1
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Medvedev AG, Medved'ko AV, Vener MV, Churakov AV, Prikhodchenko PV, Vatsadze SZ. Dioxygen-halogen bonding exemplified by crystalline peroxosolvates of N, N'-bis(haloacetyl) bispidines. Phys Chem Chem Phys 2024; 26:5195-5206. [PMID: 38261463 DOI: 10.1039/d3cp05834d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The halogen bonding in molecular crystals and supramolecular assemblies has been widely investigated. Special attention is given to the molecular structures capable of simultaneously exhibiting different types of non-covalent interactions, including conventional hydrogen bonds and halogen bonds. This paper systematically analyzes crystalline peroxosolvates of bispidine-based bis-amide derivatives, containing haloacetic acid residues, namely previously reported 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodooethanone) peroxosolvate C13H20I2N2O2·H2O2 (1) and four new crystalline compounds, 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O2·H2O2 (2), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodoethanone) peroxosolvate C13H20I2N2O5·0.5H2O2 (3), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O5·H2O2 (4), and 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-chloroethanone) peroxosolvate C13H20Cl2N2O5·H2O2 (5). Compounds 2-5 were synthesized for the first time and their crystal structures were determined by single-crystal X-ray diffractometry (SCXRD). To the best of our knowledge, 3-5 are unprecedented crystalline hydrogen peroxide adducts of organic hydroperoxides (R-OOH). Short intermolecular contacts between halogen and hydroperoxo oxygen atoms were found in 1-3. The halogen bonding of C-I(Br) fragments with dioxygen species in compounds 1-3 as well as in the previously reported cocrystal of diacetone diperoxide with triodotrinitrobenzene (6) was identified through reduced density gradient analysis, Hirshfeld surface analysis, and Bader analysis of crystalline electron density. The interactions were quantified using the electron density topological properties acquired from the periodic DFT calculations and evaluated to lie in the range of 9-19 kJ mol-1. A distinctive spectral feature was revealed for this type of interaction, involving a red shift of the characteristic O-O stretching vibration by about 6 cm-1, which appeared in IR spectra as a narrow low-intensity band in the region 837-872 cm-1.
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Affiliation(s)
- Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Aleksei V Medved'ko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Mikhail V Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Sergey Z Vatsadze
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
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2
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Song M, Yang F, Su C, Deng B. Characterizing hydrogen bonds in crystalline form of guanidinium salicylate in the terahertz range. RSC Adv 2020; 11:307-319. [PMID: 35423026 PMCID: PMC8691105 DOI: 10.1039/d0ra08053e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
For pharmaceutical compounds with poor solubility, there is an effective method to address this dilemma without tampering their intrinsic chemical properties by forming weak hydrogen bonds. Guanidinium salicylate, which is a typical pharmaceutical salt with a complex crystal structure, was systematically investigated by terahertz time-domain spectroscopy combined with density functional theory in order to obtain the complete information of weak hydrogen bonds. As a result of the influence of weak hydrogen bonds, there are substantial differences between guanidinium salicylate and its parent molecule (salicylic acid) in the experimental fingerprint spectra in the range of 0.2-2.5 THz, such as the number, amplitude and frequency positions of absorption peaks. With the help of isolated molecule density functional theory calculations, the possible sites of weak hydrogen bonds were determined by natural bond orbital analysis. It can be concluded that there is an intricate hydrogen bond network due to the polar distribution of molecular electrostatic potential. Furthermore, all THz absorption peaks were assigned to their corresponding vibrational modes and the complete information of the related hydrogen bonds (including type, role, angle, and bond length) was determined by using dispersion-corrected density functional theory. The results laid a good foundation for further study on the enhancement of solubility of pharmaceutical salts by forming weak hydrogen bonds.
