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NMR spectroscopy probes microstructure, dynamics and doping of metal halide perovskites. Nat Rev Chem 2021; 5:624-645. [PMID: 37118421 DOI: 10.1038/s41570-021-00309-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2021] [Indexed: 12/23/2022]
Abstract
Solid-state magic-angle spinning NMR spectroscopy is a powerful technique to probe atomic-level microstructure and structural dynamics in metal halide perovskites. It can be used to measure dopant incorporation, phase segregation, halide mixing, decomposition pathways, passivation mechanisms, short-range and long-range dynamics, and other local properties. This Review describes practical aspects of recording solid-state NMR data on halide perovskites and how these afford unique insights into new compositions, dopants and passivation agents. We discuss the applicability, feasibility and limitations of 1H, 13C, 15N, 14N, 133Cs, 87Rb, 39K, 207Pb, 119Sn, 113Cd, 209Bi, 115In, 19F and 2H NMR in typical experimental scenarios. We highlight the pivotal complementary role of solid-state mechanosynthesis, which enables highly sensitive NMR studies by providing large quantities of high-purity materials of arbitrary complexity and of chemical shifts calculated using density functional theory. We examine the broader impact of solid-state NMR on materials research and how its evolution over seven decades has benefitted structural studies of contemporary materials such as halide perovskites. Finally, we summarize some of the open questions in perovskite optoelectronics that could be addressed using solid-state NMR. We, thereby, hope to stimulate wider use of this technique in materials and optoelectronics research.
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Jähnigen S, Zehnacker A, Vuilleumier R. Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge. J Phys Chem Lett 2021; 12:7213-7220. [PMID: 34310135 DOI: 10.1021/acs.jpclett.1c01682] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1S,2S)-trans-1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.
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Affiliation(s)
- Sascha Jähnigen
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Rodolphe Vuilleumier
- PASTEUR Laboratory, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS,, 75005 Paris, France
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Duong NT, Aoyama Y, Kawamoto K, Yamazaki T, Nishiyama Y. Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments. Molecules 2021; 26:molecules26154652. [PMID: 34361806 PMCID: PMC8347922 DOI: 10.3390/molecules26154652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.
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Affiliation(s)
- Nghia Tuan Duong
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | | | | | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
- Correspondence:
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Morawietz T, Artrith N. Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications. J Comput Aided Mol Des 2021; 35:557-586. [PMID: 33034008 PMCID: PMC8018928 DOI: 10.1007/s10822-020-00346-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/26/2020] [Indexed: 01/13/2023]
Abstract
Atomistic simulations have become an invaluable tool for industrial applications ranging from the optimization of protein-ligand interactions for drug discovery to the design of new materials for energy applications. Here we review recent advances in the use of machine learning (ML) methods for accelerated simulations based on a quantum mechanical (QM) description of the system. We show how recent progress in ML methods has dramatically extended the applicability range of conventional QM-based simulations, allowing to calculate industrially relevant properties with enhanced accuracy, at reduced computational cost, and for length and time scales that would have otherwise not been accessible. We illustrate the benefits of ML-accelerated atomistic simulations for industrial R&D processes by showcasing relevant applications from two very different areas, drug discovery (pharmaceuticals) and energy materials. Writing from the perspective of both a molecular and a materials modeling scientist, this review aims to provide a unified picture of the impact of ML-accelerated atomistic simulations on the pharmaceutical, chemical, and materials industries and gives an outlook on the exciting opportunities that could emerge in the future.
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Affiliation(s)
- Tobias Morawietz
- Bayer AG, Pharmaceuticals, R&D, Digital Technologies, Computational Molecular Design, 42096 Wuppertal, Germany
| | - Nongnuch Artrith
- Department of Chemical Engineering, Columbia University, New York, NY 10027 USA
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Castro AC, Balcells D, Repisky M, Helgaker T, Cascella M. First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics. Inorg Chem 2020; 59:17509-17518. [PMID: 33226791 PMCID: PMC7735704 DOI: 10.1021/acs.inorgchem.0c02753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/03/2022]
Abstract
1H NMR spectroscopy has become an important technique for the characterization of transition-metal hydride complexes, whose metal-bound hydrides are often difficult to locate by X-ray diffraction. In this regard, the accurate prediction of 1H NMR chemical shifts provides a useful, but challenging, strategy to help in the interpretation of the experimental spectra. In this work, we establish a density-functional-theory protocol that includes relativistic, solvent, and dynamic effects at a high level of theory, allowing us to report an accurate and reliable interpretation of 1H NMR hydride chemical shifts of iridium polyhydride complexes. In particular, we have studied in detail the hydride chemical shifts of the [Ir6(IMe)8(CO)2H14]2+ complex in order to validate previous assignments. The computed 1H NMR chemical shifts are strongly dependent on the relativistic treatment, the choice of the DFT exchange-correlation functional, and the conformational dynamics. By combining a fully relativistic four-component electronic-structure treatment with ab initio molecular dynamics, we were able to reliably model both the terminal and bridging hydride chemical shifts and to show that two NMR hydride signals were inversely assigned in the experiment.
