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Krawczuk A, Genoni A. Current developments and trends in quantum crystallography. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624003421. [PMID: 38888407 PMCID: PMC11301899 DOI: 10.1107/s2052520624003421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 06/20/2024]
Abstract
Quantum crystallography is an emerging research field of science that has its origin in the early days of quantum physics and modern crystallography when it was almost immediately envisaged that X-ray radiation could be somehow exploited to determine the electron distribution of atoms and molecules. Today it can be seen as a composite research area at the intersection of crystallography, quantum chemistry, solid-state physics, applied mathematics and computer science, with the goal of investigating quantum problems, phenomena and features of the crystalline state. In this article, the state-of-the-art of quantum crystallography will be described by presenting developments and applications of novel techniques that have been introduced in the last 15 years. The focus will be on advances in the framework of multipole model strategies, wavefunction-/density matrix-based approaches and quantum chemical topological techniques. Finally, possible future improvements and expansions in the field will be discussed, also considering new emerging experimental and computational technologies.
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Affiliation(s)
- Anna Krawczuk
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen, 37077, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRSLaboratoire de Physique et Chimie Théoriques1 Boulevard AragoMetz57078France
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2
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Allan DR. Exploring crystal structure-physical property relationships with pressure. IUCRJ 2024; 11:438-439. [PMID: 38958012 PMCID: PMC11220890 DOI: 10.1107/s205225252400602x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
From its conception, X-ray crystallography has provided a unique understanding of the structure, bonding and electronic state of materials, which, in turn, unlocks a means of examining the properties and function of crystalline systems. Using state-of-the-art single-crystal X-ray diffraction, along with UV-Vis spectroscopy and DFT calculations, Zwolenik et al. [(2024). IUCrJ, 11, 519-527] have provided a comprehensive study of the structure-optical property relationship of 1,3-diacetylpyrene with methodologies that are increasingly accessible to non-specialist laboratories.
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Affiliation(s)
- David R. Allan
- Diamond Light Source LtdDiamond HouseChiltonOxfordshireOX11 0DEUnited Kingdom
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3
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Sizov G, Staroverov VN. Analytic Construction of One-Electron Reduced Density Matrices from Electron Densities within Finite Basis Sets. J Chem Theory Comput 2024; 20:5157-5163. [PMID: 38836443 PMCID: PMC11210478 DOI: 10.1021/acs.jctc.4c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/06/2024]
Abstract
We show how to construct analytically all one-electron reduced density matrices (1-RDMs) compatible with a given electron density within a finite basis set, provided that the density is specified as a symmetric quadratic form in terms of the basis functions. Contrary to the current belief, exact linear dependencies in the basis function products assist, rather than hinder, such constructions. By applying the N-representability conditions to the analytically reconstructed 1-RDMs, one can perform a constrained search over physically acceptable 1-RDMs that yield a given finite-basis-set density. The discussion is illustrated with worked-out examples.
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Affiliation(s)
- Georgii
N. Sizov
- Department of Chemistry, The
University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Viktor N. Staroverov
- Department of Chemistry, The
University of Western Ontario, London, Ontario N6A 5B7, Canada
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4
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Genoni A, Martín Pendás Á. Critical assessment of the x-ray restrained wave function approach: Advantages, drawbacks, and perspectives for density functional theory and periodic ab initio calculations. J Chem Phys 2024; 160:234108. [PMID: 38899684 DOI: 10.1063/5.0213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
The x-ray restrained wave function (XRW) method is a quantum crystallographic technique to extract wave functions compatible with experimental x-ray diffraction data. The approach looks for wave functions that minimize the energies of the investigated systems and also reproduce sets of x-ray structure factors. Given the strict relationship between x-ray structure factors and electron distributions, the strategy practically allows determining wave functions that correspond to given (usually experimental) electron densities. In this work, the capabilities of the XRW approach were further tested. The aim was to evaluate whether the XRW technique could serve as a tool for suggesting new exchange-correlation functionals for density functional theory or refining existing ones. Additionally, the ability of the method to address the influences of the crystalline environment was also assessed. The outcomes of XRW computations were thus compared to those of traditional gas-phase, embedding quantum mechanics/molecular mechanics, and fully periodic calculations. The results revealed that, irrespective of the initial conditions, the XRW computations practically yield a consensus electron density, in contrast to the currently employed density functional approximations (DFAs), which tend to give a too large range of electron distributions. This is encouraging in view of exploiting the XRW technique to develop improved functionals. Conversely, the calculations also emphasized that the XRW method is limited in its ability to effectively address the influences of the crystalline environment. This underscores the need for a periodic XRW technique, which would allow further untangling the shortcomings of DFAs from those inherent to the XRW approach.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, Avenida Julian Clavería 8, 33006 Oviedo, Spain
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5
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Singh A, Avinash K, Malaspina LA, Banoo M, Alhameedi K, Jayatilaka D, Grabowsky S, Thomas SP. Dynamic Covalent Bonds in the Ebselen Class of Antioxidants Probed by X-ray Quantum Crystallography. Chemistry 2024; 30:e202303384. [PMID: 38126954 DOI: 10.1002/chem.202303384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Dynamic bonds are essential structural ingredients of dynamic covalent chemistry that involve reversible cleavage and formation of bonds. Herein, we explore the electronic characteristics of Se-N bonds in the organo-selenium antioxidant ebselen and its derivatives for their propensity to function as dynamic covalent bonds by employing high-resolution X-ray quantum crystallography and complementary computational studies. An analysis of the experimentally reconstructed X-ray wavefunctions reveals the salient electronic features of the Se-N bonds with very low electron density localized at the bonding region and a positive Laplacian value at the bond critical point. Bond orders and percentage covalency and ionicity estimated from the X-ray wavefunctions, along with localized orbital locator (LOL) and electron localization function (ELF) analyses show that the Se-N bond is unique in its closed shell-like features, despite being a covalent bond. Time-dependent DFT calculations simulate the cleavage of Se-N bonds in ebselen in the excited state, further substantiating their nature as dynamic bonds.
