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Fast Quantum Approach for Evaluating the Energy of Non-Covalent Interactions in Molecular Crystals: The Case Study of Intermolecular H-Bonds in Crystalline Peroxosolvates. Molecules 2022; 27:molecules27134082. [PMID: 35807323 PMCID: PMC9268483 DOI: 10.3390/molecules27134082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Energy/enthalpy of intermolecular hydrogen bonds (H-bonds) in crystals have been calculated in many papers. Most of the theoretical works used non-periodic models. Their applicability for describing intermolecular H-bonds in solids is not obvious since the crystal environment can strongly change H-bond geometry and energy in comparison with non-periodic models. Periodic DFT computations provide a reasonable description of a number of relevant properties of molecular crystals. However, these methods are quite cumbersome and time-consuming compared to non-periodic calculations. Here, we present a fast quantum approach for estimating the energy/enthalpy of intermolecular H-bonds in crystals. It has been tested on a family of crystalline peroxosolvates in which the H∙∙∙O bond set fills evenly (i.e., without significant gaps) the range of H∙∙∙O distances from ~1.5 to ~2.1 Å typical for strong, moderate, and weak H-bonds. Four of these two-component crystals (peroxosolvates of macrocyclic ethers and creatine) were obtained and structurally characterized for the first time. A critical comparison of the approaches for estimating the energy of intermolecular H-bonds in organic crystals is carried out, and various sources of errors are clarified.
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Vener MV, Churakov AV, Voronin AP, Parashchuk OD, Artobolevskii SV, Alatortsev OA, Makhrov DE, Medvedev AG, Filarowski A. Comparison of Proton Acceptor and Proton Donor Properties of H 2O and H 2O 2 in Organic Crystals of Drug-like Compounds: Peroxosolvates vs. Crystallohydrates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030717. [PMID: 35163982 PMCID: PMC8838768 DOI: 10.3390/molecules27030717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 01/01/2023]
Abstract
Two new peroxosolvates of drug-like compounds were synthesized and studied by a combination of X-ray crystallographic, Raman spectroscopic methods, and periodic DFT computations. The enthalpies of H-bonds formed by hydrogen peroxide (H2O2) as a donor and an acceptor of protons were compared with the enthalpies of analogous H-bonds formed by water (H2O) in isomorphic (isostructural) hydrates. The enthalpies of H-bonds formed by H2O2 as a proton donor turned out to be higher than the values of the corresponding H-bonds formed by H2O. In the case of H2O2 as a proton acceptor in H-bonds, the ratio appeared reversed. The neutral O∙∙∙H-O/O∙∙∙H-N bonds formed by the lone electron pair of the oxygen atom of water were the strongest H-bonds in the considered crystals. In the paper, it was found out that the low-frequency Raman spectra of isomorphous crystalline hydrate and peroxosolvate of N-(5-Nitro-2-furfurylidene)-1-aminohydantoin are similar. As for the isostructural hydrate and peroxosolvate of the salt of protonated 2-amino-nicotinic acid and maleic acid monoanion, the Raman spectra are different.
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Affiliation(s)
- Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.V.C.); (A.G.M.)
- Correspondence: (M.V.V.); (A.F.)
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.V.C.); (A.G.M.)
| | | | - Olga D. Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Sergei V. Artobolevskii
- Faculty of Natural Science, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia; (S.V.A.); (O.A.A.); (D.E.M.)
| | - Oleg A. Alatortsev
- Faculty of Natural Science, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia; (S.V.A.); (O.A.A.); (D.E.M.)
| | - Denis E. Makhrov
- Faculty of Natural Science, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia; (S.V.A.); (O.A.A.); (D.E.M.)
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.V.C.); (A.G.M.)
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland
- Correspondence: (M.V.V.); (A.F.)
