1
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Egorov PA, Grishanov DA, Medvedev AG, Churakov AV, Mikhaylov AA, Ottenbacher RV, Bryliakov KP, Babak MV, Lev O, Prikhodchenko PV. Organoantimony Dihydroperoxides: Synthesis, Crystal Structures, and Hydrogen Bonding Networks. Inorg Chem 2023. [PMID: 37311066 DOI: 10.1021/acs.inorgchem.3c00929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite growing interest in the potential applications of p-block hydroperoxo complexes, the chemistry of inorganic hydroperoxides remains largely unexplored. For instance, single-crystal structures of antimony hydroperoxo complexes have not been reported to date. Herein, we present the synthesis of six triaryl and trialkylantimony dihydroperoxides [Me3Sb(OOH)2, Me3Sb(OOH)2·H2O, Ph3Sb(OOH)2·0.75(C4H8O), Ph3Sb(OOH)2·2CH3OH, pTol3Sb(OOH)2, pTol3Sb(OOH)2·2(C4H8O)], obtained by the reaction of the corresponding dibromide antimony(V) complexes with an excess of highly concentrated hydrogen peroxide in the presence of ammonia. The obtained compounds were characterized by single-crystal and powder X-ray diffraction, Fourier transform infrared and Raman spectroscopies, and thermal analysis. The crystal structures of all six compounds reveal hydrogen-bonded networks formed by hydroperoxo ligands. In addition to the previously reported double hydrogen bonding, new types of hydrogen-bonded motifs formed by hydroperoxo ligands were found, including infinite hydroperoxo chains. Solid-state density functional theory calculation of Me3Sb(OOH)2 revealed reasonably strong hydrogen bonding between OOH ligands with an energy of 35 kJ/mol. Additionally, the potential application of Ph3Sb(OOH)2·0.75(C4H8O) as a two-electron oxidant for the enantioselective epoxidation of olefins was investigated in comparison with Ph3SiOOH, Ph3PbOOH, t-BuOOH, and H2O2.
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Affiliation(s)
- Pavel A Egorov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russian Federation
| | - Dmitry A Grishanov
- Casali Center of Applied Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russian Federation
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russian Federation
| | - Alexey A Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russian Federation
| | - Roman V Ottenbacher
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Konstantin P Bryliakov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninskii pr. 47, Moscow 119991, Russian Federation
| | - Maria V Babak
- Drug Discovery Lab, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Ovadia Lev
- Casali Center of Applied Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russian Federation
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2
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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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3
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Voronin AP, Surov AO, Churakov AV, Parashchuk OD, Rykounov AA, Vener MV. Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate. Molecules 2020; 25:E2386. [PMID: 32455564 PMCID: PMC7287603 DOI: 10.3390/molecules25102386] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt > 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the Elatt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals.
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Affiliation(s)
- Alexander P. Voronin
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Artem O. Surov
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Andrei V. Churakov
- Department of Crystal Chemistry and X-ray Diffraction, N.S. Kurnakov Institute of General and Inorganic Chemistry of RAS, 119991 Moscow, Russia;
| | - Olga D. Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey A. Rykounov
- Theoretical Department, FSUE “RFNC-VNIITF Named after Academ. E.I. Zababakhin”, 456770 Snezhinsk, Russia;
| | - Mikhail V. Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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Churakov AV, Grishanov DA, Medvedev AG, Mikhaylov AA, Vener MV, Navasardyan MA, Tripol'skaya TA, Lev O, Prikhodchenko PV. Stabilization of hydrogen peroxide by hydrogen bonding in the crystal structure of 2-aminobenzimidazole perhydrate. CrystEngComm 2020. [DOI: 10.1039/d0ce00096e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
2-Aminobenzimidazole peroxosolvate – the third H2O2 crystalline adduct stabilized with the maximum possible number of hydrogen bonds formed by one hydrogen peroxide molecule.
