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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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2
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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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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. II. Reproducibility of electron densities in crystals of α-oxalic acid dihydrate. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:397-415. [PMID: 35695114 DOI: 10.1107/s2052520622004103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The Hirshfeld atom-based X-ray constrained wavefunction fitting (HA-XCW) procedure is tested for its reproducibility, and the information content of the fitted wavefunction is critically assessed. Fourteen different α-oxalic acid dihydrate data sets are used for this purpose, and the first joint fitting to 12 of these data sets is reported. There are systematic features in the electron density obtained from all data sets which agree with higher level benchmark calculations, but there are also many other strong systematic features which disagree with the reference calculations, most notably those associated with the electron density near the nuclei. To enhance reproducibility, three new protocols are described and tested to address the halting problem of XCW fitting, namely: an empirical power-function method, which is useful for estimating the accuracy of the structure factor uncertainties; an asymptotic extrapolation method based on ideas from density functional theory; and a `conservative method' whereby the smallest value of the regularization parameter is chosen from a series of data sets, or subsets.
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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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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: 0] [Impact Index Per Article: 0] [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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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: 4] [Impact Index Per Article: 2.0] [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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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] [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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Pal R, Jayatilaka D, Nishibori E. Structure Factors and Charge Density Description of Aluminum: A Quantum Crystallographic Study. J Phys Chem A 2022; 126:2042-2049. [PMID: 35316043 DOI: 10.1021/acs.jpca.1c10730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Static structure factors and charge density for metallic aluminum were investigated by periodic calculations using atom-centered Gaussian-type basis sets with the Perdew-Burke-Ernzerhof (PBE) functional implemented in the CRYSTAL14 package and X-ray constrained wave function (XCW) fitting. The effects of additional diffuse d and f basis functions on structure factors were compared with synchrotron powder X-ray diffraction and quantitative convergent electron beam diffraction data. Changes in structure factors from an independent atom model at 022, 113, and 222 reflections introduced d and f basis functions similar to those of the experimental data. The XCW fitting was applied to different sizes of aluminum clusters. The charge density features for a 50-atom cluster clearly demonstrated electron accumulation at tetrahedral sites and electron depletion at octahedral sites. The resolution dependence of the XCW study suggests that structure factors of the five lowest resolution reflections with 0.1% accuracy were indispensable for determining the detailed bonding description in the case of metallic aluminum.
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Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, Washington 6009, Australia
| | - Eiji Nishibori
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan.,Tsukuba Research Center for Energy Materials Science, University of Tsukuba, Tsukuba 305-8571, Japan
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Landeros-Rivera B, Gallegos M, Munarriz J, Laplaza R, Contreras García J. New venues in electron density analysis. Phys Chem Chem Phys 2022; 24:21538-21548. [DOI: 10.1039/d2cp01517j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide a comprehensive overview of the chemical information within the electron density: how to extract information, but also how to obtain and how to assess the quality of the...
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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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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: 3] [Impact Index Per Article: 1.0] [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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12
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Peng D, Nakashima PNH. Measuring Density Functional Parameters from Electron Diffraction Patterns. PHYSICAL REVIEW LETTERS 2021; 126:176402. [PMID: 33988394 DOI: 10.1103/physrevlett.126.176402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/13/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
We integrate density functional theory (DFT) into quantitative convergent-beam electron diffraction (QCBED) to create a synergy between experiment and theory called QCBED-DFT. This synergy resides entirely in the electron density which, in real materials, gives rise to the experimental CBED patterns used by QCBED-DFT to refine DFT model parameters. We use it to measure the Hubbard energy U for two strongly correlated electron systems, NiO and CeB_{6} (U=7.4±0.6 eV for d orbitals in NiO and U=3.0±0.6 eV for f orbitals in CeB_{6}), and the boron position parameter x for CeB_{6} (x=0.1992±0.0003). In verifying our measurements, we demonstrate an accuracy test for any modeled electron density.
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Affiliation(s)
- Ding Peng
- Department of Materials Science and Engineering, Monash University, Victoria 3800, Australia
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria 3800, Australia
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13
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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: 5] [Impact Index Per Article: 1.7] [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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14
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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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15
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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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16
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Abstract
In this review article, we report on the recent progresses in the field of quantum crystallography that has witnessed a massive increase of production coupled with a broadening of the scope in the last decade. It is shown that the early thoughts about extracting quantum mechanical information from crystallographic experiments are becoming reality, although a century after prediction. While in the past the focus was mainly on electron density and related quantities, the attention is now shifting toward determination of wavefunction from experiments, which enables an exhaustive determination of the quantum mechanical functions and properties of a system. Nonetheless, methods based on electron density modelling have evolved and are nowadays able to reconstruct tiny polarizations of core electrons, coupling charge and spin models, or determining the quantum behaviour at extreme conditions. Far from being routine, these experimental and computational results should be regarded with special attention by scientists for the wealth of information on a system that they actually contain.