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Affiliation(s)
- Ashi Singh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Kiran Avinash
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Lorraine A Malaspina
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012, Bern, Switzerland
| | - Masoumeh Banoo
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Khidhir Alhameedi
- School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Faculty of Education for Pure Sciences -, University of Kerbala, Karbala, Iraq
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Simon Grabowsky
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Freiestrasse 3, 3012, Bern, Switzerland
| | - Sajesh P Thomas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, 110016, India
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6
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Pawlędzio S, Ziemniak M, Trzybiński D, Arhangelskis M, Makal A, Woźniak K. Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography. RSC Adv 2024; 14:5340-5350. [PMID: 38348299 PMCID: PMC10859733 DOI: 10.1039/d3ra08081a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.
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Affiliation(s)
- Sylwia Pawlędzio
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Marcin Ziemniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Damian Trzybiński
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Mihails Arhangelskis
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Anna Makal
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
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7
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Skogh M, Dobrautz W, Lolur P, Warren C, Biznárová J, Osman A, Tancredi G, Bylander J, Rahm M. The electron density: a fidelity witness for quantum computation. Chem Sci 2024; 15:2257-2265. [PMID: 38332826 PMCID: PMC10848700 DOI: 10.1039/d3sc05269a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/19/2023] [Indexed: 02/10/2024] Open
Abstract
There is currently no combination of quantum hardware and algorithms that can provide an advantage over conventional calculations of molecules or materials. However, if or when such a point is reached, new strategies will be needed to verify predictions made using quantum devices. We propose that the electron density, obtained through experimental or computational means, can serve as a robust benchmark for validating the accuracy of quantum computation of chemistry. An initial exploration into topological features of electron densities, facilitated by quantum computation, is presented here as a proof of concept. Additionally, we examine the effects of constraining and symmetrizing measured one-particle reduced density matrices on noise-driven errors in the electron density distribution. We emphasize the potential benefits and future need for high-quality electron densities derived from diffraction experiments for validating classically intractable quantum computations of materials.
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Affiliation(s)
- Mårten Skogh
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
- Data Science & Modelling, Pharmaceutical Science, R&D, AstraZeneca Gothenburg Sweden
| | - Werner Dobrautz
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
| | - Phalgun Lolur
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
| | - Christopher Warren
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Janka Biznárová
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Amr Osman
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Giovanna Tancredi
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Jonas Bylander
- Department of Microtechnology and Nanoscience MC2, Chalmers University of Technology Gothenburg Sweden
| | - Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology Gothenburg Sweden
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8
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Yanai H. Development of Stable Carbanionic Substituents. CHEM REC 2023; 23:e202300076. [PMID: 37058109 DOI: 10.1002/tcr.202300076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Indexed: 04/15/2023]
Abstract
During the past decade, carbon (C-H) acids depicted as 'Tf2 CHR' (Tf=CF3 SO2 ) have attracted considerable attention as a new class of superacidic molecules, which show stronger acidity than sulfuric acid molecules. In recent years, the author has developed a synthetic methodology for such strong acids and has opened the door to chemistry of highly stabilised carbanions [Tf2 CR]- , which are the conjugate bases of the carbon acids. These carbanion-containing salts are stable and easy-to-handle species. Our efforts have revealed that the ionic but lipophilic characters of this type of carbanion can be used as a unique 'substituent' for increasing both the water solubility and the lipophilicity of organic compounds. This Personal Account provides an overview of our [Tf2 CR]- chemistry, including its synthesis, structure, reactivity, and applications.
