1
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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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2
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Mato M, Cornella J. Bismuth in Radical Chemistry and Catalysis. Angew Chem Int Ed Engl 2024; 63:e202315046. [PMID: 37988225 DOI: 10.1002/anie.202315046] [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: 10/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
Whereas indications of radical reactivity in bismuth compounds can be traced back to the 19th century, the preparation and characterization of both transient and persistent bismuth-radical species has only been established in recent decades. These advancements led to the emergence of the field of bismuth radical chemistry, mirroring the progress seen for other main-group elements. The seminal and fundamental studies in this area have ultimately paved the way for the development of catalytic methodologies involving bismuth-radical intermediates, a promising approach that remains largely untapped in the broad landscape of synthetic organic chemistry. In this review, we delve into the milestones that eventually led to the present state-of-the-art in the field of radical bismuth chemistry. Our focus aims at outlining the intrinsic discoveries in fundamental inorganic/organometallic chemistry and contextualizing their practical applications in organic synthesis and catalysis.
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Affiliation(s)
- Mauro Mato
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Josep Cornella
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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3
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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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4
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Woińska M, Hoser AA, Chodkiewicz ML, Woźniak K. Enhancing hydrogen positions in X-ray structures of transition metal hydride complexes with dynamic quantum crystallography. IUCRJ 2024; 11:45-56. [PMID: 37990870 PMCID: PMC10833390 DOI: 10.1107/s205225252300951x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly. In this study, we employ tools such as SHADE3 and Normal Mode Refinement (NoMoRe) to estimate anisotropic displacement parameters (ADPs) for hydrogen atoms during HAR and IAM refinements performed for seven structures of TM (Fe, Ni, Cr, Nb, Rh and Os) and metalloid (Sb) hydride complexes for which both the neutron and the X-ray structures have been determined. A direct comparison between neutron and HAR/SHADE3/NoMoRe ADPs reveals that the similarity between neutron hydrogen ADPs and those estimated with NoMoRe or SHADE3 is significantly higher than when hydrogen ADPs are refined with HAR. Regarding TM-H bond lengths, traditional HAR exhibits a slight advantage over the other methods. However, combining NoMoRe/SHADE3 with HAR results in a minor decrease in agreement with neutron TM-H bond lengths. For the Cr complex, for which high-resolution X-ray data were collected, an investigation of resolution-related effects was possible.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Anna A. Hoser
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Michał L. Chodkiewicz
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
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5
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Zhang P, Nabi R, Staab JK, Chilton NF, Demir S. Taming Super-Reduced Bi 23- Radicals with Rare Earth Cations. J Am Chem Soc 2023; 145:9152-9163. [PMID: 37043770 PMCID: PMC10141245 DOI: 10.1021/jacs.3c01058] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Here, we report the synthesis of two new sets of dibismuth-bridged rare earth molecules. The first series contains a bridging diamagnetic Bi22- anion, (Cp*2RE)2(μ-η2:η2-Bi2), 1-RE (where Cp* = pentamethylcyclopentadienyl; RE = Gd (1-Gd), Tb (1-Tb), Dy (1-Dy), Y (1-Y)), while the second series comprises the first Bi23- radical-containing complexes for any d- or f-block metal ions, [K(crypt-222)][(Cp*2RE)2(μ-η2:η2-Bi2•)]·2THF (2-RE, RE = Gd (2-Gd), Tb (2-Tb), Dy (2-Dy), Y (2-Y); crypt-222 = 2.2.2-cryptand), which were obtained from one-electron reduction of 1-RE with KC8. The Bi23- radical-bridged terbium and dysprosium congeners, 2-Tb and 2-Dy, are single-molecule magnets with magnetic hysteresis. We investigate the nature of the unprecedented lanthanide-bismuth and bismuth-bismuth bonding and their roles in magnetic communication between paramagnetic metal centers, through single-crystal X-ray diffraction, ultraviolet-visible/near-infrared (UV-vis/NIR) spectroscopy, SQUID magnetometry, DFT and multiconfigurational ab initio calculations. We find a πz* ground SOMO for Bi23-, which has isotropic spin-spin exchange coupling with neighboring metal ions of ca. -20 cm-1; however, the exchange coupling is strongly augmented by orbitally dependent terms in the anisotropic cases of 2-Tb and 2-Dy. As the first examples of p-block radicals beneath the second row bridging any metal ions, these studies have important ramifications for single-molecule magnetism, main group element, rare earth metal, and coordination chemistry at large.