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Affiliation(s)
- Abril C. Castro
- Hylleraas Centre
for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - David Balcells
- Hylleraas Centre
for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Michal Repisky
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, UiT-The Arctic University
of Norway, 9037 Tromsø, Norway
| | - Trygve Helgaker
- Hylleraas Centre
for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Hylleraas Centre
for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
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Frank I. Some simple facts about water: CPMD simulation. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1802074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Irmgard Frank
- Theoretical Chemistry, Leibniz Universität Hannover, Hannover, Germany
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Dittmer A, Stoychev GL, Maganas D, Auer AA, Neese F. Computation of NMR Shielding Constants for Solids Using an Embedded Cluster Approach with DFT, Double-Hybrid DFT, and MP2. J Chem Theory Comput 2020; 16:6950-6967. [PMID: 32966067 PMCID: PMC7659039 DOI: 10.1021/acs.jctc.0c00067] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In
this work, we explore the accuracy of post-Hartree–Fock
(HF) methods and double-hybrid density functional theory (DFT) for
the computation of solid-state NMR chemical shifts. We apply an embedded
cluster approach and investigate the convergence with cluster size
and embedding for a series of inorganic solids with long-range electrostatic
interactions. In a systematic study, we discuss the cluster design,
the embedding procedure, and basis set convergence using gauge-including
atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of
theory. We demonstrate that the accuracy obtained for the prediction
of NMR chemical shifts, which can be achieved for molecular systems,
can be carried over to solid systems. An appropriate embedded cluster
approach allows one to apply methods beyond standard DFT even for
systems for which long-range electrostatic effects are important. We find that an embedded
cluster should include at least one sphere of explicit neighbors around
the nuclei of interest, given that a sufficiently large point charge
and boundary effective potential embedding is applied. Using the pcSseg-3
basis set and GIAOs for the computation of nuclear shielding constants,
accuracies of 1.6 ppm for 7Li, 1.5 ppm for 23Na, and 5.1 ppm for 39K as well as 9.3 ppm for 19F, 6.5 ppm for 35Cl, 7.4 ppm for 79Br, and
7.5 ppm for 25Mg as well as 3.8 ppm for 67Zn
can be achieved with MP2. Comparing various DFT functionals with HF
and MP2, we report the superior quality of results for methods that
include post-HF correlation like MP2 and double-hybrid DFT.
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Affiliation(s)
- Anneke Dittmer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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31P nuclear magnetic resonance, optical and thermal spectra in MP3 (M = Ir, Co, Rh, Ni) compounds by DFT. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 844] [Impact Index Per Article: 211.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
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Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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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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Zhao D, Shen X, Cheng Z, Li W, Dong H, Li S. Accurate and Efficient Prediction of NMR Parameters of Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2020; 16:2995-3005. [DOI: 10.1021/acs.jctc.9b01298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
- Institute for Brain Sciences, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
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13
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On the calculation of magnetic properties of nucleic acids in liquid water with the sequential QM/MM method. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Hofstetter A, Balodis M, Paruzzo FM, Widdifield CM, Stevanato G, Pinon AC, Bygrave PJ, Day GM, Emsley L. Rapid Structure Determination of Molecular Solids Using Chemical Shifts Directed by Unambiguous Prior Constraints. J Am Chem Soc 2019; 141:16624-16634. [PMID: 31117663 PMCID: PMC7540916 DOI: 10.1021/jacs.9b03908] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NMR-based crystallography approaches involving the combination of crystal structure prediction methods, ab initio calculated chemical shifts and solid-state NMR experiments are powerful methods for crystal structure determination of microcrystalline powders. However, currently structural information obtained from solid-state NMR is usually included only after a set of candidate crystal structures has already been independently generated, starting from a set of single-molecule conformations. Here, we show with the case of ampicillin that this can lead to failure of structure determination. We propose a crystal structure determination method that includes experimental constraints during conformer selection. In order to overcome the problem that experimental measurements on the crystalline samples are not obviously translatable to restrict the single-molecule conformational space, we propose constraints based on the analysis of absent cross-peaks in solid-state NMR correlation experiments. We show that these absences provide unambiguous structural constraints on both the crystal structure and the gas-phase conformations, and therefore can be used for unambiguous selection. The approach is parametrized on the crystal structure determination of flutamide, flufenamic acid, and cocaine, where we reduce the computational cost by around 50%. Most importantly, the method is then shown to correctly determine the crystal structure of ampicillin, which would have failed using current methods because it adopts a high-energy conformer in its crystal structure. The average positional RMSE on the NMR powder structure is ⟨rav⟩ = 0.176 Å, which corresponds to an average equivalent displacement parameter Ueq = 0.0103 Å2.
