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Saifina AF, Kartashov SV, Saifina LF, Fayzullin RR. Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis(2-hydroxyethyl)-6-methyluracil. IUCRJ 2023; 10:584-602. [PMID: 37668216 PMCID: PMC10478519 DOI: 10.1107/s2052252523007108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
We considered it timely to test the applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. The procedure was carried out on the crystal of 1,3-bis(2-hydroxyethyl)-6-methyluracil, and some derived properties of the scalar potential and vector force fields were compared with those obtained from the experimental multipole model and from the aspherical pseudo-atom model with parameters fitted to the calculated structure factors. The procedure was shown to accurately replicate the general vector-field behavior, the peculiarities of the quantum potentials and the characteristics of the force-field pseudoatoms, such as charge, shape and volume, as well as to reproduce the relative arrangement of atomic and pseudoatomic zero-flux surfaces along internuclear regions. It was found that, in addition to the quantum-topological atoms, the force-field pseudoatoms are spatially reproduced within a single structural fragment and similar environment. In addition, the classical and nonclassical hydrogen bonds in the uracil derivative crystal, as well as the H...O, N...O and N...C interactions in the free π-stacked dimer of the uracil derivative molecules, were studied using the potential and force fields within the concepts of interatomic charge transfer and electron lone pair donation-acceptance. Remarkably, the nitrogen atoms in the N...O and N...C interactions behave rather like a Lewis base and an electron contributor. At the same time, the hydrogen atom in the H...O interaction, being a Lewis acid, also participates in the interatomic electron transfer by acting as a contributor. Thus, it has been argued that, when describing polar interatomic interactions within orbital-free considerations, it makes more physical sense to identify electronegative (electron occupier) and electropositive (electron contributor) atoms or subatomic fragments rather than nucleophilic and electrophilic sites.
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Affiliation(s)
- Alina F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Sergey V. Kartashov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Liliya F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
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2
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Anzline C, Israel S, Sujatha K, Sheeba RAJR. Structure, charge density, and Hirshfeld surface analysis of proton transfer complex 2‐amino‐4‐methylpyridinium 2‐(3‐methylphenyl)‐acetate. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Samuel Israel
- Department of Physics The American college Madurai India
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Akram S, Mehmood A, Noureen S, Ahmed M. Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis. Acta Crystallogr C Struct Chem 2022; 78:72-80. [DOI: 10.1107/s2053229621013607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.
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Bilal A, Mehmood A, Noureen S, Lecomte C, Ahmed M. Crystal engineering of a co-crystal of antipyrine and 2-chlorobenzoic acid: relative energetic contributions based on multipolar refinement. CrystEngComm 2022. [DOI: 10.1039/d2ce01179d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The growth and stability of a new 1 : 1 antipyrene–dichlorobenzoic acid cocrystal system has been analyzed in terms of electron density analysis and electrostatic interaction energy contributions.
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Affiliation(s)
- Aqsa Bilal
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
| | - Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, Texas, 76129, USA
| | - Sajida Noureen
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
| | - Claude Lecomte
- Laboratoire CRM2, UMR CNRS 7036, Université de Lorraine, Boulevard des Aiguillettes BP70239, Vandoeuvre-les-Nancy, 54506, France
- CNRS, Laboratoire CRM2, UMR CNRS 7036, Boulevard des Aiguillettes, BP70239, Vandoeuvre-les-Nancy, 54506, France
| | - Maqsood Ahmed
- Materials Chemistry Laboratory, Institute of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, 63100, Pakistan
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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9
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Kalaiarasi C, George C, Gonnade RG, Hathwar VR, Poomani K. Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:942-953. [PMID: 32830674 DOI: 10.1107/s2052520619011272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/13/2019] [Indexed: 06/11/2023]
Abstract
Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å-1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen-Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N-O and C-NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O-H...N, C-H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.
