1
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Jain P, Kumari G, Bhogra M, Yanda P, Joseph B, Waghmare UV, Narayana C. Raman Evidence of Multiple Adsorption Sites and Structural Transformation in ZIF-4. Inorg Chem 2023; 62:7703-7715. [PMID: 37163305 DOI: 10.1021/acs.inorgchem.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The zeolitic imidazolate framework, ZIF-4, exhibits soft porosity and is known to show pore volume changes with temperatures, pressures, and guest adsorption. However, the mechanism and adsorption behavior of ZIF-4 are not completely understood. In this work, we report an open to narrow pore transition in ZIF-4 around T ∼ 253 K upon lowering the temperature under vacuum (10-6 Torr) conditions, facilitated by C-H···π interactions. In the gaseous environment of N2 and CO2 around the framework, characteristic Raman peaks of adsorbed gases were observed under ambient conditions of 293 K and 1 atm. A guest-induced transition at ∼153 K resulting in the opening of new adsorption sites was inferred from the Raman spectral changes in the C-H stretching modes and low-frequency modes (<200 cm-1). In contrast to a single vibrational mode generally reported for entrapped N2, we show three Raman modes of adsorbed N2 in ZIF-4. The adsorption is facilitated by dispersive and quadrupolar interactions. From our temperature-dependent Raman results and theoretical analysis based on the density functional tight-binding approach, we conclude that the C-Hs are the preferred adsorption sites on ZIF-4 in the following order: C4-H, C5-H > C2-H > center of the Im ring (interacting with C-H centers) > center of the cavity. We also show that with an increasing concentration of N2 adsorbed at low temperatures, the ZIF-4 structure undergoes shear distortion of the window formed by 4-imidazole rings and consequent volumetric expansion. Our results have immediate implications in the field of porous materials and could be vital in identifying subtle structural transformations that may favor or hinder guest adsorption.
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Affiliation(s)
- Priyanka Jain
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
| | - Gayatri Kumari
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
| | - Meha Bhogra
- Theoretical Science Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
- Department of Mechanical Engineering, Shiv Nadar University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201314, India
| | - Premakumar Yanda
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
| | - Boby Joseph
- Elettra-Sincrotrone Trieste S.C. p. A., S.S. 14, Km 163.5 in Area Science Park, Basovizza 34149, Italy
| | - Umesh V Waghmare
- Theoretical Science Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
| | - Chandrabhas Narayana
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Karnataka 560064, India
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
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2
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Brela MZ, Didovets Y, Boczar M, Sato H, Nakajima T, Wójcik MJ. The hydrogen bond interaction dynamics in polyvinylphenol: Studied by Born-Oppenheimer molecular dynamics. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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El Foujji L, El Bourakadi K, Essassi EM, Boeré RT, Qaiss AEK, Bouhfid R. Solid-state zwitterionic tautomerization of 2-((5-methyl-1H-pyrazol-3-yl)methyl)-1H-benzimidazole: Synthesis, characterization, DFT calculation and docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Kamerin BS, Niman JW, Kresin VV. Electric deflection of imidazole dimers and trimers in helium nanodroplets: Dipole moments, structure, and fragmentation. J Chem Phys 2020; 153:081101. [DOI: 10.1063/5.0020844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Benjamin S. Kamerin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
| | - John W. Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
| | - Vitaly V. Kresin
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, USA
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5
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Direct Evidence of Interfacial Hydrogen Bonding in Proton-Electron Concerted 2D Organic Bilayer on Au Substrate. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2019. [DOI: 10.1380/ejssnt.2019.49] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Shin JY, Wang YL, Yamada SA, Hung ST, Fayer MD. Imidazole and 1-Methylimidazole Hydrogen Bonding and Nonhydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments. J Phys Chem B 2019; 123:2094-2105. [DOI: 10.1021/acs.jpcb.8b11299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jae Yoon Shin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yong-Lei Wang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Samantha T. Hung
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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7
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Tadokoro M, Isogai K, Harada S, Kouchi T, Yamane T, Sugaya T, Kamebuchi H. Evidence of proton-coupled mixed-valency by electrochemical behavior on transition metal complex dimers bridged by two Ag + ions. Dalton Trans 2019; 48:535-546. [PMID: 30525138 DOI: 10.1039/c8dt03962c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
H-Bonded metal complex dimers with reversible redox behaviour, which are connected by a low-barrier hydrogen bond (LBHB) with a very low energy barrier for proton transfer, can provide a unique mixed-valency state stabilized by the proton-coupled electron transfer (PCET) phenomenon. Using cyclic voltammetry measurements, newly prepared [ReIIICl2(PnPr3)2(Hbim)]2 (2) and [OsIIICl2(PnPr3)2(Hbim)]2 (3) existing as H-bonded dimers in a CH2Cl2 solution showed a four-step and four-electron transfer containing two mixed-valency states of ReIIReIII and ReIIIReIV, and OsIIOsIII and OsIIIOsVI, respectively. Furthermore, [ReIIICl2(PnPr3)2(Agbim)]2 (4) and [OsIIICl2(PnPr3)2(Agbim)]2 (5), bridged by two Ag+ ions instead of two H-bonding protons, were prepared, and their electrochemical behaviours changed to a two-step and four-electron transfer. It is clear that the H-bonded complex dimers 2 and 3, connected by an LBHB, can be electrochemically stabilized into unique pairs of mixed-valency states by PCET, and the H-bonding proton transfer also controls the electrochemical redox behaviour.
