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Boča R, Imrich R, Štofko J, Vranovičová B, Rajnák C. Molecular properties of linear amino acids in water. Amino Acids 2024; 56:5. [PMID: 38300332 PMCID: PMC10834582 DOI: 10.1007/s00726-023-03365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 02/02/2024]
Abstract
Four linear amino acids of increased separation of the carboxyl and amino groups, namely glycine (aminoacetic acid), β-alanine (3-aminopropanoic acid), GABA (4-aminobutanoic acid) and DAVA (5-aminopentanoic acid), have been studied by quantum chemical ab initio and DFT methods including the solvent effect in order to get electronic structure and molecular descriptors, such as ionisation energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index, dipole moment, quadrupole moment and dipole polarizability. Thermodynamic functions (zero-point energy, inner energy, enthalpy, entropy, and the Gibbs energy) were evaluated after the complete vibrational analysis at the true energy minimum provided by the full geometry optimization. Reaction Gibbs energy allows evaluating the absolute redox potentials on reduction and/or oxidation. The non-local non-additive molecular descriptors were compared along the series showing which of them behave as extensive, varying in match with the molar mass and/or separation of the carboxyl and amino groups. Amino acidic forms and zwitterionic forms of the substances were studied in parallel in order to compare their relative stability and redox properties. In total, 24 species were investigated by B3LYP/def2-TZVPD method (M1) including neutral molecules, molecular cations and molecular anions. For comparison, MP2/def2-TZVPD method (M2) with full geometry optimization and vibrational analysis in water has been applied for 12 species; analogously, for 24 substances, DLPNO-CCSD(T)/aug-cc-pVTZ method (M3) has been applied in the geometry obtained by MP2 and/or B3LYP. It was found that the absolute oxidation potential correlates with the adiabatic ionisation energy; the absolute reduction potential correlates with the adiabatic electron affinity and the electrophilicity index. In order to validate the used methodology with experimental vertical ionisation energies and vibrational spectrum obtained in gas phase, calculations were done also in vacuo.
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Affiliation(s)
- Roman Boča
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia.
| | - Richard Imrich
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Juraj Štofko
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Beáta Vranovičová
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Cyril Rajnák
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
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2
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Deiko YA, Il’in DY, Druzhinina AI, Konstantinova NM, Lukonina NS, Dmitrienko AO, Lysenko KA, Tarazanov SV, Luk’yanova VA. Thermodynamic Properties of L-Asparagine Monohydrate. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422090060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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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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4
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Cukrowski I. A unified molecular‐wide and electron density based concept of chemical bonding. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria South Africa
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5
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Rozenberg M, Fausto R, Reva I. Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119323. [PMID: 33508682 DOI: 10.1016/j.saa.2020.119323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH2) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.
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Affiliation(s)
- M Rozenberg
- The Hebrew University of Jerusalem, Department of Inorganic and Analytical Chemistry, Jerusalem, Givat Ram 91904, Israel.
| | - R Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - I Reva
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal; University of Coimbra, CIEPQPF, Department of Chemical Engineering, 3030-790 Coimbra, Portugal.
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Bojarska J, Remko M, Breza M, Madura I, Fruziński A, Wolf WM. A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. Pharmaceuticals (Basel) 2020; 13:E338. [PMID: 33114370 PMCID: PMC7692516 DOI: 10.3390/ph13110338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022] Open
Abstract
Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia;
| | - Izabela Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Andrzej Fruziński
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
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7
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Yang F, Antonietti M. Artificial Humic Acids: Sustainable Materials against Climate Change. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902992. [PMID: 32154079 PMCID: PMC7055563 DOI: 10.1002/advs.201902992] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Indexed: 05/24/2023]
Abstract
Humic acid, as a natural organic matter, is widely distributed in surface soil, oceans, rivers, and other ecological environments throughout the whole earth ecosystem. Humic acid provides abundant organic carbon and helps to maintain a hydrated, pH and redox buffered environment hosting the soil microbiome. Humic acid is however also a largely ignored polymer material full of exciting functional properties, and its scale is enormous. This perspective article discusses its synthesis and management as a tool to tackle parts of the climate crisis as well its use in technological applications, as made by chemical conversion of agricultural side products to artificial humic acids.