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Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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9
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Genoni A. Elucidating the nature of chemical bonds in a coordination compound through quantum crystallographic techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:253-254. [PMID: 37561073 DOI: 10.1107/s2052520623006364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023]
Abstract
Investigations simultaneously involving multiple techniques of quantum crystallography could be very useful to prove the consistency of obtained results or to highlight different facets of the same scientific phenomenon or problem. Pinto et al. [Acta Cryst. (2023), B79, 282-296] exploit three different quantum crystallographic techniques (Hansen & Coppens multipole model refinement, QTAIM analysis of the electron density, and Hirshfeld atom refinement) to characterize the nature of chemical bonds and of intra/intermolecular interactions in an organometallic compound.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57070, France
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10
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Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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11
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Macetti G, Genoni A. Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks. Acta Crystallogr A Found Adv 2023; 79:25-40. [PMID: 36601761 DOI: 10.1107/s2053273322010221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022] Open
Abstract
In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
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12
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Pichierri F. Tri-tert-butyl methane and its halogen analogues: a computational study of intramolecular interactions in a family of sterically crowded molecules. Struct Chem 2022. [DOI: 10.1007/s11224-022-02102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Hill NDD, Lilienthal E, Bender CO, Boeré RT. Accurate Crystal Structures of C 12H 9CN, C 12H 8(CN) 2, and C 16H 11CN Valence Isomers Using Nonspherical Atomic Scattering Factors. J Org Chem 2022; 87:16213-16229. [DOI: 10.1021/acs.joc.2c01706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Nathan D. D. Hill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - Elaura Lilienthal
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - Christopher O. Bender
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
| | - René T. Boeré
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
- The Canadian Centre for Research in Advanced Fluorine Technologies (C-CRAFT), University of Lethbridge, 4401 University Dr. W, Lethbridge, AB, Canada T1K 3M4
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14
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields. Chemistry 2022; 28:e202200985. [PMID: 35638164 DOI: 10.1002/chem.202200985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/09/2022]
Abstract
Intricate behaviour of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic ϕ e s r and kinetic ϕ k r potentials and electron density ρ r allowed partitioning any molecules and crystals into atomic ρ - and potential-based ϕ -basins; ϕ k -basins explicitly account for the electron exchange effect, which is missed for ϕ e s -ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero-flux surfaces of ρ - and ϕ -basins. The gap between ϕ e s - and ρ -basins represents the charge transfer, while the gap between ϕ k - and ρ -basins is a real-space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of ρ -, ϕ e s -, and ϕ k - basin boundaries between interacting atoms was proposed. The position of ϕ k -boundary between ϕ e s - and ρ -ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an H⋅⋅⋅O hydrogen bond is, the deeper hydrogen atom's ϕ k -basin penetrates oxygen atom's ρ -basin, while for covalent bonds a ϕ k -boundary closely approaches a ϕ e s -one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the ρ -basin of an electron occupier atom.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation.,South Ural State University, 76 Lenin Avenue, Chelyabinsk, 454080, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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15
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Genoni A. On the termination of the X-ray constrained wavefunction procedure: reformulation of the method for an unequivocal determination of λ. Acta Crystallogr A Found Adv 2022; 78:302-308. [DOI: 10.1107/s2053273322003746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
The X-ray constrained/restrained wavefunction (XCW/XRW) approach of quantum crystallography is revisited by introducing the stationary condition of the Jayatilaka functional with respect to the Lagrange multiplier λ. The theoretical derivation has unequivocally shown that the right value of λ is a maximum stationary point of the functional to optimize, thus enabling the solution of the longstanding problem of establishing the point at which to halt the XCW/XRW procedure. Based on the new finding, a reformulation of the X-ray constrained wavefunction algorithm is proposed and its implementation is envisaged. In addition to relying on more solid mathematical grounds, the new variant of the method will be intrinsically more physically meaningful, allowing a straightforward evaluation of the highest level of confidence with which the experimental X-ray diffraction data can be possibly reproduced.
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16
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Bürgi HB, Genoni A. Remarks on X-ray constrained/restrained wavefunction fitting. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:298-304. [PMID: 35695103 DOI: 10.1107/s2052520622004164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
X-ray constrained/restrained wavefunctions (XCWs/XRWs) result from a combination of theory and experiment and are therefore affected by experimental errors and model uncertainties. The present XCW/XRW procedure does not take this into account, thus limiting the meaning and significance of the obtained wavefunctions.
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Affiliation(s)
- Hans Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmacy, University of Berne, Freiestr. 12, Bern, CH-3012, Switzerland
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, 57050, France
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17
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. I. Method and review. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:312-332. [PMID: 35695105 DOI: 10.1107/s2052520622004097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The X-ray constrained wavefunction (XCW) procedure for obtaining an experimentally reconstructed wavefunction from X-ray diffraction data is reviewed. The two-center probability distribution model used to perform nuclear-position averaging in the original paper [Grimwood & Jayatilaka (2001). Acta Cryst. A57, 87-100] is carefully distinguished from the newer one-center probability distribution model. In the one-center model, Hirshfeld atoms are used, and the Hirshfeld atom based X-ray constrained wavefunction (HA-XCW) procedure is described for the first time, as well as its efficient implementation. In this context, the definition of the related X-ray wavefunction refinement (XWR) method is refined. The key halting problem for the XCW method - the procedure by which one determines when overfitting has occurred - is named and work on it reviewed.