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Affiliation(s)
- Chinnasamy Kalaiarasi
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Christy George
- Centre for Materials Characterization, National Chemical Laboratory, Pune, 411 008, India
| | - Rajesh G Gonnade
- Centre for Materials Characterization, National Chemical Laboratory, Pune, 411 008, India
| | | | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
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Novikova VV, Kulygin AK, Lepeshov GG, Avilov AS. Electronic Structure and Electrostatic Potential Distribution in Nanocrystals of Fluorides CaF2, BaF2, and LaF3 According to Electron Diffraction Data. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s106377451806024x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Pawlędzio S, Makal A, Trzybiński D, Woźniak K. Crystal structure, interaction energies and experimental electron density of the popular drug ketoprophen. IUCRJ 2018; 5:841-853. [PMID: 30443368 PMCID: PMC6211533 DOI: 10.1107/s2052252518013222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023]
Abstract
The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O-H⋯O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzo-phenone moieties bound by C-H⋯π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.
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Affiliation(s)
- Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Anna Makal
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
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12
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Shahid A, Aziz A, Noureen S, Ahmed M, Yousuf S, Choudhary MI. Biotransformation, spectroscopic investigation, crystal structure and electrostatic properties of 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate studied using transferred electron-density parameters. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:534-541. [PMID: 29726461 DOI: 10.1107/s2053229618004953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/27/2018] [Indexed: 11/11/2022]
Abstract
The biologically transformed product of estradiol valerate, namely 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate, C18H22O3·H2O, has been investigated using UV-Vis, IR, 1H and 13C NMR spectroscopic techniques, as well as by mass spectrometric analysis. Its crystal structure was determined using single-crystal X-ray diffraction based on data collected at 100 K. The structure was refined using the independent atom model (IAM) and the transferred electron-density parameters from the ELMAM2 database. The structure is stabilized by a network of hydrogen bonds and van der Waals interactions. The topology of the hydrogen bonds has been analyzed by the Bader theory of `Atoms in Molecules' framework. The molecular electrostatic potential for the transferred multipolar atom model reveals an asymmetric character of the charge distribution across the molecule due to a substantial charge delocalization within the molecule. The molecular dipole moment was also calculated, which shows that the molecule has a strongly polar character.
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Affiliation(s)
- Ammara Shahid
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
| | - Ambreen Aziz
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
| | - Sajida Noureen
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
| | - Muhammad Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
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Faroque MU, Noureen S, Ahmed M, Tahir MN. Electrostatic properties of the pyrimethamine–2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:100-107. [DOI: 10.1107/s2053229617017788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/12/2017] [Indexed: 11/11/2022]
Abstract
The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C12H14ClN4
+·C7H5O4
−·CH3OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.
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14
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Hübschle CB, van Smaalen S. The electrostatic potential of dynamic charge densities. J Appl Crystallogr 2017; 50:1627-1636. [PMID: 29217990 PMCID: PMC5713142 DOI: 10.1107/s1600576717013802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 11/10/2022] Open
Abstract
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å-3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.
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Affiliation(s)
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, 95440 Bayreuth, Germany
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Shahid A, Noureen S, Choudhary MI, Yousuf S, Ahmed M. Crystal structure and electrostatic properties of prednisolone acetate studied using a transferred multipolar atom model. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:430-436. [PMID: 28579562 DOI: 10.1107/s2053229617006556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/01/2017] [Indexed: 11/10/2022]
Abstract
Prednisolone acetate {systematic name: 2-[(8S,9S,10R,13S,14S,17R)-11,17-dihydroxy-10,13-dimethyl-3-oxo-6,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-17-yl]-2-oxoethyl acetate}, is an ophthalmic drug that belongs to the class of corticosteroids. Its crystal structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results of both refinements have been compared. The ELMAM2 refinement was found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution. The procedure proves helpful in understanding the mode of action of the drug molecule.