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17
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Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM. TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:296-306. [PMID: 32831250 DOI: 10.1107/s2052520620002917] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Michal Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
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18
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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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19
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Dos Santos LH. Applications of charge-density analysis to the rational design of molecular materials: A mini review on how to engineer optical or magnetic crystals. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Genoni A. On the use of the Obara–Saika recurrence relations for the calculation of structure factors in quantum crystallography. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:172-179. [DOI: 10.1107/s205327332000042x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022]
Abstract
Modern methods of quantum crystallography are techniques firmly rooted in quantum chemistry and, as in many quantum chemical strategies, electron densities are expressed as two-centre expansions that involve basis functions centred on atomic nuclei. Therefore, the computation of the necessary structure factors requires the evaluation of Fourier transform integrals of basis function products. Since these functions are usually Cartesian Gaussians, in this communication it is shown that the Fourier integrals can be efficiently calculated by exploiting an extension of the Obara–Saika recurrence formulas, which are successfully used by quantum chemists in the computation of molecular integrals. Implementation and future perspectives of the technique are also discussed.
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21
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Grabowsky S, Genoni A, Thomas SP, Jayatilaka D. The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting. 21ST CENTURY CHALLENGES IN CHEMICAL CRYSTALLOGRAPHY II 2020. [DOI: 10.1007/430_2020_62] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Malaspina LA, Hoser AA, Edwards AJ, Woińska M, Turner MJ, Price JR, Sugimoto K, Nishibori E, Bürgi HB, Jayatilaka D, Grabowsky S. Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density. CrystEngComm 2020. [DOI: 10.1039/d0ce00378f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.
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23
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Genoni A, Macetti G, Franchini D, Pieraccini S, Sironi M. X-ray constrained spin-coupled technique: theoretical details and further assessment of the method. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:778-797. [PMID: 31692454 DOI: 10.1107/s2053273319011021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/07/2019] [Indexed: 11/11/2022]
Abstract
One of the well-established methods of modern quantum crystallography is undoubtedly the X-ray constrained wavefunction (XCW) approach, a technique that enables the determination of wavefunctions which not only minimize the energy of the system under examination, but also reproduce experimental X-ray diffraction data within the limit of the experimental errors. Initially proposed in the framework of the Hartree–Fock method, the strategy has been gradually extended to other techniques of quantum chemistry, but always remaining limited to a single-determinant ansatz for the wavefunction to extract. This limitation has been recently overcome through the development of the novel X-ray constrained spin-coupled (XCSC) approach [Genoni et al. (2018). Chem. Eur. J.
24, 15507–15511] which merges the XCW philosophy with the traditional spin-coupled strategy of valence bond theory. The main advantage of this new technique is the possibility of extracting traditional chemical descriptors (e.g. resonance structure weights) compatible with the experimental diffraction measurements, without the need to introduce information a priori or perform analyses a posteriori. This paper provides a detailed theoretical derivation of the fundamental equations at the basis of the XCSC method and also introduces a further advancement of its original version, mainly consisting in the use of molecular orbitals resulting from XCW calculations at the Hartree–Fock level to describe the inactive electrons in the XCSC computations. Furthermore, extensive test calculations, which have been performed by exploiting high-resolution X-ray diffraction data for salicylic acid and by adopting different basis sets, are presented and discussed. The computational tests have shown that the new technique does not suffer from particular convergence problems. Moreover, all the XCSC calculations provided resonance structure weights, spin-coupled orbitals and global electron densities slightly different from those resulting from the corresponding unconstrained computations. These discrepancies can be ascribed to the capability of the novel strategy to capture the information intrinsically contained in the experimental data used as external constraints.
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24
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Bučinský L, Jayatilaka D, Grabowsky S. Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:705-717. [PMID: 31475915 DOI: 10.1107/s2053273319008027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/04/2019] [Indexed: 11/10/2022]
Abstract
Quantum crystallographic refinement of heavy-element-containing compounds is a challenge, because many physical effects have to be accounted for adequately. Here, the impact and magnitude of relativistic effects are compared with those of electron correlation, polarization through the environment, choice of basis set and treatment of thermal motion effects on the structure factors of diphenylmercury(II) [Hg(Ph)2] and dicyanomercury(II) [Hg(CN)2]. Furthermore, the individual atomic contributions to the structure factors are explored in detail (using Mulliken population analysis and the exponential decay of atomic displacement parameters) to compare the contributions of lighter atoms, especially hydrogen atoms, against mercury. Subsequently, relativistic Hirshfeld atom refinement (HAR) is validated against theoretical structure factors of Hg(Ph)2 and Hg(CN)2, starting from perturbed geometries, to test if the relativistic variant of HAR leads to multiple solutions. Generally, relativistic HAR is successful, leading to a perfect match with the reference geometries, but some limitations are pointed out.