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Affiliation(s)
- Peng Zhang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rizwan Nabi
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jakob K Staab
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Nicholas F Chilton
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Selvan Demir
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
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6
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Woińska M, Pawlędzio S, Chodkiewicz ML, Woźniak K. Hirshfeld Atom Refinement of Metal-Organic Complexes: Treatment of Hydrogen Atoms Bonded to Transition Metals. J Phys Chem A 2023; 127:3020-3035. [PMID: 36947670 PMCID: PMC10084459 DOI: 10.1021/acs.jpca.2c06998] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Hydrogen positions in hydrides play a key role in hydrogen storage materials and high-temperature superconductors. Our recently published study of five crystal structures of transition-metal-bound hydride complexes showed that using aspherical atomic scattering factors for Hirshfeld atom refinement (HAR) resulted in a systematic elongation of metal-hydrogen bonds compared to using spherical scattering factors with the Independent Atom Model (IAM). Even though only standard-resolution X-ray data was used, for the highest-quality data, we obtained excellent agreement between the X-ray and the neutron-derived bond lengths. We present an extended version of this study including 10 crystal structures of metal-organic complexes containing hydrogen atoms bonded to transition-metal atoms for which both X-ray and neutron data are available. The neutron structures were used as a benchmark, and the X-ray structures were refined by applying Hirshfeld atom refinement using various basis sets and DFT functionals in order to investigate the influence of the technical aspects on the length of metal-hydrogen bonds. The result of including relativistic effects in the Hamiltonian and using a cluster of multipoles simulating interactions with a crystal environment during wave function calculations was examined. The effect of the data quality on the final result was also evaluated. The study confirms that a high quality of experimental data is the key factor allowing us to obtain significant improvement in transition metal (TM)-hydrogen bond lengths from HAR in comparison with the IAM. Individual adjustments and better choices of the basis set can improve hydrogen positions. Average differences between TM-H bond lengths obtained with various DFT functionals upon including relativistic effects or between double-ζ and triple-ζ basis sets were not statistically significant. However, if all bonds formed by H atoms were considered, significant differences caused by different refinement strategies were observed. Finally, we examined the refinement of atomic thermal motions. Anisotropic refinement of hydrogen thermal motions with HAR was feasible only in some cases, and isotropically refined hydrogen thermal motions were in similar agreement with neutron values whether obtained with HAR or with the IAM.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Michał L Chodkiewicz
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
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7
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Dunaj T, Egorycheva M, Arebi A, Dollberg K, von Hänisch C. 2,6‐Di
iso
propylphenyl substituted Bismuth Halide and Interpnictogen Compounds. Z Anorg Allg Chem 2023. [DOI: 10.1002/zaac.202300004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Tobias Dunaj
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW) Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Marina Egorycheva
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW) Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Ahmed Arebi
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW) Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Kevin Dollberg
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW) Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Germany
| | - Carsten von Hänisch
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW) Philipps-Universität Marburg Hans-Meerwein-Straße 4 35043 Marburg Germany
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8
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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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9
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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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10
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Pawlędzio S, Malinska M, Kleemiss F, Grabowsky S, Woźniak K. Influence of modelling disorder on Hirshfeld atom refinement results of an organo-gold(I) compound. IUCRJ 2022; 9:497-507. [PMID: 35844484 PMCID: PMC9252150 DOI: 10.1107/s2052252522005309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Details of the validation of disorder modelling with Hirshfeld atom refinement (HAR) for a previously investigated organo-gold(I) compound are presented here. The impact of refining disorder on HAR results is discussed using an analysis of the differences of dynamic structure factors. These dynamic structure factor differences are calculated from thermally smeared quantum mechanical electron densities based on wavefunctions that include or exclude electron correlation and relativistic effects. When disorder is modelled, the electron densities stem from a weighted superposition of two (or more) different conformers. Here this is shown to impact the relative importance of electron correlation and relativistic effect estimates expressed by the structure factor magnitudes. The role of disorder modelling is also compared with the effect of the treatment of hydrogen anisotropic displacement parameter (ADP) values and atomic anharmonicity of the gold atom. The analysis of ADP values of gold and disordered carbon atoms showed that the effect of disorder significantly altered carbon ADP values and did not influence those of the gold atom.