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Affiliation(s)
- Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Martins Balodis
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Cory M Widdifield
- Department of Chemistry, Mathematics and Science Center , Oakland University , 146 Library Drive , Rochester , Michigan 48309-4479 , United States
| | - Gabriele Stevanato
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Peter J Bygrave
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Graeme M Day
- School of Chemistry , University of Southampton , Highfield , Southampton SO17 1BJ , United Kingdom
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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15
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Castro AC, Fliegl H, Cascella M, Helgaker T, Repisky M, Komorovsky S, Medrano MÁ, Quiroga AG, Swart M. Four-component relativistic 31P NMR calculations for trans-platinum(ii) complexes: importance of the solvent and dynamics in spectral simulations. Dalton Trans 2019; 48:8076-8083. [PMID: 30916692 DOI: 10.1039/c9dt00570f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report a combined experimental-theoretical study on the 31P NMR chemical shift for a number of trans-platinum(ii) complexes. Validity and reliability of the 31P NMR chemical shift calculations are examined by comparing with the experimental data. A successful computational protocol for the accurate prediction of the 31P NMR chemical shifts was established for trans-[PtCl2(dma)PPh3] (dma = dimethylamine) complexes. The reliability of the computed values is shown to be critically dependent on the level of relativistic effects (two-component vs. four component), choice of density functionals, dynamical averaging, and solvation effects. Snapshots obtained from ab initio molecular dynamics simulations were used to identify those solvent molecules which show the largest interactions with the platinum complex, through inspection by using the non-covalent interaction program. We observe satisfactory accuracy from the full four-component matrix Dirac-Kohn-Sham method (mDKS) based on the Dirac-Coulomb Hamiltonian, in conjunction with the KT2 density functional, and dynamical averaging with explicit solvent molecules.
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Affiliation(s)
- Abril C Castro
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17003, Girona, Spain.
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16
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Paruzzo FM, Hofstetter A, Musil F, De S, Ceriotti M, Emsley L. Chemical shifts in molecular solids by machine learning. Nat Commun 2018; 9:4501. [PMID: 30374021 PMCID: PMC6206069 DOI: 10.1038/s41467-018-06972-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/26/2018] [Indexed: 02/02/2023] Open
Abstract
Due to their strong dependence on local atonic environments, NMR chemical shifts are among the most powerful tools for strucutre elucidation of powdered solids or amorphous materials. Unfortunately, using them for structure determination depends on the ability to calculate them, which comes at the cost of high accuracy first-principles calculations. Machine learning has recently emerged as a way to overcome the need for quantum chemical calculations, but for chemical shifts in solids it is hindered by the chemical and combinatorial space spanned by molecular solids, the strong dependency of chemical shifts on their environment, and the lack of an experimental database of shifts. We propose a machine learning method based on local environments to accurately predict chemical shifts of molecular solids and their polymorphs to within DFT accuracy. We also demonstrate that the trained model is able to determine, based on the match between experimentally measured and ML-predicted shifts, the structures of cocaine and the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butylpyrazol-1-yl]benzoic acid. Solid-state nuclear magnetic resonance combined with quantum chemical shift predictions is limited by high computational cost. Here, the authors use machine learning based on local atomic environments to predict experimental chemical shifts in molecular solids with accuracy similar to density functional theory.