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Affiliation(s)
- Maojiang Song
- Guizhou Metrology Institute Guiyang Guizhou 550003 China
| | - Fei Yang
- Guizhou Metrology Institute Guiyang Guizhou 550003 China
| | - Caixia Su
- School of Big Data and Computer Science, Guizhou Nornal University Guizhou 550001 China
| | - Bing Deng
- Guizhou Metrology Institute Guiyang Guizhou 550003 China
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3
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Voronin AP, Volkova TV, Ilyukhin AB, Proshin AN, Perlovich GL. Substituent effect on the packing architecture of adamantane and memantine derivatives of sulfonamide molecular crystals. CrystEngComm 2020. [DOI: 10.1039/c9ce01750j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A specific number of structures described in this paper with adamantane and memantine fragments have been synthesised and characterised.
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Affiliation(s)
- Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Tatyana V. Volkova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Andrey B. Ilyukhin
- N.S. Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Alexey N. Proshin
- Institute of Physiologically Active Compounds
- Russian Academy of Sciences
- Chernogolovka
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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4
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Chernyshov IY, Vener MV, Shenderovich IG. Local-structure effects on 31P NMR chemical shift tensors in solid state. J Chem Phys 2019; 150:144706. [PMID: 30981271 DOI: 10.1063/1.5075519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The effect of the local structure on the 31P NMR chemical shift tensor (CST) has been studied experimentally and simulated theoretically using the density functional theory gauge-independent-atomic-orbital approach. It has been shown that the dominating impact comes from a small number of noncovalent interactions between the phosphorus-containing group under question and the atoms of adjacent molecules. These interactions can be unambiguously identified using the Bader analysis of the electronic density. A robust and computationally effective approach designed to attribute a given experimental 31P CST to a certain local morphology has been elaborated. This approach can be useful in studies of surfaces, complex molecular systems, and amorphous materials.
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Affiliation(s)
- Ivan Yu Chernyshov
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany
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5
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Churakov AV, Grishanov DA, Medvedev AG, Mikhaylov AA, Tripol'skaya TA, Vener MV, Navasardyan MA, Lev O, Prikhodchenko PV. Cyclic dipeptide peroxosolvates: first direct evidence for hydrogen bonding between hydrogen peroxide and a peptide backbone. CrystEngComm 2019. [DOI: 10.1039/c9ce00892f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystal structures of cyclic dipeptide peroxosolvates provide valuable insight into the non-redox interaction of hydrogen peroxide with the peptide backbone.
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Affiliation(s)
- Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmitry A. Grishanov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Tatiana A. Tripol'skaya
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- Department of Quantum Chemistry
| | - Mger A. Navasardyan
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Ovadia Lev
- The Casali Center of Applied Chemistry
- The Institute of Chemistry
- The Hebrew University of Jerusalem
- Jerusalem 91904
- Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
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6
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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7
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Voronin AP, Volkova TV, Ilyukhin AB, Trofimova TP, Perlovich GL. Structural and energetic aspects of adamantane and memantine derivatives of sulfonamide molecular crystals: experimental and theoretical characterisation. CrystEngComm 2018. [DOI: 10.1039/c8ce00426a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of new sulfonamide compounds with adamantane and memantine fragments were synthesised and characterised.