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Affiliation(s)
- Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Florian Kleemiss
- 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, Warsaw 02-089, Poland
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11
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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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12
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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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13
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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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14
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Pawlędzio S, Malinska M, Woińska M, Wojciechowski J, Andrade Malaspina L, Kleemiss F, Grabowsky S, Woźniak K. Relativistic Hirshfeld atom refinement of an organo-gold(I) compound. IUCRJ 2021; 8:608-620. [PMID: 34258009 PMCID: PMC8256711 DOI: 10.1107/s2052252521004541] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/28/2021] [Indexed: 06/13/2023]
Abstract
The main goal of this study is the validation of relativistic Hirshfeld atom refinement (HAR) as implemented in Tonto for high-resolution X-ray diffraction datasets of an organo-gold(I) compound. The influence of the relativistic effects on statistical parameters, geometries and electron density properties was analyzed and compared with the influence of electron correlation and anharmonic atomic motions. Recent work in this field has indicated the importance of relativistic effects in the static electron density distribution of organo-mercury compounds. This study confirms that differences in electron density due to relativistic effects are also of significant magnitude for organo-gold compounds. Relativistic effects dominate not only the core region of the gold atom, but also influence the electron density in the valence and bonding region, which has measurable consequences for the HAR refinement model parameters. To study the effects of anharmonic motion on the electron density distribution, dynamic electron density difference maps were constructed. Unlike relativistic and electron correlation effects, the effects of anharmonic nuclear motion are mostly observed in the core area of the gold atom.
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Affiliation(s)
- Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | | | - Lorraine Andrade Malaspina
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Florian Kleemiss
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
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15
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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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16
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Ramler J, Lichtenberg C. Bismuth species in the coordination sphere of transition metals: synthesis, bonding, coordination chemistry, and reactivity of molecular complexes. Dalton Trans 2021; 50:7120-7138. [PMID: 34008669 DOI: 10.1039/d1dt01300a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This contribution is focused on bismuth species in the coordination sphere of transition metals. In molecular transition metal complexes, three types of Bi-M bonding are considered, namely dative Bi→M interactions (with Bi acting as a donor), dative Bi←M interactions (with Bi acting as an acceptor) and covalent Bi-M interactions (M = transition metal). Synthetic routes to all three classes of compounds are outlined, the Bi-M bonding situation is discussed, trends in the geometric parameters and in the coordination chemistry of the compounds are addressed, and common spectroscopic properties are summarized. As an important part of this contribution, the reactivity of bismuth species in the coordination sphere of transition metal complexes in stoichiometric and catalytic reactions is highlighted.
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Affiliation(s)
- Jacqueline Ramler
- Department of Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Crispin Lichtenberg
- Department of Inorganic Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
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17
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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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18
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Woińska M, Chodkiewicz ML, Woźniak K. Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms. Chem Commun (Camb) 2021; 57:3652-3655. [PMID: 33870351 DOI: 10.1039/d0cc07661a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparison of five X-ray structures of transition-metal-bound hydride complexes, successfully refined using Hirshfeld Atom Refinement (HAR) against low resolution X-ray diffraction data (including the positions and ADPs of all hydrogen atoms), with neutron structures shows that using aspherical atomic scattering factors instead of spherical ones results in systematic elongation of metal-hydrogen bonds, which in the case of the highest-quality data leads to excellent agreement of the X-ray and the neutron-derived bond lengths.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland.