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Affiliation(s)
- Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmitry A. Grishanov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- The Casali Center
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- Department of Quantum Chemistry
| | - Mger A. Navasardyan
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Tatiana A. Tripol'skaya
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- 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
- Jerusalem 91904
- Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
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5
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Synthesis of high volumetric capacity graphene oxide-supported tellurantimony Na- and Li-ion battery anodes by hydrogen peroxide sol gel processing. J Colloid Interface Sci 2018; 512:165-171. [DOI: 10.1016/j.jcis.2017.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022]
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6
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Grishanov DA, Navasardyan MA, Medvedev AG, Lev O, Prikhodchenko PV, Churakov AV. Hydrogen Peroxide Insular Dodecameric and Pentameric Clusters in Peroxosolvate Structures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dmitry A. Grishanov
- Institute of General and Inorganic Chemistry RAS; Leninskii prosp. 31 119991 Moscow Russia
| | - Mger A. Navasardyan
- Institute of General and Inorganic Chemistry RAS; Leninskii prosp. 31 119991 Moscow Russia
| | - Alexander G. Medvedev
- Institute of General and Inorganic Chemistry RAS; Leninskii prosp. 31 119991 Moscow Russia
| | - Ovadia Lev
- The Casali Center of Applied Chemistry; The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Petr V. Prikhodchenko
- Institute of General and Inorganic Chemistry RAS; Leninskii prosp. 31 119991 Moscow Russia
- The Casali Center of Applied Chemistry; The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Andrei V. Churakov
- Institute of General and Inorganic Chemistry RAS; Leninskii prosp. 31 119991 Moscow Russia
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7
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Grishanov DA, Navasardyan MA, Medvedev AG, Lev O, Prikhodchenko PV, Churakov AV. Hydrogen Peroxide Insular Dodecameric and Pentameric Clusters in Peroxosolvate Structures. Angew Chem Int Ed Engl 2017; 56:15241-15245. [PMID: 28991407 DOI: 10.1002/anie.201709699] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 11/06/2022]
Abstract
Peroxosolvates of 2-aminonicotinic acid (I) and lidocaine N-oxide (II) including the largest insular hydrogen peroxide clusters were isolated and their crystal structures were determined by single-crystal X-ray diffraction. An unprecedented dodecameric hydrogen peroxide insular cluster was found in I. An unusual cross-like pentameric cluster was observed in the structure of II. The topology of the (H2 O2 )12 assembly was never observed for small-molecule clusters. In I and II new double and triple cross-orientational disorders of H2 O2 were found. Cluster II is the first example of a peroxosolvate crystal structure containing H2 O2 molecules with a homoleptic hydrogen peroxide environment. In II, a hydrogen bond between an H2 O2 molecule and a peptide group -CONH⋅⋅⋅O2 H2 was observed for the first time.
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Affiliation(s)
- Dmitry A Grishanov
- Institute of General and Inorganic Chemistry RAS, Leninskii prosp. 31, 119991, Moscow, Russia
| | - Mger A Navasardyan
- Institute of General and Inorganic Chemistry RAS, Leninskii prosp. 31, 119991, Moscow, Russia
| | - Alexander G Medvedev
- Institute of General and Inorganic Chemistry RAS, Leninskii prosp. 31, 119991, Moscow, Russia
| | - Ovadia Lev
- The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Petr V Prikhodchenko
- Institute of General and Inorganic Chemistry RAS, Leninskii prosp. 31, 119991, Moscow, Russia.,The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrei V Churakov
- Institute of General and Inorganic Chemistry RAS, Leninskii prosp. 31, 119991, Moscow, Russia
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8
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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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9
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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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10
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Theoretical Modeling of Vibrational Spectra and Proton Tunneling in Hydrogen-Bonded Systems. ADVANCES IN CHEMICAL PHYSICS 2016. [DOI: 10.1002/9781119165156.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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11
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Kuramshina GM, Vakula OA, Vakula NI, Majouga AG, Senyavin VM, Gorb LG, Leszczynski J. Conformations, vibrational spectra and force field of 1-methyl-2-(2′-pyridyl)benzimidazole: experimental data and density functional theory investigation in comparison with 2-(2′-pyridyl)benzimidazole. Struct Chem 2015. [DOI: 10.1007/s11224-015-0693-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Specific features of the extra strong intermolecular hydrogen bonds in crystals: Insights from the theoretical charge density analysis. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Loeffler MJ, Hudson RL. Descent without Modification? The Thermal Chemistry of H2O2 on Europa and Other Icy Worlds. ASTROBIOLOGY 2015; 15:453-461. [PMID: 26060983 DOI: 10.1089/ast.2014.1195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The strong oxidant H2O2 is known to exist in solid form on Europa and is suspected to exist on several other Solar System worlds at temperatures below 200 K. However, little is known of the thermal chemistry that H2O2 might induce under these conditions. Here, we report new laboratory results on the reactivity of solid H2O2 with eight different compounds in H2O-rich ices. Using infrared spectroscopy, we monitored compositional changes in ice mixtures during warming. The compounds CH4 (methane), C3H4 (propyne), CH3OH (methanol), and CH3CN (acetonitrile) were unaltered by the presence of H2O2 in ices, showing that exposure to either solid H2O2 or frozen H2O+H2O2 at cryogenic temperatures will not oxidize these organics, much less convert them to CO2. This contrasts strongly with the much greater reactivity of organics with H2O2 at higher temperatures, and particularly in the liquid and gas phases. Of the four inorganic compounds studied, CO, H2S, NH3, and SO2, only the last two reacted in ices containing H2O2, NH3 making NH4+ and SO2 making SO(4)2- by H+ and e- transfer, respectively. An important astrobiological conclusion is that formation of surface H2O2 on Europa and that molecule's downward movement with H2O-ice do not necessarily mean that all organics encountered in icy subsurface regions will be destroyed by H2O2 oxidation.
