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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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2
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Noonan TJ, Chibale K, Bourne SA, Caira MR. A preformulation co-crystal screening case study: Polymorphic co-crystals of an imidazopyridazine antimalarial drug lead with the coformer succinic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Noonan TJ, Chibale K, Cheuka PM, Bourne SA, Caira MR. Cocrystal and Salt Forms of an Imidazopyridazine Antimalarial Drug Lead. J Pharm Sci 2019; 108:2349-2357. [DOI: 10.1016/j.xphs.2019.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 10/27/2022]
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4
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Shenderovich IG. Simplified calculation approaches designed to reproduce the geometry of hydrogen bonds in molecular complexes in aprotic solvents. J Chem Phys 2018; 148:124313. [PMID: 29604820 DOI: 10.1063/1.5011163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The impact of the environment onto the geometry of hydrogen bonds can be critically important for the properties of the questioned molecular system. The paper reports on the design of calculation approaches capable to simulate the effect of aprotic polar solvents on the geometric and NMR parameters of intermolecular hydrogen bonds. A hydrogen fluoride and pyridine complex has been used as the main model system because the experimental estimates of these parameters are available for it. Specifically, F-H, F⋯N, and H-N distances, the values of 15N NMR shift, and spin-spin coupling constants 1J(19F1H), 1hJ(1H15N), and 2hJ(19F15N) have been analyzed. Calculation approaches based on the gas-phase and the Polarizable Continuum Model (PCM) approximations and their combinations with geometric constraints and additional noncovalent interactions have been probed. The main result of this work is that the effect of an aprotic polar solvent on the geometry of a proton-donor⋯H⋯proton-acceptor complex cannot be reproduced under the PCM approximation if no correction for solvent-solute interactions is made. These interactions can be implicitly accounted for using a simple computational protocol.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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5
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Ion AE, Dogaru A, Shova S, Madalan AM, Akintola O, Ionescu S, Voicescu M, Nica S, Buchholz A, Plass W, Andruh M. Organic co-crystals of 1,3-bis(4-pyridyl)azulene with a series of hydrogen-bond donors. CrystEngComm 2018. [DOI: 10.1039/c8ce00945g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
1,3-Bis(4-pyridyl)azulene has been employed as a hydrogen bond acceptor to construct two-component organic cocrystals.
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Gurinov AA, Denisov GS, Borissova AO, Goloveshkin AS, Greindl J, Limbach HH, Shenderovich IG. NMR Study of Solvation Effect on the Geometry of Proton-Bound Homodimers of Increasing Size. J Phys Chem A 2017; 121:8697-8705. [PMID: 29064692 DOI: 10.1021/acs.jpca.7b09285] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bond geometries in the proton-bound homodimers of quinoline and acridine derivatives in an aprotic polar solution have been experimentally studied using 1H NMR at 120 K. The reported results show that an increase of the dielectric permittivity of the medium results in contraction of the N···N distance. The degree of contraction depends on the homodimer's size and its substituent-specific solvation features. Neither of these effects can be reproduced using conventional implicit solvent models employed in computational studies. In general, the N···N distance in the homodimers of pyridine, quinoline, and acridine derivatives decreases in the sequence gas phase > solid state > polar solvent.
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Affiliation(s)
- Andrei A Gurinov
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany.,The Imaging and Characterization Core Lab, King Abdullah University of Science and Technology , Al-Khawarizimi Building 01, Thuwal 23955-6900, Saudi Arabia
| | - Gleb S Denisov
- Institute of Physics, St. Petersburg State University , Ulyanovskaya str. 1, 198504 St. Petersburg, Russian Federation
| | - Alexandra O Borissova
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , 119991, Vavilov Str., 28, Moscow, Russia
| | - Alexander S Goloveshkin
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , 119991, Vavilov Str., 28, Moscow, Russia
| | - Julian Greindl
- Institute of Organic Chemistry, University of Regensburg , Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Hans-Heinrich Limbach
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany
| | - Ilya G Shenderovich
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany.,Institute of Organic Chemistry, University of Regensburg , Universitaetstrasse 31, 93053 Regensburg, Germany
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7
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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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8
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Levina EO, Lokshin BV, Mai BD, Vener MV. Spectral features of guanidinium-carboxylate salt bridges. The combined ATR-IR and theoretical studies of aqueous solution of guanidinium acetate. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Sanphui P, Rajput L, Gopi SP, Desiraju GR. New multi-component solid forms of anti-cancer drug Erlotinib: role of auxiliary interactions in determining a preferred conformation. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:291-300. [PMID: 27240760 DOI: 10.1107/s2052520616003607] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
Erlotinib is a BCS (biopharmaceutical classification system) class II drug used for the treatment of non-small cell lung cancer. There is an urgent need to obtain new solid forms of higher solubility to improve the bioavailability of the API (active pharmaceutical ingredient). In this context, cocrystals with urea, succinic acid, and glutaric acid and salts with maleic acid, adipic acid, and saccharin were prepared via wet granulation and solution crystallizations. Crystal structures of the free base (Z' = 2), cocrystals of erlotinib-urea (1:1), erlotinib-succinic acid monohydrate (1:1:1), erlotinib-glutaric acid monohydrate (1:1:1) and salts of erlotinib-adipic acid adipate (1:0.5:0.5) are determined and their hydrogen-bonding patterns are analyzed. Self recognition via the (amine) N-H...N (pyridine) hydrogen bond between the API molecules is replaced by several heterosynthons such as acid-pyridine, amide-pyridine and carboxylate-pyridinium in the new binary systems. Auxiliary interactions play an important role in determining the conformation of the API in the crystal. FT-IR spectroscopy is used to distinguish between the salts and cocrystals in the new multi-component systems. The new solid forms are characterized by powder X-ray diffraction (PXRD) and differential scanning calorimetry (DSC) to confirm their unique phase identity.