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19
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Lipshultz JM, Li G, Radosevich AT. Main Group Redox Catalysis of Organopnictogens: Vertical Periodic Trends and Emerging Opportunities in Group 15. J Am Chem Soc 2021; 143:1699-1721. [PMID: 33464903 PMCID: PMC7934640 DOI: 10.1021/jacs.0c12816] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A growing number of organopnictogen redox catalytic methods have emerged-especially within the past 10 years-that leverage the plentiful reversible two-electron redox chemistry within Group 15. The goal of this Perspective is to provide readers the context to understand the dramatic developments in organopnictogen catalysis over the past decade with an eye toward future development. An exposition of the fundamental differences in the atomic structure and bonding of the pnictogens, and thus the molecular electronic structure of organopnictogen compounds, is presented to establish the backdrop against which organopnictogen redox reactivity-and ultimately catalysis-is framed. A deep appreciation of these underlying periodic principles informs an understanding of the differing modes of organopnictogen redox catalysis and evokes the key challenges to the field moving forward. We close by addressing forward-looking directions likely to animate this area in the years to come. What new catalytic manifolds can be developed through creative catalyst and reaction design that take advantage of the intrinsic redox reactivity of the pnictogens to drive new discoveries in catalysis?
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Affiliation(s)
- Jeffrey M Lipshultz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gen Li
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander T Radosevich
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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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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21
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Ikabata Y, Nakai H. Picture-change correction in relativistic density functional theory. Phys Chem Chem Phys 2021; 23:15458-15474. [PMID: 34278401 DOI: 10.1039/d1cp01773j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relativistic quantum chemical calculations are performed based on one of two physical pictures, namely the Dirac picture and the Schrödinger picture. With regard to the latter, the so-called picture-change effect (PCE) and picture-change correction (PCC) have been studied. The PCE, which is the change in the expectation value associated with the transformation, is not commonly a minor effect. The electron density, which is given by the expectation value of the density operator, is a fundamental variable in relativistic density functional theory (RDFT). Thus, performing the PCC in RDFT calculations is essential not only in terms of numerical agreement with the Dirac picture, but also from the viewpoint of fundamental theory. This paper explains theories and numerical studies of PCE and PCC in RDFT after overviewing those in properties, which involves the authors' works on the development of RDFT in the Schrödinger picture and relativistic exchange-correlation functionals based on picture-change-corrected variables.
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Affiliation(s)
- Yasuhiro Ikabata
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan. and Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan and Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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22
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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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23
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Abd El-Mageed H. Zinc oxide nanoclusters and nanoparticles as a drug carrier for cisplatin and nedaplatin anti-cancer drugs, insights from DFT methods and MC simulation. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1842533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- H.R. Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
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24
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Chodkiewicz ML, Woińska M, Woźniak K. Hirshfeld atom like refinement with alternative electron density partitions. IUCRJ 2020; 7:1199-1215. [PMID: 33209330 PMCID: PMC7642787 DOI: 10.1107/s2052252520013603] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/12/2020] [Indexed: 05/03/2023]
Abstract
Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree-Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.
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Affiliation(s)
- Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa, 02-089 Warszawa, Poland
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25
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Van der Maelen JF, Ceroni M, Ruiz J. The X-ray constrained wavefunction of the [Mn(CO) 4{(C 6H 5) 2P-S-C(Br 2)-P(C 6H 5) 2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:802-814. [PMID: 33017314 DOI: 10.1107/s2052520620009889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.
