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Majhi D, Stevensson B, Nguyen TM, Edén M. 1H and 13C chemical shift-structure effects in anhydrous β-caffeine and four caffeine-diacid cocrystals probed by solid-state NMR experiments and DFT calculations. Phys Chem Chem Phys 2024; 26:14345-14363. [PMID: 38700003 DOI: 10.1039/d3cp06197c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
By using density functional theory (DFT) calculations, we refined the H atom positions in the structures of β-caffeine (C), α-oxalic acid (OA; (COOH)2), α-(COOH)2·2H2O, β-malonic acid (MA), β-glutaric acid (GA), and I-maleic acid (ME), along with their corresponding cocrystals of 2 : 1 (2C-OA, 2C-MA) or 1 : 1 (C-GA, C-ME) stoichiometry. The corresponding 13C/1H chemical shifts obtained by gauge including projector augmented wave (GIPAW) calculations agreed overall very well with results from magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy experiments. Chemical-shift/structure trends of the precursors and cocrystals were examined, where good linear correlations resulted for all COO1H sites against the H⋯O and/or H⋯N H-bond distance, whereas a general correlation was neither found for the aliphatic/caffeine-stemming 1H sites nor any 13C chemical shift against either the intermolecular hydrogen- or tetrel-bond distance, except for the 13COOH sites of the 2C-OA, 2C-MA, and C-GA cocrystals, which are involved in a strong COOH⋯N bond with caffeine that is responsible for the main supramolecular stabilization of the cocrystal. We provide the first complete 13C NMR spectral assignment of the structurally disordered anhydrous β-caffeine polymorph. The results are discussed in relation to previous literature on the disordered α-caffeine polymorph and the ordered hydrated counterpart, along with recommendations for NMR experimentation that will secure sufficient 13C signal-resolution for reliable resonance/site assignments.
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Affiliation(s)
- Debashis Majhi
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Baltzar Stevensson
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Tra Mi Nguyen
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Mattias Edén
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91, Stockholm, Sweden.
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Brette F, Kourati D, Paris M, Loupias L, Célérier S, Cabioc'h T, Deschamps M, Boucher F, Mauchamp V. Assessing the Surface Chemistry of 2D Transition Metal Carbides (MXenes): A Combined Experimental/Theoretical 13C Solid State NMR Approach. J Am Chem Soc 2023; 145:4003-4014. [PMID: 36779668 DOI: 10.1021/jacs.2c11290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The surface functionalization of 2D transition metal carbides or nitrides, so-called MXenes, is one of the fundamental levers allowing to deeply modify their physicochemical properties. Beyond new approaches to control this pivotal parameter, the ability to unambiguously assess their surface chemistry is thus key to expand the application fields of this large class of 2D materials. Using a combination of experiments and state of the art density functional theory calculations, we show that the NMR signal of the carbon─the element common to all MXene carbides and corresponding MAX phase precursors─is extremely sensitive to the MXene functionalization, although carbon atoms are not directly bonded to the surface groups. The simulations include the orbital part to the NMR shielding and the contribution from the Knight shift, which is crucial to achieve good correlation with the experimental data, as demonstrated on a set of reference MXene precursors. Starting with the Ti3C2Tx MXene benchmark system, we confirm the high sensitivity of the 13C NMR shift to the exfoliation process. Developing a theoretical protocol to straightforwardly simulate different surface chemistries, we show that the 13C NMR shift variations can be quantitatively related to different surface compositions and number of surface chemistry variants induced by the different etching agents. In addition, we propose that the etching agent affects not only the nature of the surface groups but also their spatial distribution. The direct correlation between surface chemistry and 13C NMR shift is further confirmed on the V2CTx, Mo2CTx, and Nb2CTx MXenes.
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Affiliation(s)
- Florian Brette
- Université de Poitiers, ISAE-ENSMA, CNRS, PPRIME, 86073 Poitiers, France
- Nantes Université, CNRS, Institut des Matériaux De Nantes Jean Rouxel, IMN, F-44000 Nantes, France
| | - Dani Kourati
- CNRS, CEMHTI UPR3079, Université D'Orléans, 45071 Orléans, France
| | - Michael Paris
- Nantes Université, CNRS, Institut des Matériaux De Nantes Jean Rouxel, IMN, F-44000 Nantes, France
| | - Lola Loupias
- Institut De Chimie Des Milieux Et Matériaux De Poitiers (IC2MP), Université De Poitiers, CNRS, F-86073 Poitiers, France
| | - Stéphane Célérier
- Institut De Chimie Des Milieux Et Matériaux De Poitiers (IC2MP), Université De Poitiers, CNRS, F-86073 Poitiers, France
| | - Thierry Cabioc'h
- Université de Poitiers, ISAE-ENSMA, CNRS, PPRIME, 86073 Poitiers, France
| | | | - Florent Boucher
- Nantes Université, CNRS, Institut des Matériaux De Nantes Jean Rouxel, IMN, F-44000 Nantes, France
| | - Vincent Mauchamp
- Université de Poitiers, ISAE-ENSMA, CNRS, PPRIME, 86073 Poitiers, France
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Mathew R, Stevensson B, Edén M. Refined Structures of O-Phospho-l-serine and Its Calcium Salt by New Multinuclear Solid-State NMR Crystallography Methods. J Phys Chem B 2021; 125:10985-11004. [PMID: 34553936 PMCID: PMC8503883 DOI: 10.1021/acs.jpcb.1c05587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/17/2022]
Abstract
O-phospho-l-serine (Pser) and its Ca salt, Ca[O-phospho-l-serine]·H2O (CaPser), play important roles for bone mineralization and were recently also proposed to account for the markedly improved bone-adhesive properties of Pser-doped calcium phosphate-based cements for biomedical implants. However, the hitherto few proposed structural models of Pser and CaPser were obtained by X-ray diffraction, thereby leaving the proton positions poorly defined. Herein, we refine the Pser and CaPser structures by density functional theory (DFT) calculations and contrast them with direct interatomic-distance constraints from two-dimensional (2D) nuclear magnetic resonance (NMR) correlation experimentation at fast magic-angle spinning (MAS), encompassing double-quantum-single-quantum (2Q-1Q) 1H NMR along with heteronuclear 13C{1H} and 31P{1H} correlation NMR experiments. The Pser and CaPser structures before and after refinements by DFT were validated against sets of NMR-derived effective 1H-1H, 1H-31P, and 1H-13C distances, which confirmed the improved accuracy of the refined structures. Each distance set was derived from one sole 2D NMR experiment applied to a powder without isotopic enrichment. The distances were extracted without invoking numerical spin-dynamics simulations or approximate phenomenological models. We highlight the advantages and limitations of the new distance-extraction procedure. Isotropic 1H, 13C, and 31P chemical shifts obtained by DFT calculations using the gauge including projector augmented wave (GIPAW) method agreed very well with the experimental results. We discuss the isotropic and anisotropic 13C and 31P chemical-shift parameters in relation to the previous literature, where most data on CaPser are reported herein for the first time.
