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Electrochemical oxygen reduction reaction at conductive polymer PEDOT: Insight from ab initio molecular dynamics simulations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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2
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Lozynski M, Rusinska-Roszak D. Finding the direct energy-structure correlations in intramolecular aromaticity assisted hydrogen bonding (AAHB). J Mol Graph Model 2021; 105:107884. [PMID: 33725643 DOI: 10.1016/j.jmgm.2021.107884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 11/25/2022]
Abstract
A predictive model for intramolecular hydrogen bond energy (EHB) calculation of polyaromatic ortho-hydroxyaldehydes based on a set of small, functionalized hydrocarbons is developed. The complete data set of 18 compounds was used for this study. The model is based on one of four optional categories of molecular descriptors: geometric, spectroscopic, bond order and topological indices. The model of Wiberg bond indices (WBIs) as descriptors of the CC involved bond based on stepwise regression has acceptable prediction abilities for 14 structures of ortho-hydroxyformylobenzo[a]pyrene derivatives already at the semiempirical level. The presented correlation enables a significantly more rapid and quantitative description of the hydrogen bonding strength than the much more time-consuming MTA method. Thus, WBIs are shown to provide a reliable means for fast prescreening of the energy of chelate hydrogen bonds potentially for any polyaromatic derivatives.
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Affiliation(s)
- Marek Lozynski
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland
| | - Danuta Rusinska-Roszak
- Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland.
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3
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Nakahara K, Yamaguchi K, Kansui H. Stepwise Reactions between Cyclic 1,4-Diazadienes and Ketenes: Characteristics and Mechanism. HETEROCYCLES 2021. [DOI: 10.3987/com-20-14401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Yang Y, Li D, Li C, Liu Y, Jiang K. Asymmetric substitution changes the UV-induced nonradiative decay pathway and the spectra behaviors of β-diketones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 207:209-215. [PMID: 30240982 DOI: 10.1016/j.saa.2018.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Asymmetric substitution has not been termed as an essential factor in studying photo-induced ultrafast dynamics of molecular system. Asymmetric 4-hydroxybut-3-en-2-one (HEO), together with symmetric malonaldehyde (MA) and acetylacetone (AA), have been provided as target sample to study the nonradiative decay (ND) processes of β-diketones. An effective ND pathway of the three molecules is presented that their excited second (S2) states transfer to first (S1) state by nonadiabatic surface hopping, and then transfer to triplet (T1) state by crossing minimum energy crossing point (MECP), after which decay to ground (S0) state through MECP. More importantly, the asymmetric substitution of HEO induces the proton transfer in the S1 state and generates a proton-transferred conformer with lowest energy, which does not occur for MA and AA. This change exploits a new ND pathway that the S1 state decays to the proton transferred T1 state and then undergoes reverse proton transfer to S0 state through the MECPs between the three states. The two pathways of HEO give detailed energy and geometric information on surface hopping of S2/S1 and MECPs of S1/T1/S0, and interpret the reason of the ND pathway while not spectra emission. This result is significantly different from the previous reported ND pathway of photoisomerization or conical intersection between different states. This work shows that asymmetric substitution changes the molecular structure and then changes their spectra behaviors.
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Affiliation(s)
- Yonggang Yang
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Donglin Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Chaozheng Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China.
| | - Kai Jiang
- School of Environment, Henan Normal University, Xinxiang 453007, China
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Hollas D, Šištík L, Hohenstein EG, Martínez TJ, Slavíček P. Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method. J Chem Theory Comput 2017; 14:339-350. [DOI: 10.1021/acs.jctc.7b00958] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Hollas
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Lukáš Šištík
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Edward G. Hohenstein
- Department
of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
- PhD
Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Todd J. Martínez
- Department
of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 3, 18223 Prague 8, Czech Republic
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Hossein Bagi A, Khaledi Y, Ghari H, Arndt S, Hashmi ASK, Yates BF, Ariafard A. A Mechanistic Investigation of the Gold(III)-Catalyzed Hydrofurylation of C–C Multiple Bonds. J Am Chem Soc 2016; 138:14599-14608. [DOI: 10.1021/jacs.6b05742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amin Hossein Bagi
- Department
of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran 1467686831, Iran
| | - Yousef Khaledi
- Department
of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran 1467686831, Iran
| | - Hossein Ghari
- Department
of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran 1467686831, Iran
| | - Sebastian Arndt
- Organisch-Chemisches
Institut, Universität Heidelberg, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
| | - A. Stephen K. Hashmi
- Organisch-Chemisches
Institut, Universität Heidelberg, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
| | - Brian F. Yates
- School
of Physical Sciences (Chemistry), University of Tasmania, Private
Bag 75, Hobart, Tasmania 7001, Australia
| | - Alireza Ariafard
- Department