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Affiliation(s)
- Max L Davidson
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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18
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Pal R, Jelsch C, Momma K, Grabowsky S. π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:231-246. [PMID: 35411861 PMCID: PMC9004022 DOI: 10.1107/s2052520622001457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.
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Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | | | - Koichi Momma
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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19
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Pawlȩdzio S, Malinska M, Kleemiss F, Grabowsky S, Woźniak K. Aurophilic Interactions Studied by Quantum Crystallography. Inorg Chem 2022; 61:4235-4239. [PMID: 35230099 PMCID: PMC8924918 DOI: 10.1021/acs.inorgchem.1c03333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
This is the first
use of a wave-function-based crystallographic
method to characterize aurophilic interactions from X-ray diffraction
data. Theoretical calculations previously suggested the importance
of electron correlation and dispersion forces, but no influence of
relativistic corrections to the Au...Au interaction energy was found.
In this study, we confirm the importance of relativistic corrections
in the characterization of aurophilic interactions in addition to
electron correlation and dispersion. Hirshfeld
atom refinement was used to characterize aurophilic
interactions from X-ray diffraction data. An intermediate closed-shell
type of aurophilic interaction with some features of covalency was
identified when both electron correlation and relativistic corrections
were applied. Relativistic correction changes the electron density
distribution more than electron correlation. Relativistic effects
strongly dominate the metal core region also in the direction of the
noncovalent interactions and all of the valence and bonding regions
with regard to the Au···Au interaction.
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Affiliation(s)
- Sylwia Pawlȩdzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.,Faculty for Chemistry und Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
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20
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Yanai H. Chemistry of Carbanions Stabilised by (Trifluoromethyl) sulfonyl Group: Synthesis, Structure and Applications. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hikaru Yanai
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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21
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Jiang XM, Deng S, Whangbo MH, Guo GC. Material research from the viewpoint of functional motifs. Natl Sci Rev 2022; 9:nwac017. [PMID: 35983369 PMCID: PMC9379984 DOI: 10.1093/nsr/nwac017] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
As early as 2001, the need for the ‘functional motif theory’ was pointed out to assist the rational design of functional materials. The properties of materials are determined by their functional motifs and by how they are arranged in the materials. Uncovering the functional motifs and their arrangements is crucial in understanding the properties of materials and rationally designing new materials of desired properties. The functional motifs of materials are the critical microstructural units (e.g. constituent components and building blocks) that play a decisive role in generating certain material functions, and could not be replaced with other structural units without losing or significantly suppressing the relevant functions. The role of functional motifs and their arrangements in materials with representative examples was presented. These examples could be classified into six types of material microscopic structures on a length scale smaller than ∼10 nm with maximum subatomic resolution, i.e. the crystal, magnetic, aperiodic, defect, local, and electronic structures. The method of functional motif analysis could be employed in the function-oriented design of materials, as elucidated by taking infrared nonlinear optical materials as an example. Machine learning is more efficient in predicting material properties and screening materials with high efficiency than high-throughput experimentation and high-throughput calculations. In extracting the functional motifs and finding their quantitative relationships, developing sufficiently reliable databases for material structures and properties is imperative.
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Affiliation(s)
- Xiao-Ming Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Shuiquan Deng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Myung-Hwan Whangbo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
- Department of Chemistry, North Carolina State University, Raleigh, NC27695-8204, USA
| | - Guo-Cong Guo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
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22
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Matta CF, Huang L, Massa L. Quantum Crystallography:
N
‐Representability Big and Small**. Isr J Chem 2021. [DOI: 10.1002/ijch.202100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chérif F. Matta
- Department of Chemistry and Physics Mount Saint Vincent University Halifax Nova Scotia Canada B3M 2J6
- Department of Chemistry Dalhousie University Halifax Nova Scotia Canada B3H 4J3
- Department of Chemistry Saint Mary's University Halifax Nova Scotia Canada B3H 3C3
- Département de chimie Université Laval, Québec Québec Canada G1V 0A6
| | - Lulu Huang
- Department of Chemistry Hunter College City University of New York NY 10065 USA
| | - Lou Massa
- Department of Chemistry Hunter College City University of New York NY 10065 USA
- Departments of Chemistry and Physics Graduate Center City University of New York NY 10016 USA
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23
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Wenger JS, Wang X, Johnstone TC. H-Atom Assignment and Sb-O Bonding of [Mes 3SbOH][O 3SPh] Confirmed by Neutron Diffraction, Multipole Modeling, and Hirshfeld Atom Refinement. Inorg Chem 2021; 60:16048-16052. [PMID: 34661394 DOI: 10.1021/acs.inorgchem.1c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neutron wavelength-resolved Laue diffraction experiments permit accurate refinement of the H-atom positions and anisotropic displacement parameters of [Mes3SbOH][O3SPh]. A multipole-based charge density refinement and a topological analysis of the refined electron density were also performed. Hirshfeld atom refinement (HAR) recovers the neutron-determined H-atom parameters, and the quantum-mechanical electron density used in HAR recovers the electron density topology from the refined multipole model. These results confirm that [Mes3SbOH][O3SPh] does indeed feature a hydroxystibonium cation with a nominal Sb-O single bond and not a stibine oxide with an Sb=O/Sb+-O- bond.