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Affiliation(s)
- Makoto Tadokoro
- Tokyo University of Science, Faculty of Science, Department of Chemistry, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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8
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Forsting T, Zischang J, Suhm MA, Eckhoff M, Schröder B, Mata RA. Strained hydrogen bonding in imidazole trimer: a combined infrared, Raman, and theory study. Phys Chem Chem Phys 2019; 21:5989-5998. [DOI: 10.1039/c9cp00399a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is not how three imidazole molecules prefer to arrange, as a combined IR, Raman and computational analysis unambiguously shows.
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Affiliation(s)
- Thomas Forsting
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Julia Zischang
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Marco Eckhoff
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Benjamin Schröder
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Ricardo A. Mata
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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9
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Brela MZ, Boczar M, Malec LM, Wójcik MJ, Nakajima T. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:194-201. [PMID: 29395929 DOI: 10.1016/j.saa.2018.01.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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10
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Cosby T, Vicars Z, Heres M, Sangoro J. Associating Imidazoles: Elucidating the Correlation between the Static Dielectric Permittivity and Proton Conductivity. PHYSICAL REVIEW LETTERS 2018; 120:136001. [PMID: 29694165 DOI: 10.1103/physrevlett.120.136001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Broadband dielectric spectroscopy is employed to investigate the impact of supramolecular structure on charge transport and dynamics in hydrogen-bonded 2-ethyl-4-methylimidazole and 4-methylimidazole. Detailed analyses reveal (i) an inverse relationship between the average supramolecular chain length and proton conductivity and (ii) no direct correlation between the static dielectric permittivity and proton conductivity in imidazoles. These findings raise fundamental questions regarding the widespread notion that extended supramolecular hydrogen-bonded networks facilitate proton conduction in hydrogen bonding materials.
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Affiliation(s)
- Tyler Cosby
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Zachariah Vicars
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Maximilian Heres
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Joshua Sangoro
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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11
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Kato HS, Yoshimoto S, Ueda A, Yamamoto S, Kanematsu Y, Tachikawa M, Mori H, Yoshinobu J, Matsuda I. Strong Hydrogen Bonds at the Interface between Proton-Donating and -Accepting Self-Assembled Monolayers on Au(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2189-2197. [PMID: 29359939 DOI: 10.1021/acs.langmuir.7b03451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations. Here, we report the formation of the catechol-fused bis(methylthio)tetrathiafulvalene (H2Cat-BMT-TTF) adlayer hydrogen bonding with an imidazole-terminated alkanethiolate self-assembled monolayer (Im-SAM) on Au(111). The heterogeneous bilayer is realized by sequential two-step immersions in solutions for the individual Im-SAM and H2Cat-BMT-TTF adlayer formations. In the measurements by AFM, a grained H2Cat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of H2Cat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between H2Cat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm-1, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm-1). The OH stretching mode frequency and the adsorption strength for the H2Cat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations.
