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Saifina AF, Kartashov SV, Saifina LF, Fayzullin RR. Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis(2-hydroxyethyl)-6-methyluracil. IUCRJ 2023; 10:584-602. [PMID: 37668216 PMCID: PMC10478519 DOI: 10.1107/s2052252523007108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
We considered it timely to test the applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. The procedure was carried out on the crystal of 1,3-bis(2-hydroxyethyl)-6-methyluracil, and some derived properties of the scalar potential and vector force fields were compared with those obtained from the experimental multipole model and from the aspherical pseudo-atom model with parameters fitted to the calculated structure factors. The procedure was shown to accurately replicate the general vector-field behavior, the peculiarities of the quantum potentials and the characteristics of the force-field pseudoatoms, such as charge, shape and volume, as well as to reproduce the relative arrangement of atomic and pseudoatomic zero-flux surfaces along internuclear regions. It was found that, in addition to the quantum-topological atoms, the force-field pseudoatoms are spatially reproduced within a single structural fragment and similar environment. In addition, the classical and nonclassical hydrogen bonds in the uracil derivative crystal, as well as the H...O, N...O and N...C interactions in the free π-stacked dimer of the uracil derivative molecules, were studied using the potential and force fields within the concepts of interatomic charge transfer and electron lone pair donation-acceptance. Remarkably, the nitrogen atoms in the N...O and N...C interactions behave rather like a Lewis base and an electron contributor. At the same time, the hydrogen atom in the H...O interaction, being a Lewis acid, also participates in the interatomic electron transfer by acting as a contributor. Thus, it has been argued that, when describing polar interatomic interactions within orbital-free considerations, it makes more physical sense to identify electronegative (electron occupier) and electropositive (electron contributor) atoms or subatomic fragments rather than nucleophilic and electrophilic sites.
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Affiliation(s)
- Alina F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Sergey V. Kartashov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Liliya F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
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2
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Vener MV, Kharlanov OG, Sosorev AY. High-Mobility Naphthalene Diimide Derivatives Revealed by Raman-Based In Silico Screening. Int J Mol Sci 2022; 23:13305. [PMID: 36362092 PMCID: PMC9653651 DOI: 10.3390/ijms232113305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 08/27/2023] Open
Abstract
Charge transport in crystalline organic semiconductors (OSCs) is considerably hindered by low-frequency vibrations introducing dynamic disorder in the charge transfer integrals. Recently, we have shown that the contributions of various vibrational modes to the dynamic disorder correlate with their Raman intensities and suggested a Raman-based approach for estimation of the dynamic disorder and search for potentially high-mobility OSCs. In the present paper, we showcase this approach by revealing the highest-mobility OSC(s) in two series of crystalline naphthalene diimide derivatives bearing alkyl or cycloalkyl substituents. In contrast to our previous studies, Raman spectra are not measured, but are instead calculated using periodic DFT. As a result, an OSC with a potentially high charge mobility is revealed in each of the two series, and further mobility calculations corroborate this choice. Namely, for the naphthalene diimide derivatives with butyl and cyclopentyl substituents, the estimated room-temperature isotropic electron mobilities are as high as 6 and 15 cm2 V-1 s-1, respectively, in the latter case even exceeding 20 cm2 V-1 s-1 in a two-dimensional plane. Thus, our results highlight the potential of using the calculated Raman spectra to search for high-mobility crystalline OSCs and reveal two promising OSCs, which were previously overlooked.
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Affiliation(s)
- Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, Leninskii Prosp. 31, Moscow 119991, Russia
| | - Oleg G. Kharlanov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/2, Moscow 119991, Russia
| | - Andrey Yu. Sosorev
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/2, Moscow 119991, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, Moscow 117997, Russia
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Janczak J. Supramolecular architecture formed between amidinothiourea and 2-pyridinecarboxylic acid. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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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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Bartashevich E, Mukhitdinova S, Yushina I, Tsirelson V. Electronic criterion for categorizing the chalcogen and halogen bonds: sulfur–iodine interactions in crystals. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2019; 75:117-126. [DOI: 10.1107/s2052520618018280] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/24/2018] [Indexed: 11/10/2022]
Abstract
Diversity of mutual orientations of Y–S and I–X and covalent bonds in molecular crystals complicate categorizing noncovalent chalcogen and halogen bonds. Here, the different types of S...I interactions with short interatomic distances are analysed. The selection of S...I interactions for the categorization of the chalcogen and halogen bonds has been made using angles that determine the mutual orientation of electron lone pairs and σ-holes interacted S and I atoms. In complicated cases of noncovalent interactions with `hole-to-hole' of S and I orientations, distinguishing the chalcogen and halogen bonds is only possible if the atom is uniquely determined, which also provides the electrophilic site. The electronic criterion for chalcogen/halogen bonds categorizing that is based on analysis of dispositions of electron density and electrostatic potential minima along the interatomic lines has been suggested and its effectiveness has been demonstrated.
