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Chodkiewicz ML, Olech B, Jha KK, Dominiak PM, Woźniak K. Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data. IUCRJ 2024; 11:730-736. [PMID: 39078666 PMCID: PMC11364029 DOI: 10.1107/s2052252524006808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/11/2024] [Indexed: 07/31/2024]
Abstract
Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural parameters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (Ih). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O-H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O-H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Å for HAR. The refinement results changed considerably when dynamical scattering effects were modelled - with extinction correction or with dynamical refinement. The latter led to an improvement of the O-H bond length accuracy to 0.021 Å on average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.
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Affiliation(s)
- Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of ChemistryUniversity of WarsawŻwirki i Wigury 101WarszawaWarszawa02-089Poland
| | - Barbara Olech
- Biological and Chemical Research Centre, Department of ChemistryUniversity of WarsawŻwirki i Wigury 101WarszawaWarszawa02-089Poland
- Centre of New TechnologiesUniversity of WarsawS. Banacha 2cWarsaw02-097Poland
| | - Kunal Kumar Jha
- Centre of New TechnologiesUniversity of WarsawS. Banacha 2cWarsaw02-097Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of ChemistryUniversity of WarsawŻwirki i Wigury 101WarszawaWarszawa02-089Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of ChemistryUniversity of WarsawŻwirki i Wigury 101WarszawaWarszawa02-089Poland
- Centre of New TechnologiesUniversity of WarsawS. Banacha 2cWarsaw02-097Poland
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2
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Pinto CB, Dos Santos LHR, Rodrigues BL. Experimental charge density and topological analysis of tetraaquabis(hydrogenmaleato)nickel(II): a comparison with Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:281-295. [PMID: 37402161 DOI: 10.1107/s2052520623004377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/20/2023] [Indexed: 07/06/2023]
Abstract
Experimental charge density analysis is conducted on the coordination compound tetraaquabis(hydrogenmaleato)nickel(II), which exhibits a short intramolecular hydrogen bond. Through topological analysis, the nature of Ni-O bonds is concluded to be intermediate between ionic and covalent, but mainly presenting an ionic character, while the short hydrogen bond is classified as covalent in nature. The compound was also analysed after Hirshfeld atom refinement performed using NoSpherA2. A topological analysis was conducted on the molecular wavefunction and the results are compared with those obtained from experiment. In general, there is good agreement between the refinements, and the chemical bonds involving H atoms are in better agreement with what is expected from neutron data after HAR than they are after multipole refinement.
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Affiliation(s)
- Camila B Pinto
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Leonardo H R Dos Santos
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Bernardo L Rodrigues
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Muddassir M, Alarifi A, Abduh NAY, Saeed WS, Karami AM, Afzal M. Multifunctional Zn(II) Coordination Polymer as Highly Selective Fluorescent Sensor and Adsorbent for Dyes. Int J Mol Sci 2023; 24:ijms24108512. [PMID: 37239860 DOI: 10.3390/ijms24108512] [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: 01/25/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
A new Zn(II)-based coordination polymer (1) comprising the Schiff base ligand obtained by the condensation of 5-aminosalicylic acid and salicylaldehyde has been synthesized. This newly synthesized compound has been characterized by analytical and spectroscopic methods, and finally, by single-crystal X-ray diffraction technique in this study. The X-ray analysis reveals a distorted tetrahedral environment around the central Zn(II) center. This compound has been used as a sensitive and selective fluorescent sensor for acetone and Ag+ cations. The photoluminescence measurements indicate that in the presence of acetone, the emission intensity of 1 displays quenching at room temperature. However, other organic solvents caused meagre changes in the emission intensity of 1. Additionally, the fluorescence intensity of 1 has been examined in the presence of different ketones viz. cyclohexanone, 4-heptanone, and 5-nonanone, to assess the interaction between the C=O group of the ketones and the molecular framework of 1. Moreover, 1 displays a selective recognition of Ag+ in the aqueous medium by an enhancement in its fluorescence intensity, representing its high sensitivity for the detection of Ag+ ions in a water sample. Additionally, 1 displays the selective adsorption of cationic dyes (methylene blue and rhodamine B). Hence, 1 showcases its potential as an excellent luminescent probe to detect acetone, other ketones, and Ag+ with an exceptional selectivity, and displaying a selective adsorption of cationic dye molecules.