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Affiliation(s)
- Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Tatiana V. Volkova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Andrey B. Ilyukhin
- N. S. Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
| | - Tatiana P. Trofimova
- Institute of Physiologically Active Compounds
- Russian Academy of Sciences
- Chernogolovka
- Russia
- Lomonosov Moscow State University
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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8
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Bondarchuk SV, Minaev BF. DFT design of polyguanidine – a unique two-dimensional material with high-energy density. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1321157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sergey V. Bondarchuk
- Department of Chemistry and Nanomaterials Science, Bogdan Khmelnitsky Cherkasy National University, Cherkasy, Ukraine
| | - Boris F. Minaev
- Department of Chemistry and Nanomaterials Science, Bogdan Khmelnitsky Cherkasy National University, Cherkasy, Ukraine
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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9
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Katsyuba SA, Vener MV, Zvereva EE, Brandenburg JG. The role of London dispersion interactions in strong and moderate intermolecular hydrogen bonds in the crystal and in the gas phase. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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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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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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Manin AN, Voronin AP, Shishkina AV, Vener MV, Churakov AV, Perlovich GL. Influence of Secondary Interactions on the Structure, Sublimation Thermodynamics, and Solubility of Salicylate:4-Hydroxybenzamide Cocrystals. Combined Experimental and Theoretical Study. J Phys Chem B 2015; 119:10466-77. [PMID: 26258951 DOI: 10.1021/acs.jpcb.5b05082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cocrystal screening of 4-hydroxybenzamide with a number of salicylates (salicylic acid, SA; 4-aminosalicylic acid, PASA; acetylsalicylic acid, ASA; and salicylsalicylic acid, SSA) was conducted to confirm the formation of two cocrystals, [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1). Their structures were determined using single-crystal X-ray diffraction, and the hydrogen-bond network topology was studied. Thermodynamic characteristics of salicylic acid cocrystal sublimation were obtained experimentally. It was proved that PASA cocrystallization with 4-OHBZA makes the drug more stable and prevents the irreversible process of decarboxylation of PASA resulting in formation of toxic 3-aminophenol. The pattern of non-covalent interactions in the cocrystals is described quantitatively using solid-state density functional theory followed by Bader analysis of the periodic electron density. It has been found that the total energy of secondary interactions between synthon atoms and the side hydroxyl group of the acid molecule in [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1) cocrystals is comparable to the energy of the primary acid-amide heterosynthon. The theoretical value of the sublimation enthalpy of [SA+4-OHBZA], 231 kJ/mol, agrees fairly well with the experimental one, 272 kJ/mol. The dissolution experiments with [SA+4-OHBZA] have proved that the relatively large cocrystal stability in relation to the stability of its components has a negative effect on the dissolution rate and equilibrium solubility. The [PASA+4-OHBZA] (1:1) cocrystal showed an enhancement of apparent solubility compared to that of the corresponding pure active pharmaceutical ingredient, while their intrinsic dissolution rates are comparable.
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Affiliation(s)
- Alex N Manin
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
| | - Alexander P Voronin
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
| | - Anastasia V Shishkina
- ‡Mendeleev University of Chemical Technology, 9, Miusskaya Square, 125047 Moscow, Russia
| | - Mikhail V Vener
- ‡Mendeleev University of Chemical Technology, 9, Miusskaya Square, 125047 Moscow, Russia
| | - Andrei V Churakov
- §Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia
| | - German L Perlovich
- †G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 1, Academicheskaya, 153045 Ivanovo, Russian Federation
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13
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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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14
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Surov AO, Voronin AP, Simagina AA, Churakov AV, Skachilova SY, Perlovich GL. Saccharin salts of biologically active hydrazone derivatives. NEW J CHEM 2015. [DOI: 10.1039/c5nj01532d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Crystal structures, solubility and formation thermodynamics of saccharin salts with biologically active hydrazone derivatives were investigated.
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Affiliation(s)
- Artem O. Surov
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Alexander P. Voronin
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | - Anna A. Simagina
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
| | | | | | - German L. Perlovich
- Institution of Russian Academy of Sciences
- G.A. Krestov Institute of Solution Chemistry RAS
- Ivanovo
- Russia
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15
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Manin AN, Voronin AP, Manin NG, Vener MV, Shishkina AV, Lermontov AS, Perlovich GL. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations. J Phys Chem B 2014; 118:6803-14. [PMID: 24861612 DOI: 10.1021/jp5032898] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.
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Affiliation(s)
- Alex N Manin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences , 1, Academicheskaya, 153045 Ivanovo, Russia
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16
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Plumley JA, Ali-Torres J, Pohl G, Dannenberg JJ. Capping amyloid β-sheets of the tau-amyloid structure VQIVYK with hexapeptides designed to arrest growth. An ONIOM and density functional theory study. J Phys Chem B 2014; 118:3326-34. [PMID: 24601594 PMCID: PMC3983367 DOI: 10.1021/jp501890p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
We
present ONIOM calculations using density functional theory (DFT)
as the high and AM1 as the medium level that explore the abilities
of different hexapeptide sequences to terminate the growth of a model
for the tau-amyloid implicated in Alzheimer’s disease. We delineate
and explore several design principles (H-bonding in the side chains,
using antiparallel interactions on the growing edge of a parallel
sheet, using all-d residues to form rippled interactions
at the edge of the sheet, and replacing the H-bond donor N–H’s
that inhibit further growth) that can be used individually and in
combination to design such peptides that will have a greater affinity
for binding to the parallel β-sheet of acetyl-VQIVYK-NHCH3 than the natural sequence and will prevent another strand
from binding to the sheet, thus providing a cap to the growing sheet
that arrests further growth. We found peptides in which the Q is replaced
by an acetyllysine (aK) residue to be particularly promising candidates,
particularly if the reverse sequence (KYVIaKV) is used to form an
antiparallel interaction with the sheet.