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Affiliation(s)
- Fan Yang
- School of Water Conservancy and Civil EngineeringNortheast Agricultural UniversityHarbin150030China
- Joint laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU‐MPICI)Harbin150030China
- Max Planck Institute of Colloids and Interfaces Department of Colloid Chemistry14476PotsdamGermany
| | - Markus Antonietti
- Joint laboratory of Northeast Agricultural University and Max Planck Institute of Colloids and Interfaces (NEAU‐MPICI)Harbin150030China
- Max Planck Institute of Colloids and Interfaces Department of Colloid Chemistry14476PotsdamGermany
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8
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Fukin GK, Cherkasov AV, Baranov EV, Rumyantcev RV, Sazonova EV, Artemov AN. The Electron Density Distribution in Crystals of η
6
–[1,4–dihydrospiro(2
H
–3,1–benzoxazine–2,1′–cyclohexane)]tricarbonylchromium(0): Experiment
vs
Molecular Invariom. ChemistrySelect 2019. [DOI: 10.1002/slct.201901394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Georgy K. Fukin
- G.A. Razuvaev Institute of Organometallic Chemistry of Russian Academy of Sciences Tropinina str., 49, Nizhny Novgorod 603137 Russian Federation
| | - Anton V. Cherkasov
- G.A. Razuvaev Institute of Organometallic Chemistry of Russian Academy of Sciences Tropinina str., 49, Nizhny Novgorod 603137 Russian Federation
| | - Evgeny V. Baranov
- G.A. Razuvaev Institute of Organometallic Chemistry of Russian Academy of Sciences Tropinina str., 49, Nizhny Novgorod 603137 Russian Federation
| | - Roman V. Rumyantcev
- G.A. Razuvaev Institute of Organometallic Chemistry of Russian Academy of Sciences Tropinina str., 49, Nizhny Novgorod 603137 Russian Federation
| | - Elena V. Sazonova
- Chemical DepartmentLobachevsky State University of Nizhny Novgorod Gagarina Pr., 23, Nizhny Novgorod 603950 Russian Federation
| | - Alexander N. Artemov
- Chemical DepartmentLobachevsky State University of Nizhny Novgorod Gagarina Pr., 23, Nizhny Novgorod 603950 Russian Federation
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9
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A density functional theory investigation of the fragmentation mechanism of deprotonated asparagine. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Zobel D, Strumpel M. Electron density: historical remarks with a focus on the Berlin school. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The history of electron density (ED) research is surveyed and its historical highlights in the 20th century are summarized. The progress, reached at the beginnig of the 21st century, is described including contributions from the Berlin school. Key experimental advances concern X-ray sources and synchrotron radiation, measuring reflection data at very low temperatures (down to ~10 K), as well as the introduction of area detectors. Methodological progress was reached by new software systems for the refinement and analysis of ED data sets. This allowed to obtain quantitative ED properties, making use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM). More recently methods, which combine experimental X-ray data and quantum-chemically derived wave functions, established the rapidly developing new field of “Quantum Crystallography.”
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Affiliation(s)
- Dieter Zobel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
| | - Marianna Strumpel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
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11
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Koenig JJ, Neudörfl JM, Hansen A, Breugst M. Redetermination of the solvent-free crystal structure of l-proline. Acta Crystallogr E Crystallogr Commun 2018; 74:1067-1070. [PMID: 30116563 PMCID: PMC6072995 DOI: 10.1107/s2056989018009490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/02/2018] [Indexed: 12/03/2022]
Abstract
The title compound, (S)-pyrrolidine-2-carb-oxy-lic acid (C5H9NO2), commonly known as l-proline, crystallized without the inclusion of any solvent or water mol-ecules through the slow diffusion of diethyl ether into a saturated solution of l-proline in ethanol. l-Proline crystallized in its zwitterionic form and the mol-ecules are linked via N-H⋯O hydrogen bonds, resulting in a two-dimensional network. In comparison to the only other publication of a single-crystal structure of l-proline without inclusions [Kayushina & Vainshtein (1965 ▸). Kristallografiya, 10, 833-844], the R1 value is significantly improved (0.039 versus 0.169) and thus, our data provides higher precision structural information.