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Buldashov IA, Medvedev AG, Mikhaylov AA, Churakov AV, Lev O, Prikhodchenko PV. Non-covalent interactions of the hydroperoxo group in crystalline adducts of organic hydroperoxides and their potassium salts. CrystEngComm 2022. [DOI: 10.1039/d2ce01017h] [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
X-ray diffraction of three new stable cocrystals of potassium salts of organic hydroperoxides with molecular hydroperoxides reveals strong charge-assisted ROO−⋯HOOR H-bonds.
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Affiliation(s)
- Ivan A. Buldashov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
- Faculty of Chemistry, National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow 101000, Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Ovadia Lev
- The Casali Center, The Institute of Chemistry, and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
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Saunders LK, Pallipurath AR, Gutmann MJ, Nowell H, Zhang N, Allan DR. A quantum crystallographic approach to short hydrogen bonds. CrystEngComm 2021; 23:6180-6190. [PMID: 34588923 PMCID: PMC8436739 DOI: 10.1039/d1ce00355k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
Abstract
In this work we use high-resolution synchrotron X-ray diffraction for electron density mapping, in conjunction with ab initio modelling, to study short O-H⋯O and O+-H⋯O- hydrogen bonds whose behaviour is known to be tuneable by temperature. The short hydrogen bonds have donor-acceptor distances in the region of 2.45 Å and are formed in substituted urea and organic acid molecular complexes of N,N'-dimethylurea oxalic acid 2 : 1 (1), N,N-dimethylurea 2,4-dinitrobenzoate 1 : 1 (2) and N,N-dimethylurea 3,5-dinitrobenzoic acid 2 : 2 (3). From the combined analyses, these complexes are found to fall within the salt-cocrystal continuum and exhibit short hydrogen bonds that can be characterised as both strong and electrostatic (1, 3) or very strong with a significant covalent contribution (2). An additional charge assisted component is found to be important in distinguishing the relatively uncommon O-H⋯O pseudo-covalent interaction from a typical strong hydrogen bond. The electron density is found to be sensitive to the extent of static proton transfer, presenting it as a useful parameter in the study of the salt-cocrystal continuum. From complementary calculated hydrogen atom potentials, we attribute changes in proton position to the molecular environment. Calculated potentials also show zero barrier to proton migration, forming an 'energy slide' between the donor and acceptor atoms. The better fundamental understanding of the short hydrogen bond in the 'zone of fluctuation' presented in a salt-cocrystal continuum, enabled by studies like this, provide greater insight into their related properties and can have implications in the regulation of pharmaceutical materials.
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Affiliation(s)
- Lucy K Saunders
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Anuradha R Pallipurath
- School of Chemical and Process Engineering, University of Leeds Leeds LS2 9JT UK
- Research Complex at Harwell Didcot Oxfordshire OX11 0DE UK
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Advanced Crystallization, University of Strathclyde G1 1RD UK
| | - Matthias J Gutmann
- ISIS Pulsed Muon and Neutron Source, Rutherford Appleton Laboratory, Harwell Oxford Didcot OX11 0QX UK
| | - Harriott Nowell
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Ningjin Zhang
- Chemistry, Faculty of Natural and Environmental Sciences, Highfield Campus, University of Southampton Southampton SO17 1HE UK
| | - David R Allan
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
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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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Medvedev AG, Churakov AV, Prikhodchenko PV, Lev O, Vener MV. Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions. Molecules 2020; 26:E26. [PMID: 33374602 PMCID: PMC7793138 DOI: 10.3390/molecules26010026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 01/22/2023] Open
Abstract
Despite the technological importance of urea perhydrate (percarbamide) and sodium percarbonate, and the growing technological attention to solid forms of peroxide, fewer than 45 peroxosolvates were known by 2000. However, recent advances in X-ray diffractometers more than tripled the number of structurally characterized peroxosolvates over the last 20 years, and even more so, allowed energetic interpretation and gleaning deeper insight into peroxosolvate stability. To date, 134 crystalline peroxosolvates have been structurally resolved providing sufficient insight to justify a first review article on the subject. In the first chapter of the review, a comprehensive analysis of the structural databases is carried out revealing the nature of the co-former in crystalline