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Affiliation(s)
- Joshua A Plumley
- Department of Chemistry Hunter College and the Graduate School, City University of New York , 695 Park Avenue, New York, New York 10065, United States
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Abstract
Abstract
The interaction between various proton donors (indole, CF3CH2OH, (CF3)2CHOH, (CF3)3COH) and (NNC)PtH hydrido complex (NNC-H=6-(1,1'-dimethylbenzyl)-2,2'-bipyridine) was investigated through low-temperature IR and NMR spectroscopy in combination with density functional theory calculations at the M06 level of theory. The experiment shows formation of very weak hydrogen bonded complexes (Δ HºHB
ca. -1.0 kcal mol-1), which undergo subsequent proton transfer surprisingly easy. Computational analysis of the hydrogen bonded complexes geometry, electronic parameters (obtained by NBO and AIM analysis), and orbital interaction energies shows that all the complexes are better described as bonded to the metal atom. At that in case of weak alcohols (CH3OH, TFE) there is also the additional interaction with the hydride ligand. These computational results allow explaining the observed experimental trends and give the first example of hydrogen bonding to a metal atom in the presence of hydride ligand.
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Filippov OA, Belkova NV, Epstein LM, Lledos A, Shubina ES. Directionality of Dihydrogen Bonds: The Role of Transition Metal Atoms. Chemphyschem 2012; 13:2677-87. [DOI: 10.1002/cphc.201200097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/19/2012] [Indexed: 11/11/2022]
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Marianski M, Dannenberg JJ. Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory. J Phys Chem B 2012; 116:1437-45. [PMID: 22201227 DOI: 10.1021/jp209177u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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20
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Comparative Study of Vibrational Spectra of Two Bioactive Natural Products Lupeol and Lupenone Using MM/QM Method. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/486304] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This work deals with the theoretical study on the molecular structure and vibrational spectra of two well-known natural products: lupeol and lupenone. The spectra were interpreted with the aid of normal mode analysis following full-structure optimization carried out with the hybrid two-level ONIOM (B3LYP/6-31G: PM3) method. A detailed interpretation of the infrared spectra of Lupeol and Lupenone is also reported in the present work. The similarities and differences between the vibrational spectra of the two molecules studied have been highlighted. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The thermodynamic calculations related to the title compounds were also performed at B3LYP/6-31G: PM3 level of theory. Quantum chemical calculations have been carried out to understand the dynamical behavior of the bioactive molecules Lupeol and Lupenone.
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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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22
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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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23
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Plumley JA, Dannenberg JJ. Comparison of β-sheets of capped polyalanine with those of the tau-amyloid structures VQIVYK and VQIINK. A density functional theory study. J Phys Chem B 2011; 115:10560-6. [PMID: 21797271 DOI: 10.1021/jp205388q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high and AM1 as the low level on parallel β-sheets containing from two to ten strands of Ac-VQIVYK-NHMe and Ac-VQIINK-NHMe, as well as both parallel and antiparallel Ac-AAAAAA-NHMe. We find that the first two sequences form more stable sheets due to the additional H-bonding between the Q's in the side chains of both and the N's in the side chain of Ac-VQIINK-NHMe. However, the H-bonds in the amyloid chains are significantly weakened by attractive strain, which prevents all the interstrand H-bonds from achieving their optimal geometries simultaneously and requires high distortion energies for the individual strands in the sheets. The antiparallel Ac-AAAAAA-NHMe's are generally more stable and more cooperative than the parallel sheets, principally due to the higher distortion energies of the latter.