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Affiliation(s)
- Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Albert Hofstetter
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Félix Musil
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandip De
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michele Ceriotti
- Institut des Sciences et Génie Matériaux, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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17
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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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18
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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19
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Luber S. Localized molecular orbitals for calculation and analysis of vibrational Raman optical activity. Phys Chem Chem Phys 2018; 20:28751-28758. [DOI: 10.1039/c8cp05880f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First calculations of vibrational Raman optical activity based on localized molecular orbitals are presented, which pave the way for novel insight into spectroscopic signatures of chiral systems.
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Affiliation(s)
- Sandra Luber
- Department of Chemistry
- University of Zurich
- Zurich
- Switzerland
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20
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21
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Liu J, Ma J, Zhang K, Ravat P, Machata P, Avdoshenko S, Hennersdorf F, Komber H, Pisula W, Weigand JJ, Popov AA, Berger R, Müllen K, Feng X. π-Extended and Curved Antiaromatic Polycyclic Hydrocarbons. J Am Chem Soc 2017; 139:7513-7521. [DOI: 10.1021/jacs.7b01619] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | - Ke Zhang
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Prince Ravat
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Peter Machata
- Leibniz Institute for Solid State and Materials Research, 01069 Dresden, Germany
| | - Stanislav Avdoshenko
- Leibniz Institute for Solid State and Materials Research, 01069 Dresden, Germany
| | | | - Hartmut Komber
- Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Strasse 6, 01069 Dresden, Germany
| | - Wojciech Pisula
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Molecular Physics, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | | | - Alexey A. Popov
- Leibniz Institute for Solid State and Materials Research, 01069 Dresden, Germany
| | | | - Klaus Müllen
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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22
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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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23
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Nikmaram FR, Khoddamzadeh A. Chemical shielding of doped nitrogen on C20 cage and bowl fullerenes. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617010231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Scherrer A, Vuilleumier R, Sebastiani D. Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase. J Chem Phys 2016; 145:084101. [DOI: 10.1063/1.4960653] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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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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26
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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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27
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Alkan F, Dybowski C. Effect of Co-Ordination Chemistry and Oxidation State on the (207)Pb Magnetic-Shielding Tensor: A DFT/ZORA Investigation. J Phys Chem A 2015; 120:161-8. [PMID: 26683366 DOI: 10.1021/acs.jpca.5b10991] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The magnetic shielding tensor of (207)Pb is calculated for various solids exhibiting (1) a holodirected lead(II) center containing a stereochemically inactive lone pair, (2) a hemidirected lead(II) center with a stereochemically active lone-pair, or (3) a lead(IV) center. Tensors investigated at the scalar relativistic level are compared with those calculated with the full ZORA/spin-orbit Hamiltonian. The effect of using GGA density functionals is compared to the use of hybrid density functionals.
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Affiliation(s)
- Fahri Alkan
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716-2522 United States
| | - C Dybowski
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716-2522 United States
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28
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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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29
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Elgabarty H, Khaliullin RZ, Kühne TD. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments. Nat Commun 2015; 6:8318. [PMID: 26370179 PMCID: PMC4647854 DOI: 10.1038/ncomms9318] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 08/10/2015] [Indexed: 12/29/2022] Open
Abstract
The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of 10 m while the stabilization energy due to this charge transfer is ∼15 kJ mol−1. The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems. Covalency is a fundamental concept in chemical bonding, but experimentally it is not possible to measure the degree of covalency of a particular bond. Here, the authors report a model to link the covalency of hydrogen bonds in water with the anisotropy of the magnetic shielding tensor in the proton NMR.