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Affiliation(s)
- Ammara Shahid
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajida Noureen
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Iqbal Choudhary
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sammer Yousuf
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
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Kalaiarasi C, Pavan MS, Kumaradhas P. Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:775-786. [PMID: 27698320 DOI: 10.1107/s2052520616010581] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen-Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed using CRYSTAL09.
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Affiliation(s)
- Chinnasamy Kalaiarasi
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Mysore S Pavan
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
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Faroque MU, Yousuf S, Zafar S, Choudhary MI, Ahmed M. Transferred multipolar atom model for 10β,17β-dihydroxy-17α-methylestr-4-en-3-one dihydrate obtained from the biotransformation of methyloestrenolone. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:398-404. [PMID: 27146568 DOI: 10.1107/s2053229616005441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/31/2016] [Indexed: 11/10/2022]
Abstract
Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.
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Affiliation(s)
- Muhammad Umer Faroque
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Salman Zafar
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
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18
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Kandhakumar G, Kalaiarasi C, Kumaradhas P. Structure and charge density distribution of amine azide based hypergolic propellant molecules: a theoretical study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A quantum chemical calculation and charge density analysis of some amine azide based propellants (DMAZ, DMAEH, ADMCPA, AMCBA and ACPA) have been carried out to understand the geometry, bond topological, electrostatic, and energetic properties. The topological properties of electron density of the molecules were determined using Bader’s theory of atoms in molecules from the wave functions obtained from the density functional method (B3LYP) with the 6-311G** basis set. The electron density distribution of these molecules reveals the nature of chemical bonding in the molecules. The azide group attached C−N bonds of all molecules exhibit the electron density of ρbcp(r) ∼1.639 e Å−3 and the Laplacian of electron density ∇2ρbcp(r) is ∼–14.0 e Å−5, in which the corresponding values of the ADMCPA molecule are relatively high, 1.725 e Å–3 and –15.2 e Å−5 respectively, whereas for the methylamine group attached C–N bonds, these values are found to be higher (1.824 e Å–3 and –17.25 e Å−5). The Laplacian of terminal N–N bonds of the azide group is highly negative, indicating that these charges are highly concentrated, whereas the charge concentration of the dimethylamine group attached N–N bond of DMEAH is very much less, confirming that the bond is the weakest bond among the molecules. The energy density has been calculated for each bond of the molecules, which insights the energy density distribution of the molecules. Relatively, the molecules exhibit distinct electrostatic properties that are related to different charge distribution in the molecules. Large negative electrostatic potential regions are found at the vicinity of the amine and azide groups of the molecules. The charge imbalance parameter of the molecules has been determined and shows that the DMAEH molecule is the least sensitive molecule in this series.
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Affiliation(s)
- Gopal Kandhakumar
- Department of Physics, Periyar University, Salem 636 011, India
- Department of Physics, Periyar University, Salem 636 011, India
| | - Chinnasamy Kalaiarasi
- Department of Physics, Periyar University, Salem 636 011, India
- Department of Physics, Periyar University, Salem 636 011, India
| | - Poomani Kumaradhas
- Department of Physics, Periyar University, Salem 636 011, India
- Department of Physics, Periyar University, Salem 636 011, India
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Macchi P, Gillet JM, Taulelle F, Campo J, Claiser N, Lecomte C. Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges. IUCRJ 2015; 2:441-51. [PMID: 26175903 PMCID: PMC4491316 DOI: 10.1107/s2052252515007538] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/16/2015] [Indexed: 06/01/2023]
Abstract
Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.