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Affiliation(s)
- Mohd Muddassir
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naaser A Y Abduh
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Waseem Sharaf Saeed
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Four-Coordinate Monoboron Complexes with 8-Hydroxyquinolin-5-Sulfonate: Synthesis, Crystal Structures, Theoretical Studies, and Luminescence Properties. CRYSTALS 2022. [DOI: 10.3390/cryst12060783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
8-Hydroxyquinolin-5-sulfonic acid (8HQSA) was combined with 3-pyridineboronic acid (3PBA) or 4-pyridineboronic acid (4PBA) to give two zwitterionic monoboron complexes in crystalline form. The compounds were characterized by elemental analysis, single-crystal X-ray diffraction studies, and IR, 1H NMR, UV-Visible, and luminescence spectroscopy. The analyses revealed compounds with boron atoms adopting tetrahedral geometry. In the solid state, the molecular components are linked by charge-assisted (B)(O-H···−O(S) and N+-H···O(S) hydrogen bonds aside from C-H···O contacts and π···π interactions, as shown by Hirshfeld surface analyses and 2D fingerprint plots. The luminescence properties were characterized in terms of the emission behavior in solution and the solid state, showing emission in the bluish-green region in solution and large positive solvatofluorochromism, caused by intramolecular charge transfer. According to TD-DFT calculations at the M06-2X/6-31G(d) level of theory simulating an ethanol solvent environment, the emission properties are originated from π-π * and n-π * HOMO-LUMO transitions.
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Ruth PN, Herbst-Irmer R, Stalke D. Hirshfeld atom refinement based on projector augmented wave densities with periodic boundary conditions. IUCRJ 2022; 9:286-297. [PMID: 35371508 PMCID: PMC8895013 DOI: 10.1107/s2052252522001385] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Hirshfeld atom refinement (HAR) is an X-ray diffraction refinement method that, in numerous publications, has been shown to give H-atom bond lengths in close agreement with neutron diffraction derived values. Presented here is a first evaluation of an approach using densities derived from projector augmented wave (PAW) densities with three-dimensional periodic boundary conditions for HAR. The results show an improvement over refinements that neglect the crystal environment or treat it classically, while being on a par with non-periodic approximations for treating the solid-state environment quantum mechanically. A suite of functionals were evaluated for this purpose, showing that the SCAN and revSCAN functionals are most suited to these types of calculation.
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Affiliation(s)
- Paul Niklas Ruth
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, Göttingen, Lower Saxony 37077, Germany
| | - Regine Herbst-Irmer
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, Göttingen, Lower Saxony 37077, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstraße 4, Göttingen, Lower Saxony 37077, Germany
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Feliciano IO, Silva DP, Piedade MFM, Bernardes CES, Minas da Piedade ME. First and Second Dissociation Enthalpies in Bi-Component Crystals Consisting of Maleic Acid and L-Phenylalanine. Molecules 2021; 26:molecules26185714. [PMID: 34577186 PMCID: PMC8469174 DOI: 10.3390/molecules26185714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
The energetics of the stepwise dissociation of a A:B2 bi-component crystal, according to A:B2(cr) → A:B(cr) + B(cr) and A:B(cr) → A(cr) + B(cr), was investigated using MA:Phe2 and MA:Phe (MA = maleic acid; Phe = L-phenylalanine) as model systems. The enthalpy changes associated with these sequential processes and with the overall dissociation reaction A:B2(cr) → A(cr) + 2B(cr) were determined by solution calorimetry. It was found that they are all positive, indicating that there is a lattice enthalpy gain when MA:Phe2 is formed, either from the individual precursors or by adding Phe to MA:Phe. Single-crystal X-ray diffraction (SCXRD) analysis showed that MA:Phe2 is best described as a protic salt containing a maleate anion (MA−) and two non-equivalent L-phenylalanine units, both linked to MA− by NH···O hydrogen bonds (H-bond): one of these units is protonated (HPhe+) and the other zwitterionic (Phe±). Only MA− and HPhe+ molecules are present in the MA:Phe lattice. In this case, however, NH···O and OH···O H-bonds are formed between each