, Ashbrook SE, Hodgkinson P, Brown SP. Towards homonuclear J solid-state NMR correlation experiments for half-integer quadrupolar nuclei: experimental and simulated 11B MAS spin-echo dephasing and calculated 2JBB coupling constants for lithium diborate. Phys Chem Chem Phys 2011; 13:5778-89. [DOI: 10.1039/c0cp02343d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Sadoc A, Body M, Legein C, Biswal M, Fayon F, Rocquefelte X, Boucher F. NMR parameters in alkali, alkaline earth and rare earth fluorides from first principle calculations. Phys Chem Chem Phys 2011; 13:18539-50. [DOI: 10.1039/c1cp21253b] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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