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Affiliation(s)
- Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jean-Michel Gillet
- Laboratoire Structures Propriétés et Modélisation des Solides, UMR 8580, Université Paris Saclay CentraleSupélec, CNRS, Grande Voie des Vignes, 92295 Chatenay-Malabry, France
| | - Francis Taulelle
- Institut Lavoisier de Versailles, Université de Versailles Saint Quentin en Yvelines, 45 Avenue des Etats-Unis, Versailles, 78035, France
| | - Javier Campo
- Materials Science Institute of Aragón, CSIC-University of Zaragoza, Zaragoza, 50009, Spain
| | - Nicolas Claiser
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
| | - Claude Lecomte
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
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Stash AI, Tsirelson VG. DevelopingWinXPRO: a software for determination of the multipole-model-based properties of crystals. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714021566] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The new release of the computer program packageWinXPRO v.3xfor determination of the crystal properties from parameters of the multipole-modeled experimental electron density and anharmonic atomic displacement coefficients is described. The set of properties is significantly extended by using the density functional and information theories. In addition, a built-in multi-functional viewer and programs to display the output data, including the mapping of the chosen functional bonding descriptors onto surfaces of the other properties, are included.
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Rajalakshmi G, Hathwar VR, Kumaradhas P. Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2014; 70:568-79. [DOI: 10.1107/s205252061303388x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 12/15/2013] [Indexed: 11/10/2022]
Abstract
An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.
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Nguyen TH, Howard ST, Hanrahan JR, Groundwater PW, Platts JA, Hibbs DE. Experimental and Theoretical Charge Density Distribution in a Host–Guest System: Synthetic Terephthaloyl Receptor Complexed to Adipic Acid. J Phys Chem A 2012; 116:5618-28. [DOI: 10.1021/jp210803m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thanh Ha Nguyen
- Faculty of
Pharmacy, University of Sydney, NSW 2006,
Australia
| | - Sian T. Howard
- Faculty of
Pharmacy, University of Sydney, NSW 2006,
Australia
| | | | | | - James A. Platts
- School
of Chemistry, Main Building, Cardiff University, Park
Place, Cardiff CF10 3AT, United Kingdom
| | - David E. Hibbs
- Faculty of
Pharmacy, University of Sydney, NSW 2006,
Australia
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Schürmann CJ, Pröpper K, Wagner T, Dittrich B. Invariom modeling of ceftazidime pentahydrate: molecular properties from a 200 second synchrotron microcrystal experiment. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2012; 68:313-7. [PMID: 22610682 DOI: 10.1107/s0108768112017831] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 04/21/2012] [Indexed: 11/10/2022]
Abstract
The structure of ceftazidime pentahydrate, a third generation cephalosporin antibiotic, is reported. Data collection was carried out in a remarkably short time with synchrotron radiation and the latest detector technology, illustrating that single-crystal X-ray diffraction can be used as a technique for screening hundreds of compounds in a short amount of time. Structure refinement made use of invarioms, namely non-spherical scattering factors, which allow more information to be derived from a diffraction experiment. Properties that can be screened are bond-topological parameters, empirical hydrogen-bond energies, molecular dipole moments and electrostatic potentials.
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Affiliation(s)
- C J Schürmann
- Institut für Anorganische Chemie der Universität Göttingen, Göttingen, Germany
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24
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Holstein JJ, Hübschle CB, Dittrich B. Electrostatic properties of nine fluoroquinoloneantibiotics derived directly from their crystal structure refinements. CrystEngComm 2012. [DOI: 10.1039/c1ce05966a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Holstein JJ, Luger P, Kalinowski R, Mebs S, Paulman C, Dittrich B. Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycin. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:568-77. [DOI: 10.1107/s0108768110026480] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 07/05/2010] [Indexed: 11/10/2022]
Abstract
Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed.