MA− unit and two HPhe+ molecules. Despite these structural differences, the enthalpy cost for the removal of the zwitterionic Phe± unit from the MA:Phe2 lattice to yield MA:Phe is only 0.9 ± 0.4 kJ mol−1 higher than that for the dissociation of MA:Phe, which requires a proton transfer from HPhe+ to MA− and the rearrangement of L-phenylalanine to the zwitterionic, Phe±, form. Finally, a comparison of the dissociation energetics and structures of MA:Phe and of the previously reported glycine maleate (MA:Gly) analogue indicated that parameters, such as the packing coefficient, density, hydrogen bonds formed, or fusion temperature, are not necessarily good descriptors of dissociation enthalpy or lattice enthalpy trends when bi-component crystals with different molecular composition are being compared, even if the stoichiometry is the same.
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Affiliation(s)
- Inês O. Feliciano
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Daniela P. Silva
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - M. Fátima M. Piedade
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Carlos E. S. Bernardes
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Manuel E. Minas da Piedade
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
- Correspondence: ; Tel.: +351-217500005
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Fischer A, Eickerling G, Scherer W. The Effects of Chemical Bonding at Subatomic Resolution: A Case Study on α-Boron. Molecules 2021; 26:molecules26144270. [PMID: 34299544 PMCID: PMC8303496 DOI: 10.3390/molecules26144270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/22/2022] Open
Abstract
Similar to classical asphericity shifts, aspherical deformations of the electron density in the atomic core region can result in core asphericity shifts in refinements using a Hansen-Coppens multipolar model (HCM), especially when highly precise experimental datasets with resolutions far beyond sin(θ)/λ ≤ 1.0 Å−1 are employed. These shifts are about two orders of magnitude smaller than their counterparts caused by valence shell deformations, and their underlying deformations are mainly of dipolar character for 1st row atoms. Here, we analyze the resolution dependence of core asphericity shifts in α-boron. Based on theoretical structure factors, an appropriate Extended HCM (EHCM) is developed, which is tested against experimental high-resolution (sin(θ)/λ ≤ 1.6 Å−1) single-crystal diffraction data. Bond length deviations due to core asphericity shifts of α-boron in the order of 4–6·10−4 Å are small but significant at this resolution and can be effectively compensated by an EHCM, although the correlation of the additional model parameters with positional parameters prevented a free refinement of all core model parameters. For high quality, high resolution data, a proper treatment with an EHCM or other equivalent methods is therefore highly recommended.
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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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9
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Taherzadeh M, Pourayoubi M, Vahdani Alviri B, Shoghpour Bayraq S, Ariani M, Nečas M, Dušek M, Eigner V, Amiri Rudbari H, Bruno G, Mancilla Percino T, Leyva-Ramírez MA, Damodaran K. Hydrogen-bond directionality and symmetry in [C(O)NH](N) 2P(O)-based structures: a comparison between X-ray crystallography data and neutron-normalized values, and evaluation of reliability. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2021; 77:384-396. [PMID: 34096521 DOI: 10.1107/s2052520621003371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
For [C(O)NH](N)2P(O)-based structures, the magnitude of the differences in the N-H...O, H...O=P and H...O=C angles has been evaluated when the N-H bond lengths, determined by X-ray diffraction, were compared to the neutron normalized values and the maximum percentage difference was obtained, i.e. about 3% for the angle even if the N-H bond lengths have a difference of about 30% (0.7 Å for the X-ray and 1.03 Å for the neutron-normalized value). The symmetries of the crystals are discussed with respect to the symmetry of the molecules, as well as to the symmetry of hydrogen-bonded motifs, and the role of the most directional hydrogen bond in raising the probability of obtaining centrosymmetric crystal structures is investigated. The work was performed by considering nine new X-ray crystal structures and 204 analogous structures retrieved from the Cambridge Structural Database.