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Affiliation(s)
- Renny Mathew
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mattias Edén
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
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Scarperi A, Barcaro G, Pajzderska A, Martini F, Carignani E, Geppi M. Structural Refinement of Carbimazole by NMR Crystallography. Molecules 2021; 26:molecules26154577. [PMID: 34361730 PMCID: PMC8347463 DOI: 10.3390/molecules26154577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave’s disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.
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Affiliation(s)
- Andrea Scarperi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
| | - Giovanni Barcaro
- Institute For Chemical And Physical Processes, Italian National Council for Research, CNR/IPCF, Via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Aleksandra Pajzderska
- Department of Radiospectroscopy, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614 Poznan, Poland;
| | - Francesca Martini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Center for Instrument Sharing, University of Pisa (CISUP), 56126 Pisa, Italy
| | - Elisa Carignani
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Institute for the Chemistry of OrganoMetallic Compounds, Italian National Council for Research, CNR/ICCOM, Via G. Moruzzi 1, 56124 Pisa, Italy
- Correspondence: (E.C.); (M.G.); Tel.: +39-050-2219353 (E.C.); +39-050-2219289 (M.G.)
| | - Marco Geppi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; (A.S.); (F.M.)
- Center for Instrument Sharing, University of Pisa (CISUP), 56126 Pisa, Italy
- Institute for the Chemistry of OrganoMetallic Compounds, Italian National Council for Research, CNR/ICCOM, Via G. Moruzzi 1, 56124 Pisa, Italy
- Correspondence: (E.C.); (M.G.); Tel.: +39-050-2219353 (E.C.); +39-050-2219289 (M.G.)
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Gupta A, Chakraborty S, Ramakrishnan R. Revving up 13C NMR shielding predictions across chemical space: benchmarks for atoms-in-molecules kernel machine learning with new data for 134 kilo molecules. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abe347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles method for training. Herein we report the QM9-NMR dataset comprising isotropic shielding of over 0.8 million C atoms in 134k molecules of the QM9 dataset in gas and five common solvent phases. Using these data for training, we present benchmark results for the prediction transferability of kernel-ridge regression models with popular local descriptors. Our best model, trained on 100k samples, accurately predicts isotropic shielding of 50k ‘hold-out’ atoms with a mean error of less than 1.9 ppm. For the rapid prediction of new query molecules, the models were trained on geometries from an inexpensive theory. Furthermore, by using a Δ-ML strategy, we quench the error below 1.4 ppm. Finally, we test the transferability on non-trivial benchmark sets that include benchmark molecules comprising 10–17 heavy atoms and drugs.
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Ludwig M, Hillebrecht H. First-principles calculation of 11B solid-state NMR parameters of boron-rich compounds II: the orthorhombic phases MgB 7 and MgB 12C 2 and the boron modification γ-B 28. Phys Chem Chem Phys 2021; 23:3883-3897. [PMID: 33539490 DOI: 10.1039/d0cp06073a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the work on referencing 11B nuclear magnetic resonance (NMR) spectra for molecular icosahedral boranes and the subsequent transfer to the rhombohedral boron-rich borides of the α-rB12 type, we show that the magic angle spinning (MAS) NMR spectra of boron-rich borides with four or five symmetry-independent boron atoms can also be calculated. The calculations are performed on the level of density functional theory (DFT) using the gauge-including projector-augmented wave (GIPAW) approach. As model compounds o-MgB12C2 and MgB7 are used, for which the experimental spectra could be calculated in excellent agreement with a deviation of 1 to 2 ppm. Based on the calculations, the different B atoms can be assigned to the respective signals, taking into account the quadrupolar coupling constants Cq from computation of the electric field gradient (EFG) with its main axis Vzz. It is shown that due to the specific geometric conditions of icosahedra, the magnitudes of Vzz for the boron atoms involved in exohedral B-B bonds to neighbouring icosahedra depend only on the valence electron density of the bond critical point and the distance. This also applies to the bonds to the interstitial B2 unit in MgB7, but not to bonds to the heteroatom of the C2 dumbbell in o-MgB12C2. Both results are in line with our previous observations for the rhombohedral species (α-rB12; B12X2 with X = P, As, O). Finally, the spectrum of γ-B28 was calculated, whose structure also contains B12 icosahedra and interstitial B2 dumbbells. Here, a very similar bonding situation is found for the icosahedron, but the calculations show that the situation for the B2 unit is clearly different. In general, the only parameter that needs to be varied to fit calculated and measured spectra is the linewidth, as this cannot be calculated. For the cases of o-MgB12C2 and MgB7 signal areas are related to corresponding site multiplicities. A prerequisite for the successful application of the chosen method seems to be the presence of a semiconductor with a sufficiently large band gap, which is the case for the compounds investigated.
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Affiliation(s)
- Martin Ludwig
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg, Germany.
| | - Harald Hillebrecht
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg, Germany.
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Shi M, Jin X, Wan Z, He X. Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals. J Chem Phys 2021; 154:064502. [PMID: 33588539 DOI: 10.1063/5.0039115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the 13C and 1H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For 13C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the 1H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental 13C and 1H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for 13C chemical shift calculations, but not for the 1H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the 13C and 1H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.
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Affiliation(s)
- Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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Ludwig M, Hillebrecht H. First-principles calculation of 11B solid-state NMR parameters of boron-rich compounds I: the rhombohedral boron modifications and B 12X 2 (X = P, As, O). Phys Chem Chem Phys 2021; 23:470-486. [PMID: 33320120 DOI: 10.1039/d0cp04061d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the present study, solid-state nuclear magnetic resonance (NMR) spectra under magic angle spinning conditions of the rhombohedral structures α-B and B12P2 are reported together with the corresponding parameter sets from first principles calculations on α-B B12X2 (X = P, As, O). With the combination of density functional theory (DFT) and the gauge-including projector-augmented wave (GIPAW) approach as the theoretical tools at hand the computed 11B parameters lead to unambiguous explanation of the measurements. Thereby, we overcome common obstacles of processing recorded NMR spectra of solid-state compounds with several crystallographic positions, in particular non-trivial signal assignments and parameter determination due to peak overlap or even unexpected intensity/area ratios. In fact, we find very good agreement between the theoretical results and measured spectra without applying fitting procedures. Using the Perdew-Burke-Ernzerhof (PBE) functional, the results of the common construction types for pseudopotentials and referencing methods for the chemical shift determination are compared. Suggestions and conclusions from experimental 11B NMR studies on parameters according to the icosahedral positions are critically discussed, for instance the early suspected correlation to chemical shifts is not confirmed. Regarding the electric field gradient (EFG) a detailed explanation for obtaining small deviations amongst all investigated structures of the icosahedral polar sites compared to the equatorial sites is given. Our results show an important link between the exohedral bonding situation of compounds with icosahedral structure elements and the main axis of the EFG and therefore, also measurable quadrupole coupling constants if certain geometrical conditions are fulfilled. Finally, this work also contributes to establishing the number of unique sites measured by solid-state NMR methods within the modification of β-B.
