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Shaik S, Danovich D, Zare RN. Valence Bond Theory Allows a Generalized Description of Hydrogen Bonding. J Am Chem Soc 2023; 145:20132-20140. [PMID: 37664980 PMCID: PMC10510329 DOI: 10.1021/jacs.3c08196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 09/05/2023]
Abstract
This paper describes the nature of the hydrogen bond (HB), B:---H-A, using valence bond theory (VBT). Our analysis shows that the most important HB interactions are polarization and charge transfer, and their corresponding sum displays a pattern that is identical for a variety of energy decomposition analysis (EDA) methods. Furthermore, the sum terms obtained with the different EDA methods correlate linearly with the corresponding VB quantities. The VBT analysis demonstrates that the total covalent-ionic resonance energy (RECS) of the HB portion (B---H in B:---H-A) correlates linearly with the dissociation energy of the HB, ΔEdiss. In principle, therefore, RECS(HB) can be determined by experiment. The VBT wavefunction reveals that the contributions of ionic structures to the HB increase the positive charge on the hydrogen of the corresponding external/free O-H bonds in, for example, the water dimer compared with a free water molecule. This increases the electric field of the external O-H bonds of water clusters and contributes to bringing about catalysis of reactions by water droplets and in water-hydrophobic interfaces.
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Affiliation(s)
- Sason Shaik
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - David Danovich
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Richard N. Zare
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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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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3
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Petelski AN, Duarte DJR, Peruchena NM. Nature and Strength of Weak O⋅⋅⋅O Interactions in Nitryl Halide Dimers. Chemphyschem 2022; 24:e202200768. [PMID: 36515410 DOI: 10.1002/cphc.202200768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/15/2022]
Abstract
The use of real space functions and molecular graphs has pushed some chemists to wonder: Are interactions between negatively charged oxygen atoms possible? In this contribution we analyze whether there is a real interaction between oxygen atoms in nitryl halide dimers (XNO2 )2 (X=F, Cl, Br and I) and in tetranitromethane and derivatives. Based on ab-initio and density functional theories (DFT) methods, we show these complexes are weakly stabilized. Energy decomposition analyses based on local molecular orbitals (LMOEDA) and interacting quantum atoms (IQA) reveal both dispersion and exchange play a crucial role in the stabilization of these complexes. Electron charge density and IQA analyses indicate that the oxygen atoms are connected by privileged exchange channels. In addition, electrostatic interactions between O and N atoms are also vital for the stabilization of the complexes. Finally, a reasonable explanation is given for the dynamic behavior of nitryl groups in tetranitromethane and derivatives.
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Affiliation(s)
- Andre Nicolai Petelski
- Departamento de Ingeniería Química, Grupo de Investigación en Química Teórica y Experimental (QUITEX), Universidad Tecnológica Nacional, Facultad Regional Resistencia, French 414, H3500CHJ), Resistencia, Chaco, Argentina
| | - Darío Jorge Roberto Duarte
- Laboratorio de Estructura Molecular y Propiedades, Instituto de Química Básica y Aplicada del Nordeste Argentino IQUIBA-NEA (UNNE-CONICET), Avenida Libertad 5460, 3400, Corrientes, Argentina.,Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, 3400, Corrientes, Argentina
| | - Nélida María Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Instituto de Química Básica y Aplicada del Nordeste Argentino IQUIBA-NEA (UNNE-CONICET), Avenida Libertad 5460, 3400, Corrientes, Argentina.,Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460, 3400, Corrientes, Argentina
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4
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Surov AO, Voronin AP, Drozd KV, Gruzdev MS, Perlovich GL, Prashanth J, Balasubramanian S. Polymorphic forms of antiandrogenic drug nilutamide: structural and thermodynamic aspects. Phys Chem Chem Phys 2021; 23:9695-9708. [PMID: 33908506 DOI: 10.1039/d1cp00793a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attempts to obtain new cocrystals of nonsteroidal antiandrogenic drug nilutamide produced alternative polymorphic forms of the compound (Form II and Form III) and their crystal structures were elucidated by single-crystal X-ray diffraction. Apart from the cocrystallization technique, lyophilization was found to be an effective strategy for achieving polymorph control of nilutamide, which was difficult to obtain by other methods. The physicochemical properties and relative stability of the commercial Form I and newly obtained Form II were comprehensively investigated by a variety of analytical methods (thermal analysis, solution calorimetry, solubility, and sublimation), whereas for Form III, only a handful of experimental parameters were obtained due to the elusive nature of the polymorph. Form I and Form II were found to be monotropically related, with Form I being confirmed as the thermodynamically most stable solid phase. In addition, the performance of different DFT-D and semi-empirical schemes for lattice energy calculation and polymorph energy ranking was compared and analysed. Lattice energy calculations using periodic DFT at B3LYP-D3/6-31(F+)G(d,p) and PBEh-3c/def2-mSVP levels of theory were found to provide the most accurate lattice energy values for Form I against experimental data, while PIXEL and PBEh-3c/def2-mSVP were the only methods that predicted the correct order of stability of Forms I and II.
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Affiliation(s)
- Artem O Surov
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., 153045 Ivanovo, Russia.