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Affiliation(s)
- Joshua A Plumley
- Department of Chemistry, City University of New York-Hunter College and Graduate School, 695 Park Avenue, New York, New York 10065, United States
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24
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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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Solís-Calero C, Ortega-Castro J, Muñoz F. Reactivity of a phospholipid monolayer model under periodic boundary conditions: a density functional theory study of the Schiff base formation between phosphatidylethanolamine and acetaldehyde. J Phys Chem B 2010; 114:15879-85. [PMID: 21077587 DOI: 10.1021/jp1088367] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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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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Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy. Proc Natl Acad Sci U S A 2010; 107:14008-13. [PMID: 20660784 DOI: 10.1073/pnas.1006435107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogen K-edge spectra of aqueous triglycine were measured using liquid microjets, and the effects of Hofmeister-active salts on the spectra were observed. Spectra simulated using density functional theory, sampled from room temperature classical molecular dynamics trajectories, capture all major features in the measured spectra. The spectrum of triglycine in water is quite similar to that in the presence of chaotropic sodium bromide (and other halides), which raises the solubility of proteins. However, a new feature is found when kosmotropic Na(2)SO(3), which lowers solubility, is present; this feature results from excitations of the nitrogen atom in the terminal amino group of triglycine. Both direct interactions between this salt and the protonated amino terminus, as well as corresponding changes in the conformational dynamics of the system, contribute to this new feature. These molecular measurements support a different mechanism for the Hofmeister effect than has previously been suggested based on thermodynamic measurements. It is also shown that near edge X-ray absorption fine structure (NEXAFS) is sensitive to strong direct interaction between certain salts and charged peptides. However, by investigating the sensitivity of NEXAFS to the extreme structural differences between model beta-sheets and alpha-helices, we conclude that this technique is relatively insensitive to secondary structure of peptides and proteins.
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Kong S, Shenderovich IG, Vener MV. Density functional study of the proton transfer effect on vibrations of strong (short) intermolecular O-H...N/O-...H-N+ hydrogen bonds in aprotic solvents. J Phys Chem A 2010; 114:2393-9. [PMID: 20104882 DOI: 10.1021/jp911694r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and spectroscopic properties of the 1:1 complexes of substituted pyridines with benzoic acid and phenol derivatives in aprotic solvents are studied using B3LYP functional combined with the polarizable continuum model approximation. Two extreme structures are investigated: the state without (HB) and with proton transfer (PT). In the presence of an external electric field the O...N distance is contracted and the PT state does appear. The PT state of both the pyridine-benzoic and the pyridine-phenol complexes displays the only IR-active band in the 2800-1800 frequency region, which is located around 2000 cm(-1). However, the nature of the band is different for these two complexes. In the pyridine-benzoic acid complex it is practically a pure stretching vibration of the HN(+) group, while in the pyridine-phenol complex it is the mixed vibration of the bridging proton. A specific feature of the PT state in the pyridine-phenol complex is an IR-intensive band near 600 cm(-1), associated with the asymmetric stretching vibrations of the O(-)...HN(+) fragment. Its intensity is reciprocally proportional to the O...N distance. The appearance of this band provides an efficient criterion to differentiate between the HB and PT states of the 1:1 complexes of phenols with pyridines in aprotic solvents.
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Affiliation(s)
- Shushu Kong
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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29
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DFT study of H-bonds in the peptide secondary structures: The backbone–side-chain and polar side-chains interactions. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.01.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Computational study of hydrogen-bonding complex formation of helical polypeptides with water molecule. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum. Int J Mol Sci 2009; 10:3358-3370. [PMID: 20111685 PMCID: PMC2812828 DOI: 10.3390/ijms10083358] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/21/2009] [Accepted: 07/27/2009] [Indexed: 11/29/2022] Open
Abstract
Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ɛ-polylysine (ɛ-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and α-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6°. The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.
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