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Affiliation(s)
- Jonas J. Koenig
- Department für Chemie, Universität zu Köln, Greinstrasse 4, 50939 Köln, Germany
| | - Jörg-M. Neudörfl
- Department für Chemie, Universität zu Köln, Greinstrasse 4, 50939 Köln, Germany
| | - Anne Hansen
- Department für Chemie, Universität zu Köln, Greinstrasse 4, 50939 Köln, Germany
| | - Martin Breugst
- Department für Chemie, Universität zu Köln, Greinstrasse 4, 50939 Köln, Germany
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12
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Famiano MA, Boyd RN, Kajino T, Onaka T, Mo Y. Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life. Sci Rep 2018; 8:8833. [PMID: 29891867 PMCID: PMC5995967 DOI: 10.1038/s41598-018-27110-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/25/2018] [Indexed: 11/12/2022] Open
Abstract
Magnetochiral phenomena may be responsible for the selection of chiral states of biomolecules in meteoric environments. For example, the Supernova Amino Acid Processing (SNAAP) Model was proposed previously as a possible mode of magnetochiral selection of amino acids by way of the weak interaction in strong magnetic fields. In earlier work, this model was shown to produce an enantiomeric excess (ee) as high as 0.014% for alanine. In this paper we present the results of molecular quantum chemistry calculations from which ees are determined for the α-amino acids plus isovaline and norvaline, which were found to have positive ees in meteorites. Calculations are performed for both isolated and aqueous states. In some cases, the aqueous state was found to produce larger ees reaching values as high as a few percent under plausible conditions.
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Affiliation(s)
- Michael A Famiano
- Department of Physics and Joint Institute for Nuclear Astrophysics, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA. .,National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.
| | - Richard N Boyd
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Physics, Department of Astronomy, The Ohio State Univ., Columbus, OH, 43210, USA
| | - Toshitaka Kajino
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Physics and Nuclear Energy Engineering, Beihang Univ. (Beijing Univ. of Aeronautics and Astronautics), Beijing, 100083, P.R. China
| | - Takashi Onaka
- Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yirong Mo
- Department of Chemistry, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA
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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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14
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Woińska M, Grabowsky S, Dominiak PM, Woźniak K, Jayatilaka D. Hydrogen atoms can be located accurately and precisely by x-ray crystallography. SCIENCE ADVANCES 2016; 2:e1600192. [PMID: 27386545 PMCID: PMC4928899 DOI: 10.1126/sciadv.1600192] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/28/2016] [Indexed: 05/14/2023]
Abstract
Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2–Biologie/Chemie, Universität Bremen, Leobener Str. NW2, 28359 Bremen, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
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15
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Michaelis VK, Keeler EG, Ong TC, Craigen KN, Penzel S, Wren JEC, Kroeker S, Griffin RG. Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR. J Phys Chem B 2015; 119:8024-36. [PMID: 25996165 PMCID: PMC4894719 DOI: 10.1021/acs.jpcb.5b04647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Kimberley N. Craigen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Susanne Penzel
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - John E. C. Wren
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Scott Kroeker
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
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Abstract
Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak through to very strong H-bonds.
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Affiliation(s)
- Patricia A Hunt
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
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17
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Görbitz CH. Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2014.964229] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Görbitz CH, Karen P. Twin displacive phase transitions in amino acid quasiracemates. J Phys Chem B 2015; 119:4975-84. [PMID: 25794326 DOI: 10.1021/acs.jpcb.5b01483] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three quasiracemates, L-norleucine:D-methionine, L-norvaline:D-norleucine, and L-norvaline:D-methionine, were crystallized to see how they differ from regular racemates in terms of crystal structure (studied by single-crystal X-ray diffraction) and of thermally induced phase transitions (studied by differential scanning calorimetry). Two types of transitions are detected between 100 and 450 K and structurally characterized: (1) displacive transitions of the molecular bilayers that form the crystal and (2) continuous or discontinuous disordering transitions in the amino acid side chains. Uniquely for the quasiracemates, the displacive transition proceeds in two close steps as only one surface of each molecular bilayer slides at first, upon forming an intermediate phase, while the other surface follows at a slightly higher temperature. Altogether, 18 new single-crystal structure-refinement data sets are reported for these three quasiracemates.