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Affiliation(s)
- Mark J Loeffler
- Astrochemistry Laboratory, NASA Goddard Space Flight Center , Greenbelt, Maryland
| | - Reggie L Hudson
- Astrochemistry Laboratory, NASA Goddard Space Flight Center , Greenbelt, Maryland
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14
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Surov AO, Voronin AP, Simagina AA, Churakov AV, Skachilova SY, Perlovich GL. Saccharin salts of biologically active hydrazone derivatives. NEW J CHEM 2015. [DOI: 10.1039/c5nj01532d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Crystal structures, solubility and formation thermodynamics of saccharin salts with biologically active hydrazone derivatives were investigated.
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Affiliation(s)
- Artem O. Surov
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Alexander P. Voronin
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Anna A. Simagina
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | | | | | - German L. Perlovich
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
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15
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Medvedev AG, Shishkina AV, Prikhodchenko PV, Lev O, Vener MV. The applicability of the dimeric heterosynthon concept to molecules with equivalent binding sites. A DFT study of crystalline urea–H2O2. RSC Adv 2015. [DOI: 10.1039/c5ra02498f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The limited applicability of the dimeric heterosynthon concept to a two-component urea–H2O2crystal is reported.
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Affiliation(s)
- A. G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- RAS
- Moscow
- Russia
- The Casali Institute of Applied Chemistry
| | | | | | - O. Lev
- The Casali Institute of Applied Chemistry
- The Institute of Chemistry
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - M. V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- RAS
- Moscow
- Russia
- Mendeleev University of Chemical Technology
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16
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Manin AN, Voronin AP, Manin NG, Vener MV, Shishkina AV, Lermontov AS, Perlovich GL. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations. J Phys Chem B 2014; 118:6803-14. [PMID: 24861612 DOI: 10.1021/jp5032898] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.
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Affiliation(s)
- Alex N Manin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences , 1, Academicheskaya, 153045 Ivanovo, Russia
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17
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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18
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Katsyuba SA, Vener MV, Zvereva EE, Fei Z, Scopelliti R, Laurenczy G, Yan N, Paunescu E, Dyson PJ. How strong is hydrogen bonding in ionic liquids? Combined X-ray crystallographic, infrared/Raman spectroscopic, and density functional theory study. J Phys Chem B 2013; 117:9094-105. [PMID: 23822750 DOI: 10.1021/jp405255w] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hydrogen bonding in ionic liquids based on the 1-(2'-hydroxylethyl)-3-methylimidazolium cation ([C₂OHmim](+)) and various anions ([A](-)) of differing H-bond acceptor strength, viz. hexafluorophosphate [PF6](-), tetrafluoroborate [BF₄](-), bis(trifluoromethanesulfonimide) [Tf₂N](-), trifluoromethylsulfonate [OTf](-), and trifluoroacetate [TFA](-), was studied by a range of spectroscopic and computational techniques and, in the case of [C₂OHmim][PF6], by single crystal X-ray diffraction. The first quantitative estimates of the energy (E(HB)) and the enthalpy (-ΔH(HB)) of H-bonds in bulk ILs were obtained from a theoretical analysis of the solid-state electron-density map of crystalline [C₂OHmim][PF6] and an analysis of the IR spectra in crystal and liquid samples. E(HB) for OH···[PF6](-) H-bonds amounts to ~3.4-3.8 kcal·mol(-1), whereas weaker H-bonds (2.8-3.1 kcal·mol(-1)) are formed between aromatic C2H group of imidazolium ring and the [PF6](-) anion. The enthalpy of the OH···[A](-) H-bonds follows the order: [PF6] (2.4 kcal·mol(-1)) < [BF₄] (3.3 kcal·mol(-1)) < [Tf₂N] (3.4 kcal·mol(-1)) < [OTf] (4.7 kcal·mol(-1)l) < [TFA] (6.2 kcal·mol(-1)). The formation of aggregates of self-associated [C₂OHmim](+) cations is present in liquid [C₂OHmim][PF6], [C₂OHmim][BF₄], and [C₂OHmim][Tf₂N], with the energy of the OH···OH H-bonds amounting to ~6 kcal·mol(-1). Multiple secondary interactions in the bulk ILs influence their structure, vibrational spectra, and H-bond strength. In particular, these interactions can blue-shift the stretching frequencies of the CH groups of the imidazolium ring in spite of red-shifting CH···[A](-) H-bonds. They also weaken the H-bonding in the IL relative to the isolated ion pairs, with these anticooperative effects amounting to ca. 50% of the E(HB) value.