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Affiliation(s)
- Martin Ludwig
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg, Germany.
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Wang SS, Zhang YY, Guan JH, Yu Y, Xia Y, Li SS. Numerical study of disorder on the orbital magnetization in two dimensions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:335302. [PMID: 32294636 DOI: 10.1088/1361-648x/ab8985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The modern theory of orbital magnetization (OM) was developed by using Wannier function method, which has a formalism similar with the Berry phase. In this manuscript, we perform a numerical study on the fate of the OM under disorder, by using this method on the Haldane model in two dimensions, which can be tuned between a normal insulator or a Chern insulator at half filling. The effects of increasing disorder on OM for both cases are simulated. Energy renormalization shifts are observed in the weak disorder regime and topologically trivial case, which was predicted by a self-consistentT-matrix approximation. Besides this, two other phenomena can be seen. One is the localization trend of the band orbital magnetization. The other is the remarkable contribution from topological chiral states arising from nonzero Chern number or large value of integrated Berry curvature. If the fermi energy is fixed at the gap center of the clean system, there is an enhancement of |M| at the intermediate disorder, for both cases of normal and Chern insulators, which can be attributed to the disorder induced topological metal state before localization.
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Affiliation(s)
- Si-Si Wang
- SKLSM, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yan-Yang Zhang
- School of Physics and Electronic Engineering, Guangzhou University, 510006 Guangzhou, People's Republic of China
| | - Ji-Huan Guan
- SKLSM, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yan Yu
- SKLSM, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yang Xia
- Microelectronic Instrument and Equipment Research Center, Institute of Microelectronics of Chinese Academy of Sciences, Beijing 100029, People's Republic of China
- School of Microelectronics, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shu-Shen Li
- SKLSM, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Ludwig M, Himmel D, Hillebrecht H. GIAO versus GIPAW: Comparison of Methods To Calculate 11B NMR Shifts of Icosahedral Closo-Heteroboranes toward Boron-Rich Borides. J Phys Chem A 2020; 124:2173-2185. [PMID: 31999459 DOI: 10.1021/acs.jpca.9b06582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we perform first-principle density functional theory calculations with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional to compare the results of the gauge-including atomic orbital (GIAO) method with the gauge-including projector-augmented wave (GIPAW) approach for isotropic 11B nuclear magnetic resonance shifts. GIPAW had been used successfully for the theoretical calculation of nuclear magnetic parameters of 11B species in strong ionic solid-phase compounds such as borates but had been applied very rarely to structures where boron is mainly involved in complex covalent bonding situations, for example, in icosahedra of boron-rich borides. Thus, we investigate the accuracy of both well-known methods and reliability of the effective treatment of core electrons on a test set containing 16 experimentally known closo-(hetero)dodecaboranes. In general, we find very good agreement between GIAO and GIPAW when compared to experimental observations. However, accidental degeneracies of the shift values are better predicted by GIPAW. The optimized molecular geometries on the PBE level agree well with gaseous electron diffraction data and lead to theoretical isotropic chemical 11B shifts with root-mean-square errors of 2.1 and 1.0 ppm depending on the used model of converting absolute shieldings to chemical shifts. The comparison with results from hybrid functionals (B3LYP, B3LYP-D2, and PBE0) shows a minor improvement in accuracy, which is in agreement with 13C shifts of sp3-hybridized species. In order to prove the reliability of the conversion parameters obtained by PBE, we report the calculated 11B shifts of 1,2-, 1,7-, and 1,12-PCB10H11 with GIAO and GIPAW to our knowledge for the first time. Additionally, Bader's analysis is carried out on the converged electron density for all boron species within the molecular test set, yielding no simple direct relation between charge and isotropic shifts.
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Affiliation(s)
- Martin Ludwig
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Daniel Himmel
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Harald Hillebrecht
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
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11
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Bashi M, Rahnamaye Aliabad HA. Investigation of 205 Tl NMR shielding, structural, and electronical properties in thallium halides by applying PBE-GGA, YS-PBE0 and mBJ functionals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:223-231. [PMID: 31715051 DOI: 10.1002/mrc.4970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
We report the structural, electronical, and heavy nuclear 205 Tl Nuclear Magnetic Resonance (NMR) shielding properties of thallium halides TlX (X = F, Cl, Br, and I) by the first principles calculation. The Perdew-Burke-Ernzerhof Generalized Gradient Approximation, Yukawa Screened-PBE0 hybrid functional, and modified Becke-Johnson (mBJ) functionals including the relativistic and spin-orbit coupling effects are applied for calculation of the exchange-correlation potentials. Calculated PDOS spectra display that the valence band is composed of the X-s, Tl-5d, X-p, and Tl-6s states, and these states play an important role in 205 Tl NMR shielding. Our findings indicate that the nuclear magnetic shielding parameters depend on the electronic properties. Obtained results by mBJ show that there is a close agreement between the experimental and the calculated NMR parameters.
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Affiliation(s)
- M Bashi
- Department of Physics, Hakim Sabzevari University, Sabzevar, Iran
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12
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Blaha P, Schwarz K, Tran F, Laskowski R, Madsen GKH, Marks LD. WIEN2k: An APW+lo program for calculating the properties of solids. J Chem Phys 2020; 152:074101. [DOI: 10.1063/1.5143061] [Citation(s) in RCA: 585] [Impact Index Per Article: 146.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter Blaha
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Karlheinz Schwarz
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Fabien Tran
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Robert Laskowski
- Institute of High Performance Computing, A*STAR, 1 Fusionopolis Way, #16-16, Connexis 138632, Singapore
| | - Georg K. H. Madsen
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Laurence D. Marks
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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13
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Guo R, Uddin MN, Price LS, Price SL. Calculation of Diamagnetic Susceptibility Tensors of Organic Crystals: From Coronene to Pharmaceutical Polymorphs. J Phys Chem A 2020; 124:1409-1420. [PMID: 31951408 PMCID: PMC7145345 DOI: 10.1021/acs.jpca.9b07104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Understanding
why crystallization in strong magnetic fields can
lead to new polymorphs requires methods to calculate the diamagnetic
response of organic molecular crystals. We develop the calculation
of the macroscopic diamagnetic susceptibility tensor, χcryst, for organic molecular crystals using periodic density
functional methods. The crystal magnetic susceptibility tensor, χcryst, for all experimentally known polymorphs,
and its molecular counterpart, χmol,
are calculated for flexible pharmaceuticals such as carbamazepine,
flufenamic acid, and chalcones, and rigid molecules, such as benzene,
pyridine, acridine, anthracene, and coronene, whose molecular magnetic
properties have been traditionally studied. A tensor addition method
is developed to approximate the crystal diamagnetic susceptibility
tensor, χcryst, from the molecular one, χmol, giving good agreement with those calculated
directly using the more costly periodic density functional method
for χcryst. The response of pharmaceutical
molecules and crystals to magnetic fields, as embodied by χcryst, is largely determined by the packing in the crystal,
as well as the molecular conformation. The anisotropy of χcryst can vary considerably between polymorphs though
the isotropic terms are fairly constant. The implications for developing
a computational method for predicting whether crystallization in a
magnetic field could produce a novel or different polymorph are discussed.