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Affiliation(s)
- Maryam Taherzadeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mehrdad Pourayoubi
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Samad Shoghpour Bayraq
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maral Ariani
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Marek Nečas
- Department of Chemistry, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Michal Dušek
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 8, 182 21, Czech Republic
| | - Václav Eigner
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 8, 182 21, Czech Republic
| | - Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Giuseppe Bruno
- Department of Chemical Sciences, University of Messina, Via F. Stagnod'Alcontres 31, Messina 98166, Italy
| | - Teresa Mancilla Percino
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, 07000, Ciudad de México, México
| | - Marco A Leyva-Ramírez
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, 07000, Ciudad de México, México
| | - Krishnan Damodaran
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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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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11
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Macetti G, Wieduwilt EK, Genoni A. QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals. J Phys Chem A 2021; 125:2709-2726. [DOI: 10.1021/acs.jpca.0c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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12
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Wieduwilt EK, Macetti G, Genoni A. Climbing Jacob's Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions. J Phys Chem Lett 2021; 12:463-471. [PMID: 33369421 DOI: 10.1021/acs.jpclett.0c03421] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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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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14
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A new 1D Cu(II)-W(Cn)8 based coordination polymer: Crystallographic structural architecture, Hirshfeld surface, DFT and luminescent analyses. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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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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16
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Sanjuan-Szklarz WF, Woińska M, Domagała S, Dominiak PM, Grabowsky S, Jayatilaka D, Gutmann M, Woźniak K. On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model. IUCRJ 2020; 7:920-933. [PMID: 32939284 PMCID: PMC7467170 DOI: 10.1107/s2052252520010441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 05/20/2023]
Abstract
X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.
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Affiliation(s)
- W. Fabiola Sanjuan-Szklarz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Sławomir Domagała
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
| | - Simon Grabowsky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Matthias Gutmann
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa, Poland
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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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Vénosová B, Koziskova J, Kožíšek J, Herich P, Lušpai K, Petricek V, Hartung J, Müller M, Hübschle CB, van Smaalen S, Bucinsky L. Charge density of 4-methyl-3-[(tetrahydro-2H-pyran-2-yl)oxy]thiazole-2(3H)-thione. A comprehensive multipole refinement, maximum entropy method and density functional theory study. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:450-468. [PMID: 32831263 DOI: 10.1107/s2052520620005533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
The structure of 4-methyl-3-[(tetrahydro-2H-pyran-2-yl)oxy]thiazole-2(3H)-thione (MTTOTHP) was investigated using X-ray diffraction and computational chemistry methods for determining properties of the nitrogen-oxygen bond, which is the least stable entity upon photochemical excitation. Experimentally measured structure factors have been used to determine and characterize charge density via the multipole model (MM) and the maximum entropy method (MEM). Theoretical investigation of the electron density and the electronic structure has been performed in the finite basis set density functional theory (DFT) framework. Quantum Theory of Atoms In Molecules (QTAIM), deformation densities and Laplacians maps have been used to compare theoretical and experimental results. MM experimental results and predictions from theory differ with respect to the sign and/or magnitude of the Laplacian at the N-O bond critical point (BCP), depending on the treatment of n values of the MM radial functions. Such Laplacian differences in the N-O bond case are discussed with respect to a lack of flexibility in the MM radial functions also reported by Rykounov et al. [Acta Cryst. (2011), B67, 425-436]. BCP Hessian eigenvalues show qualitatively matching results between MM and DFT. In addition, the theoretical analysis used domain-averaged fermi holes (DAFH), natural bond orbital (NBO) analysis and localized (LOC) orbitals to characterize the N-O bond as a single σ bond with marginal π character. Hirshfeld atom refinement (HAR) has been employed to compare to the MM refinement results and/or neutron dataset C-H bond lengths and to crystal or single molecule geometry optimizations, including considerations of anisotropy of H atoms. Our findings help to understand properties of molecules like MTTOTHP as progenitors of free oxygen radicals.