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Stevens ED, Dowd MK, Johnson GP, French AD. Experimental and theoretical electron density distribution of α,α-trehalose dihydrate. Carbohydr Res 2010; 345:1469-81. [DOI: 10.1016/j.carres.2010.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 03/10/2010] [Accepted: 03/14/2010] [Indexed: 10/19/2022]
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Dittrich B, Bond CS, Kalinowski R, Spackman MA, Jayatilaka D. Revised electrostatics from invariom refinement of the 18-residue peptaibol antibiotic trichotoxin A50E. CrystEngComm 2010. [DOI: 10.1039/c001072c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mebs S, Messerschmidt M, Luger P. Experimental charge density of an L-phenylalanine formic acid complex with a short hydrogen bond determined at 25 K. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.2006.221.9.656] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The experimental charge density and related atomic and bond topological properties of an L-phenylalanine formic acid complex were derived from a high resolution X-ray data set (sin θ/λ = 1.18 Å–1/d = 0.42 Å) measured at 25 K. The complex consists of a zwitterionic and a cationic phenylalanine molecule with formate as counterion. Special focus was directed on the density distribution in the region of a strong O—H ·· O hydrogen bond (O ·· O = 2.491(1) Å) which is formed between the two phenylalanine units. The obtained results are compared with the 15 previously derived experimental amino acid charge density data, with various theoretical calculations at experimental geometries and with the complete set of topological descriptors based on ab initio calculations of the neutral forms of all 20 amino acids published recently in the literature. A comparison of all available data in this biologically important class of compounds gives an impression about the significance of the quantitative results from experimental and theoretical charge density determinations.
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Mebs S, Lüth A, Löwe W, Paulmann C, Luger P. Electron density of a new EGFR Tyrokinase-inhibitor at 100 K, consideration of different models. Z KRIST-CRYST MATER 2009. [DOI: 10.1524/zkri.2008.0055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The electron density (ED) of a substituted 4-(indol-3-yl)-quinazoline, a newly developed anti-cancer drug, was determined from a high resolution X-ray data set measured at 100 K using synchrotron radiation. Because the structure contains a chlorine atom, which has a diffuse outer electron shell and is therefore beyond standard modeling, the influence of the model on the bond topological and atomic properties was studied following Bader's approach of ‘Atoms In Molecules’ (AIM). The expansion/contraction parameters κ and κ′ of the four atoms being constitutive for the Cl—C-bond and the F—C-bond were obtained by calculation of theoretical structure factors of a model compound and assigned in subsequent multipole refinements. The κ and κ′-values for all other non H-atoms atoms were taken from the literature. The effect of two different sets of κ and κ′ (1.20/1.20 and 1.13/1.29) for the hydrogen atoms was evaluated for the topological properties at bonds to hydrogen atoms (including hydrogen bonds) and to the atomic properties of the hydrogen atoms. Furthermore the effect of particular n
l
-sets for the chlorine atom to bond topological descriptors of the Cl—C-bond was investigated for the theoretical structure factors and compared with experiment. All results were compared with corresponding theoretical findings from a single point calculation at experimental geometry.
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31
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Chopra D, Zhurov VV, Zhurova EA, Pinkerton AA. Chemical Bonding and Structure−Reactivity Correlation in Meldrum’s Acid: A Combined Experimental and Theoretical Electron Density Study. J Org Chem 2009; 74:2389-95. [DOI: 10.1021/jo8027054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepak Chopra
- Department of Chemistry, University of Toledo, Toledo, Ohio 43606
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32
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Förster D, Hübschle CB, Luger P, Hügle T, Lentz D. On the 2-Electron 3-Center B−H−B Bond: Charge Density Determination of Tetraborane(10). Inorg Chem 2008; 47:1874-6. [DOI: 10.1021/ic701924r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diana Förster
- Institut für Chemie und Biochemie/Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34−36, 14195 Berlin, Germany, and Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
| | - Christian B. Hübschle
- Institut für Chemie und Biochemie/Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34−36, 14195 Berlin, Germany, and Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
| | - Peter Luger
- Institut für Chemie und Biochemie/Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34−36, 14195 Berlin, Germany, and Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
| | - Thomas Hügle
- Institut für Chemie und Biochemie/Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34−36, 14195 Berlin, Germany, and Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie/Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34−36, 14195 Berlin, Germany, and Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
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33
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Luger P. Fast electron density methods in the life sciences--a routine application in the future? Org Biomol Chem 2008; 5:2529-40. [PMID: 18019525 DOI: 10.1039/b706235d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The understanding of mutual recognition of biologically interacting systems on an atomic scale is of paramount importance in the life sciences. Electron density distributions that can be obtained from a high resolution X-ray diffraction experiment can provide--in addition to steric information--electronic properties of the species involved in these interactions. In recent years experimental ED methods have seen several favourable developments towards successful application in the life sciences. Experimental and methodological advances have made possible on the one hand high-speed X-ray diffraction experiments, and have allowed on the other hand the quantitative derivation of bonding, non-bonding and atomic electronic properties. This has made the investigation of a large number of molecules possible, and moreover, molecules with 200 or more atoms can be subject of experimental ED studies, as has been demonstrated by the example of vitamin B12. Supported by the experimentally verified transferability concept of submolecular electronic properties, a key issue in Bader's The Quantum Theory of Atoms in Molecules, activities have emerged to establish databases for the additive generation of electron densities of macromolecules from submolecular building blocks. It follows that the major aims of any experimental electron density work in the life sciences, namely the generation of electronic information for a series of molecules in a reasonable time and the study of biological macromolecules (proteins, polynucleotides), are within reach in the near future.