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Affiliation(s)
| | - Pavel Karen
- Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
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Breuers V, Lehmann CW, Frank W. Unusual Bonding and Properties in Main Group Element Chemistry: Rational Synthesis, Characterization, and Experimental Electron Density Determination of Mixed-Valent Tetraphosphetes. Chemistry 2015; 21:4596-606. [PMID: 25703334 DOI: 10.1002/chem.201406131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Verena Breuers
- Institut für Anorganische Chemie und Strukturchemie, Lehrstuhl II: Material- und Strukturforschung, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany), Fax: (+49) 211 81-14146.
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Krawczuk A, Macchi P. Charge density analysis for crystal engineering. Chem Cent J 2014; 8:68. [PMID: 25520749 PMCID: PMC4266768 DOI: 10.1186/s13065-014-0068-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/30/2014] [Indexed: 07/13/2024] Open
Abstract
This review reports on the application of charge density analysis in the field of crystal engineering, which is one of the most growing and productive areas of the entire field of crystallography. While methods to calculate or measure electron density are not discussed in detail, the derived quantities and tools, useful for crystal engineering analyses, are presented and their applications in the recent literature are illustrated. Potential developments and future perspectives are also highlighted and critically discussed. Graphical abstractᅟ
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Affiliation(s)
- Anna Krawczuk
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, Krakow, 30-060 Poland
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, 3012 Switzerland
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21
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Derrar SN, Sekkal-Rahal M, Derreumaux P, Springborg M. Theoretical study of the NLO responses of some natural and unnatural amino acids used as probe molecules. J Mol Model 2014; 20:2388. [DOI: 10.1007/s00894-014-2388-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
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Held J, van Smaalen S. The active site of hen egg-white lysozyme: flexibility and chemical bonding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1136-46. [PMID: 24699657 PMCID: PMC3975892 DOI: 10.1107/s1399004714001928] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 01/27/2014] [Indexed: 11/10/2022]
Abstract
Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.
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Affiliation(s)
- Jeanette Held
- Laboratory of Crystallography, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, D-95440 Bayreuth, Germany
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23
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Cukrowski I, de Lange JH, Mitoraj M. Physical Nature of Interactions in ZnII Complexes with 2,2′-Bipyridyl: Quantum Theory of Atoms in Molecules (QTAIM), Interacting Quantum Atoms (IQA), Noncovalent Interactions (NCI), and Extended Transition State Coupled with Natural Orbitals for Chemical Valence (ETS-NOCV) Comparative Studies. J Phys Chem A 2014; 118:623-37. [DOI: 10.1021/jp410744x] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural
and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Jurgens H. de Lange
- Department of Chemistry, Faculty of Natural
and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Mariusz Mitoraj
- K. Gumiński Department of Theoretical
Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena
3, 30-060 Cracow, Poland
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24
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Görbitz CH, Leirvåg AB, Jacobsen Ø. Hydrogen bond architecture in crystal structures of N-alkylated hydrophobic amino acids. CrystEngComm 2014. [DOI: 10.1039/c4ce01412j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of N-alkylated hydrophobic amino acids, including five new compounds, show robust and characteristic hydrogen bond patterns.