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5
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Suryaprasad B, Chandra S, Ramanathan N, Sundararajan K. Pentavalent P…π phosphorus bonding with associated Cl…π halogen bonding in influencing the geometry of POCl3-Phenylacetylene heterodimers: Evidence from matrix isolation infrared spectroscopy and ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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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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7
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Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Dominance of unique Pπ phosphorus bonding with π donors: evidence using matrix isolation infrared spectroscopy and computational methodology. Phys Chem Chem Phys 2020; 22:20771-20791. [PMID: 32909555 DOI: 10.1039/d0cp02880k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albeit the first account of hypervalentπ interactions has been reported with halogenπ interactions, the feasibility of their extension to other hypervalent atoms as possible Lewis acids is still open. In this work, the role of phosphorus as an acceptor from the π electron cloud (Pπ pnicogen or phosphorus bonding) in PCl3-C2H2 and PCl3-C2H4 heterodimers is explored, by combining matrix isolation infrared spectroscopy with ab initio and DFT computational methodologies. The respective potential energy surfaces of the PCl3-C2H2 and PCl3-C2H4 heterodimers reveal unique minima stabilized by a concert of reasonably strong to weak interactions, of which Pπ phosphorus bonding was energetically dominant. Heterodimers, trimers and tetramers bound primarily by this unique phosphorus bond were generated at low temperatures. The dominance of phosphorus bonding in the PCl3-C2H2 and PCl3-C2H4 heterodimers over other interactions (such as Hπ, HCl, HP, Clπ and lone pair-π interactions) was confirmed and substantiated using extended quantum theory of atoms in molecules, natural bond orbital, electrostatic potential mapping and energy decomposition analyses. The following inferences in correlation with results from non-covalent-interaction analysis offer a complete understanding of the nature of the Pπ phosphorus bonding interactions. The significance of electrostatic forces kinetically favoring the formation of phosphorus bonded heterodimers, in addition to thermodynamic stabilization, is demonstrated experimentally.
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Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
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8
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Levina EO, Chernyshov IY, Voronin AP, Alekseiko LN, Stash AI, Vener MV. Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals. RSC Adv 2019; 9:12520-12537. [PMID: 35515880 PMCID: PMC9063672 DOI: 10.1039/c9ra02116g] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 01/22/2023] Open
Abstract
The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C–F⋯F–C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C–F⋯F–C and C–H⋯F–C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C–H⋯F–C interactions due to the dominant electrostatic contribution to these contacts. C–H⋯F–C and C–H⋯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions. The nature and strength of weak C–H⋯F–C and C–F⋯F–C interactions and their role in organofluorine molecular crystals were studied using periodic DFT coupled with CSD data mining and experimental sublimation enthalpies.![]()
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Affiliation(s)
- Elena O. Levina
- Moscow Institute of Physics and Technology
- Russia
- Research Centre of Biotechnology
- Russian Academy of Sciences
- Moscow
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9
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Experimental and theoretical study on the molecular structure, covalent and non-covalent interactions of 2,4-dinitrodiphenylamine: X-ray diffraction and QTAIM approach. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Chernyshov IY, Vener MV, Feldman EV, Paraschuk DY, Sosorev AY. Inhibiting Low-Frequency Vibrations Explains Exceptionally High Electron Mobility in 2,5-Difluoro-7,7,8,8-tetracyanoquinodimethane (F 2-TCNQ) Single Crystals. J Phys Chem Lett 2017; 8:2875-2880. [PMID: 28590744 DOI: 10.1021/acs.jpclett.7b01003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Organic electronics requires materials with high charge mobility. Despite decades of intensive research, charge transport in high-mobility organic semiconductors has not been well understood. In this Letter, we address the physical mechanism underlying the exceptionally high band-like electron mobility in F2-TCNQ (2,5-difluoro-7,7,8,8-tetracyanoquinodimethane) single crystals among a crystal family of similar compounds Fn-TCNQ (n = 0, 2, 4) using a combined experimental and theoretical approach. While electron transfer integrals and reorganization energies did not show outstanding features for F2-TCNQ, Raman spectroscopy and solid-state DFT indicated that the frequency of the lowest vibrational mode is nearly twice higher in the F2-TCNQ crystal than in TCNQ and F4-TCNQ. This phenomenon is explained by the specific packing motif of F2-TCNQ with only one molecule per primitive cell so that electron-phonon interaction decreases and the electron mobility increases. We anticipate that our findings will encourage investigators for the search and design of organic semiconductors with one molecule per primitive cell and/or the poor low-frequency vibrational spectrum.