of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran 1467686831, Iran
- School
of Physical Sciences (Chemistry), University of Tasmania, Private
Bag 75, Hobart, Tasmania 7001, Australia
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Shayan K, Nowroozi A. The first singlet excited state (S1) intramolecular hydrogen bond of malonaldehyde derivatives: a TD-DFT and CIS study. Struct Chem 2016. [DOI: 10.1007/s11224-016-0796-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Iyer S, Lopez-Hilfiker F, Lee BH, Thornton JA, Kurtén T. Modeling the Detection of Organic and Inorganic Compounds Using Iodide-Based Chemical Ionization. J Phys Chem A 2016; 120:576-87. [DOI: 10.1021/acs.jpca.5b09837] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Siddharth Iyer
- Department
of Chemistry, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Felipe Lopez-Hilfiker
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Ben H. Lee
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Joel A. Thornton
- Department
of Atmospheric Sciences, University of Washington, Seattle, Washington 98195-1640, United States
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, Helsinki, FIN-00014, Finland
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Romero-Fernández MP, Ávalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. A further look at π-delocalization and hydrogen bonding in 2-arylmalondialdehydes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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D'Cunha C, Morozov AN, Chatfield DC. Theoretical study of HOCl-catalyzed keto-enol tautomerization of β-cyclopentanedione in an explicit water environment. J Phys Chem A 2013; 117:8437-48. [PMID: 23902476 DOI: 10.1021/jp401409y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of acid-catalyzed keto-enol tautomerization of β-cyclopentanedione (CPD) in solution is studied computationally. Reaction profiles are first calculated for a limited solvation environment using ab initio and density functional methods. Barrier heights for systems including up to one hydration shell of explicit water molecules depend strongly on the number of waters involved in proton transfer and to a lesser but significant extent on the number of waters forming hydrogen bonds with waters in the proton-transfer chain (each such water reduces the barrier by 4.4 kcal/mol on average). Barriers of 8-13 kcal/mol were obtained when a full or nearly full hydration shell was present, consistent with calculations for nonacid-catalyzed keto-enol tautomerization of related molecules. The presence of HOCl reduced the barrier by 4.5 kcal/mol in relation to the gas phase, consistent with the well-known principle that keto-enol tautomerization can be acid- or base-catalyzed. The reaction was also modeled beginning with snapshots of reactant conformations taken from a 300 K molecular dynamics simulation of CPD, HOCl, and 324 explicit waters. Reaction profiles were calculated at a QM/MM level with waters in the first hydration shell either fixed or energy-minimized at each step along the reaction coordinate. A substantial variation in barrier height was observed in both cases, depending primarily on electrostatic interactions (hydrogen bonding) with first-hydration-shell waters and, to a lesser extent, on electrostatic interactions with more distant waters and geometric distortion effects. For the lowest barriers, the extent of barrier reduction by waters involved in proton transfer is consistent with the limited solvation results, but further barrier reduction due to hydrogen bonding to waters involved in proton transfer is not observed. It is postulated that this is because highly flexible structures such as extensive hydrogen bonding networks optimal for reaction are entropically disfavored and so may not contribute significantly to the observed reaction rate.
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Affiliation(s)
- Cassian D'Cunha
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA
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Alagona G, Ghio C, Nagy PI. The catalytic effect of water on the keto–enol tautomerism. Pyruvate and acetylacetone: a computational challenge. Phys Chem Chem Phys 2010; 12:10173-88. [DOI: 10.1039/c003999c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Fedorov DG, Gordon MS. A combined effective fragment potential–fragment molecular orbital method. I. The energy expression and initial applications. J Chem Phys 2009; 131:024101. [DOI: 10.1063/1.3156313] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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13
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Substituent effects on the tautomerism of monochalcogenocarboxylic acids XC(O)YH (X=H, F, NH2, OH, CN, and CH3; Y=S, Se, and Te): A theoretical study. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Mturi GJ, Martincigh BS. Photostability of the sunscreening agent 4-tert-butyl-4′-methoxydibenzoylmethane (avobenzone) in solvents of different polarity and proticity. J Photochem Photobiol A Chem 2008. [DOI: 10.1016/j.jphotochem.2008.09.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Erdtman E, Eriksson LA. Theoretical Study of 5-Aminolevulinic Acid Tautomerization: A Novel Self-Catalyzed Mechanism. J Phys Chem A 2008; 112:4367-74. [DOI: 10.1021/jp7118197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edvin Erdtman
- Department of Natural Sciences and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden, and Modelling and Simulation Research Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Department of Natural Sciences and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden, and Modelling and Simulation Research Center, Örebro University, 701 82 Örebro, Sweden
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Bertolasi V, Ferretti V, Gilli P, Yao X, Li CJ. Substituent effects on keto–enol tautomerization of β-diketones from X-ray structural data and DFT calculations. NEW J CHEM 2008. [DOI: 10.1039/b714708b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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