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Affiliation(s)
- C. H. Görbitz
- Department of Chemistry
- University of Oslo
- N0315 Oslo, Norway
| | - A. B. Leirvåg
- Department of Chemistry
- University of Oslo
- N0315 Oslo, Norway
| | - Ø. Jacobsen
- Department of Chemistry
- University of Oslo
- N0315 Oslo, Norway
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25
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Jagannatha Prathapa S, Held J, van Smaalen S. Topological Properties of Chemical Bonds from Static and Dynamic Electron Densities. Z Anorg Allg Chem 2013; 639:2047-2056. [PMID: 25995522 PMCID: PMC4431502 DOI: 10.1002/zaac.201200535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 11/18/2022]
Abstract
Dynamic and static electron densities (EDs) based on the independent spherical atom model (IAM) and multipole (MP) models of crambin were successfully computed, holding no series-termination effects. The densities are compared to EDs of small biological molecules at diverse temperatures. It is outlined that proteins exhibit an intrinsic flexibility, present as frozen disorder at 100 K, in contrast to small molecules. The flexibility of the proteins is reflected by atomic displacement parameters (B-factors), which are considerably larger than for small molecules at 298 K. Thus, an optimal deconvolution of deformation density and thermal motion is not guaranteed, which prevents a free refinement of MP parameters but allows an application of transferable, fixed MP parameters. The analysis of the topological properties, such as the density at bond critical points (BCPs) and the Laplacian, reveals systematic differences between static and dynamic EDs. Zero-point-vibrations, yet present in dynamic EDs at low temperature, affect but marginally the EDs of small molecules. The zero-point-vibrations cause a smearing of the ED, which becomes more pronounced with increasing temperature. Topological properties, primarily the Laplacian, of covalent bonds appear to be more sensitive to effects by temperature and the polarity of the bonds. However, dynamic EDs at ca. 20 K based on MP models provide a good characterization of chemical bonding. Both the density at BCPs and the Laplacian of hydrogen bonds constitute similar values from static and dynamic EDs for all studied temperatures. Deformation densities demonstrate the necessity of the employment of MP parameters in order to comprise the nature of covalent bonds. The character of hydrogen bonds can be roughly pictured by IAM, whereas MP parameters are recommended for a classification of hydrogen bonds beyond a solely interpretation of topological properties.
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Affiliation(s)
| | - Jeanette Held
- Laboratory of Crystallography, University of Bayreuth Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth Universitaetsstrasse 30, 95447 Bayreuth, Germany
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26
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Williams MRC, Aschaffenburg DJ, Ofori-Okai BK, Schmuttenmaer CA. Intermolecular Vibrations in Hydrophobic Amino Acid Crystals: Experiments and Calculations. J Phys Chem B 2013; 117:10444-61. [DOI: 10.1021/jp406730a] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael R. C. Williams
- Department of Chemistry, Yale University, P.O.
Box 208107, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Daniel J. Aschaffenburg
- Department of Chemistry, Yale University, P.O.
Box 208107, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Benjamin K. Ofori-Okai
- Department of Chemistry, Yale University, P.O.
Box 208107, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Charles A. Schmuttenmaer
- Department of Chemistry, Yale University, P.O.
Box 208107, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
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27
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Zhurov VV, Pinkerton AA. Charge Density Analysis of an Organic Ferroelectric. Croconic Acid: an Experimental and Theoretical Study. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201200506] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Tyunina EY, Badelin VG. Sublimation effects and volume effects in the crystals of amino acids, peptides, and their some acetyl derivatives. RUSS J GEN CHEM+ 2013. [DOI: 10.1134/s1070363213040178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Görbitz CH, Alebachew F, Petříček V. Solid-State Phase Transitions of dl-Aminobutyric Acid. J Phys Chem B 2012; 116:10715-21. [DOI: 10.1021/jp305016k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fassil Alebachew
- Department
of Chemistry, University of Oslo, N-0315
Oslo, Norway
| | - Václav Petříček
- Institute
of Physics, Academy of Sciences of the Czech Republic v.v.i., Na
Slovance 2, 182 21, Praha 8, Czech Republic
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30
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Jamróz MH, Rode JE, Ostrowski S, Lipiński PFJ, Dobrowolski JC. Chirality Measures of α-Amino Acids. J Chem Inf Model 2012; 52:1462-79. [DOI: 10.1021/ci300057h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał H. Jamróz
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Joanna E. Rode
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Sławomir Ostrowski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Piotr F. J. Lipiński
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Industrial Chemistry Research
Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
- National Medicines Institute,
30/34 Chełmska Street, 00-725 Warsaw, Poland
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31
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Berendt RT, Munson EJ. Effect of enantiomeric ratio and preparation method on proline crystal form. CrystEngComm 2012. [DOI: 10.1039/c2ce06445f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Rykounov AA, Stash AI, Zhurov VV, Zhurova EA, Pinkerton AA, Tsirelson VG. On the transferability of QTAIMC descriptors derived from X-ray diffraction data and DFT calculations: substituted hydropyrimidine derivatives. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2011; 67:425-36. [DOI: 10.1107/s0108768111033015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/15/2011] [Indexed: 11/11/2022]
Abstract
The combined study of electron-density features in three substituted hydropyrimidines of the Biginelli compound family has been fulfilled. Results of the low-temperature X-ray diffraction measurements and density functional theory (DFT) B3LYP/6-311++G** calculations of these compounds are described. The experimentally derived atomic and bonding characteristics determined within the quantum-topological theory of atoms in molecules and crystals (QTAIMC) were demonstrated to be fully transferable within chemically similar structures such as the Biginelli compounds. However, for certain covalent bonds they differ significantly from the theoretical results because of insufficient flexibility of the atom-centered multipole electron density model. It was concluded that currently analysis of the theoretical electron density provides a more reliable basis for the determination of the transferability of QTAIMC descriptors for molecular structures. Empirical corrections making the experimentally derived QTAIMC bond descriptors more transferable are proposed.