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Affiliation(s)
- Hossam Elgabarty
- Department of Chemistry, Dynamics of Condensed Matter, University of Paderborn, Warburger Street 100, D-33098 Paderborn, Germany
| | - Rustam Z Khaliullin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, 801 Sherbrooke Str. West, Montreal, Quebec, Canada H3A 0B8
| | - Thomas D Kühne
- Department of Chemistry, Dynamics of Condensed Matter, University of Paderborn, Warburger Street 100, D-33098 Paderborn, Germany.,Paderborn Center for Parallel Computing and Institute for Lightweight Design with Hybrid Systems, Warburger Street 100, D-33098 Paderborn, Germany
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30
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Scherrer A, Agostini F, Sebastiani D, Gross EKU, Vuilleumier R. Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function. J Chem Phys 2015; 143:074106. [DOI: 10.1063/1.4928578] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arne Scherrer
- Martin-Luther-University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle, Germany
- UMR 8640 ENS-CNRS-UPMC, Département de Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
| | - Federica Agostini
- Max-Planck-Institute of Microstructure Physics, Weinberg 2, D-06120 Halle, Germany
| | - Daniel Sebastiani
- Martin-Luther-University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle, Germany
| | - E. K. U. Gross
- Max-Planck-Institute of Microstructure Physics, Weinberg 2, D-06120 Halle, Germany
| | - Rodolphe Vuilleumier
- UMR 8640 ENS-CNRS-UPMC, Département de Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
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31
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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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32
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Vela S, Deumal M, Shiga M, Novoa JJ, Ribas-Arino J. Dynamical effects on the magnetic properties of dithiazolyl bistable materials. Chem Sci 2015; 6:2371-2381. [PMID: 29308151 PMCID: PMC5645919 DOI: 10.1039/c4sc03930k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/22/2015] [Indexed: 12/13/2022] Open
Abstract
The magnetic properties of molecule-based magnets are commonly rationalized by considering only a single nuclear configuration of the system under study (usually an X-ray crystal structure). Here, by means of a computational study, we compare the results obtained using such a static approach with those obtained by explicitly accounting for thermal fluctuations, and uncover the serious limitations of the static perspective when dealing with magnetic crystals whose radicals undergo wide-amplitude motions. As a proof of concept, these limitations are illustrated for the magnetically bistable 1,3,5-trithia-2,4,6-triazapentalenyl (TTTA) material. For its high-temperature phase at 300 K, we show that nuclear dynamics induce large fluctuations in the magnetic exchange interactions (JAB) between spins (up to 1000% of the average value). These deviations result in a ∼20% difference between the 300 K magnetic susceptibility computed by explicitly considering the nuclear dynamics and that computed using the X-ray structure, the former being in better agreement with the experimental data. The unveiled strong coupling between JAB interactions and intermolecular vibrations reveals that considering JAB as a constant value at a given temperature (as always done in molecular magnetism) leads to a flawed description of the magnetism of TTTA. Instead, the physically relevant concept in this case is the statistical distribution of JAB values. The discovery that a single X-ray structure is not adequate enough to interpret the magnetic properties of TTTA is also expected to be decisive in other organic magnets with dominant exchange interactions propagating through labile π-π networks.
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Affiliation(s)
- Sergi Vela
- Departament de Química Física and IQTCUB , Facultat de Química , Universitat de Barcelona , Av. Diagonal 645 , 08028-Barcelona , Spain . ;
| | - Mercè Deumal
- Departament de Química Física and IQTCUB , Facultat de Química , Universitat de Barcelona , Av. Diagonal 645 , 08028-Barcelona , Spain . ;
| | - Motoyuki Shiga
- Center for Computational Science and E-Systems , Japan Atomic Energy Agency , 148-4, Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa , Chiba , 277-0871 , Japan
| | - Juan J Novoa
- Departament de Química Física and IQTCUB , Facultat de Química , Universitat de Barcelona , Av. Diagonal 645 , 08028-Barcelona , Spain . ;
| | - Jordi Ribas-Arino
- Departament de Química Física and IQTCUB , Facultat de Química , Universitat de Barcelona , Av. Diagonal 645 , 08028-Barcelona , Spain . ;
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33
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Raimbault N, de Boeij PL, Romaniello P, Berger JA. Gauge-invariant calculation of static and dynamical magnetic properties from the current density. PHYSICAL REVIEW LETTERS 2015; 114:066404. [PMID: 25723234 DOI: 10.1103/physrevlett.114.066404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 06/04/2023]
Abstract
In this work we solve two problems related to the calculation of static and dynamical magnetic properties with ab initio theories. First, we show that the dependence of the dynamical magnetic dipole moment on the reference point of the multipole expansion and on the gauge origin of the vector potential have a clear physical significance. They are due to a dynamical electric dipole moment and an electric field, respectively. Both are fully determined by the experimental setup and do not pose any fundamental problem, contrary to what is commonly assumed. Second, in the static case, any dependence on the gauge origin is an artifact of the computational method. We show that the artificial dependence on the gauge origin can be removed in an elegant way by the introduction of a sum rule that puts the diamagnetic and paramagnetic contributions on equal footing. Our approach can be applied to calculate any magnetic observable that can be derived from the current density, and can be used in combination with any ab initio theory from which it can be obtained. To illustrate our method we apply it here to time-dependent current-density-functional theory for the calculation of static and dynamical magnetizabilities of molecules.