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Affiliation(s)
- Rui Guo
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - M Nadia Uddin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - Louise S Price
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - Sarah L Price
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
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14
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Cuny J, Jolibois F, Gerber IC. Evaluation of Gas-to-Liquid 17O Chemical Shift of Water: A Test Case for Molecular and Periodic Approaches. J Chem Theory Comput 2018; 14:4041-4051. [DOI: 10.1021/acs.jctc.8b00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC), Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Franck Jolibois
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
| | - Iann C. Gerber
- LPCNO, Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS, 135 avenue de Rangueil, 31077 Cedex 4 Toulouse, France
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15
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Springborg M, Molayem M, Kirtman B. Electronic orbital response of regular extended and infinite periodic systems to magnetic fields. I. Theoretical foundations for static case. J Chem Phys 2018; 147:104101. [PMID: 28915743 DOI: 10.1063/1.5001261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical treatment for the orbital response of an infinite, periodic system to a static, homogeneous, magnetic field is presented. It is assumed that the system of interest has an energy gap separating occupied and unoccupied orbitals and a zero Chern number. In contrast to earlier studies, we do not utilize a perturbation expansion, although we do assume the field is sufficiently weak that the occurrence of Landau levels can be ignored. The theory is developed by analyzing results for large, finite systems and also by comparing with the analogous treatment of an electrostatic field. The resulting many-electron Hamilton operator is forced to be hermitian, but hermiticity is not preserved, in general, for the subsequently derived single-particle operators that determine the electronic orbitals. However, we demonstrate that when focusing on the canonical solutions to the single-particle equations, hermiticity is preserved. The issue of gauge-origin dependence of approximate solutions is addressed. Our approach is compared with several previously proposed treatments, whereby limitations in some of the latter are identified.
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Affiliation(s)
- Michael Springborg
- Physical and Theoretical Chemistry, University of Saarland, 66123 Saarbrücken, Germany
| | - Mohammad Molayem
- Physical and Theoretical Chemistry, University of Saarland, 66123 Saarbrücken, Germany
| | - Bernard Kirtman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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16
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Tavares SR, Vaiss VS, Antunes FPN, Fonseca CG, Nangoi IM, Moraes PIR, Soares CV, Haddad JFS, Lima LL, Silva BNN, Leitão AA. DFT calculations for structural prediction and applications of intercalated lamellar compounds. Dalton Trans 2018; 47:2852-2866. [DOI: 10.1039/c7dt03730a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This review lists some relevant types of intercalated lamellar materials and applications of DFT calculations in these materials.
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17
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Zilka M, Sturniolo S, Brown SP, Yates JR. Visualising crystal packing interactions in solid-state NMR: Concepts and applications. J Chem Phys 2017; 147:144203. [DOI: 10.1063/1.4996750] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Miri Zilka
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Simone Sturniolo
- Scientific Computing Department, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX,
United Kingdom
| | - Steven P. Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan R. Yates
- Department of Materials, University of Oxford, Oxford OX1 3PH, United Kingdom
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18
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19
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Bashi M, Aliabad HAR, Mowlavi AA, Ahmad I. 127I NMR calculations in binary metal iodides by PBE-GGA, YS-PBE0 and mBJ exchange correlation potentials. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 82-83:10-15. [PMID: 28040584 DOI: 10.1016/j.ssnmr.2016.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/20/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
We have calculated Nuclear Magnetic Resonance (NMR) spectroscopy for 127I (quadrupolar nuclei I=5/2) in binary metal iodides XI (X=Li, Na, K, Rb and Cs) by using PBE- GGA, YS- PBE0 and mBJ exchange correlation potentials. The results show that the nature of bonds between Iodine and metal atoms are ionic. The main contribution in NMR spectroscopy is related to the induced current inside the atomic sphere and the remainder of the unit cell volume contributes only a few ppm. Obtained NMR shifts are compared with the NMR shielding data and the NMR shielding for metal-p band varies across the series about 221ppm. Density of states results indicate that the largest contribution in the shielding comes from the I-core electrons (1s and 4d). The NMR shielding graphs show that there are negative linear correlation with slope -1.18, -1.16 and -1.01 by PBE- GGA, YS- PBE0 and mBJ, respectively. The computed results by mBJ are in good agreement with the experimental values.