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Affiliation(s)
- Juan F Van der Maelen
- Dept. Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
| | - Mario Ceroni
- Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Javier Ruiz
- Dept. Química Orgánica e Inorgánica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
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26
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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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27
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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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28
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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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29
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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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30
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Ramler J, Hofmann K, Lichtenberg C. Neutral and Cationic Bismuth Compounds: Structure, Heteroaromaticity, and Lewis Acidity of Bismepines. Inorg Chem 2019; 59:3367-3376. [DOI: 10.1021/acs.inorgchem.9b03189] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jacqueline Ramler
- Institute of Inorganic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Klaus Hofmann
- Institute of Inorganic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Crispin Lichtenberg
- Institute of Inorganic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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31
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Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A. Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy. J Phys Chem Lett 2019; 10:6973-6982. [PMID: 31633355 DOI: 10.1021/acs.jpclett.9b02646] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.
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Affiliation(s)
- Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Justin Bergmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Benjamin Meyer
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Manuel F Ruiz-López
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alessandro Genoni
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
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32
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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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33
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Woinska M, Wanat M, Taciak P, Pawinski T, Minor W, Wozniak K. Energetics of interactions in the solid state of 2-hydroxy-8- X-quinoline derivatives ( X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements. IUCRJ 2019; 6:868-883. [PMID: 31576220 PMCID: PMC6760436 DOI: 10.1107/s2052252519007358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2019] [Indexed: 05/20/2023]
Abstract
In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) - together with X-ray wavefunction refinement (XWR) - are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures - the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions.
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Affiliation(s)
- Magdalena Woinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Monika Wanat
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences (MISMaP), University of Warsaw, Stefana Banacha 2C, Warszawa 02-097, Poland
| | - Przemyslaw Taciak
- Department of Drug Chemistry, Faculty of Pharmacy, Medicinal University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
- Department of Pharmacodynamics, Centre of Preclinical Research and Technology, Faculty of Pharmacy, Medical University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
| | - Tomasz Pawinski
- Department of Drug Chemistry, Faculty of Pharmacy, Medicinal University of Warsaw, Stefana Banacha 1, Warszawa 02-091, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Chemistry, University of Warsaw, Pasteura 1, Warszawa 02-093, Poland
| | - Krzysztof Wozniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warszawa 02-089, Poland
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34
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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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35
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Ikabata Y, Oyama T, Hayami M, Seino J, Nakai H. Extension and acceleration of relativistic density functional theory based on transformed density operator. J Chem Phys 2019; 150:164104. [DOI: 10.1063/1.5090523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yasuhiro Ikabata
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takuro Oyama
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masao Hayami
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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36
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Anderson JSM, Rodríguez JI, Ayers PW, Trujillo-González DE, Götz AW, Autschbach J, Castillo-Alvarado FL, Yamashita K. Molecular QTAIM Topology Is Sensitive to Relativistic Corrections. Chemistry 2019; 25:2538-2544. [PMID: 30393899 DOI: 10.1002/chem.201804464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 11/11/2022]
Abstract
The topology of the molecular electron density of benzene dithiol gold cluster complex Au4 -S-C6 H4 -S'-Au'4 changed when relativistic corrections were made and the structure was close to a minimum of the Born-Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.