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Williams MRC, True AB, Izmaylov AF, French TA, Schroeck K, Schmuttenmaer CA. Terahertz spectroscopy of enantiopure and racemic polycrystalline valine. Phys Chem Chem Phys 2011; 13:11719-30. [PMID: 21603704 DOI: 10.1039/c1cp20594c] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Experimental and computational THz (or far-infrared) spectra of polycrystalline valine samples are reported. The experimental spectra have been measured using THz time-domain spectroscopy. Spectra of the pure enantiomers, both D and L, as well as the dl racemate have been taken at room temperature and low temperature (78 K). The spectra of the pure D and L enantiomers are essentially identical, and they are markedly different from the DL racemate. In addition, a temperature-dependent study of L-valine was undertaken in which the absorption maxima were found to red shift as a function of increasing temperature. The vibrational absorption spectra (frequencies and intensities) were calculated using the harmonic approximation with the Perdew-Burke-Ernzerhof (PBE) functional, localized atomic orbital basis sets, and periodic boundary conditions. The calculated and experimental spectra are in good qualitative agreement. A general method of quantifying the degree to which a calculated mode is intermolecular versus intramolecular is demonstrated, with the intermolecular motions further separated into translational versus rotational/librational motion. This allows straightforward comparison of spectra calculated using different basis sets or other constraints.
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Affiliation(s)
- Michael R C Williams
- Yale University, Department of Chemistry, PO Box 208107, 225 Prospect St., New Haven, CT 06520-8107, USA
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34
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Chiral recognition and complexation behaviour of β-CyD vs. l- and dl-serine by FTIR-ATR spectroscopy. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Görbitz CH. Solid-State Phase Transitions in dl-Norvaline Studied by Single-Crystal X-ray Diffraction. J Phys Chem B 2011; 115:2447-53. [DOI: 10.1021/jp111332m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Ejgenberg M, Mastai Y. Conglomerate crystallization on self-assembled monolayers. Chem Commun (Camb) 2011; 47:12161-3. [DOI: 10.1039/c1cc14952k] [Citation(s) in RCA: 13] [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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37
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Koritsanszky T, Volkov A, Chodkiewicz M. New Directions in Pseudoatom-Based X-Ray Charge Density Analysis. ELECTRON DENSITY AND CHEMICAL BONDING II 2011. [DOI: 10.1007/430_2010_32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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38
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Prikhodchenko PV, Medvedev AG, Tripol'skaya TA, Churakov AV, Wolanov Y, Howard JAK, Lev O. Crystal structures of natural amino acid perhydrates. CrystEngComm 2011. [DOI: 10.1039/c0ce00481b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Engels B, Schmidt TC, Gatti C, Schirmeister T, Fink RF. Challenging Problems in Charge Density Determination: Polar Bonds and Influence of the Environment. ELECTRON DENSITY AND CHEMICAL BONDING II 2011. [DOI: 10.1007/430_2010_36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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40
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New SY, Wu X, Bai SQ, Koh LL, Hor TSA, Xue F. Lipid-bilayer-mimicking solid-state structures of Cu(ii) and Ni(ii) with l-tryptophan and l-tyrosine Schiff base derivatives. CrystEngComm 2011. [DOI: 10.1039/c0ce00986e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Tadeusiak E, Kruszynski R, Trzesowska-Kruszynska A, Sieranski T, Lewinski B. Determination of enantiomeric excess of leucine and valine by X-ray powder diffraction. ACTA ACUST UNITED AC 2010. [DOI: 10.5155/eurjchem.1.4.319-321.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Görbitz CH. L-2-Aminobutyric acid: two fully ordered polymorphs with Z′ = 4. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:253-9. [DOI: 10.1107/s0108768110005732] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 02/11/2010] [Indexed: 11/10/2022]
Abstract
The crystal structure of L-2-aminobutyric acid, an L-alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z′ = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than α-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network.