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Affiliation(s)
- M Bashi
- Department of Physics, Hakim Sabzevari University, Sabzevar 9617976487, Iran
| | | | - A A Mowlavi
- Department of Physics, Hakim Sabzevari University, Sabzevar 9617976487, Iran; ICTP, Associate federation Scheme, Medical Physics Field, Trieste, Italy
| | - Iftikhar Ahmad
- Center for Computational Materials Science, University of Malakand, Chakdara, Pakistan; Vice-Chancellor, Abbottabad University of Science & Technology, Havelian, Pakistan
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20
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de Wijs GA, Laskowski R, Blaha P, Havenith RWA, Kresse G, Marsman M. NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations. J Chem Phys 2017; 146:064115. [DOI: 10.1063/1.4975122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- G. A. de Wijs
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
| | - R. Laskowski
- Institute of High Performance Computing, A∗STAR, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632
| | - P. Blaha
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - R. W. A. Havenith
- Zernike Institute for Advanced Materials, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
- Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), B-9000 Gent, Belgium
| | - G. Kresse
- University of Vienna, Faculty of Physics and Center for Computational Materials Science, Sensengasse 8/12, A-1090 Vienna, Austria
| | - M. Marsman
- University of Vienna, Faculty of Physics and Center for Computational Materials Science, Sensengasse 8/12, A-1090 Vienna, Austria
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21
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Veinberg SL, Friedl ZW, Lindquist AW, Kispal B, Harris KJ, O'Dell LA, Schurko RW. 14N Solid-State NMR Spectroscopy of Amino Acids. Chemphyschem 2016; 17:4011-4027. [DOI: 10.1002/cphc.201600873] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Stanislav L. Veinberg
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Zachary W. Friedl
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Austin W. Lindquist
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Brianna Kispal
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Kristopher J. Harris
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Luke A. O'Dell
- Institute for Frontier Materials; Deakin University; Waurn Ponds Campus Geelong Victoria 3220 Australia
| | - Robert W. Schurko
- Department of Chemistry and Biochemistry; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
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22
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Sundholm D, Fliegl H, Berger RJ. Calculations of magnetically induced current densities: theory and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1270] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dage Sundholm
- Department of Chemistry; University of Helsinki; Helsinki Finland
| | - Heike Fliegl
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry; University of Oslo; Oslo Norway
| | - Raphael J.F. Berger
- Paris-Lodron University of Salzburg; Chemistry of Materials; Salzburg Austria
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23
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Mandal A, Hunt KLC. Gauge-invariant expectation values of the energy of a molecule in an electromagnetic field. J Chem Phys 2016; 144:044109. [PMID: 26827204 DOI: 10.1063/1.4938564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we show that the full Hamiltonian for a molecule in an electromagnetic field can be separated into a molecular Hamiltonian and a field Hamiltonian, both with gauge-invariant expectation values. The expectation value of the molecular Hamiltonian gives physically meaningful results for the energy of a molecule in a time-dependent applied field. In contrast, the usual partitioning of the full Hamiltonian into molecular and field terms introduces an arbitrary gauge-dependent potential into the molecular Hamiltonian and leaves a gauge-dependent form of the Hamiltonian for the field. With the usual partitioning of the Hamiltonian, this same problem of gauge dependence arises even in the absence of an applied field, as we show explicitly by considering a gauge transformation from zero applied field and zero external potentials to zero applied field, but non-zero external vector and scalar potentials. We resolve this problem and also remove the gauge dependence from the Hamiltonian for a molecule in a non-zero applied field and from the field Hamiltonian, by repartitioning the full Hamiltonian. It is possible to remove the gauge dependence because the interaction of the molecular charges with the gauge potential cancels identically with a gauge-dependent term in the usual form of the field Hamiltonian. We treat the electromagnetic field classically and treat the molecule quantum mechanically, but nonrelativistically. Our derivation starts from the Lagrangian for a set of charged particles and an electromagnetic field, with the particle coordinates, the vector potential, the scalar potential, and their time derivatives treated as the variables in the Lagrangian. We construct the full Hamiltonian using a Lagrange multiplier method originally suggested by Dirac, partition this Hamiltonian into a molecular term Hm and a field term Hf, and show that both Hm and Hf have gauge-independent expectation values. Any gauge may be chosen for the calculations; but following our partitioning, the expectation values of the molecular Hamiltonian are identical to those obtained directly in the Coulomb gauge. As a corollary of this result, the power absorbed by a molecule from a time-dependent, applied electromagnetic field is equal to the time derivative of the non-adiabatic term in the molecular energy, in any gauge.
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Affiliation(s)
- Anirban Mandal
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Katharine L C Hunt
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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24
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Cuny J, Xie Y, Pickard CJ, Hassanali AA. Ab Initio Quality NMR Parameters in Solid-State Materials Using a High-Dimensional Neural-Network Representation. J Chem Theory Comput 2016; 12:765-73. [PMID: 26730889 DOI: 10.1021/acs.jctc.5b01006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental tools to probe the local atomic order of a wide range of solid-state compounds. However, due to the complexity of the related spectra, in particular for amorphous materials, their interpretation in terms of structural information is often challenging. These difficulties can be overcome by combining molecular dynamics simulations to generate realistic structural models with an ab initio evaluation of the corresponding chemical shift and quadrupolar coupling tensors. However, due to computational constraints, this approach is limited to relatively small system sizes which, for amorphous materials, prevents an adequate statistical sampling of the distribution of the local environments that is required to quantitatively describe the system. In this work, we present an approach to efficiently and accurately predict the NMR parameters of very large systems. This is achieved by using a high-dimensional neural-network representation of NMR parameters that are calculated using an ab initio formalism. To illustrate the potential of this approach, we applied this neural-network NMR (NN-NMR) method on the (17)O and (29)Si quadrupolar coupling and chemical shift parameters of various crystalline silica polymorphs and silica glasses. This approach is, in principal, general and has the potential to be applied to predict the NMR properties of various materials.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse [UPS] and CNRS , 118 Route de Narbonne, F-31062 Toulouse, France
| | - Yu Xie
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Chris J Pickard
- Department of Materials Science & Metallurgy, University of Cambridge , 27 Charles Babbage Road, Cambridge CB3 0FS, United Kingdom
| | - Ali A Hassanali
- Condensed Matter Physics Section, The Abdus Salaam International Center for Theoretical Physics , Strada Costiera 11, I-34151 Trieste, Trieste, Italy
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25
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Skachkov D, Krykunov M, Kadantsev E, Ziegler T. The Calculation of NMR Chemical Shifts in Periodic Systems Based on Gauge Including Atomic Orbitals and Density Functional Theory. J Chem Theory Comput 2015; 6:1650-9. [PMID: 26615697 DOI: 10.1021/ct100046a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here a method that can calculate NMR shielding tensors from first principles for systems with translational invariance. Our approach is based on Kohn-Sham density functional theory and gauge-including atomic orbitals. Our scheme determines the shielding tensor as the second derivative of the total electronic energy with respect to an external magnetic field and a nuclear magnetic moment. The induced current density due to a periodic perturbation from nuclear magnetic moments is obtained through numerical differentiation, whereas the influence of the responding perturbation in terms of the external magnetic field is evaluated analytically. The method is implemented into the periodic program BAND. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn-Sham potential fully without the use of effective core potentials. Results from calculations of NMR shielding constants based on the present approach are presented for isolated molecules as well as systems with one-, two- and three-dimensional periodicity. The reported values are compared to experiment and results from calculations on cluster models.