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Affiliation(s)
- Palash Sanphui
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnatakla 560012, India
| | - Lalit Rajput
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnatakla 560012, India
| | - Shanmukha Prasad Gopi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnatakla 560012, India
| | - Gautam R Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Avenue, Bangalore, Karnatakla 560012, India
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Affiliation(s)
- Susanta K. Sen Gupta
- Department of Chemistry, Faculty of Science; Banaras Hindu University; Varanasi 221005 India
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11
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Katsyuba SA, Vener MV, Zvereva EE, Fei Z, Scopelliti R, Brandenburg JG, Siankevich S, Dyson PJ. Quantification of Conventional and Nonconventional Charge-Assisted Hydrogen Bonds in the Condensed and Gas Phases. J Phys Chem Lett 2015; 6:4431-4436. [PMID: 26496074 DOI: 10.1021/acs.jpclett.5b02175] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Charge-assisted hydrogen bonds (CAHBs) play critical roles in many systems from biology through to materials. In none of these areas has the role and function of CAHBs been explored satisfactorily because of the lack of data on the energy of CAHBs in the condensed phases. We have, for the first time, quantified three types of CAHBs in both the condensed and gas phases for 1-(2'-hydroxylethyl)-3-methylimidazolium acetate ([C2OHmim][OAc]). The energy of conventional OH···[OAc](-) CAHBs is ∼10 kcal·mol(-1), whereas nonconventional C(sp2)H···[OAc](-) and C(sp3)H···[OAc](-) CAHBs are weaker by ∼5-7 kcal·mol(-1). In the gas phase, the strength of the nonconventional CAHBs is doubled, whereas the conventional CAHBs are strengthened by <20%. The influence of cooperativity effects on the ability of the [OAc](-) anion to deprotonate the imidazolium cation is evaluated. The ability to quantify CAHBs in the condensed phase on the basis of easier accessible gas-phase estimates is highlighted.
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Affiliation(s)
- Sergey A Katsyuba
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences , Arbuzov Street 8, 420088 Kazan, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology , Miusskaya Square 9, 125047 Moscow, Russia
| | - Elena E Zvereva
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences , Arbuzov Street 8, 420088 Kazan, Russia
- Institut de Nanosciences et Cryogénie, SP2M/L_sim, CEA , 17 Rue des Martyrs, 38054 Grenoble, France
| | - Zhaofu Fei
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstrasse 4, 53115 Bonn, Germany
| | - Sviatlana Siankevich
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL) EPFL - BCH , CH-1015 Lausanne, Switzerland
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12
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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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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Frantsuzov I, Ford SJ, Radosavljevic Evans I, Horsewill AJ, Trommsdorff HP, Johnson MR. Measurement of proton tunneling in short hydrogen bonds in single crystals of 3,5 pyridinedicarboxylic acid using nuclear magnetic resonance spectroscopy. PHYSICAL REVIEW LETTERS 2014; 113:018301. [PMID: 25032933 DOI: 10.1103/physrevlett.113.018301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Indexed: 06/03/2023]
Abstract
In this Letter, we present NMR spin-lattice and relaxometry data for proton transfer in one of the shortest known N-H⋯O hydrogen bonds in a single crystal of 3,5 pyridinedicarboxylic acid (35PDCA). It is widely believed that proton transfer by quantum tunneling does not occur in short hydrogen bonds since the ground state energy level lies above the potential barrier, yet these data show a temperature independent, proton tunneling rate below 77 K and a clear deviation from classical dynamics below 91 K. This study therefore suggests that proton tunneling occurs in all hydrogen bonds at low temperature and the crossover temperature to classical hopping must be determined when evaluating whether proton tunneling persists at higher temperature, for example in enzyme catalysis under physiological conditions.