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Affiliation(s)
- Barbora Vénosová
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
| | - Julia Koziskova
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
| | - Jozef Kožíšek
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
| | - Peter Herich
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
| | - Karol Lušpai
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
| | - Vaclav Petricek
- Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, Praha 8, 182 21, Czech Republic
| | - Jens Hartung
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern, D-67663, Germany
| | - Mike Müller
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern, D-67663, Germany
| | - Christian B Hübschle
- Laboratory of Crystallography, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Lukas Bucinsky
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University of Technology in Bratislava, Radlinského 9, Bratislava, SK-81237, Slovak Republic
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19
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Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM. TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:296-306. [PMID: 32831250 DOI: 10.1107/s2052520620002917] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Michal Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
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20
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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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21
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Bergmann J, Davidson M, Oksanen E, Ryde U, Jayatilaka D. fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins. IUCRJ 2020; 7:158-165. [PMID: 32148844 PMCID: PMC7055371 DOI: 10.1107/s2052252519015975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/27/2019] [Indexed: 05/20/2023]
Abstract
The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Chemical Center, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Max Davidson
- School of Molecular Sciences M310, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
| | - Esko Oksanen
- Instruments Division, European Spallation Source ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Center, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Dylan Jayatilaka
- School of Molecular Sciences M310, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
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22
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Genoni A. On the use of the Obara–Saika recurrence relations for the calculation of structure factors in quantum crystallography. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:172-179. [DOI: 10.1107/s205327332000042x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022]
Abstract
Modern methods of quantum crystallography are techniques firmly rooted in quantum chemistry and, as in many quantum chemical strategies, electron densities are expressed as two-centre expansions that involve basis functions centred on atomic nuclei. Therefore, the computation of the necessary structure factors requires the evaluation of Fourier transform integrals of basis function products. Since these functions are usually Cartesian Gaussians, in this communication it is shown that the Fourier integrals can be efficiently calculated by exploiting an extension of the Obara–Saika recurrence formulas, which are successfully used by quantum chemists in the computation of molecular integrals. Implementation and future perspectives of the technique are also discussed.
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23
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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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24
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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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25
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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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26
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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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27
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Svane B, Tolborg K, Jørgensen LR, Roelsgaard M, Jørgensen MRV, Brummerstedt Iversen B. Multipole electron densities and atomic displacement parameters in urea from accurate powder X-ray diffraction. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2019; 75:600-609. [PMID: 31264644 DOI: 10.1107/s205327331900799x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 11/10/2022]
Abstract
Electron density determination based on structure factors obtained through powder X-ray diffraction has so far been limited to high-symmetry inorganic solids. This limit is challenged by determining high-quality structure factors for crystalline urea using a bespoke vacuum diffractometer with imaging plates. This allows the collection of data of sufficient quality to model the electron density of a molecular system using the multipole method. The structure factors, refined parameters as well as chemical bonding features are compared with results from the high-quality synchrotron single-crystal study by Birkedal et al. [Acta Cryst. (2004), A60, 371-381] demonstrating that powder X-ray diffraction potentially provides a viable alternative for electron density determination in simple molecular crystals where high-quality single crystals are not available.
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Affiliation(s)
- Bjarke Svane
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Kasper Tolborg
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Lasse Rabøl Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Martin Roelsgaard
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Mads Ry Vogel Jørgensen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
| | - Bo Brummerstedt Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, Aarhus, DK-8000, Denmark
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29
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Lübben J, Wandtke CM, Hübschle CB, Ruf M, Sheldrick GM, Dittrich B. Aspherical scattering factors for SHELXL - model, implementation and application. Acta Crystallogr A Found Adv 2019; 75:50-62. [PMID: 30575583 PMCID: PMC6302932 DOI: 10.1107/s2053273318013840] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/29/2018] [Indexed: 11/23/2022] Open
Abstract
A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.