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Affiliation(s)
- Peter Luger
- Institute for Chemistry and Biochemistry/Crystallography, Free University of Berlin, Fabeckstr. 36a, 14 195, Berlin, Germany.
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34
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Förster D, Scheins S, Luger P, Lentz D, Preetz W. Electron Density and Bonding in Borates: An Experimental Study of Tetrabutylammonium Heptahydridohexaborate, [(C4H9)4N][B6H7]. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700444] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Avilov A, Kuligin K, Nicolopoulos S, Nickolskiy M, Boulahya K, Portillo J, Lepeshov G, Sobolev B, Collette J, Martin N, Robins A, Fischione P. Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination. Ultramicroscopy 2007; 107:431-44. [PMID: 17258859 DOI: 10.1016/j.ultramic.2006.09.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Accepted: 09/07/2006] [Indexed: 11/29/2022]
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36
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Jaradat DMM, Mebs S, Checińska L, Luger P. Experimental charge density of sucrose at 20K: bond topological, atomic, and intermolecular quantitative properties. Carbohydr Res 2007; 342:1480-9. [PMID: 17506999 DOI: 10.1016/j.carres.2007.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/29/2007] [Accepted: 04/02/2007] [Indexed: 11/30/2022]
Abstract
The charge density of sucrose was determined from a high-resolution X-ray data set measured at 20K. The density distribution so obtained was analyzed quantitatively by application of Bader's atoms in molecules (AIM) formalism, and a comparison was made with corresponding results from a B3LYP (6-311++G(3df,3pd)) calculation at the experimental geometry. Bond topological and atomic properties (volumes and charges) were derived and compared. The influence of hydrogen bonding on the experimental charge density was also studied qualitatively and quantitatively by means of topological properties. In terms of the hydrogen-bond energies, a grouping into strong, medium and very weak hydrogen bonds was made, the latter of which were involved in a bifurcated bond.
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Affiliation(s)
- Da'san M M Jaradat
- Institute for Chemistry and Biochemistry/Crystallography, Free University Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany
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37
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Checińska L, Troyanov SI, Mebs S, Hübschle CB, Luger P. Examination of intermolecular electronic interactions in the crystal structure of C60(CF3)12 by experimental electron density determination. Chem Commun (Camb) 2007:4003-5. [PMID: 17912396 DOI: 10.1039/b712694h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From a high resolution X-ray data set measured at 20 K the experimental electron density of the fullerene C(60)(CF(3))(12) was derived and topologically analyzed to yield, in addition to bond topological and atomic properties, information about the density distribution in the region where hexagons of adjacent molecules approach closely at only 3.3 A.