peroxosolvates. In the majority of cases, the coformers can be classified into three groups: (1) salts of inorganic and carboxylic acids; (2) amino acids, peptides, and related zwitterions; and (3) molecular compounds with a lone electron pair on nitrogen and/or oxygen atoms. The second chapter of the review is devoted to H-bonding in peroxosolvates. The database search and energy statistics revealed the importance of intermolecular hydrogen bonds (H-bonds) which play a structure-directing role in the considered crystals. H2O2 always forms two H-bonds as a proton donor, the energy of which is higher than the energy of analogous H-bonds existing in isostructural crystalline hydrates. This phenomenon is due to the higher acidity of H2O2 compared to water and the conformational mobility of H2O2. The dihedral angle H-O-O-H varies from 20 to 180° in crystalline peroxosolvates. As a result, infinite H-bonded 1D chain clusters are formed, consisting of H2O2 molecules, H2O2 and water molecules, and H2O2 and halogen anions. H2O2 can form up to four H-bonds as a proton acceptor. The third chapter of the review is devoted to energetic computations and in particular density functional theory with periodic boundary conditions. The approaches are considered in detail, allowing one to obtain the H-bond energies in crystals. DFT computations provide deeper insight into the stability of peroxosolvates and explain why percarbamide and sodium percarbonate are stable to H2O2/H2O isomorphic transformations. The review ends with a description of the main modern trends in the synthesis of crystalline peroxosolvates, in particular, the production of peroxosolvates of high-energy compounds and mixed pharmaceutical forms with antiseptic and analgesic effects.
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Affiliation(s)
- Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
| | - Ovadia Lev
- The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia; (A.G.M.); (A.V.C.); (P.V.P.)
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia
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Levina EO, Khrenova MG, Tsirelson VG. Effect of Substituents in Hydrolyzed Cephalosporins on Intramolecular O–H···N Bond. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420050131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Saunders LK, Nowell H, Hatcher LE, Shepherd HJ, Teat SJ, Allan DR, Raithby PR, Wilson CC. Exploring short strong hydrogen bonds engineered in organic acid molecular crystals for temperature dependent proton migration behaviour using single crystal synchrotron X-ray diffraction (SCSXRD). CrystEngComm 2019. [DOI: 10.1039/c9ce00925f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Short strong hydrogen bonds in multi-component organic acid molecular crystals exhibit temperature dependent proton migration for certain HB donor–acceptor distances.
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Affiliation(s)
- Lucy K. Saunders
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot OX11 0DE
- UK
| | - Harriott Nowell
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot OX11 0DE
- UK
| | | | - Helena J. Shepherd
- School of Physical Sciences
- Ingram Building
- University of Kent
- Canterbury
- UK
| | - Simon J. Teat
- Advanced Light Source
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - David R. Allan
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot OX11 0DE
- UK
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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Vener MV, Chernyshov IY, Rykounov AA, Filarowski A. Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1380860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. V. Vener
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - I. Yu. Chernyshov
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A. A. Rykounov
- Theoretical Department, Russian Federal Nuclear Center – All-Russian Research Institute of Technical Physics (RFNC-VNIITF), Snezhinsk, Russia
| | - A. Filarowski
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
- Department of Physics, Industrial University of Tyumen, Tyumen, Russia
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Fedorov IA, Zhuravlev YN. First-principles study of the pressure effects on the structural and electronic properties of crystalline organic azide C10H8N6O4. J STRUCT CHEM+ 2016. [DOI: 10.1134/s0022476616060032] [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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Effects of the crystal structure and thermodynamic stability on solubility of bioactive compounds: DFT study of isoniazid cocrystals. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhurov VV, Pinkerton AA. Inter- and Intramolecular Interactions in Crystalline 2-Nitrobenzoic Acid—An Experimental and Theoretical QTAIM Analysis. J Phys Chem A 2015; 119:13092-100. [DOI: 10.1021/acs.jpca.5b10027] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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