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Affiliation(s)
- Jens Lübben
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
- Bruker AXS Inc., 5465 E. Cheryl Parkway, Madison, WI 53711, USA
| | - Claudia M. Wandtke
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
| | | | - Michael Ruf
- Bruker AXS Inc., 5465 E. Cheryl Parkway, Madison, WI 53711, USA
| | - George M. Sheldrick
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstrasse 4, Göttingen, D-37077, Germany
| | - Birger Dittrich
- Heinrich-Heine Universität Düsseldorf, Institut für Anorganische Chemie und Strukturchemie, Material- und Strukturforschung, Gebäude: 26.42, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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30
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Meyer B, Genoni A. Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks. J Phys Chem A 2018; 122:8965-8981. [PMID: 30339393 DOI: 10.1021/acs.jpca.8b09056] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.
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Affiliation(s)
- Benjamin Meyer
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 , 1 Boulevard Arago , F-57078 Metz , France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 , 1 Boulevard Arago , F-57078 Metz , France
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31
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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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32
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Tchoń D, Makal A, Gutmann M, Woźniak K. Doxycycline hydrate and doxycycline hydrochloride dihydrate – crystal structure and charge density analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/zkri-2018-2058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
High-resolution low-temperature X-ray diffraction experiments for doxycycline monohydrate and hydrochloride dihydrate have been performed. Translation-Libration-Screw (TLS) analysis for both crystal forms as well as the data from neutron diffraction experiment for hydrochloride combined with the Hansen-Coppens formalism resulted in precise charge density distribution models for both the zwitterionic monohydrate and a protonated hydrochloride crystal forms. Their detailed topological analysis suggested that the electron structure of doxycycline’s amide moiety undergoes significant changes during protonation due to formation of a very strong resonance-assisted hydrogen bond. A notably increased participation of amide nitrogen atom and hydrogen-accepting oxygen atom in the resonance upon doxycycline protonation was observed. A comparison of TLS- and neutron data-derived hydrogen parameters confirmed the experimental neutron data to be vital for proper description of intra- and inter-molecular interactions in this compound. Finally, calculated lattice and interaction energies quantified repulsive Dox-Dox interactions in the protonated crystal form of the antibiotic, relating with a good solubility of doxycycline hydrochloride relative to its hydrate.
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Affiliation(s)
- Daniel Tchoń
- Biological and Chemical Research Centre , Department of Chemistry , University of Warsaw, Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Anna Makal
- Biological and Chemical Research Centre , Department of Chemistry , University of Warsaw, Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Matthias Gutmann
- ISIS Facility , STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus , Chilton, Didcot, Oxfordshire OX11 OQX , England
| | - 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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33
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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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34
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Brewitz L, Noda H, Kumagai N, Shibasaki M. Structural and Computational Investigation of Intramolecular N···H Interactions in α‐ and β‐Fluorinated 7‐Azaindoline Amides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lennart Brewitz
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23 141‐0021 Shinagawa‐ku, Tokyo Japan
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23 141‐0021 Shinagawa‐ku, Tokyo Japan
| | - Naoya Kumagai
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23 141‐0021 Shinagawa‐ku, Tokyo Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23 141‐0021 Shinagawa‐ku, Tokyo Japan
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35
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Tautomerism in acyl-pyrazolones and in a novel photolysis product—importance and impact of the accurate localization of hydrogen atoms in crystal structures. Struct Chem 2017. [DOI: 10.1007/s11224-017-1005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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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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37
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38
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Dittrich B, Lübben J, Mebs S, Wagner A, Luger P, Flaig R. Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks. Chemistry 2017; 23:4605-4614. [PMID: 28295691 PMCID: PMC5434951 DOI: 10.1002/chem.201604705] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/21/2016] [Indexed: 11/21/2022]
Abstract
Amino acid structures are an ideal test set for method-development studies in crystallography. High-resolution X-ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non-standard amino acid. Structures were re-investigated to study a widely applicable treatment that permits accurate X-H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen-atom parameters with aspherical scattering factors with constrained "TLS+INV" estimated hydrogen anisotropic displacement parameters (H-ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H-ADPs, as free refinement frequently leads to over-parameterization and non-positive definite H-ADPs irrespective of the aspherical scattering model used. Using estimated H-ADPs, both methods yield accurate and precise X-H distances in best quantitative agreement with neutron diffraction data (available for five of the test-set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.