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Affiliation(s)
- Dmitry Skachkov
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Mykhaylo Krykunov
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Eugene Kadantsev
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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26
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Laskowski R, Blaha P. NMR Shielding in Metals Using the Augmented Plane Wave Method. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:19390-19396. [PMID: 26322148 PMCID: PMC4547173 DOI: 10.1021/acs.jpcc.5b05947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/28/2015] [Indexed: 06/04/2023]
Abstract
We present calculations of solid state NMR magnetic shielding in metals, which includes both the orbital and the complete spin response of the system in a consistent way. The latter contains an induced spin-polarization of the core states and needs an all-electron self-consistent treatment. In particular, for transition metals, the spin hyperfine field originates not only from the polarization of the valence s-electrons, but the induced magnetic moment of the d-electrons polarizes the core s-states in opposite direction. The method is based on DFT and the augmented plane wave approach as implemented in the WIEN2k code. A comparison between calculated and measured NMR shifts indicates that first-principle calculations can obtain converged results and are more reliable than initially concluded based on previous publications. Nevertheless large k-meshes (up to 2 000 000 k-points in the full Brillouin-zone) and some Fermi-broadening are necessary. Our results show that, in general, both spin and orbital components of the NMR shielding must be evaluated in order to reproduce experimental shifts, because the orbital part cancels the shift of the usually highly ionic reference compound only for simple sp-elements but not for transition metals. This development paves the way for routine NMR calculations of metallic systems.
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Affiliation(s)
- Robert Laskowski
- Institute of High
Performance Computing, A*STAR, 1 Fusionopolis
Way, #16-16, Connexis, Singapore 138632
| | - Peter Blaha
- Institute
of Materials Chemistry, Vienna University
of Technology, Getreidemarkt
9/165-TC, A-1060 Vienna, Austria
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27
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Štěpánek P, Bouř P. Origin-independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method. J Comput Chem 2015; 36:723-30. [DOI: 10.1002/jcc.23845] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/05/2015] [Accepted: 01/09/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Petr Štěpánek
- Group of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences; Flemingovo nám. 2 16610 Prague Czech Republic
- Institute of Physics, Faculty of Mathematics and Physics; Charles University; Ke Karlovu 5 121 16 Prague Czech Republic
| | - Petr Bouř
- Group of Molecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences; Flemingovo nám. 2 16610 Prague Czech Republic
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28
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Ren P, Zheng A, Xiao J, Pan X, Bao X. Exploring the ring current of carbon nanotubes by first-principles calculations. Chem Sci 2015; 6:902-908. [PMID: 29560175 PMCID: PMC5811143 DOI: 10.1039/c4sc01996b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/26/2014] [Indexed: 11/29/2022] Open
Abstract
Ring current is a fundamental concept to understand the nuclear magnetic resonance (NMR) properties and aromaticity for conjugated systems, such as carbon nanotubes (CNTs). Employing the recently developed gauge including projector augmented wave (GIPAW) method, we studied the ring currents of CNTs systematically and visualized their distribution. The ring current patterns are determined by the semiconducting or metallic properties of CNTs. The discrepancy is mainly caused by the axial component of external magnetic fields, whereas the radial component induced ring currents are almost independent of the electronic structures of CNTs, where the intensities of the ring currents are linearly related to the diameters of the CNTs. Although the ring currents induced by the radial component are more intense than those by the axial component, only the latter determines the overall NMR responses and aromaticity of the CNTs as well. Furthermore, the semiconducting CNTs are more aromatic than their metallic counterparts due to the existence of delocalized ring currents on the semiconducting CNTs. These fundamental features are of vital importance for the development of CNT-based nanoelectronics and applications in magnetic fields.
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Affiliation(s)
- Pengju Ren
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China .
| | - Anmin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Center for Magnetic Resonance , Wuhan Institute of Physics and Mathematics , Chinese Academy of Sciences , Wuhan 430071 , China
| | - Jianping Xiao
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China .
| | - Xiulian Pan
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China .
| | - Xinhe Bao
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Zhongshan Road 457 , Dalian 116023 , China .
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29
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Bevilaqua RCA, Rigo VA, Veríssimo-Alves M, Miranda CR. NMR characterization of hydrocarbon adsorption on calcite surfaces: a first principles study. J Chem Phys 2014; 141:204705. [PMID: 25429955 DOI: 10.1063/1.4902251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The electronic and coordination environment of minerals surfaces, as calcite, are very difficult to characterize experimentally. This is mainly due to the fact that there are relatively few spectroscopic techniques able to detect Ca(2+). Since calcite is a major constituent of sedimentary rocks in oil reservoir, a more detailed characterization of the interaction between hydrocarbon molecules and mineral surfaces is highly desirable. Here we perform a first principles study on the adsorption of hydrocarbon molecules on calcite surface (CaCO3 (101¯4)). The simulations were based on Density Functional Theory with Solid State Nuclear Magnetic Resonance (SS-NMR) calculations. The Gauge-Including Projector Augmented Wave method was used to compute mainly SS-NMR parameters for (43)Ca, (13)C, and (17)O in calcite surface. It was possible to assign the peaks in the theoretical NMR spectra for all structures studied. Besides showing different chemical shifts for atoms located on different environments (bulk and surface) for calcite, the results also display changes on the chemical shift, mainly for Ca sites, when the hydrocarbon molecules are present. Even though the interaction of the benzene molecule with the calcite surface is weak, there is a clearly distinguishable displacement of the signal of the Ca sites over which the hydrocarbon molecule is located. A similar effect is also observed for hexane adsorption. Through NMR spectroscopy, we show that aromatic and alkane hydrocarbon molecules adsorbed on carbonate surfaces can be differentiated.
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Affiliation(s)
- Rochele C A Bevilaqua
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Vagner A Rigo
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Marcos Veríssimo-Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
| | - Caetano R Miranda
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Santo André, SP, Brazil
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30
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Kupka T, Stachów M, Chełmecka E, Pasterny K, Stobińska M, Stobiński L, Kaminský J. Efficient Modeling of NMR Parameters in Carbon Nanosystems. J Chem Theory Comput 2013; 9:4275-86. [DOI: 10.1021/ct4002812] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teobald Kupka
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Michał Stachów
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Elżbieta Chełmecka
- Division of Statistics, Department
of Instrumental Analysis, Medical University of Silesia, 30 Ostrogórska Street, 41-200 Sosnowiec, Poland
| | - Karol Pasterny
- A. Chełkowski Institute of
Physics, University of Silesia, 4 Uniwersytecka
Street, 40-007 Katowice, Poland
| | - Magdalena Stobińska
- Institute of Theoretical Physics and Astrophysics, University of Gdańsk, 57 Wita Stwosza Street, 80-952 Gdańsk,
Poland
- Institute of Physics, Polish Academy of Sciences, 32/46, al. Lotników,
02-668 Warsaw, Poland
| | - Leszek Stobiński
- Institute
of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka Street, 01-224 Warsaw, Poland
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2., 166
10 Prague, Czech Republic
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31
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Vasconcelos F, de Wijs GA, Havenith RWA, Marsman M, Kresse G. Finite-field implementation of NMR chemical shieldings for molecules: Direct and converse gauge-including projector-augmented-wave methods. J Chem Phys 2013; 139:014109. [DOI: 10.1063/1.4810799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Vasconcelos F, Cristol S, Paul JF, Delevoye L, Mauri F, Charpentier T, Le Caër G. Extended Czjzek model applied to NMR parameter distributions in sodium metaphosphate glass. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:255402. [PMID: 23719213 DOI: 10.1088/0953-8984/25/25/255402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The extended Czjzek model (ECM) is applied to the distribution of NMR parameters of a simple glass model (sodium metaphosphate, NaPO3) obtained by molecular dynamics (MD) simulations. Accurate NMR tensors, electric field gradient (EFG) and chemical shift anisotropy (CSA) are calculated from density functional theory (DFT) within the well-established PAW/GIPAW framework. The theoretical results are compared to experimental high-resolution solid-state NMR data and are used to validate the considered structural model. The distributions of the calculated coupling constant C(Q) is proportional to |V(zz)| and the asymmetry parameter η(Q) that characterize the quadrupolar interaction are discussed in terms of structural considerations with the help of a simple point charge model. Finally, the ECM analysis is shown to be relevant for studying the distribution of CSA tensor parameters and gives new insight into the structural characterization of disordered systems by solid-state NMR.