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Affiliation(s)
- Hiroyuki S Kato
- Department of Chemistry, Graduate School of Science, Osaka University , Toyonaka, Osaka 560-0043, Japan
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Shinya Yoshimoto
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Akira Ueda
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Susumu Yamamoto
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Yusuke Kanematsu
- Faculty of Information Sciences, Hiroshima City University , 3-4-1, Hiroshima, Hiroshima 731-3194, Japan
| | - Masanori Tachikawa
- Graduate School of Nanobioscience, Yokohama City University , Yokohama, Kanagawa 236-0027, Japan
| | - Hatsumi Mori
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Jun Yoshinobu
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
| | - Iwao Matsuda
- The Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwa, Chiba 277-8581, Japan
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12
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Gług M, Brela MZ, Boczar M, Turek AM, Boda Ł, Wójcik MJ, Nakajima T, Ozaki Y. Infrared Spectroscopy and Born–Oppenheimer Molecular Dynamics Simulation Study on Deuterium Substitution in the Crystalline Benzoic Acid. J Phys Chem B 2017; 121:479-489. [DOI: 10.1021/acs.jpcb.6b10617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Gług
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
| | - Mateusz Z. Brela
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Marek Boczar
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
| | - Andrzej M. Turek
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
| | - Łukasz Boda
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
| | - Marek J. Wójcik
- Faculty
of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland
| | - Takahito Nakajima
- Advanced
Institute for Computational Science, RIKEN, 7-1-26, Minatojima-minami-machi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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13
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Mukherjee V, Yadav T. Conformational study of neutral histamine monomer and their vibrational spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 165:167-175. [PMID: 27155558 DOI: 10.1016/j.saa.2016.04.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/13/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Molecular modeling and potential energy scanning of histamine molecule, which is an important neurotransmitter, with respect to the dihedral angle of methylamine side chain have done which prefer three different conformers of histamine monomer. We have calculated molecular structures and vibrational spectra with IR and Raman intensities of these conformers using Density Functional Theory (DFT) with the exchange functional B3LYP incorporated with the basis set 6-31++G(d,p) and Hartree-Fock (HF) with the same basis set. We have also employed normal coordinate analysis (NCA) to scale the theoretical frequencies and to calculate potential energy distributions (PEDs) for the conspicuous assignments. Normal modes assignments of some of the vibrational frequencies of all the three conformers are in good agreement with the earlier reported experimental frequencies of histamine whereas others have modified. The standard deviations between the theoretical and experimental frequencies fall in the region 13-20cm(-1) for the three conformers. NBO analyses of histamine conformers were also performed. The net charge transfers from ethylamine side chain to the imidazole ring. The intensive interactions between bonding and anti-bonding orbitals are found in imidazole ring. The HOMO-LUMO energy gap is nearly 5.50eV.
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Affiliation(s)
- V Mukherjee
- SUIIT, Sambalpur University, Sambalpur, 768019, Odisha, India.
| | - T Yadav
- SUIIT, Sambalpur University, Sambalpur, 768019, Odisha, India
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14
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Theoretical Modeling of Vibrational Spectra and Proton Tunneling in Hydrogen-Bonded Systems. ADVANCES IN CHEMICAL PHYSICS 2016. [DOI: 10.1002/9781119165156.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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15
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Trachsel MA, Ottiger P, Frey HM, Pfaffen C, Bihlmeier A, Klopper W, Leutwyler S. Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene. J Phys Chem B 2015; 119:7778-90. [DOI: 10.1021/jp512766r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Maria A. Trachsel
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Angela Bihlmeier
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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16
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Brela MZ, Wójcik MJ, Boczar M, Witek Ł, Yasuda M, Ozaki Y. Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds. J Phys Chem B 2015; 119:7922-30. [DOI: 10.1021/acs.jpcb.5b02777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mateusz Z. Brela
- Research
Group of Molecular Modelling of Catalytic Processes, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek J. Wójcik
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek Boczar
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Łukasz Witek
- Photochemistry
and Luminescence Research Group, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Mitsuru Yasuda
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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17