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Affiliation(s)
- Birger Dittrich
- Heinrich-Heine Universität DüsseldorfInstitut für Anorganische Chemie und Strukturchemie, Material- und Strukturforschung, Gebäude: 26.42Universitätsstraße 140225DüsseldorfGermany
| | - Jens Lübben
- Heinrich-Heine Universität DüsseldorfInstitut für Anorganische Chemie und Strukturchemie, Material- und Strukturforschung, Gebäude: 26.42Universitätsstraße 140225DüsseldorfGermany
| | - Stefan Mebs
- Institut für Chemie und Biochemie–Anorganische Chemie derFreien Universität Berlin14195BerlinGermany
| | - Armin Wagner
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUK
| | - Peter Luger
- Institut für Chemie und Biochemie–Anorganische Chemie derFreien Universität Berlin14195BerlinGermany
| | - Ralf Flaig
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUK
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39
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Bučinský L, Jayatilaka D, Grabowsky S. Importance of Relativistic Effects and Electron Correlation in Structure Factors and Electron Density of Diphenyl Mercury and Triphenyl Bismuth. J Phys Chem A 2016; 120:6650-69. [PMID: 27434184 DOI: 10.1021/acs.jpca.6b05769] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study investigates the possibility of detecting relativistic effects and electron correlation in single-crystal X-ray diffraction experiments using the examples of diphenyl mercury (HgPh2) and triphenyl bismuth (BiPh3). In detail, the importance of electron correlation (ECORR), relativistic effects (REL) [distinguishing between total, scalar and spin-orbit (SO) coupling relativistic effects] and picture change error (PCE) on the theoretical electron density, its topology and its Laplacian using infinite order two component (IOTC) wave functions is discussed. This is to develop an understanding of the order of magnitude and shape of these different effects as they manifest in the electron density. Subsequently, the same effects are considered for the theoretical structure factors. It becomes clear that SO and PCE are negligible, but ECORR and scalar REL are important in low- and medium-order reflections on absolute and relative scales-not in the high-order region. As a further step, Hirshfeld atom refinement (HAR) and subsequent X-ray constrained wavefunction (XCW) fitting have been performed for the compound HgPh2 with various relativistic and nonrelativistic wave functions against the experimental structure factors. IOTC calculations of theoretical structure factors and relativistic HAR as well as relativistic XCW fitting are presented for the first time, accounting for both scalar and spin-orbit relativistic effects.
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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
- Fachbereich 2 - Biologie/Chemie, Universität Bremen , Leobener Straβe NW2, 28359 Bremen, Germany
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40
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Wall ME. Quantum crystallographic charge density of urea. IUCRJ 2016; 3:237-46. [PMID: 27437111 PMCID: PMC4937779 DOI: 10.1107/s2052252516006242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/13/2016] [Indexed: 05/20/2023]
Abstract
Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.
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Affiliation(s)
- Michael E. Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Mail Stop B256, Los Alamos, New Mexico 87545, USA
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41
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Sovago I, Gutmann MJ, Senn HM, Thomas LH, Wilson CC, Farrugia LJ. Electron density, disorder and polymorphism: high-resolution diffraction studies of the highly polymorphic neuralgic drug carbamazepine. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:39-50. [PMID: 26830795 DOI: 10.1107/s2052520615019538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Analysis of neutron and high-resolution X-ray diffraction data on form (III) of carbamazepine at 100 K using the atoms in molecules (AIM) topological approach afforded excellent agreement between the experimental results and theoretical densities from the optimized gas-phase structure and from multipole modelling of static theoretical structure factors. The charge density analysis provides experimental confirmation of the partially localized π-bonding suggested by the conventional structural formula, but the evidence for any significant C-N π bonding is not strong. Hirshfeld atom refinement (HAR) gives H atom positional and anisotropic displacement parameters that agree very well with the neutron parameters. X-ray and neutron diffraction data on the dihydrate of carbemazepine strongly indicate a disordered orthorhombic crystal structure in the space group Cmca, rather than a monoclinic crystal structure in space group P2(1)/c. This disorder in the dihydrate structure has implications for both experimental and theoretical studies of polymorphism.