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Affiliation(s)
- James S M Anderson
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada.,iTHES Research Group, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Instituto de Química, Universidad Nacional Autónoma de México, Universidad 300, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Juan I Rodríguez
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Paul W Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada
| | - Daniel E Trujillo-González
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093-0505, California, USA
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, 14260-3000, NY, USA
| | - Fray L Castillo-Alvarado
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Koichi Yamashita
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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37
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Wrobel L, Rüffer T, Korb M, Krautscheid H, Meyer J, Andrews PC, Lang H, Mehring M. Homo- and Heteroleptic Coordination Polymers and Oxido Clusters of Bismuth(III) Vinylsulfonates. Chemistry 2018; 24:16630-16644. [DOI: 10.1002/chem.201803664] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Lydia Wrobel
- Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie; Technische Universität Chemnitz; 09107 Chemnitz Germany
| | - Tobias Rüffer
- Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie; Technische Universität Chemnitz; 09107 Chemnitz Germany
| | - Marcus Korb
- Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie; Technische Universität Chemnitz; 09107 Chemnitz Germany
| | - Harald Krautscheid
- Fakultät für Chemie und Mineralogie, Institut für Anorganische Chemie; Universität Leipzig; 04103 Leipzig Germany
| | - Jens Meyer
- STOE & Cie GmbH; 64295 Darmstadt Germany
| | - Philip C. Andrews
- School of Chemistry; Monash University; Melbourne Victoria 3800 Australia
| | - Heinrich Lang
- Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie; Technische Universität Chemnitz; 09107 Chemnitz Germany
| | - Michael Mehring
- Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie; Technische Universität Chemnitz; 09107 Chemnitz Germany
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38
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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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39
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Preda AM, Krasowska M, Wrobel L, Kitschke P, Andrews PC, MacLellan JG, Mertens L, Korb M, Rüffer T, Lang H, Auer AA, Mehring M. Evaluation of dispersion type metal···π arene interaction in arylbismuth compounds - an experimental and theoretical study. Beilstein J Org Chem 2018; 14:2125-2145. [PMID: 30202466 PMCID: PMC6122404 DOI: 10.3762/bjoc.14.187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/12/2018] [Indexed: 11/25/2022] Open
Abstract
The dispersion type Bi···π arene interaction is one of the important structural features in the assembly process of arylbismuth compounds. Several triarylbismuth compounds and polymorphs are discussed and compared based on the analysis of single crystal X-ray diffraction data and computational studies. First, the crystal structures of polymorphs of Ph3Bi (1) are described emphasizing on the description of London dispersion type bismuth···π arene interactions and other van der Waals interactions in the solid state and the effect of it on polymorphism. For comparison we have chosen the substituted arylbismuth compounds (C6H4-CH═CH2-4)3Bi (2), (C6H4-OMe-4)3Bi (3), (C6H3-t-Bu2-3,5)3Bi (4) and (C6H3-t-Bu2-3,5)2BiCl (5). The structural analyses revealed that only two of them show London dispersion type bismuth···π arene interactions. One of them is the styryl derivative 2, for which two polymorphs were isolated. Polymorph 2a crystallizes in the orthorhombic space group P212121, while polymorph 2b exhibits the monoclinic space group P21/c. The general structure of 2a is similar to the monoclinic C2/c modification of Ph3Bi (1a), which leads to the formation of zig-zag Bi-arenecentroid ribbons formed as a result of bismuth···π arene interactions and π···π intermolecular contacts. In the crystal structures of the polymorph 2b as well as for 4 bismuth···π arene interactions are not observed, but both compounds revealed C-HPh···π intermolecular contacts, as likewise observed in all of the three described polymorphs of Ph3Bi. For compound 3 intermolecular contacts as a result of coordination of the methoxy group to neighboring bismuth atoms are observed overruling Bi···π arene contacts. Compound 5 shows a combination of donor acceptor Bi···Cl and Bi···π arene interactions, resulting in an intermolecular pincer-type coordination at the bismuth atom. A detailed analysis of three polymorphs of Ph3Bi (1), which were chosen as model systems, at the DFT-D level of theory supported by DLPNO-CCSD(T) calculations reveals how van der Waals interactions between different structural features balance in order to stabilize molecular arrangements present in the crystal structure. Furthermore, the computational results allow to group this class of compounds into the range of heavy main group element compounds which have been characterized as dispersion energy donors in previous work.