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Takahashi H, Takahashi K, Yabushita S. Interpretation of semiclassical transition moments through wave function expansion of dipole moment functions with applications to the OH stretching spectra of simple acids and alcohols. J Phys Chem A 2015; 119:4834-45. [PMID: 25919505 DOI: 10.1021/acs.jpca.5b02050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Semiclassical description of molecular vibrations has provided us with various computational approximations and enhanced our conceptual understanding of quantum mechanics. In this study, the transition moments of the OH stretching fundamental and overtone intensities (Δv = 1-6) of some alcohols and acids are calculated by three kinds of semiclassical methods, correspondence-principle (CP) approximation, quasiclassical approximation, and uniform WKB approximation, and their respective transition moments are compared to those by the quantum theory. On the basis of the local mode picture, the one-dimensional potential energy curves and the dipole moment functions (DMFs) were obtained by density functional theory calculations and then fitted to Morse functions and sixth-order polynomials, respectively. It was shown that both the transition energies and the absorption intensities derived in the semiclassical methods reproduced their respective quantum values. In particular, the CP approximation reproduces the quantum transition moments if the formula given by Naccache is used for the action integral value. On the basis of these semiclassical results, we present a picture to understand the small variance in the overtone intensities of these acids and alcohols. Another important result is the ratios of semiclassical-to-quantum transition moment are almost independent of the applied molecules even with a great molecular variance of the DMFs, and they depend only on the nature of the semiclassical approximations and the quantum number. The difference between the semiclassical and quantum transition moments was analyzed in terms of a hitherto unrecognized concept that the Fourier expansion of the time dependent DMF in the CP treatment is a kind of the wave function expansion method using trigonometric functions as the quotient functions. For a Morse oscillator, we derive the analytic and approximate expressions of the quotient functions in terms of the bond displace coordinate in both the CP and the quantum mechanical frameworks and discuss the methodological dependence of the calculated transition moments. As a byproduct, we have found a simple derivation of the DMF expression first derived by Timm and Mecke long time ago.
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Affiliation(s)
- Hirokazu Takahashi
- †Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan
| | - Kaito Takahashi
- ‡Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan
| | - Satoshi Yabushita
- †Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 Japan
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Wierzbicka E, Boczar M, Wójcik MJ. Investigation of hydrogen bonds properties in the terephthalic acid crystal, using molecular dynamics method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:488-493. [PMID: 24813277 DOI: 10.1016/j.saa.2014.03.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/19/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.
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Affiliation(s)
- Ewa Wierzbicka
- Department of Physical Chemistry & Electrochemistry, Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30060 Krakow, Poland
| | - Marek Boczar
- Department of Physical Chemistry & Electrochemistry, Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30060 Krakow, Poland
| | - Marek J Wójcik
- Department of Physical Chemistry & Electrochemistry, Faculty of Chemistry, Jagiellonian University in Krakow, Ingardena 3, 30060 Krakow, Poland.
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19
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Wójcik MJ, Kwiendacz J, Boczar M, Boda Ł, Ozaki Y. Quantum-mechanical and Car–Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Car–Parrinello simulation of the vibrational spectra of strong hydrogen bonds with isotopic substitution effects: Application to oxalic acid dihydrate. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Güntepe F, Saraçoğlu H, Çalışkan N, Yüksektepe Ç, Cukurovali A. Synthesis, molecular and crystal structure analysis of 2-bromo-4-chloro-6-{[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-hydrazonomethyl}-phenol by experimental methods and theoretical calculations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Futami Y, Morisawa Y, Ozaki Y, Hamada Y, Wojcik MJ, Ozaki Y. The dielectric constant dependence of absorption intensities and wavenumbers of the fundamental and overtone transitions of stretching vibration of the hydrogen fluoride studied by quantum chemistry calculations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.01.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Zerroukhi A, Jeanmaire T, Raveyre C, Ainser A. Synthesis and characterization of hydrophobically modified starch by ring opening polymerization using imidazole as catalyst. STARCH-STARKE 2012. [DOI: 10.1002/star.201100154] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Brela M, Stare J, Pirc G, Sollner-Dolenc M, Boczar M, Wójcik MJ, Mavri J. Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide. J Phys Chem B 2012; 116:4510-8. [PMID: 22429110 DOI: 10.1021/jp2094559] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.