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Affiliation(s)
- Lilianna Checińska
- Department of Crystallography and Crystal Chemistry, University of Lodz, Pomorska 149/153, 90-236 Lodz, Poland
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38
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Brown AS, Spackman MA. The determination of electric field gradients from X-ray diffraction data. Mol Phys 2006. [DOI: 10.1080/00268979400101421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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39
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Checińska L, Mebs S, Hübschle CB, Förster D, Morgenroth W, Luger P. Reproducibility and transferability of topological data: experimental charge density study of two modifications ofl-alanyl-l-tyrosyl-l-alanine. Org Biomol Chem 2006; 4:3242-51. [PMID: 17036112 DOI: 10.1039/b607744g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two crystalline modifications of the tripeptide L-Ala-L-Tyr-L-Ala, which have different solvent molecules in the crystal structure (water and ethanol for modifications 1 and 2), were the subject of experimental charge density studies based on high resolution X-ray data collected at ultra-low temperatures of 9 K (1) and 20 K (2), respectively. The molecular structures and the intermolecular interactions were found to be rather similar in the two crystal lattices, so that this study allowed the reproducibility of the charge density of a given molecule in different (but widely comparable) crystalline environments to be examined. With respect to bond topological and atomic properties, the agreement between the two modifications of the title tripeptide was in the same range as found from the comparison with the previously reported results of tri-L-alanine. It follows that the reproducibility and transferability of quantitative topological data are comparable and that within the accuracy of experimental charge density work the replacement of the central amino acid residue L-Ala by L-Tyr has no significant influence, neither on bond nor on the atomic properties of the oligopeptide main chain. Intermolecular interactions in the form of hydrogen bonds were characterized quantitatively and qualitatively by topological criteria and by mapping the charge density distribution on the Hirshfeld surface.
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Affiliation(s)
- Lilianna Checińska
- Department of Crystallography and Crystal Chemistry, University of Łódź, Pomorska 149/153, 90 236, Łódź, Poland
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40
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Stash AI, Tsirelson VG. Modern possibilities for calculating some properties of molecules and crystals from the experimental electron density. CRYSTALLOGR REP+ 2005. [DOI: 10.1134/1.1887890] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Hibbs DE, Overgaard J, Howard ST, Nguyen TH. Experimental charge density of a potential DHO synthetase inhibitor: dimethyl-trans-2-oxohexahydro-pyrimidine-4,6-dicarboxylate. Org Biomol Chem 2005; 3:441-7. [PMID: 15678181 DOI: 10.1039/b416118a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimental charge density distribution of dimethyl-trans-2-oxohexahydro-pyrimidine-4,6-dicarboxylate 1 has been determined using single-crystal X-ray diffraction data measured at 100 K, in terms of the rigid-pseudoatom formalism. Multipole refinement converged at R(F) = 0.034 for 7283 reflections with I > 3 sigma (I) and sin theta/lambda < or = 1.13 A(-1). Covalent and hydrogen bonding interactions are analyzed using a topological analysis of the Laplacian of the charge density. The experimentally derived electrostatic potential mapped onto the reactive surface of the molecule reveals the potential binding sites of 1.