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Affiliation(s)
- John S Wenger
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Xiaoping Wang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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24
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Midgley L, Bourhis LJ, Dolomanov OV, Grabowsky S, Kleemiss F, Puschmann H, Peyerimhoff N. Vanishing of the atomic form factor derivatives in non-spherical structural refinement - a key approximation scrutinized in the case of Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:519-533. [PMID: 34726630 DOI: 10.1107/s2053273321009086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/02/2021] [Indexed: 11/10/2022]
Abstract
When calculating derivatives of structure factors, there is one particular term (the derivatives of the atomic form factors) that will always be zero in the case of tabulated spherical atomic form factors. What happens if the form factors are non-spherical? The assumption that this particular term is very close to zero is generally made in non-spherical refinements (for example, implementations of Hirshfeld atom refinement or transferable aspherical atom models), unless the form factors are refinable parameters (for example multipole modelling). To evaluate this general approximation for one specific method, a numerical differentiation was implemented within the NoSpherA2 framework to calculate the derivatives of the structure factors in a Hirshfeld atom refinement directly as accurately as possible, thus bypassing the approximation altogether. Comparing wR2 factors and atomic parameters, along with their uncertainties from the approximate and numerically differentiating refinements, it turns out that the impact of this approximation on the final crystallographic model is indeed negligible.
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Affiliation(s)
- Laura Midgley
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
| | - Luc J Bourhis
- Bruker, 4 Allée Lorentz, Champs-sur-Marne, 77447 Marne-la-Vallée cedex 2, France
| | - Oleg V Dolomanov
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Kleemiss
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Horst Puschmann
- OlexSys Ltd, Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Norbert Peyerimhoff
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, United Kingdom
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25
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Pinto CB, Rodrigues BL, Dos Santos LHR. Estimating electron density at the bond critical point through atomic Hirshfeld surfaces. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721009213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Interatomic surfaces often carry information related to the electron distribution in a molecule or crystal, not only being a visual aid but also enabling quantitative analyses. Under certain conditions, atomic Hirshfeld surfaces present a high resemblance to the interatomic surfaces obtained through the quantum theory of atoms in molecules (QTAIM), with the advantage of being easily calculated, even for crystal structures determined at low resolutions (i.e. when a charge-density refinement is not performed). Here an empirical relation between the curvedness property of the Hirshfeld surfaces and the electron density at the bond critical point for certain types of covalent and coordination interactions involving carbon atoms has been obtained. The exponential function was tested to estimate the electron density in different crystalline systems, and the highest deviation from reference values obtained through QTAIM was just 16%. Additionally, fine details of this fit may be salient to the difference in electronegativity of the atoms involved in the bond.
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26
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Hoser AA, Sztylko M, Trzybiński D, Madsen AØ. Theoretically derived thermodynamic properties can be improved by the refinement of low-frequency modes against X-ray diffraction data. Chem Commun (Camb) 2021; 57:9370-9373. [PMID: 34528955 DOI: 10.1039/d1cc02608a] [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
Herein, a framework for the estimation of the thermodynamic properties of molecular crystals via the refinement of frequencies from density functional theory calculations against X-ray diffraction data is presented. The framework provides an efficient approach to including the contribution of acoustic modes in the thermodynamic properties. The obtained heat capacities for urea, the α- and β-glycine polymorphs, benzoic acid, and 4'-hydroxyacetophenone are in good agreement with those from adiabatic calorimetry.