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Affiliation(s)
- Filipe Vasconcelos
- Unité de Catalyse et Chimie du Solide, UMR CNRS 8181, École Nationale Supérieure de Chimie de Lille, Université de Lille, BP Villeneuve d'Ascq, France.
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33
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da Silva BHST, Marana NL, Mafud AC, da Silva-Filho LC. A theoretical and experimental study to unequivocal structural assignment of tetrahydroquinoline derivatives. Struct Chem 2013. [DOI: 10.1007/s11224-013-0297-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Bouzková K, Babinský M, Novosadová L, Marek R. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and 13C NMR Chemical Shift Tensors. J Chem Theory Comput 2013; 9:2629-38. [DOI: 10.1021/ct400209b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kateřina Bouzková
- CEITEC—Central
European Institute of Technology, ‡National Center for Biomolecular Research, and §Department of
Chemistry, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Martin Babinský
- CEITEC—Central
European Institute of Technology, ‡National Center for Biomolecular Research, and §Department of
Chemistry, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Lucie Novosadová
- CEITEC—Central
European Institute of Technology, ‡National Center for Biomolecular Research, and §Department of
Chemistry, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Radek Marek
- CEITEC—Central
European Institute of Technology, ‡National Center for Biomolecular Research, and §Department of
Chemistry, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
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35
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Timilsina R, Biswas P. A study of hydrogen microstructure in amorphous silicon via inversion of nuclear magnetic resonance spectra. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:165801. [PMID: 23552017 DOI: 10.1088/0953-8984/25/16/165801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We present an inverse approach for studying hydrogen microstructure in amorphous silicon. The approach consists of generating a prior distribution (of spins/hydrogen) by inverting experimental nuclear magnetic resonance (NMR) data, which is subsequently superimposed on a network of amorphous silicon. The resulting network is then relaxed using a total-energy functional to obtain a stable, low-energy configuration such that the initial spin distribution is minimally perturbed. The efficacy of this approach is demonstrated by generating model configurations that not only have the correct NMR spectra but also satisfy simultaneously experimental structural, electronic and vibrational properties of hydrogenated amorphous silicon.
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Affiliation(s)
- Rajendra Timilsina
- Department of Physics and Astronomy, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
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36
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Lopez MG, Canepa P, Thonhauser T. NMR study of small molecule adsorption in MOF-74-Mg. J Chem Phys 2013; 138:154704. [DOI: 10.1063/1.4800952] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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37
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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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38
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Vähäkangas J, Ikäläinen S, Lantto P, Vaara J. Nuclear magnetic resonance predictions for graphenes: concentric finite models and extrapolation to large systems. Phys Chem Chem Phys 2013; 15:4634-41. [DOI: 10.1039/c3cp44631j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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39
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Cuny J, Cordier S, Perrin C, Pickard CJ, Delevoye L, Trébosc J, Gan Z, Pollès LL, Gautier R. 95Mo Solid-State Nuclear Magnetic Resonance Spectroscopy and Quantum Simulations: Synergetic Tools for the Study of Molybdenum Cluster Materials. Inorg Chem 2012; 52:617-27. [DOI: 10.1021/ic301648s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jérôme Cuny
- Institut des Sciences Chimiques
de Rennes, UMR 6226, CNRS - Université de Rennes 1 - Ecole Nationale Supérieure de Chimie de Rennes,
Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex
7, France
| | - Stéphane Cordier
- Institut des Sciences Chimiques
de Rennes, UMR 6226, CNRS - Université de Rennes 1 - Ecole Nationale Supérieure de Chimie de Rennes,
Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex
7, France
| | - Christiane Perrin
- Institut des Sciences Chimiques
de Rennes, UMR 6226, CNRS - Université de Rennes 1 - Ecole Nationale Supérieure de Chimie de Rennes,
Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex
7, France
| | - Chris J. Pickard
- Department of Physics & Astronomy, University College London, Gower Street, London WC1E 6BT, U.K
| | - Laurent Delevoye
- Unité de Catalyse et
Chimie du Solide, UMR 8181, CNRS - Université de Lille 1, 59655 Villeneuve d’Ascq, France
| | - Julien Trébosc
- Unité de Catalyse et
Chimie du Solide, UMR 8181, CNRS - Université de Lille 1, 59655 Villeneuve d’Ascq, France
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee,
Florida 32310, United States
| | - Laurent Le Pollès
- Institut des Sciences Chimiques
de Rennes, UMR 6226, CNRS - Université de Rennes 1 - Ecole Nationale Supérieure de Chimie de Rennes,
Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex
7, France
| | - Régis Gautier
- Institut des Sciences Chimiques
de Rennes, UMR 6226, CNRS - Université de Rennes 1 - Ecole Nationale Supérieure de Chimie de Rennes,
Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex
7, France
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40
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Maschio L, Kirtman B, Orlando R, Rèrat M. Ab initioanalytical infrared intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method. J Chem Phys 2012. [DOI: 10.1063/1.4767438] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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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: 27.2] [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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42
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Pavan B, Ceresoli D, Tecklenburg MMJ, Fornari M. First principles NMR study of fluorapatite under pressure. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 45-46:59-65. [PMID: 22770669 PMCID: PMC3435879 DOI: 10.1016/j.ssnmr.2012.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 06/01/2023]
Abstract
NMR is the technique of election to probe the local properties of materials. Herein we present the results of density functional theory (DFT) ab initio calculations of the NMR parameters for fluorapatite (FAp), a calcium orthophosphate mineral belonging to the apatite family, by using the GIPAW method (Pickard and Mauri, 2001). Understanding the local effects of pressure on apatites is particularly relevant because of their important role in many solid state and biomedical applications. Apatites are open structures, which can undergo complex anisotropic deformations, and the response of NMR can elucidate the microscopic changes induced by an applied pressure. The computed NMR parameters proved to be in good agreement with the available experimental data. The structural evaluation of the material behavior under hydrostatic pressure (from -5 to +100 kbar) indicated a shrinkage of the diameter of the apatitic channel, and a strong correlation between NMR shielding and pressure, proving the sensitivity of this technique to even small changes in the chemical environment around the nuclei. This theoretical approach allows the exploration of all the different nuclei composing the material, thus providing a very useful guidance in the interpretation of experimental results, particularly valuable for the more challenging nuclei such as (43)Ca and (17)O.