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Affiliation(s)
- Nathaniel Raimbault
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Toulouse III - Paul Sabatier, CNRS and European Theoretical Spectroscopy Facility (ETSF), 118 Route de Narbonne, 31062 Toulouse Cedex, France and Laboratoire de Physique Théorique, CNRS, IRSAMC, Université Toulouse III - Paul Sabatier and European Theoretical Spectroscopy Facility (ETSF), 118 Route de Narbonne, 31062 Toulouse Cedex, France
| | - Paul L de Boeij
- Scientific Computing & Modeling NV, Vrije Universiteit, Theoretical Chemistry, De Boelelaan 1083, 1081 HV Amsterdam, Netherlands
| | - Pina Romaniello
- Laboratoire de Physique Théorique, CNRS, IRSAMC, Université Toulouse III - Paul Sabatier and European Theoretical Spectroscopy Facility (ETSF), 118 Route de Narbonne, 31062 Toulouse Cedex, France
| | - J A Berger
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Toulouse III - Paul Sabatier, CNRS and European Theoretical Spectroscopy Facility (ETSF), 118 Route de Narbonne, 31062 Toulouse Cedex, France
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34
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Mondal A, Balasubramanian S. Vibrational Signatures of Cation–Anion Hydrogen Bonding in Ionic Liquids: A Periodic Density Functional Theory and Molecular Dynamics Study. J Phys Chem B 2015; 119:1994-2002. [DOI: 10.1021/jp5113679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Anirban Mondal
- Chemistry and Physics of
Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of
Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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35
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Alkan F, Dybowski C. Chemical-shift tensors of heavy nuclei in network solids: a DFT/ZORA investigation of 207Pb chemical-shift tensors using the bond-valence method. Phys Chem Chem Phys 2015; 17:25014-26. [DOI: 10.1039/c5cp03348a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate computation of 207Pb magnetic shielding principal components is within the reach of quantum chemistry methods by employing relativistic ZORA/DFT and cluster models adapted from the bond valence model.
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Affiliation(s)
- Fahri Alkan
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark
- USA
| | - C. Dybowski
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark
- USA
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36
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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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37
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Calandrini V, Nguyen TH, Arnesano F, Galliani A, Ippoliti E, Carloni P, Natile G. Structural Biology of Cisplatin Complexes with Cellular Targets: The Adduct with Human Copper Chaperone Atox1 in Aqueous Solution. Chemistry 2014; 20:11719-25. [DOI: 10.1002/chem.201402834] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Indexed: 12/17/2022]
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38
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Caputo MC, Provasi PF, Benitez L, Georg HC, Canuto S, Coutinho K. Monte Carlo–Quantum Mechanics Study of Magnetic Properties of Hydrogen Peroxide in Liquid Water. J Phys Chem A 2014; 118:6239-47. [DOI: 10.1021/jp411303n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- María Cristina Caputo
- Departamento de Fı́sica, FCEN,
UBA and IFIBA, Conicet, Ciudad Universitaria, 1428, Buenos Aires, Argentina
| | - Patricio F. Provasi
- Department of Physics - IMIT, Northeastern University, Av. Libertad 5500, Corrientes, Argentina
| | - Lucía Benitez
- Department of Physics - IMIT, Northeastern University, Av. Libertad 5500, Corrientes, Argentina
| | - Herbert C. Georg
- Instituto
de Fı́sica, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
| | - Sylvio Canuto
- Instituto de Fı́sica, Universidade de São Paulo, CP
66318, 05315-970 São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Fı́sica, Universidade de São Paulo, CP
66318, 05315-970 São Paulo, Brazil
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39
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Calandrini V, Arnesano F, Galliani A, Nguyen TH, Ippoliti E, Carloni P, Natile G. Platination of the copper transporter ATP7A involved in anticancer drug resistance. Dalton Trans 2014; 43:12085-94. [DOI: 10.1039/c4dt01339e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Franco de Carvalho F, Curchod BFE, Penfold TJ, Tavernelli I. Derivation of spin-orbit couplings in collinear linear-response TDDFT: A rigorous formulation. J Chem Phys 2014; 140:144103. [DOI: 10.1063/1.4870010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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41
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Hassanali AA, Cuny J, Verdolino V, Parrinello M. Aqueous solutions: state of the art in ab initio molecular dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20120482. [PMID: 24516179 DOI: 10.1098/rsta.2012.0482] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
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Affiliation(s)
- Ali A Hassanali
- Department of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, , via G. Buffi 13, 6900 Lugano, Switzerland
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42
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Alkan F, Dybowski C. Calculation of chemical-shift tensors of heavy nuclei: a DFT/ZORA investigation of 199Hg chemical-shift tensors in solids, and the effects of cluster size and electronic-state approximations. Phys Chem Chem Phys 2014; 16:14298-308. [DOI: 10.1039/c4cp01682c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A ZORA/DFT investigation of the NMR chemical shielding of a suite of 199Hg-containing solid materials shows the importance of calculations with the molecular-cluster method.