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Affiliation(s)
- Anna A Hoser
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Marcin Sztylko
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
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27
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Macetti G, Genoni A. Initial Maximum Overlap Method for Large Systems by the Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Technique. J Chem Theory Comput 2021; 17:4169-4182. [PMID: 34196174 DOI: 10.1021/acs.jctc.1c00388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum chemistry offers a large variety of methods to treat excited states. Many of them are based on a multireference wave function ansatz and are therefore characterized by an intrinsic complexity and high computational costs. To overcome these drawbacks and also some limitations of simpler single-reference approaches (e.g., configuration interaction singles and time-dependent density functional theory), the single-determinant Δself-consistent field-initial maximum overlap method (ΔSCF-IMOM) has been proposed. This strategy substitutes the aufbau principle with a criterion that occupies molecular orbitals at successive SCF iterations on the basis of their maximum overlap with a proper set of guess orbitals for the target excited state. In this way, it prevents the SCF process to collapse to the ground state wave function and provides excited state single Slater determinant solutions to the SCF equations. Here, we propose to extend the applicability of the IMOM to the treatment of localized excited states of large systems. To accomplish this task, we coupled it with the QM/ELMO (quantum mechanics/extremely localized molecular orbitals) strategy, a quantum mechanical embedding method in which the most chemically relevant part of the system is treated with traditional quantum chemical approaches, while the rest is described by extremely localized molecular orbitals transferred from recently constructed libraries or proper model molecules. After presenting the theoretical foundations of the new IMOM/ELMO technique, in this paper, we will show and discuss the results of preliminary test calculations carried out on both model systems (i.e., decanoic acid, decene, decapentaene, and solvated acrolein) and a system of biological interest (flavin mononucleotide in the flavodoxin protein). We observed that, for localized excited states, the new IMOM/ELMO method provides reliable results, and it reproduces the outcomes of fully IMOM calculations within the chemical accuracy threshold (i.e., 0.043 eV) by including only a limited number of atoms in the QM region. Furthermore, the first application of our embedding technique to a larger biological system gave completely plausible results in line with those obtained through more traditional quantum mechanical methods, thus opening the possibility of using the new approach in future investigations of photobiology problems.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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28
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Milašinović V, Molčanov K, Krawczuk A, Bogdanov NE, Zakharov BA, Boldyreva EV, Jelsch C, Kojić-Prodić B. Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure. IUCRJ 2021; 8:644-654. [PMID: 34258012 PMCID: PMC8256703 DOI: 10.1107/s2052252521005273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano-N-methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals.
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Affiliation(s)
- Valentina Milašinović
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Krešimir Molčanov
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Anna Krawczuk
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, Göttingen 37077, Germany
- Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, Krakow 30-387, Poland
| | - Nikita E. Bogdanov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Boris A. Zakharov
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Elena V. Boldyreva
- Boreskov Institute of Catalysis, SB RAS, Lavrentiev Avenue 5, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova Street 2, Novosibirsk 630090 Russian Federation
| | - Christian Jelsch
- CRM2, CNRS, UMR 7036, Université de Lorraine, BP 70239 Nancy, France
| | - Biserka Kojić-Prodić
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
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29
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Macetti G, Genoni A. Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions. J Phys Chem A 2021; 125:6013-6027. [PMID: 34190569 DOI: 10.1021/acs.jpca.1c05040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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30
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Holsten S, Malaspina LA, Kleemiss F, Mebs S, Hupf E, Grabowsky S, Beckmann J. Different Reactivities of (5-Ph2P-Ace-6-)2MeSiH toward the Rhodium(I) Chlorides [(C2H4)2RhCl]2 and [(CO)2RhCl]2. Hirshfeld Atom Refinement of a Rh–H···Si Interaction. Organometallics 2021. [DOI: 10.1021/acs.organomet.0c00804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sebastian Holsten
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Lorraine A. Malaspina
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Kleemiss
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
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Malaspina LA, Genoni A, Grabowsky S. lamaGOET: an interface for quantum crystallography. J Appl Crystallogr 2021; 54:987-995. [PMID: 34188618 PMCID: PMC8202027 DOI: 10.1107/s1600576721002545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/08/2021] [Indexed: 11/24/2022] Open
Abstract
In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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Malaspina LA, Genoni A, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Grabowsky S. The advanced treatment of hydrogen bonding in quantum crystallography. J Appl Crystallogr 2021; 54:718-729. [PMID: 34188611 PMCID: PMC8202034 DOI: 10.1107/s1600576721001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/31/2021] [Indexed: 11/16/2022] Open
Abstract
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Michael J. Turner
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute/Diffraction and Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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Macetti G, Wieduwilt EK, Genoni A. QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals. J Phys Chem A 2021; 125:2709-2726. [DOI: 10.1021/acs.jpca.0c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
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Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
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Crystallographic and Computational Electron Density of d x2-y2 Orbitals of Azo-Schiff Base Metal Complexes Using Conventional Programs. Molecules 2021; 26:molecules26030551. [PMID: 33494463 PMCID: PMC7865803 DOI: 10.3390/molecules26030551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 11/23/2022] Open
Abstract
The crystal structures of two azobenzene derivative Schiff base metal complexes (new C44H40CuN6O2 of P-1 and known C44H38MnN6O7 of P21/c abbreviated as Cu and Mn, respectively) were (re-)determined experimentally using conventional X-ray analysis to obtain electron density using a PLATON program. Cu affords a four-coordinated square planar geometry, while Mn affords a hexa-coordinated distorted octahedral geometry whose apical sites are occupied by an acetate ion and water ligands, which are associated with hydrogen bonds. The π-π or CH-π and hydrogen bonding intermolecular interactions were found in both crystals, which were also analyzed using a Hirshfeld surface analysis program. To compare these results with experimental results, a density functional theory (DFT) calculation was also carried out based on the crystal structures to obtain calculated electron density using a conventional Gaussian program. These results revealed that the axial Mn-O coordination bonds of Mn were relatively weaker than the in-plane M-N or M-O coordination bonds.