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Affiliation(s)
- Mateusz Brela
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
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25
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Piela K, Szostak MM. Electrical Anharmonicity and Vibronic Couplings Contributions to Optical Nonlinearity of N-Benzyl-2-methyl-4-nitroaniline Crystal Studied by FT-IR, Polarized FT-NIR, Resonance Raman and UV–Vis Spectroscopy. J Phys Chem A 2012; 116:1730-45. [PMID: 22263616 DOI: 10.1021/jp211476c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katarzyna Piela
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - M. Magdalena Szostak
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
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26
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Wu BD, Zhang JG, Zhang TL, Yang L, Zhou ZN. Two Environmentally Friendly Energetic Compounds, [Mn(AZT)4(H2O)2](PA)2·4H2O and [Co(AZT)2(H2O)4](PA)2, Based on 3-Azido-1,2,4-triazole (AZT) and Picrate (PA). Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201100806] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Flakus HT, Hachuła B, Stolarczyk A. H/D isotopic recognition in hydrogen bonded systems: H/D isotopic self-organization effects in the IR spectra of the hydrogen bond in 2-methylimidazole crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 85:7-16. [PMID: 22019215 DOI: 10.1016/j.saa.2011.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/04/2011] [Accepted: 08/14/2011] [Indexed: 05/31/2023]
Abstract
Polarized IR spectra of H12(3)45 2-methylimidazole and of its H1D2(3)45, D1H2(3)45 and D12(3)45 deuterium derivative crystals are reported and interpreted within the limits of the "strong-coupling" theory. The spectra interpretation facilitated the recognition of the H/D isotopic "self-organization" phenomenon, which depends on a non-random distribution of protons and deuterons in the lattices of isotopically diluted crystal samples. The H/D isotopic "self-organization" mechanism engaged all four hydrogen bonds from each unit cell. These effects basically resulted from the dynamical co-operative interactions involving adjacent hydrogen bonds in each hydrogen bond chain. A weaker exciton coupling involved the closely spaced hydrogen bonds; each belonging to a different chain of associated 2-methylimidazole molecules. The high intensity of the narrow band at ca. 1880cm(-1) was interpreted as the result of coupling between the γ(N-H⋯N) proton bending "out of plane" vibration overtone and the ν(N-H) proton stretching vibration.
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Affiliation(s)
- Henryk T Flakus
- Institute of Chemistry, University of Silesia, 9 Szkolna Street, Pl-40-006 Katowice, Poland.
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28
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Maiti KS, Samsonyuk A, Scheurer C, Steinel T. Hydrogen bonding characteristics of 2-pyrrolidinone: a joint experimental and theoretical study. Phys Chem Chem Phys 2012; 14:16294-300. [DOI: 10.1039/c2cp43114a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Wu BD, Wang SW, Yang L, Zhang TL, Zhang JG, Zhou ZN. Preparation, Crystal Structure, and Thermal Decomposition of Two Novel Energetic Compounds [Ni(IMI)6](L)2 (L = ClO4- and NO3-) and one Carbonate Compound [Ni(IMI)6](CO3)·5H2O (IMI = Imidazole). Z Anorg Allg Chem 2011. [DOI: 10.1002/zaac.201100279] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Ghalla H, Issaoui N, Oujia B. Theoretical study of the polarized infrared spectra of the hydrogen bond in 2-furoic acid crystal dimer. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2011. [DOI: 10.1002/qua.23117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Wu B, Wang S, Yang L, Zhang T, Zhang J, Zhou Z, Yu K. Preparation, Crystal Structures, Thermal Decomposition and Explosive Properties of Two Novel Energetic Compounds M(IMI)
4
(N
3
)
2
(M = Cu
II
and Ni
II
, IMI = Imidazole): The New High–Nitrogen Materials (N > 46 %). Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100054] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bi‐dong Wu
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Shi‐wei Wang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Li Yang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Tong‐lai Zhang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Jian‐guo Zhang
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Zun‐ning Zhou
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
| | - Kai‐bei Yu
- State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing 100081, China, Fax: +86‐10‐68‐911‐202
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32
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Stare J, Mavri J, Grdadolnik J, Zidar J, Maksić ZB, Vianello R. Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study. J Phys Chem B 2011; 115:5999-6010. [DOI: 10.1021/jp111175e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jernej Zidar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | | | - Robert Vianello
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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33
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Kwiendacz J, Boczar M, Wójcik MJ. Car–Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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