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Affiliation(s)
- Fahri Alkan
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark, USA
| | - C. Dybowski
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark, USA
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43
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Xu Y, Watermann T, Limbach HH, Gutmann T, Sebastiani D, Buntkowsky G. Water and small organic molecules as probes for geometric confinement in well-ordered mesoporous carbon materials. Phys Chem Chem Phys 2014; 16:9327-36. [DOI: 10.1039/c4cp00808a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Confinement effects on water, benzene and pyridine in mesoporous carbon materials were probed by 1H-MAS NMR and chemical shift calculations.
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Affiliation(s)
- Yeping Xu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Technische Universität Darmstadt
- D-64287 Darmstadt, Germany
| | - Tobias Watermann
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle, Germany
| | - Hans-Heinrich Limbach
- Institut für Physikalische und Theoretische Chemie
- Freie Universität Berlin
- D-14195 Berlin, Germany
| | - Torsten Gutmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Technische Universität Darmstadt
- D-64287 Darmstadt, Germany
| | - Daniel Sebastiani
- Institut für Chemie
- Martin-Luther-Universität Halle-Wittenberg
- 06120 Halle, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
- Technische Universität Darmstadt
- D-64287 Darmstadt, Germany
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44
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Scherrer A, Vuilleumier R, Sebastiani D. Nuclear Velocity Perturbation Theory of Vibrational Circular Dichroism. J Chem Theory Comput 2013; 9:5305-12. [DOI: 10.1021/ct400700c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Scherrer
- UMR 8640 ENS-CNRS-UPMC, Département de
Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
| | - R. Vuilleumier
- UMR 8640 ENS-CNRS-UPMC, Département de
Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
| | - D. Sebastiani
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
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45
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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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46
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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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47
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Yu W, Lopes PEM, Roux B, MacKerell AD. Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys 2013; 138:034508. [PMID: 23343286 PMCID: PMC3562330 DOI: 10.1063/1.4774577] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/21/2012] [Indexed: 01/23/2023] Open
Abstract
A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed SWM4-NDP model, additional sites representing oxygen lone-pairs were introduced. The geometry of the sites is assumed to be rigid. Considering the large number of adjustable parameters, simulated annealing together with polynomial fitting was used to facilitate model optimization. The new water model was shown to yield the correct self-diffusion coefficient after taking the system size effect into account, and the dimer geometry is better reproduced than in the SWM4 models. Moreover, the experimental oxygen-oxygen radial distribution is better reproduced, indicating that the new model more accurately describes the local hydrogen bonding structure of bulk phase water. This was further validated by its ability to reproduce the experimental nuclear magnetic shielding and related chemical shift of the water hydrogen in the bulk phase, a property sensitive to the local hydrogen bonding structure. In addition, comparison of the liquid properties of the SWM6 model is made with those of a number of widely used additive and polarizable models. Overall, improved balance between the description of monomer, dimer, clustered, and bulk phase water is obtained with the new model compared to its SWM4-NDP polarizable predecessor, though application of the model requires an approximately twofold increase on computational resources.
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Affiliation(s)
- Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
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48
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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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49
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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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50
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Bonhomme C, Gervais C, Babonneau F, Coelho C, Pourpoint F, Azaïs T, Ashbrook SE, Griffin JM, Yates JR, Mauri F, Pickard CJ. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: a chemist's point of view. Chem Rev 2012; 112:5733-79. [PMID: 23113537 DOI: 10.1021/cr300108a] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris, Université Pierre et Marie Curie, CNRS UMR, Collège de France, France.
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