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Affiliation(s)
- 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 Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 - Biology/Chemistry, University of Bremen, Leobener Strasse 3, 28359 Bremen, Germany
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25
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Fugel M, Malaspina LA, Pal R, Thomas SP, Shi MW, Spackman MA, Sugimoto K, Grabowsky S. Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent? Chemistry 2019; 25:6523-6532. [PMID: 30759315 DOI: 10.1002/chem.201806247] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/05/2022]
Abstract
There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO4 3- ), sulfate (SO4 2- ) and perchlorate (ClO4 - ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH4 PO4 ⋅6 H2 O, Li2 SO4 ⋅H2 O, and KClO4 ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.
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Affiliation(s)
- Malte Fugel
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Lorraine A Malaspina
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
| | - Rumpa Pal
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany.,Current address: Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Sajesh P Thomas
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.,Current address: Interdisciplinary Nanoscience Center - INANO-Kemi, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Ming W Shi
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Mark A Spackman
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Kunihisa Sugimoto
- SPring-8, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Simon Grabowsky
- Department 2-Chemistry/Biology, Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobener Str. 3 and 7, 28359, Bremen, Germany
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27
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Meyer B, Genoni A. Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks. J Phys Chem A 2018; 122:8965-8981. [PMID: 30339393 DOI: 10.1021/acs.jpca.8b09056] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.
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Affiliation(s)
- Benjamin Meyer
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 , 1 Boulevard Arago , F-57078 Metz , France
| | - Alessandro Genoni
- Université de Lorraine and 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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Genoni A, Franchini D, Pieraccini S, Sironi M. X‐ray Constrained Spin‐Coupled Wavefunction: a New Tool to Extract Chemical Information from X‐ray Diffraction Data. Chemistry 2018; 24:15507-15511. [DOI: 10.1002/chem.201803988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Alessandro Genoni
- Université de Lorraine CNRS, Laboratoire LPCT 1 Boulevard Arago 57078 Metz France
| | - Davide Franchini
- Dipartimento di Chimica Università degli Studi di Milano Via Golgi 19 20133 Milano Italy
| | - Stefano Pieraccini
- Dipartimento di Chimica Università degli Studi di Milano Via Golgi 19 20133 Milano Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), CNR Via Golgi 19 20133 Milano Italy
- Consorzio Interuniversitario Nazionale per la, Scienza e Tecnologia dei Materiali (INSTM), UdR Milano Via Golgi 19 20133 Milano Italy
| | - Maurizio Sironi
- Dipartimento di Chimica Università degli Studi di Milano Via Golgi 19 20133 Milano Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), CNR Via Golgi 19 20133 Milano Italy
- Consorzio Interuniversitario Nazionale per la, Scienza e Tecnologia dei Materiali (INSTM), UdR Milano Via Golgi 19 20133 Milano Italy
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29
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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30
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Fugel M, Jayatilaka D, Hupf E, Overgaard J, Hathwar VR, Macchi P, Turner MJ, Howard JAK, Dolomanov OV, Puschmann H, Iversen BB, Bürgi HB, Grabowsky S. Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2. IUCRJ 2018; 5:32-44. [PMID: 29354269 PMCID: PMC5755575 DOI: 10.1107/s2052252517015548] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/25/2017] [Indexed: 05/20/2023]
Abstract
Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r(X-H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X-H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro-carbon rubrene (orthorhombic 5,6,11,12-tetra-phenyl-tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element-hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.
