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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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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3
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/04/2023] [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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4
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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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5
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Davidson ML, Grabowsky S, Jayatilaka D. X-ray constrained wavefunctions based on Hirshfeld atoms. II. Reproducibility of electron densities in crystals of α-oxalic acid dihydrate. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:397-415. [PMID: 35695114 DOI: 10.1107/s2052520622004103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
The Hirshfeld atom-based X-ray constrained wavefunction fitting (HA-XCW) procedure is tested for its reproducibility, and the information content of the fitted wavefunction is critically assessed. Fourteen different α-oxalic acid dihydrate data sets are used for this purpose, and the first joint fitting to 12 of these data sets is reported. There are systematic features in the electron density obtained from all data sets which agree with higher level benchmark calculations, but there are also many other strong systematic features which disagree with the reference calculations, most notably those associated with the electron density near the nuclei. To enhance reproducibility, three new protocols are described and tested to address the halting problem of XCW fitting, namely: an empirical power-function method, which is useful for estimating the accuracy of the structure factor uncertainties; an asymptotic extrapolation method based on ideas from density functional theory; and a `conservative method' whereby the smallest value of the regularization parameter is chosen from a series of data sets, or subsets.
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Affiliation(s)
- Max L Davidson
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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6
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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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7
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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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8
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Jiang XM, Deng S, Whangbo MH, Guo GC. Material research from the viewpoint of functional motifs. Natl Sci Rev 2022; 9:nwac017. [PMID: 35983369 PMCID: PMC9379984 DOI: 10.1093/nsr/nwac017] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
As early as 2001, the need for the ‘functional motif theory’ was pointed out to assist the rational design of functional materials. The properties of materials are determined by their functional motifs and by how they are arranged in the materials. Uncovering the functional motifs and their arrangements is crucial in understanding the properties of materials and rationally designing new materials of desired properties. The functional motifs of materials are the critical microstructural units (e.g. constituent components and building blocks) that play a decisive role in generating certain material functions, and could not be replaced with other structural units without losing or significantly suppressing the relevant functions. The role of functional motifs and their arrangements in materials with representative examples was presented. These examples could be classified into six types of material microscopic structures on a length scale smaller than ∼10 nm with maximum subatomic resolution, i.e. the crystal, magnetic, aperiodic, defect, local, and electronic structures. The method of functional motif analysis could be employed in the function-oriented design of materials, as elucidated by taking infrared nonlinear optical materials as an example. Machine learning is more efficient in predicting material properties and screening materials with high efficiency than high-throughput experimentation and high-throughput calculations. In extracting the functional motifs and finding their quantitative relationships, developing sufficiently reliable databases for material structures and properties is imperative.
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Affiliation(s)
- Xiao-Ming Jiang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Shuiquan Deng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
| | - Myung-Hwan Whangbo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
- Department of Chemistry, North Carolina State University, Raleigh, NC27695-8204, USA
| | - Guo-Cong Guo
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou350002, China
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9
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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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10
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Holsten S, Malaspina LA, Kleemiss F, Mebs S, Hupf E, Grabowsky S, Beckmann J. Different Reactivities of (5-Ph2P-Ace-6-)2MeSiH toward the Rhodium(I) Chlorides [(C2H4)2RhCl]2 and [(CO)2RhCl]2. Hirshfeld Atom Refinement of a Rh–H···Si Interaction. Organometallics 2021. [DOI: 10.1021/acs.organomet.0c00804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sebastian Holsten
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Lorraine A. Malaspina
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Kleemiss
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Simon Grabowsky
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
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11
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Wanat M, Malinska M, Hoser AA, Woźniak K. Further Validation of Quantum Crystallography Approaches. Molecules 2021; 26:molecules26123730. [PMID: 34207308 PMCID: PMC8233966 DOI: 10.3390/molecules26123730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.
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Affiliation(s)
- Monika Wanat
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences (MISMaP), University of Warsaw, 2C Stefana Banacha, 02-097 Warszawa, Poland
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
| | - Anna A. Hoser
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Żwirki i Wigury, 02-089 Warszawa, Poland; (M.W.); (M.M.); (A.A.H.)
- Correspondence:
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12
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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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13
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Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
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Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
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14
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Podhorský M, Bučinský L, Jayatilaka D, Grabowsky S. HgH 2 meets relativistic quantum crystallography. How to teach relativity to a non-relativistic wavefunction. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:54-66. [PMID: 33399131 DOI: 10.1107/s2053273320014837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022]
Abstract
The capability of X-ray constrained wavefunction (XCW) fitting to introduce relativistic effects into a non-relativistic wavefunction is tested. It is quantified how much of the reference relativistic effects can be absorbed in the non-relativistic XCW calculation when fitted against relativistic structure factors of a model HgH2 molecule. Scaling of the structure-factor sets to improve the agreement statistics is found to introduce a significant systematic error into the XCW fitting of relativistic effects.
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Affiliation(s)
- Michal Podhorský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Lukáš Bučinský
- Institute of Physical Chemistry and Chemical Physics FCHPT, Slovak University of Technology, Radlinskeho 9, Bratislava SK-812 37, Slovakia
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Perth WA 6009, Australia
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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15
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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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16
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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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17
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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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18
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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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19
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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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20
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Malaspina LA, Hoser AA, Edwards AJ, Woińska M, Turner MJ, Price JR, Sugimoto K, Nishibori E, Bürgi HB, Jayatilaka D, Grabowsky S. Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density. CrystEngComm 2020. [DOI: 10.1039/d0ce00378f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.
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