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Affiliation(s)
- Sergey A Katsyuba
- A. E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Centre of the Russian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia.
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A qualitative study of the effect of a counterion and polar environment on the structure and spectroscopic signatures of a hydrated hydroxyl anion. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1361-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Martyniak A, Panek J, Jezierska-Mazzarello A, Filarowski A. Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines. J Comput Aided Mol Des 2012; 26:1045-53. [PMID: 22955961 PMCID: PMC3474916 DOI: 10.1007/s10822-012-9597-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/29/2012] [Indexed: 11/17/2022]
Abstract
First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.
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Affiliation(s)
- Agata Martyniak
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383, Wrocław, Poland
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Vener MV, Egorova AN, Churakov AV, Tsirelson VG. Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions. J Comput Chem 2012; 33:2303-9. [PMID: 22786749 DOI: 10.1002/jcc.23062] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/14/2012] [Accepted: 06/19/2012] [Indexed: 11/11/2022]
Abstract
The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.
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Affiliation(s)
- M V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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Liang C, Knoester J, Jansen TLC. Proton Transport in a Membrane Protein Channel: Two-Dimensional Infrared Spectrum Modeling. J Phys Chem B 2012; 116:6336-45. [DOI: 10.1021/jp3019827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chungwen Liang
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Center for Theoretical
Physics and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Vener MV, Medvedev AG, Churakov AV, Prikhodchenko PV, Tripol'skaya TA, Lev O. H-bond network in amino acid cocrystals with H2O or H2O2. The DFT study of serine-H2O and serine-H2O2. J Phys Chem A 2011; 115:13657-63. [PMID: 22004006 DOI: 10.1021/jp207899z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure, IR spectrum, and H-bond network in the serine-H(2)O and serine-H(2)O(2) crystals were studied using DFT computations with periodic boundary conditions. Two different basis sets were used: the all-electron Gaussian-type orbital basis set and the plane wave basis set. Computed frequencies of the IR-active vibrations of the titled crystals are quite different in the range of 10-100 cm(-1). Harmonic approximation fails to reproduce IR active bands in the 2500-2800 frequency region of serine-H(2)O and serine-H(2)O(2). The bands around 2500 and 2700 cm(-1) do exist in the anharmonic IR spectra and are caused by the first overtone of the OH bending vibrations of H(2)O and a combination vibration of the symmetric and asymmetric bendings of H(2)O(2). The quantum-topological analysis of the crystalline electron density enables us to describe quantitatively the H-bond network. It is much more complex in the title crystals than in a serine crystal. Appearance of water leads to an increase of the energy of the amino acid-amino acid interactions, up to ~50 kJ/mol. The energy of the amino acid-water H-bonds is ~30 kJ/mol. The H(2)O/H(2)O(2) substitution does not change the H-bond network; however, the energy of the amino acid-H(2)O(2) contacts increases up to 60 kJ/mol. This is caused by the fact that H(2)O(2) is a much better proton donor than H(2)O in the title crystals.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Moscow, Russia.
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Bartashevich E, Nikulov D, Vener M, Tsirelson V. QTAIMC study of the X–H/H⋯O bond order indices (X=O, N, C) in molecular systems. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.06.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lasave J, Koval S, Migoni RL, Dalal NS. Ab initio studies of the para- and antiferroelectric structures and local polarized configurations in NH4H2PO4. J Chem Phys 2011; 135:084504. [DOI: 10.1063/1.3624616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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