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Affiliation(s)
- Barbara Pavan
- Science of Advanced Materials, Central Michigan University, Mt. Pleasant, MI 48859, USA.
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43
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Hassanali AA, Cuny J, Ceriotti M, Pickard CJ, Parrinello M. The Fuzzy Quantum Proton in the Hydrogen Chloride Hydrates. J Am Chem Soc 2012; 134:8557-69. [DOI: 10.1021/ja3014727] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ali A. Hassanali
- Department of Chemistry and
Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano,
Switzerland
| | - Jérôme Cuny
- Department of Chemistry and
Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano,
Switzerland
| | - Michele Ceriotti
- Physical and
Theoretical Chemistry
Laboratory, University of Oxford, South
Parks Road, United Kingdom
| | - Chris J. Pickard
- Department of Physics and Astronomy, University College London, Gower Street, United Kingdom
| | - Michele Parrinello
- Department of Chemistry and
Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, via G. Buffi 13, CH-6900 Lugano,
Switzerland
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44
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Skachkov D, Krykunov M, Ziegler T. An improved scheme for the calculation of NMR chemical shifts in periodic systems based on gauge including atomic orbitals and density functional theory. CAN J CHEM 2011. [DOI: 10.1139/v11-050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report here on an improved first principles method that can determine NMR shielding tensors for periodic systems. Our scheme evaluates the shielding tensor as the second derivative of the total electronic energy with respect to a nuclear magnetic moment and an external magnetic field. Both the induced current density J(α) due to the first perturbation from the nuclear magnetic moment as well as the interaction of J(α) with the second perturbation in the form of an external magnetic field are evaluated analytically. Our approach is based on Kohn–Sham density functional theory and gauge-including atomic orbitals. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn–Sham potential fully without the use of effective core potentials. The method is implemented into the periodic program BAND. The new scheme represents an improvement over a previously proposed method in that use can be made of the zero-order Kohn–Sham orbitals from a calculation based on a primitive cell instead of a supercell. Further, J(α) is evaluated analytically rather than by a finite difference approach. The improvements reduce the required computational time by up to two orders of magnitude for three-dimensional systems. Such a reduction is made possible by the fact that we are using atomic centered basis functions. The new implementation is further able to take into account scalar relativistic effects within the zero-order regular approximation. Results from calculations of NMR shielding constants based on the present approach are presented for systems with one-, two-, and three-dimensional periodicity. The reported values are compared to experiment and results from the previously proposed scheme.
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Affiliation(s)
- Dmitry Skachkov
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mykhaylo Krykunov
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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45
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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: 18.1] [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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46
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Kibalchenko M, Payne MC, Yates JR. Magnetic response of single-walled carbon nanotubes induced by an external magnetic field. ACS NANO 2011; 5:537-545. [PMID: 21171576 DOI: 10.1021/nn102590b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Using first-principles density functional calculations, magnetically induced currents are obtained for zigzag single-walled carbon nanotubes. Clear differences and trends in current flow are observed between the different nanotube families. In particular, for a magnetic field applied along the tube axis, the current response of the λ = 0 infinite nanotubes is paramagnetic, whereas for λ = 1 and 2 nanotubes, the response is diamagnetic. The results are used to predict and interpret the significant changes in NMR properties for small molecules encapsulated inside a tube.
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Affiliation(s)
- Mikhail Kibalchenko
- TCM Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom.
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47
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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48
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Gowda CM, Vasconcelos F, Schwartz E, van Eck ERH, Marsman M, Cornelissen JJLM, Rowan AE, de Wijs GA, Kentgens APM. Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations. Phys Chem Chem Phys 2011; 13:13082-95. [DOI: 10.1039/c1cp20304e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Robinson M, Haynes PD. Dynamical effects in ab initio NMR calculations: classical force fields fitted to quantum forces. J Chem Phys 2010; 133:084109. [PMID: 20815562 DOI: 10.1063/1.3474573] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
NMR chemical shifts for an L-alanine molecular crystal are calculated using ab initio plane wave density functional theory. Dynamical effects including anharmonicity may be included by averaging chemical shifts over an ensemble of structural configurations generated using molecular dynamics (MD). The time scales required mean that ab initio MD is prohibitively expensive. Yet the sensitivity of chemical shifts to structural details requires that the methodologies for performing MD and calculating NMR shifts be consistent. This work resolves these previously competing requirements by fitting classical force fields to reproduce ab initio forces. This methodology is first validated by reproducing the averaged chemical shifts found using ab initio molecular dynamics. Study of a supercell of L-alanine demonstrates that finite size effects can be significant when accounting for dynamics.
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Affiliation(s)
- Mark Robinson
- Theory of Condensed Matter, Cavendish Laboratory, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom.
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50
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Vasconcelos F, Cristol S, Paul JF, Montagne L, Mauri F, Delevoye L. First-principles calculations of NMR parameters for phosphate materials. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48 Suppl 1:S142-50. [PMID: 20821412 DOI: 10.1002/mrc.2667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this short review, we discuss the ability to reproduce NMR parameters in the case of phosphates materials through electronic structure calculation within density functional theory linear response. Indeed, the gauge-including projector-augmented wave is today largely used by the solid-state NMR community as a tool for structural determination and it has been applied to a large variety of materials. We emphasise on the crucial points that should be taken into account to perform such calculations. In particular, we discuss the influence of the electronic structure and of the geometry on the calculation of NMR parameters. To illustrate the review, we present experimental and theoretical comparison of (31)P, (1)H and (23)Na NMR data on a series of sodium phosphate systems.
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Affiliation(s)
- Filipe Vasconcelos
- UCCS-Unité de Catalyse et Chimie du Solide, UMR CNRS 8181, École Nationale Supérieure de Chimie de Lille, Université des Sciences et Technologies de Lille, BP 108, 59652 Villeneuve d'Ascq Cedex, France
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