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Affiliation(s)
- I Frantsuzov
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - S J Ford
- Institute Laue Langevin, BP 156, 38042 Grenoble, France and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | | | - A J Horsewill
- School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - H P Trommsdorff
- Institute Laue Langevin, BP 156, 38042 Grenoble, France and University of Grenoble 1/CNRS, LIPhy UMR 5588, BP 87, 38041 Grenoble, France
| | - M R Johnson
- Institute Laue Langevin, BP 156, 38042 Grenoble, France
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Brancatelli G, Pappalardo S, Gattuso G, Notti A, Pisagatti I, Parisi MF, Geremia S. Hydrogen bond-assisted solid-state formation of a salt-bridged calix[5]arene pseudo-dimer. CrystEngComm 2014. [DOI: 10.1039/c3ce41667d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Wang L, Xue R, Li Y, Zhao Y, Liu F, Huang K. Hydrogen-bonding patterns in a series of multi-component molecular solids formed by 2,3,5,6-tetramethylpyrazine with selected carboxylic acids. CrystEngComm 2014. [DOI: 10.1039/c4ce00749b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonding patterns in a series of cocrystals of 2,3,5,6-tetramethylpyrazine with selected carboxylic acids are discussed.
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Affiliation(s)
- Lei Wang
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, PR China
| | - Ruiyu Xue
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, PR China
| | - Yuanxin Li
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, PR China
| | - Yiran Zhao
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, PR China
| | - Faqian Liu
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042, PR China
| | - Keke Huang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- Jilin University
- Changchun, PR China
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17
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Maiorov VD, Kislina IS, Rykounov AA, Vener MV. The structure and vibrational features of proton disolvates in water-ethanol solutions of HCl: the combined spectroscopic and theoretical study. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Vladimir D. Maiorov
- Semenov Institute of Chemical Physics; Russian Academy of Sciences; Moscow Russia
| | - Irina S. Kislina
- Semenov Institute of Chemical Physics; Russian Academy of Sciences; Moscow Russia
| | - Alexey A. Rykounov
- Snezhinsk Physics and Technology Institute; National Research Nuclear University MEPhI; Snezhinsk Russia
| | - Mikhail V. Vener
- Quantum Chemistry Department; Mendeleev University of Chemical Technology; 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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Katsyuba SA, Zvereva EE, Burganov TI. Is there a simple way to reliable simulations of infrared spectra of organic compounds? J Phys Chem A 2013; 117:6664-70. [PMID: 23805975 DOI: 10.1021/jp404574m] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To assess the ability of the quantum-chemical computations to reproduce the experimental relative intensities in the infrared (IR) spectra of both the gas- and condensed-phase systems, the hybrid DFT functional B3LYP has been applied to simulation of IR spectra for species containing from three to twelve first- or second-row atoms, both in the gas phase and in CCl4 solutions. The results demonstrate that B3LYP, combined with the highly compact double-ζ basis set 6-31+G* and "scaled quantum mechanics" techniques, offers excellent quantitative performance in the calculations of relative IR intensities and frequencies (ν ≤ 2200 cm(-1)) for the bands of vibrations of medium-size isolated molecules, whereas it produces unsatisfactory results for the solutions of the same species. Neither larger basis sets nor implicit treatment of the media effects improve the agreement of the simulated spectra with the condensed-phase experiment. At the same time, some preliminary results suggest that explicit modeling of media effects could offer better quality of the IR spectral simulations for the condensed-phase systems.
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Affiliation(s)
- Sergey A Katsyuba
- A. E. Arbuzov Institute of Organic and Physical Chemistry of Kazan Scientific Centre of Russian Academy of Sciences, Arbuzov str, 8, Kazan 420088, Russia.
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Borissova AO, Lyssenko KA, Gurinov AA, Shenderovich IG. Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction. ACTA ACUST UNITED AC 2013. [DOI: 10.1524/zpch.2013.0400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The hydrogen bond pattern and the types of non-covalent interactions in the crystals of the 1:1 and 1:2 adducts of 2,4,6-trimethylpyridine and benzoic acids are studied using high-resolution X-ray diffraction. The geometries of the hydrogen bonds are estimated using a combined XRD/DFT approach that provides the geometrical parameters within the margin of error of neutron diffraction studies. The energies of the non-covalent interactions are estimated on the base of the experimental electron density distribution function. It is shown that the structures of the adducts are governed by the NOH and OHO hydrogen bonds. In turn, C-H...O contacts and stacking interactions define the packing of the adducts in the crystal. On the other hand, it is important to note that the latter interactions affect the competition of the former hydrogen bonds in some 1:2 adducts.
