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The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123690. [PMID: 35744821 PMCID: PMC9229234 DOI: 10.3390/molecules27123690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022]
Abstract
The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.
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Malaspina LA, Genoni A, Grabowsky S. lamaGOET: an interface for quantum crystallography. J Appl Crystallogr 2021; 54:987-995. [PMID: 34188618 PMCID: PMC8202027 DOI: 10.1107/s1600576721002545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/08/2021] [Indexed: 11/24/2022] Open
Abstract
In quantum crystallography, theoretical calculations and crystallographic refinements are closely intertwined. This means that the employed software must be able to perform both quantum-mechanical calculations and crystallographic least-squares refinements. So far, the program Tonto is the only one able to do that. The lamaGOET interface described herein deals with this issue since it interfaces dedicated quantum-chemical software (the widely used Gaussian package and the specialized ELMOdb program) with the refinement capabilities of Tonto. Three different flavours of quantum-crystallographic refinements of the dipetide glycyl-l-threonine dihydrate are presented to showcase the capabilities of lamaGOET: Hirshfeld atom refinement (HAR), HAR-ELMO, namely HAR coupled with extremely localized molecular orbitals, and X-ray constrained wavefunction fitting.
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Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
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Pochekutova TS, Khamylov VK, Fukin GK, Petrov BI, Shavyrin AS, Arapova AV, Lazarev NM, Faerman VI, Kulikova TI, Baranov EV, Khamaletdinova NM. Synthesis, structures, thermal behavior and vapour pressures of new strontium and barium β-diketonate complexes [M(t-BuCOCHCOCF3)2(18-crown-6)] and [M(t-BuCOCHCOC3F7)2(18-crown-6)] (M = Sr, Ba). Polyhedron 2020. [DOI: 10.1016/j.poly.2019.114263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Experimental and experimental-theoretical topological characteristics of the electron density distribution in the crystal of NCN-(2-pyridinecarbonitrile)-(3,6-di-tert-butylcatecholato)triphenylantimony(v). Russ Chem Bull 2019. [DOI: 10.1007/s11172-019-2607-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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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Novaković SB, Bogdanović GA, Heering C, Makhloufi G, Francuski D, Janiak C. Charge-Density Distribution and Electrostatic Flexibility of ZIF-8 Based on High-Resolution X-ray Diffraction Data and Periodic Calculations. Inorg Chem 2015; 54:2660-70. [DOI: 10.1021/ic5028256] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sladjana B. Novaković
- Vinča Institute
of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia
| | - Goran A. Bogdanović
- Vinča Institute
of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia
| | - Christian Heering
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
| | - Gamall Makhloufi
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
| | - Djordje Francuski
- Institute of Molecular Genetics and Genetic
Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade, Serbia
| | - Christoph Janiak
- Institut für Anorganische
Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse
1, 40225 Düsseldorf, Germany
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - 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 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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Pröpper K, Holstein JJ, Hübschle CB, Bond CS, Dittrich B. Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 Å resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1530-9. [DOI: 10.1107/s0907444913010664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 04/18/2013] [Indexed: 11/10/2022]
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Dittrich B, Hübschle CB, Pröpper K, Dietrich F, Stolper T, Holstein J. The generalized invariom database (GID). ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2013. [DOI: 10.1107/s0108768113002280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Dittrich B, Jayatilaka D. Reliable Measurements of Dipole Moments from Single-Crystal Diffraction Data and Assessment of an In-Crystal Enhancement. ELECTRON DENSITY AND CHEMICAL BONDING II 2012. [DOI: 10.1007/430_2012_78] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Bąk JM, Domagała S, Hübschle C, Jelsch C, Dittrich B, Dominiak PM. Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases. Acta Crystallogr A 2011; 67:141-53. [PMID: 21325717 DOI: 10.1107/s0108767310049731] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/28/2010] [Indexed: 11/11/2022] Open
Abstract
The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high-resolution single-crystal X-ray diffraction experiment on L-His-L-Ala dihydrate and 23 K high-resolution data for L-Ala [Destro & Marsh (1988). J. Phys. Chem. 92, 966-973], the structural properties, electron-density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal-field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly-L-His dihydrate, D,L-His and the above-mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root-mean-square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X-H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high-resolution and low-resolution data, respectively. Differences in dipole-moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9-15 and 22-33 kJ mol(-1) for UBDB and the other database models, respectively.
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Affiliation(s)
- Joanna Maria Bąk
- Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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