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37
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Wieduwilt EK, Macetti G, Genoni A. Climbing Jacob's Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions. J Phys Chem Lett 2021; 12:463-471. [PMID: 33369421 DOI: 10.1021/acs.jpclett.0c03421] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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38
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Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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Podhorský M, Bučinský L, Jayatilaka D, Grabowsky S. HgH 2 meets relativistic quantum crystallography. How to teach relativity to a non-relativistic wavefunction. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:54-66. [PMID: 33399131 DOI: 10.1107/s2053273320014837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022]
Abstract
The capability of X-ray constrained wavefunction (XCW) fitting to introduce relativistic effects into a non-relativistic wavefunction is tested. It is quantified how much of the reference relativistic effects can be absorbed in the non-relativistic XCW calculation when fitted against relativistic structure factors of a model HgH2 molecule. Scaling of the structure-factor sets to improve the agreement statistics is found to introduce a significant systematic error into the XCW fitting of relativistic effects.
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Affiliation(s)
- Michal Podhorský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Perth WA 6009, Australia
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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40
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Quantum mechanics/extremely localized molecular orbital embedding technique: Theoretical foundations and further validation. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Mapp LK, Cadden J, Klooster WT, Aitipamula S, Coles SJ. Insights into the structure-property relationship of pharmaceutical co-crystals: Charge density and quantum chemical approaches. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Affiliation(s)
- Piero Macchi
- Department, Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Milano, Italy
- Center for Nano Science and Technology CNST@polimi, Italian Institute of Technology, Milano, Italy
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43
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Macetti G, Genoni A. Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Strategy for Excited States: Coupling to Time-Dependent Density Functional Theory and Equation-of-Motion Coupled Cluster. J Chem Theory Comput 2020; 16:7490-7506. [PMID: 33241930 DOI: 10.1021/acs.jctc.0c00956] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.
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Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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44
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Kleemiss F, Dolomanov OV, Bodensteiner M, Peyerimhoff N, Midgley L, Bourhis LJ, Genoni A, Malaspina LA, Jayatilaka D, Spencer JL, White F, Grundkötter-Stock B, Steinhauer S, Lentz D, Puschmann H, Grabowsky S. Accurate crystal structures and chemical properties from NoSpherA2. Chem Sci 2020; 12:1675-1692. [PMID: 34163928 PMCID: PMC8179328 DOI: 10.1039/d0sc05526c] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022] Open
Abstract
The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure - at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples.
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Affiliation(s)
- Florian Kleemiss
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | | | - Michael Bodensteiner
- Universität Regensburg, Fakultät für Chemie und Pharmazie, Universitätsstr. 31 93053 Regensburg Germany
| | - Norbert Peyerimhoff
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Laura Midgley
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Luc J Bourhis
- Bruker France 4 Allée Lorentz, Champs-sur-Marne 77447 Marne-la-Vallée cedex 2 France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 1 Boulevard Arago 57078 Metz France
| | - Lorraine A Malaspina
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | - Dylan Jayatilaka
- University of Western Australia, School of Molecular Sciences 35 Stirling Highway WA 6009 Perth Australia
| | - John L Spencer
- Victoria University of Wellington, School of Chemical and Physical Sciences Wellington 6012 New Zealand
| | - Fraser White
- Rigaku Europe SE Hugenottenallee 167 63263 Neu-Isenburg Germany
| | - Bernhard Grundkötter-Stock
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Simon Steinhauer
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Dieter Lentz
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | | | - Simon Grabowsky
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
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Sadjadi S, Matta CF, Hamilton IP. Bonding and metastability for Group 12 dications. J Comput Chem 2020; 42:40-49. [PMID: 33063900 DOI: 10.1002/jcc.26431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/06/2022]
Abstract
Electronic structure and bonding properties of the Group 12 dications M2 2+ (M = Zn, Cd, Hg) are investigated and electron density-derived quantities are used to characterize the metastability of these species. Of particular interest are the complementary descriptions afforded by the Laplacian of the electron density ∇2 ρ(r) and the one-electron Bohm quantum potential (Q = ∇ 2 ρ r / 2 ρ r ) along the bond path. Further, properties derived from the pair density including the localization-delocalization matrices (LDMs) and the interacting quantum atoms (IQA) energies are analyzed within the framework of the quantum theory of atoms in molecules (QTAIM). From the crossing points of the singlet (ground) and triplet (excited) potential energy curves, the barriers for dissociation (BFD) are estimated to be 25.2 kcal/mol (1.09 eV) for Zn2 2+ , 22.8 kcal/mol (0.99 eV) for Cd2 2+ , and 26.4 kcal/mol (1.14 eV) for Hg2 2+ . For comparison and benchmarking purposes, the case of N2 2+ is considered as a texbook example of metastability. At the equilibrium geometries, LDMs, which are used here as an electronic fingerprinting tool, discriminate and group together Group 12 M2 2+ from its isoelectronic Group 11 M2 . While "classical" bonding indices are inconclusive in establishing regions of metastability in the bonding, it is shown that the one-electron Bohm quantum potential is promising in this regard.