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Affiliation(s)
| | - Konstantin A. Lyssenko
- Russian Academy of Sciences, A.N. Nesmeyanov Institute of Organoelement Compoun, Moscow, Russische Föderation
| | - Andrey A. Gurinov
- St. Petersburg State University, Department of Physics, St. Petersburg, Russische Föderation
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Abstract
Abstract
Fluorescence and absorption spectral parameters of acridine have been studied in solution at room temperature in the presence of different proton donors aiming to inspect whether or not acridine can be used as a spectroscopic probe suitable to measure the geometry of hydrogen bonds under different conditions. It has been shown that the most appropriate spectral parameter is the position of fluorescence maximum that changes heavily upon a contraction of the N···H distance. Presumably, also the intensity of the maximum strongly depends on the hydrogen bond geometry. These two parameters can be used to establish two independent, mutually complementary correlations connecting the spectral manifestations and the geometry of hydrogen bond.
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Pang XF. Properties of proton transfer in hydrogen-bonded systems and its experimental evidences and applications in biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:1-32. [DOI: 10.1016/j.pbiomolbio.2012.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 11/25/2022]
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23
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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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24
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Mukherjee A, Tothadi S, Chakraborty S, Ganguly S, Desiraju GR. Synthon identification in co-crystals and polymorphs with IR spectroscopy. Primary amides as a case study. CrystEngComm 2013. [DOI: 10.1039/c3ce40286j] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Draguta S, Fonari MS, Masunov AE, Zazueta J, Sullivan S, Antipin MY, Timofeeva TV. New acentric materials constructed from aminopyridines and 4-nitrophenol. CrystEngComm 2013. [DOI: 10.1039/c3ce40291f] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Melikova S, Rutkowski K, Gurinov A, Denisov G, Rospenk M, Shenderovich I. FTIR study of the hydrogen bond symmetry in protonated homodimers of pyridine and collidine in solution. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.12.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Houjou H. Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond? J Chem Phys 2012; 135:154111. [PMID: 22029301 DOI: 10.1063/1.3652102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.
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Affiliation(s)
- Hirohiko Houjou
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Tokyo 153-8505, Japan.
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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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31
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Kong S, Borissova AO, Lesnichin SB, Hartl M, Daemen LL, Eckert J, Antipin MY, Shenderovich IG. Geometry and spectral properties of the protonated homodimer of pyridine in the liquid and solid states. A combined NMR, X-ray diffraction and inelastic neutron scattering study. J Phys Chem A 2011; 115:8041-8. [PMID: 21644583 DOI: 10.1021/jp203543g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and spectral signatures of the protonated homodimer of pyridine in its complex with a poorly coordinating anion have been studied in solution in CDF(3)/CDClF(2) down to 120 K and in a single crystal. In both phases, the hydrogen bond is asymmetric. In the solution, the proton is involved in a fast reversible transfer that determines the multiplicity of NMR signals and the sign of the primary H/D isotope effect of --0.95 ppm. The proton resonates at 21.73 ppm that is above any value reported in the past and is indicative of a very short hydrogen bond. By combining X-ray diffraction analysis with model computations, the position of the proton in the crystal has been defined as d(N-H) = 1.123 Å and d(H···N) = 1.532 Å. The same distances have been estimated using a (15)N NMR correlation. The frequency of the protonic out-of-plane bending mode is 822 cm(-1) in agreement with Novak's correlation.
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Affiliation(s)
- S Kong
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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Horbatenko Y, Vyboishchikov SF. Hydrogen Motion in Proton Sponge Cations: A Theoretical Study. Chemphyschem 2011; 12:1118-29. [DOI: 10.1002/cphc.201000721] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 01/21/2011] [Indexed: 11/12/2022]
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Churakov AV, Prikhodchenko PV, Lev O, Medvedev AG, Tripol'skaya TA, Vener MV. A model proton-transfer system in the condensed phase: NH4(+)OOH(-), a crystal with short intermolecular H-bonds. J Chem Phys 2011; 133:164506. [PMID: 21033804 DOI: 10.1063/1.3493688] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G(∗∗) level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P2(1)/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.
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Affiliation(s)
- Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
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Hydrogen bonds and O⋯O interactions in proton-ordered ices. DFT computations with periodic boundary conditions. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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