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Affiliation(s)
- Ivan Yu Chernyshov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences , Leninskii prosp. 31, Moscow 119991, Russia
| | - Mikhail V Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences , Leninskii prosp. 31, Moscow 119991, Russia
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences , Academicheskaya 1, 153045 Ivanovo, Russia
| | - Elizaveta V Feldman
- Faculty of Physics and International Laser Center, M.V. Lomonosov Moscow State University , Moscow 119991, Russia
| | - Dmitry Yu Paraschuk
- Faculty of Physics and International Laser Center, M.V. Lomonosov Moscow State University , Moscow 119991, Russia
| | - Andrey Yu Sosorev
- Faculty of Physics and International Laser Center, M.V. Lomonosov Moscow State University , Moscow 119991, Russia
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11
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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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12
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Joshi PR, Ramanathan N, Sundararajan K, Sankaran K. Evidence for Phosphorus Bonding in Phosphorus Trichloride–Methanol Adduct: A Matrix Isolation Infrared and ab Initio Computational Study. J Phys Chem A 2015; 119:3440-51. [DOI: 10.1021/jp511156d] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Prasad Ramesh Joshi
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - N. Ramanathan
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sundararajan
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sankaran
- Chemistry
Group, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
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13
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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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14
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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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15
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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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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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Sirsch P, Che FN, Titah JT, McGrady GS. Hydride-Hydride Bonding Interactions in the Hydrogen Storage Materials AlH3, MgH2, and NaAlH4. Chemistry 2012; 18:9476-80. [DOI: 10.1002/chem.201200803] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Indexed: 11/11/2022]
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Rozenberg M, Loewenschuss A, Nielsen CJ. H-Bonded Clusters in the Trimethylamine/Water System: A Matrix Isolation and Computational Study. J Phys Chem A 2012; 116:4089-96. [DOI: 10.1021/jp3020035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mark Rozenberg
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904,
Israel
| | - Aharon Loewenschuss
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904,
Israel
| | - Claus J. Nielsen
- Centre for Theoretical and Computational Chemistry, Department of
Chemistry, University of Oslo, 1033 Blindern,
N-0315 Oslo, Norway
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Adhikari U, Scheiner S. Comparison of P⋯D (D = P,N) with other noncovalent bonds in molecular aggregates. J Chem Phys 2011; 135:184306. [DOI: 10.1063/1.3660355] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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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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Santra B, Klimeš J, Alfè D, Tkatchenko A, Slater B, Michaelides A, Car R, Scheffler M. Hydrogen bonds and van der waals forces in ice at ambient and high pressures. PHYSICAL REVIEW LETTERS 2011; 107:185701. [PMID: 22107644 DOI: 10.1103/physrevlett.107.185701] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Indexed: 05/31/2023]
Abstract
The first principles methods, density-functional theory and quantum Monte Carlo, have been used to examine the balance between van der Waals (vdW) forces and hydrogen bonding in ambient and high-pressure phases of ice. At higher pressure, the contribution to the lattice energy from vdW increases and that from hydrogen bonding decreases, leading vdW to have a substantial effect on the transition pressures between the crystalline ice phases. An important consequence, likely to be of relevance to molecular crystals in general, is that transition pressures obtained from density-functional theory exchange-correlation functionals which neglect vdW forces are greatly overestimated.
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Affiliation(s)
- Biswajit Santra
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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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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Scheiner S, Adhikari U. Abilities of Different Electron Donors (D) to Engage in a P···D Noncovalent Interaction. J Phys Chem A 2011; 115:11101-10. [DOI: 10.1021/jp2082787] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S. On the properties of X···N noncovalent interactions for first-, second-, and third-row X atoms. J Chem Phys 2011; 134:164313. [PMID: 21528966 DOI: 10.1063/1.3585611] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In addition to a structure with a PH···N H-bond, a second complex of greater stability is formed when the PH(3) is rotated such that its P-H bond is pointing away from the approaching N lone pair of NH(3). Quantum calculations are applied to examine whether such a complex is characteristic only of P, or may occur as well for other atoms of the first, second, or third rows of the periodic table. The molecules PH(3), H(2)S, HCl, AsH(3), and NH(3) are all paired with NH(3) as electron donor. While NH(3) will not engage in an N···N attraction, all the others do form a X···N complex. The energetics, geometries, and other properties of these complexes are relatively insensitive to the nature of the X atom. This uniformity contrasts sharply with the H-bonded XH···N complexes where a strong sensitivity to X is observed. The three-dimensional nature of the electrostatic potential, in conjunction with the striving for a linear H-X···N orientation that maximizes charge transfer, serves as an excellent tool in understanding both the shape of the potential energy surface and the proclivity to engage in a X···N interaction.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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Scheiner S. Effects of Substituents upon the P···N Noncovalent Interaction: The Limits of Its Strength. J Phys Chem A 2011; 115:11202-9. [DOI: 10.1021/jp203964b] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S. A new noncovalent force: comparison of P···N interaction with hydrogen and halogen bonds. J Chem Phys 2011; 134:094315. [PMID: 21384977 DOI: 10.1063/1.3562209] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(∗) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(∗) orbital that is closest to the P. In contrast to halogen bonds, there is no requirement of a σ-hole of positive electrostatic potential on the P atom, nor is it necessary for the two interacting atoms to be of differing potential. In fact, the two atoms can be identical, as the global minimum of the PH(3) homodimer has the same structure, characterized by a P···P attraction. Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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Mata I, Alkorta I, Espinosa E, Molins E. Relationships between interaction energy, intermolecular distance and electron density properties in hydrogen bonded complexes under external electric fields. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.03.055] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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