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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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Bol’shakov O, Yushina I, Bartashevich E, Nelyubina Y, Aysin R, Rakitin O. Asymmetric triiodide-diiodine interactions in the crystal of (Z)-4-chloro-5-((2-((4-chloro-5H-1,2,3-dithiazol-5-ylidene)amino)phenyl)amino)-1,2,3-dithiazol-1-ium oligoiodide. Struct Chem 2017. [DOI: 10.1007/s11224-017-0987-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Bartashevich EV, Pendás ÁM, Tsirelson VG. An anatomy of intramolecular atomic interactions in halogen-substituted trinitromethanes. Phys Chem Chem Phys 2015; 16:16780-9. [PMID: 25001471 DOI: 10.1039/c4cp01257g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The intramolecular interactions in substituted trinitromethanes, XC(NO2)3 (X = F, Cl, I, H) are studied and clarified by using a combination of the Quantum Theory of Atoms in Molecules (QTAIM), the non-covalent interaction analysis and the Interacting Quantum Atoms (IQA) methods. The stretching vibration modes are formed by the concerted displacements of atoms involved in the covalent bonds showing the significant multiatomic influence in substituted trinitromethanes. In agreement with that, the arrangement of the local reduced density gradient minima indicates that the electron density favors the non-covalent intramolecular interactions X···O and N···O. However, the corresponding QTAIM bond paths are not formed; instead, contacts, which we call uncompleted links in this context, are accompanied by "quasi-bonding channels" corresponding to the λ2() ≤ 0 regions on the sign[λ2(r)]ρ(r) contour maps. The intramolecular IQA energy contributions signal the appreciable electron exchange between the pairs of atoms associated with potential atomic interactions or the bond-path-free non-covalent links. The IQA analysis shows that the electrostatic term destabilizes FC(NO2)3 and distinctly stabilizes IC(NO2)3, whereas it is close to neutral in ClC(NO2)3. The exchange energy between the X atom and the NO2 groups, in contrast, stabilizes all the molecules.
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Affiliation(s)
- Ekaterina V Bartashevich
- Department of Chemistry, South Ural State University (National Research University), 454080 Chelyabinsk, Russia.
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11
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Understanding the bifurcated halogen bonding N⋯Hal⋯N in bidentate diazaheterocyclic compounds. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.09.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Bartashevich EV, Tsirelson VG. Interplay between non-covalent interactions in complexes and crystals with halogen bonds. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rcr4440] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Stash AI, Tsirelson VG. DevelopingWinXPRO: a software for determination of the multipole-model-based properties of crystals. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714021566] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The new release of the computer program packageWinXPRO v.3xfor determination of the crystal properties from parameters of the multipole-modeled experimental electron density and anharmonic atomic displacement coefficients is described. The set of properties is significantly extended by using the density functional and information theories. In addition, a built-in multi-functional viewer and programs to display the output data, including the mapping of the chosen functional bonding descriptors onto surfaces of the other properties, are included.
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Characterizing the multiple non-covalent interactions in N, S-heterocycles–diiodine complexes with focus on halogen bonding. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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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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Bertolotti F, Curetti N, Benna P, Gervasio G. The effects of P–T changes on intermolecular interactions in crystal structure of iodoform. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Mata I, Alkorta I, Molins E, Espinosa E. Tracing environment effects that influence the stability of anion–anion complexes: The case of phosphate–phosphate interactions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.10.073] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Gibbs GV, Crawford TD, Wallace AF, Cox DF, Parrish RM, Hohenstein EG, Sherrill CD. Role of Long-Range Intermolecular Forces in the Formation of Inorganic Nanoparticle Clusters. J Phys Chem A 2011; 115:12933-40. [DOI: 10.1021/jp204044k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - A. F. Wallace
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - R. M. Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - E. G. Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. D. Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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Nelyubina YV, Antipin MY, Lyssenko KA. Extremely short halogen bond: the nature and energy of iodine–oxygen interactions in crystalline iodic acid. MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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