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Affiliation(s)
- Ana-Maria Preda
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, Germany
| | - Małgorzata Krasowska
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Lydia Wrobel
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, Germany
| | - Philipp Kitschke
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, Germany
| | - Phil C Andrews
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | | | - Lutz Mertens
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, Germany
| | - Marcus Korb
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie, 09107 Chemnitz, Germany
| | - Tobias Rüffer
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie, 09107 Chemnitz, Germany
| | - Heinrich Lang
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Anorganische Chemie, 09107 Chemnitz, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Michael Mehring
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, Germany
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40
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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: 85] [Impact Index Per Article: 14.2] [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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41
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Preda AM, Schneider WB, Rainer M, Rüffer T, Schaarschmidt D, Lang H, Mehring M. Heteroaryl bismuthines: a novel synthetic concept and metalπ heteroarene interactions. Dalton Trans 2018; 46:8269-8278. [PMID: 28617492 DOI: 10.1039/c7dt01437f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The alkoxide Bi[OCMe2(2-C4H3S)]3 (1) is formed by the reaction of three equiv. of the alcohol HOCMe2(2-C4H3S) with Bi(OtBu)3 and subsequent hydrolysis provides the bismuth oxido cluster [Bi4O2{OCMe2(2-C4H3S)}8] (2). In contrast, the reaction of Bi(OtBu)3 and Bi[N(SiMe3)2]3 with the silanols HOSiMe2(2-C4H3X) (X = O, S, Se, and NMe), HOSiMe2(2-C4H2S-5-SiMe3) and HOSiMe2(3-C4H3S) leads to the formation of tris(heteroaryl)bismuthines Bi(2-C4H2X-5-R)3 [where X = O, R = H (3); X = S, R = H (4); X = S, R = SiMe3 (5); X = NMe, R = H (6); X = Se, R = H (7)] and Bi(3-C4H3S)3 (8). For the silanols, bismuth-carbon bond formation is observed rather than silanol-alcoholate or silanol-amide exchange. The structures of compounds 1, 2, and 4-7a in the solid state were established by single crystal X-ray diffraction and all compounds except 5 show London dispersion type bismuthπ heteroarene interactions. For the bismuthine Bi(2-C4H3Se)3 (7), two polymorphs were isolated depending on the conditions of crystallization. At 8 °C, polymorph I (7a) crystallizes from an n-hexane solution in the triclinic space group P1[combining macron], whereas polymorph II (7b) crystallizes at 20 °C from a CH2Cl2/n-pentane solution in the monoclinic space group P21/c. The heteroaryl bismuthines 3 and 4 exhibit 2D network structures as a result of bismuthπ heteroarene interactions, whereas for the pyrrole derivative 6 the dispersion type interactions provide separated dimers.
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Affiliation(s)
- A M Preda
- Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Professur Koordinationschemie, 09107 Chemnitz, 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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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: 97] [Impact Index Per Article: 13.9] [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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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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Genoni A, Dos Santos LHR, Meyer B, Macchi P. Can X-ray constrained Hartree-Fock wavefunctions retrieve electron correlation? IUCRJ 2017; 4:136-146. [PMID: 28250952 PMCID: PMC5330524 DOI: 10.1107/s2052252516019217] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 05/29/2023]
Abstract
The X-ray constrained wavefunction (XC-WF) method proposed by Jayatilaka [Jayatilaka & Grimwood (2001) ▸, Acta Cryst. A57, 76-86] has attracted much attention because it represents a possible third way of theoretically studying the electronic structure of atoms and molecules, combining features of the more popular wavefunction- and DFT-based approaches. In its original formulation, the XC-WF technique extracts statistically plausible wavefunctions from experimental X-ray diffraction data of molecular crystals. A weight is used to constrain the pure Hartree-Fock solution to the observed X-ray structure factors. Despite the wavefunction being a single Slater determinant, it is generally assumed that its flexibility could guarantee the capture, better than any other experimental model, of electron correlation effects, absent in the Hartree-Fock Hamiltonian but present in the structure factors measured experimentally. However, although the approach has been known for long time, careful testing of this fundamental hypothesis is still missing. Since a formal demonstration is impossible, the validation can only be done heuristically and, to accomplish this task, X-ray constrained Hartree-Fock calculations have been performed using structure factor amplitudes computed at a very high correlation level (coupled cluster) for selected molecules in isolation, in order to avoid the perturbations due to intermolecular interactions. The results show that a single-determinant XC-WF is able to capture the electron correlation effects only partially. The largest amount of electron correlation is extracted when: (i) a large external weight is used (much larger than what has normally been used in XC-WF calculations using experimental data); and (ii) the high-order reflections, which carry less information on the electron correlation, are down-weighted (or even excluded), otherwise they would bias the fitting towards the unconstrained Hartree-Fock wavefunction.