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Affiliation(s)
- Ioana Sovago
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Matthias J Gutmann
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0QX, England
| | - Hans Martin Senn
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Lynne H Thomas
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Chick C Wilson
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - Louis J Farrugia
- WESTChem School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
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42
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Lübben J, Bourhis LJ, Dittrich B. Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program. J Appl Crystallogr 2015; 48:1785-1793. [PMID: 26664341 PMCID: PMC4665659 DOI: 10.1107/s1600576715018075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/27/2015] [Indexed: 11/10/2022] Open
Abstract
Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation-libration-screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.
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Affiliation(s)
- Jens Lübben
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Luc J Bourhis
- Bruker-AXS SAS, 4 Allée Lorents, F-77447 Marne-la-Vallée, France
| | - Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany ; Heinrich-Heine Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Universitätsstrasse 1, Gebäude 26.42.01.21, 40225 Düsseldorf, Germany
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43
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Thomas SP, Jayatilaka D, Guru Row TN. S⋯O chalcogen bonding in sulfa drugs: insights from multipole charge density and X-ray wavefunction of acetazolamide. Phys Chem Chem Phys 2015; 17:25411-20. [DOI: 10.1039/c5cp04412j] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental charge density analysis combined with the quantum crystallographic technique of X-ray wavefunction refinement (XWR) provides quantitative insights into the intra- and intermolecular interactions formed by acetazolamide, a diuretic drug.
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Affiliation(s)
- Sajesh P. Thomas
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
- Solid state and Structural Chemistry Unit
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
| | - T. N. Guru Row
- Solid state and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore
- India
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44
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Capelli SC, Bürgi HB, Dittrich B, Grabowsky S, Jayatilaka D. Hirshfeld atom refinement. IUCRJ 2014; 1:361-79. [PMID: 25295177 PMCID: PMC4174878 DOI: 10.1107/s2052252514014845] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/24/2014] [Indexed: 05/20/2023]
Abstract
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
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Affiliation(s)
- Silvia C. Capelli
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Hans-Beat Bürgi
- Department of Chemistry and Biochemistry, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Department of Chemistry, Universität Zürich, Winterthurstrasse 190, 8057 Zürich, Switzerland
| | - Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
| | - Simon Grabowsky
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
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45
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Lübben J, Volkmann C, Grabowsky S, Edwards A, Morgenroth W, Fabbiani FPA, Sheldrick GM, Dittrich B. On the temperature dependence of H-U(iso) in the riding hydrogen model. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2014; 70:309-16. [PMID: 25970187 PMCID: PMC4075069 DOI: 10.1107/s2053273314010626] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/09/2014] [Indexed: 11/10/2022]
Abstract
The temperature dependence of hydrogen Uiso and parent Ueq in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-Uiso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.
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Affiliation(s)
- Jens Lübben
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Christian Volkmann
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Simon Grabowsky
- School of Chemistry and Biochemistry, Stirling Highway 35, WA-6009 Crawley, Australia
| | - Alison Edwards
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Wolfgang Morgenroth
- Institut für Geowissenschaften, Abteilung Kristallographie, Goethe-Universität, Altenhöferallee 1, 60438 Frankfurt am Main, Germany
| | - Francesca P A Fabbiani
- GZG, Abteilung Kristallographie, Georg-August Universität, Goldschmidtstrasse 1, 37077 Göttingen, Germany
| | - George M Sheldrick
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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