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Affiliation(s)
- David E Hibbs
- Faculty of Pharmacy, University of Sydney, NSW 2006, Australia
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42
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Volkov A, Koritsanszky T, Coppens P. Combination of the exact potential and multipole methods (EP/MM) for evaluation of intermolecular electrostatic interaction energies with pseudoatom representation of molecular electron densities. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.04.097] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Bach A, Lentz D, Luger P, Messerschmidt M, Olesch C, Patzschke M. Kristallstrukturanalyse von 1,1,4,4-Tetrafluorbutadien und experimentelle Bestimmung der Ladungsdichte von 1,1,4,4-Tetrafluorbutatrien. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020118)114:2<311::aid-ange311>3.0.co;2-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Macchi P, Schultz AJ, Larsen FK, Iversen BB. Experimental and Theoretical Electron Density Study of the Peroxo Function in Oxoperoxo(pyridine-2,6-dicarboxylato)(hexamethylphosphoramide)molybdenum(VI): Implications for Olefin Epoxidation by Peroxo Transition Metal Complexes. J Phys Chem A 2001. [DOI: 10.1021/jp011328x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Macchi
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy, Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - A. J. Schultz
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy, Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - F. K. Larsen
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy, Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - B. B. Iversen
- Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy, Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
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Ellena J, Goeta AE, Howard JAK, Punte G. Role of the Hydrogen Bonds in Nitroanilines Aggregation: Charge Density Study of 2-Methyl-5-nitroaniline. J Phys Chem A 2001. [DOI: 10.1021/jp010688h] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javier Ellena
- IFLP & LANADI. Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, (1900), La Plata, Argentina, and Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, C.P. 369, 13560, São Carlos (SP), Brazil, and Department of Chemistry, University of Durham, Durham, DH1 3LE, United Kingdom
| | - Andrés E. Goeta
- IFLP & LANADI. Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, (1900), La Plata, Argentina, and Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, C.P. 369, 13560, São Carlos (SP), Brazil, and Department of Chemistry, University of Durham, Durham, DH1 3LE, United Kingdom
| | - Judith A. K. Howard
- IFLP & LANADI. Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, (1900), La Plata, Argentina, and Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, C.P. 369, 13560, São Carlos (SP), Brazil, and Department of Chemistry, University of Durham, Durham, DH1 3LE, United Kingdom
| | - Graciela Punte
- IFLP & LANADI. Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC 67, (1900), La Plata, Argentina, and Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, C.P. 369, 13560, São Carlos (SP), Brazil, and Department of Chemistry, University of Durham, Durham, DH1 3LE, United Kingdom
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Bach A, Lentz D, Luger P. Charge Density and Topological Analysis of Pentafluorobenzoic Acid. J Phys Chem A 2001. [DOI: 10.1021/jp004626n] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ansgar Bach
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Institut für Chemie/Anorganische und Analytische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, D-14195 Berlin, Germany
| | - Dieter Lentz
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Institut für Chemie/Anorganische und Analytische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, D-14195 Berlin, Germany
| | - Peter Luger
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Institut für Chemie/Anorganische und Analytische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, D-14195 Berlin, Germany
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Affiliation(s)
- T S Koritsanszky
- Department of Chemistry, University of the Witwatersrand, WITS 2050, Johannesburg, South Africa
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Flaig R, Koritsánszky T, Soyka R, Häming L, Luger P. Electronic Insight into an Antithrombotic Agent by High-Resolution X-Ray Crystallography. Angew Chem Int Ed Engl 2001; 40:355-359. [DOI: 10.1002/1521-3773(20010119)40:2<355::aid-anie355>3.0.co;2-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2000] [Indexed: 11/08/2022]
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Flaig R, Koritsánszky T, Soyka R, Häming L, Luger P. Einblick in die elektronische Struktur eines antithrombotischen Wirkstoffs durch hochaufgelöste Röntgenbeugung. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010119)113:2<368::aid-ange368>3.0.co;2-#] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ralf Flaig
- Institut für Chemie/Kristallographie der Freien Universität Berlin Takustraße 6, 14195 Berlin (Deutschland) Fax: (+49) 30‐838‐53464
| | - Tibor Koritsánszky
- Department of Chemistry, University of the Witwatersrand Private Bag 3, WITS 2050, Johannesburg (Südafrika)
| | - Rainer Soyka
- Research and Development, Boehringer Ingelheim Pharma KG Birkendorfer Straße 65, 88397 Biberach (Deutschland)
| | - Ludger Häming
- Bruker Analytical X‐ray Systems Östliche Rheinbrückenstraße 50, 76187 Karlsruhe (Deutschland)
| | - Peter Luger
- Institut für Chemie/Kristallographie der Freien Universität Berlin Takustraße 6, 14195 Berlin (Deutschland) Fax: (+49) 30‐838‐53464
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