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Affiliation(s)
- Alessandro Genoni
- CNRS, Laboratoire SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-lès-Nancy, F-54506, France
- Université de Lorraine, Laboratoire SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-lès-Nancy, F-54506, France
| | - Leonardo H. R. Dos Santos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Benjamin Meyer
- CNRS, Laboratoire SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-lès-Nancy, F-54506, France
- Université de Lorraine, Laboratoire SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-lès-Nancy, F-54506, France
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
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Preda AM, Schneider WB, Schaarschmidt D, Lang H, Mertens L, Auer AA, Mehring M. The role of dispersion type metal⋯π interaction in the enantiotropic phase transition of two polymorphs of tris-(thienyl)bismuthine. Dalton Trans 2017; 46:13492-13501. [PMID: 28951920 DOI: 10.1039/c7dt02567j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bi(2-C4H3S)3 shows an enantiotropic phase transition that is dominated by London dispersion forces. DFT calculations on model compounds were carried out in order to investigate the competition between Bi⋯S and Bi⋯π heteroarene interaction.
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Affiliation(s)
- A. M. Preda
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - W. B. Schneider
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - D. Schaarschmidt
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Anorganische Chemie
- 09107 Chemnitz
| | - H. Lang
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Anorganische Chemie
- 09107 Chemnitz
| | - L. Mertens
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
| | - A. A. Auer
- Max-Planck-Institut für Chemische Energiekonversion
- 45470 Mülheim an der Ruhr
- Germany
| | - M. Mehring
- Technische Universität Chemnitz
- Fakultät für Naturwissenschaften
- Institut für Chemie
- Professur Koordinationschemie
- 09107 Chemnitz
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Characterization of B-H agostic compounds involved in the dehydrogenation of amine-boranes by group 4 metallocenes. J Mol Model 2016; 22:294. [PMID: 27888405 DOI: 10.1007/s00894-016-3165-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/08/2016] [Indexed: 10/20/2022]
Abstract
For over a decade, amine-borane has been considered as a potential chemical hydrogen vector in the context of a search for cleaner energy sources. When catalyzed by organometallic complexes, the reaction mechanisms currently considered involve the formation of β-BH agostic intermediates. A thorough understanding of these intermediates may constitute a crucial step toward the identification of ideal catalysts. Topological approaches such as QTAIM and ELF revealed to be particularly suitable for the description of β-agostic interactions. When studying model catalysts, accurate theoretical calculations may be carried out. However, for a comparison with experimental data, calculations should also be carried out on large organo-metallic species, often including transition metals belonging to the second or the third row. In such a case, DFT methods are particularly attractive. Unfortunately, triple-ζ all electrons basis sets are not easily available for heavy transition metal elements. Thus, a subtle balance should be reached between the affordable level of calculations and the required accuracy of the electronic description of the systems. Herein we propose the use of B3LYP functional in combination with the LanL2DZ pseudopotential for the metal atom and 6-311++G(2d,2p) basis set for the other atoms, followed by a single point using the DKH2 relativistic Hamiltonian in combination with the B3LYP/DZP-DKH level, as a "minimum level of theory" leading to a consistent topological description of the interaction within the ELF and QTAIM framework, in the context of isolated (gas-phase) group 4 metallocene catalysts.
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