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Dobrowolski JC, Jamróz MH, Kołos R, Rode JE, Cyrański MK, Sadlej J. IR low-temperature matrix, X-ray and ab initio study on l-isoserine conformations. Phys Chem Chem Phys 2010; 12:10818-30. [DOI: 10.1039/c0cp00016g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Abstract
This account takes to task papers that criticize the definition of a bond path as a criterion for the bonding between the atoms it links by mistakenly identifying it with a chemical bond. It is argued that the notion of a chemical bond is too restrictive to account for the physics underlying the broad spectrum of interactions between atoms and molecules that determine the properties of matter. A bond path on the other hand, as well as being accessible to experimental verification and subject to the theorems of quantum mechanics, is applicable to any and all of the interactions that account for the properties of matter. It is shown that one may define a bond path operator as a Dirac observable, making the bond path the measurable expectation value of a quantum mechanical operator. Particular attention is given to van der Waals interactions that traditionally are assumed to represent attractive interactions that are distinct from chemical bonding. They are assumed by some to act in concert with Pauli repulsions to account for the existence of condensed states of molecules. It is such dichotomies of interpretation that are resolved by the experimental detection of bond paths and the delineation of their properties in molecular crystals. Specific criticisms of the stabilization afforded by the presence of bond paths derived from spectroscopic measurements performed on dideuteriophenanthrene are shown to be physically unsound. The concept of a bond path as a "bridge of density" linking bonded atoms was introduced by London in 1928 following the definition of the electron density by Schrödinger in 1926. These papers marked the beginning of the theory of atoms in molecules linked by bond paths.
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Affiliation(s)
- Richard F W Bader
- Department of Chemistry, McMaster University, Hamilton, ON L7L 2T1, Canada
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46
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Netzel J, van Smaalen S. Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM). ACTA CRYSTALLOGRAPHICA. SECTION B, STRUCTURAL SCIENCE 2009; 65:624-38. [PMID: 19767685 PMCID: PMC2749645 DOI: 10.1107/s0108768109026767] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 07/08/2009] [Indexed: 11/10/2022]
Abstract
Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T approximately 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l(max) = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C-C, C-N and C-O bonds, and for hydrogen bonds together with covalent C-H and N-H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds.
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Affiliation(s)
- Jeanette Netzel
- Laboratory of Crystallography, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, D-95440 Bayreuth, Germany
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Sousa SF, Fernandes PA, Ramos MJ. Gas-Phase Geometry Optimization of Biological Molecules as a Reasonable Alternative to a Continuum Environment Description: Fact, Myth, or Fiction? J Phys Chem A 2009; 113:14231-6. [DOI: 10.1021/jp902213t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sérgio Filipe Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro Alexandrino Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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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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Boldyreva EV, Kolesnik EN, Drebushchak TN, Sowa H, Ahsbahs H, Seryotkin YV. A comparative study of the anisotropy of lattice strain induced in the crystals of DL-serine by cooling down to 100 K, or by increasing pressure up to 8.6 GPa. A comparison with L-serine. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.2006.221.2.150] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SummaryThe anisotropy of lattice strain in the crystals of DL-serine (P21/n) on cooling down to 100 K and with increasing hydrostatic pressure up to 8.6 GPa was studied by single-crystal X-ray diffraction. In contrast to L-serine undergoing pressure-induced phase transitions at about 5 and 8 GPa, no phase transitions were observed in DL-serine at least up to 8.6 GPa (the highest pressure reached in the experiment). The anisotropy of strain in DL-serine on cooling was shown to be radically different from that with increasing pressure. The response of the crystal structure of DL-serine to cooling and to increasing pressure was considerably different from that of L-serine.
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Vener MV, Egorova AN, Fomin DP, Tsirel’son VG. A quantum-topological analysis of noncovalent interactions in secondary polyalanine structures. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2009. [DOI: 10.1134/s1990793109040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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