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Affiliation(s)
- Malte Fugel
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Emanuel Hupf
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Venkatesha R. Hathwar
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
- Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, Bern 3012, Switzerland
| | - Michael J. Turner
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | | | - Oleg V. Dolomanov
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - Horst Puschmann
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - Bo B. Iversen
- Center for Materials Crystallography, Department of Chemistry and iNano, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Hans-Beat Bürgi
- Department of Chemistry and Biochemistry, University of Bern, Freiestraße 3, Bern 3012, Switzerland
- Department of Chemistry, University of Zürich, Winterthurerstraße 190, Zürich 8057, Switzerland
| | - Simon Grabowsky
- Department 2: Biology/Chemistry, University of Bremen, Leobener Straße NW2, 28359 Bremen, Germany
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Woińska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Woźniak K, Dominiak PM, Grabowsky S. Validation of X-ray Wavefunction Refinement. Chemphyschem 2017; 18:3334-3351. [PMID: 29168318 DOI: 10.1002/cphc.201700810] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/22/2017] [Indexed: 11/10/2022]
Abstract
In this work, the quality of the electron density in crystals reconstructed by the multipolar model (MM) and by X-ray wavefunction refinement (XWR) is tested on a set of high-resolution X-ray diffraction data sets of four amino acids and six tripeptides. It results in the first thorough validation of XWR. Agreement statistics, figures of merit, residual- and deformation-density maps, as well as atomic displacement parameters are used to measure the quality of the reconstruction relative to the measured structure factors. Topological analysis of the reconstructed density is carried out to obtain atomic and bond-topological properties, which are subsequently compared to the values derived from benchmarking periodic DFT geometry optimizations. XWR is simultaneously in better agreement than the MM with both benchmarking theory and the measured diffraction pattern. In particular, the obvious problems with the description of polar bonds in the MM are significantly reduced by using XWR. Similarly, modeling of electron density in the vicinity of hydrogen atoms with XWR is visibly improved.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Birger Dittrich
- Heinrich-Heine-Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Gebäude 26.42.01.21, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ralf Flaig
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxon, OX11 0DE, UK
| | - Peter Luger
- Freie Universität Berlin, Institut für Chemie und Biochemie, Fabeckstraße 36a, 14195, Berlin, Germany
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2-Biologie/Chemie, Universität Bremen, Leobener Straße NW2, 28359, Bremen, Germany
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Casati N, Genoni A, Meyer B, Krawczuk A, Macchi P. Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:584-597. [DOI: 10.1107/s2052520617008356] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/06/2017] [Indexed: 11/10/2022]
Abstract
The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casatiet al.(2016).Nat. Commun.7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the speciessyn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.
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Macchi P. The future of topological analysis in experimental charge-density research. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:330-336. [PMID: 28572543 DOI: 10.1107/s2052520617006989] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
In a recent paper, Dittrich (2017) critically discussed the benefits of analysing experimental electron density within the framework of the quantum theory of atoms in molecules, often called simply the topological analysis of the charge density. The point he raised is important because it challenges the scientific production of a very active community. The question whether this kind of investigation is still sensible is intriguing and it fosters a multifaceted answer. Granted that none can predict the future of any field of science, but an alternative point of view emerges after answering three questions: Why should we investigate the electron charge (and spin) density? Is the interpretative scheme proposed by the quantum theory of atoms in molecules useful? Is an experimental charge density necessary?
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Affiliation(s)
- Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
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34
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Grabowsky S, Genoni A, Bürgi HB. Quantum crystallography. Chem Sci 2017; 8:4159-4176. [PMID: 28878872 PMCID: PMC5576428 DOI: 10.1039/c6sc05504d] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/03/2017] [Indexed: 12/12/2022] Open
Abstract
Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated tool. The development of quantum crystallographic research is reviewed. Some results obtained by quantum crystallography illustrate the potential and limitations of this field.
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Affiliation(s)
- Simon Grabowsky
- Universität Bremen , Fachbereich 2 - Biologie/Chemie , Institut für Anorganische Chemie und Kristallographie , Leobener Str. NW2 , 28359 Bremen , Germany .
| | - Alessandro Genoni
- CNRS , Laboratoire SRSMC , UMR 7565 , Vandoeuvre-lès-Nancy , F-54506 , France
- Université de Lorraine , Laboratoire SRSMC , UMR 7565 , Vandoeuvre-lès-Nancy , F-54506 , France .
| | - Hans-Beat Bürgi
- Universität Bern , Departement für Chemie und Biochemie , Freiestr. 3 , CH-3012 Bern , Switzerland .
- Universität Zürich , Institut für Chemie , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
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35
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Genoni A. A first-prototype multi-determinant X-ray constrained wavefunction approach: the X-ray constrained extremely localized molecular orbital–valence bond method. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2017; 73:312-316. [DOI: 10.1107/s2053273317005903] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/19/2017] [Indexed: 11/10/2022]
Abstract
All the current variants of Jayatilaka's X-ray constrained wavefunction (XCW) approach work within the framework of the single-determinant wavefunctionansatz. In this paper, a first-prototype multi-determinant XCW technique is proposed. The strategy assumes that the desired XCW is written as a valence-bond-like expansion in terms of pre-determined single Slater determinants constructed with extremely localized molecular orbitals. The method, which can be particularly suitable to investigate systems with a multi-reference character, has been applied to determine the weights of the resonance structures of naphthalene at different temperatures by exploiting experimental high-resolution X-ray diffraction data. The results obtained have shown that the explicit consideration of experimental structure factors in the determination of the resonance structure weights may lead to results significantly different compared with those resulting only from the simple energy minimization.
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Catlow CRA. Developments in the structural science of materials. IUCRJ 2017; 4:199-201. [PMID: 28512565 PMCID: PMC5414392 DOI: 10.1107/s2052252517006145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent developments in the structural science of materials and the growing power of computational methods in this field are discussed.
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Affiliation(s)
- C. Richard A. Catlow
- Department of Chemistry, University College London, 20 Gordon St., London WC1H OAJ, UK
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
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