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Affiliation(s)
- SeyedAbdolreza Sadjadi
- Department of Physics, Faculty of Science, Laboratory for Space Research, The University of Hong Kong, Hong Kong SAR, China
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian P Hamilton
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada
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Sanjuan-Szklarz WF, Woińska M, Domagała S, Dominiak PM, Grabowsky S, Jayatilaka D, Gutmann M, Woźniak K. On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model. IUCRJ 2020; 7:920-933. [PMID: 32939284 PMCID: PMC7467170 DOI: 10.1107/s2052252520010441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 05/20/2023]
Abstract
X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.
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Affiliation(s)
- W. Fabiola Sanjuan-Szklarz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Sławomir Domagała
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Matthias Gutmann
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
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47
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Tsirelson V, Stash A. Orbital-free quantum crystallography: view on forces in crystals. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2020; 76:769-778. [DOI: 10.1107/s2052520620009178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/06/2020] [Indexed: 11/11/2022]
Abstract
Quantum theory of atoms in molecules and the orbital-free density functional theory (DFT) are combined in this work to study the spatial distribution of electrostatic and quantum electronic forces acting in stable crystals. The electron distribution is determined by electrostatic electron mutual repulsion corrected for exchange and correlation, their attraction to nuclei and by electron kinetic energy. The latter defines the spread of permissible variations in the electron momentum resulting from the de Broglie relationship and uncertainty principle, as far as the limitations of Pauli principle and the presence of atomic nuclei and other electrons allow. All forces are expressed via kinetic and DFT potentials and then defined in terms of the experimental electron density and its derivatives; hence, this approach may be considered as orbital-free quantum crystallography. The net force acting on an electron in a crystal at equilibrium is zero everywhere, presenting a balance of the kinetic
F
kin(
r
) and potential forces
F
(
r
). The critical points of both potentials are analyzed and they are recognized as the points at which forces
F
kin(
r
) and
F
(
r
) individually are zero (the Lagrange points). The positions of these points in a crystal are described according to Wyckoff notations, while their types depend on the considered scalar field. It was found that
F
(
r
) force pushes electrons to the atomic nuclei, while the kinetic force
F
kin(
r
) draws electrons from nuclei. This favors formation of electron concentration bridges between some of the nearest atoms. However, in a crystal at equilibrium, only kinetic potential v
kin(
r
) and corresponding force exhibit the electronic shells and atomic-like zero-flux basins around the nuclear attractors. The force-field approach and quantum topological theory of atoms in molecules are compared and their distinctions are clarified.
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48
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Moreno JR, Carleo G, Georges A. Deep Learning the Hohenberg-Kohn Maps of Density Functional Theory. PHYSICAL REVIEW LETTERS 2020; 125:076402. [PMID: 32857556 DOI: 10.1103/physrevlett.125.076402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
A striking consequence of the Hohenberg-Kohn theorem of density functional theory is the existence of a bijection between the local density and the ground-state many-body wave function. Here we study the problem of constructing approximations to the Hohenberg-Kohn map using a statistical learning approach. Using supervised deep learning with synthetic data, we show that this map can be accurately constructed for a chain of one-dimensional interacting spinless fermions in different phases of this model including the charge ordered Mott insulator and metallic phases and the critical point separating them. However, we also find that the learning is less effective across quantum phase transitions, suggesting an intrinsic difficulty in efficiently learning nonsmooth functional relations. We further study the problem of directly reconstructing complex observables from simple local density measurements, proposing a scheme amenable to statistical learning from experimental data.
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Affiliation(s)
- Javier Robledo Moreno
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
- Center for Quantum Phenomena, Department of Physics, New York University, 726 Broadway, New York, New York 10003, USA
| | - Giuseppe Carleo
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Antoine Georges
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
- Collège de France, 11 place Marcelin Berthelot, 75005 Paris, France
- CPHT, CNRS, École Polytechnique, IP Paris, F-91128 Palaiseau, France
- DQMP, Université de Genève, 24 quai Ernest Ansermet, CH-1211 Genève, Suisse
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49
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Post-Hartree-Fock methods for Hirshfeld atom refinement: are they necessary? Investigation of a strongly hydrogen-bonded molecular crystal. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127934] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Ernst M, Genoni A, Macchi P. Analysis of crystal field effects and interactions using X-ray restrained ELMOs. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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