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Computational investigation on potential energy surface evolution: The tautomerization from enediyne to enyne-allene. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wang XD, Xuan CJ, Feng WL, Tian SX. Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study. J Chem Phys 2015; 142:064316. [DOI: 10.1063/1.4907940] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Xu-Dong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Center of Advanced Chemical Physics, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chuan-Jin Xuan
- Hefei National Laboratory for Physical Sciences at the Microscale, Center of Advanced Chemical Physics, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wen-Ling Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, Center of Advanced Chemical Physics, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, Center of Advanced Chemical Physics, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Mayer PM, Staedter D, Blanchet V, Hemberger P, Bodi A. Comparing femtosecond multiphoton dissociative ionization of tetrathiafulvene with imaging photoelectron photoion coincidence spectroscopy. J Phys Chem A 2013; 117:2753-9. [PMID: 23463913 DOI: 10.1021/jp311066y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper we describe femtosecond photoionization and the imaging photoelectron photoion coincidence spectroscopy of tetrathiafulvene, TTF. Femtosecond photoionization of TTF results in the absorption of up to twelve 808 nm photons leading to ion internal energies up to 12.1 eV as deduced from the photoelectron spectrum. Within this internal energy a variety of dissociation channels are accessible. In order to disentangle the complex ionic dissociation, we utilized the imaging photoelectron photoion coincidence (iPEPICO) technique. Above the dissociation threshold, iPEPICO results show that the molecular ion (m/z = 204) dissociates into seven product ions, six of which compete in a 1.0 eV internal energy window and are formed with the same appearance energy. Ab initio calculations are reported on the possible fragment ion structures of five dissociation channels as well as trajectories showing the loss of C2H2 and C2H2S from high internal energy TTF cations. A three-channel dissociation model is used to fit the PEPICO data in which two dissociation channels are treated as simple dissociations (one with a reverse barrier), while the rest involve a shared barrier. The two lower energy dissociation channels, m/z = 146 and the channel leading to m/z = 178, 171, 159, 140, and 127, have E0 values of 2.77 ± 0.10 and 2.38 ± 0.10 eV, respectively, and are characterized by ΔS(‡)(600 K) values of -9 ± 6 and 1 ± 6 J K(-1) mol(-1), respectively. Competing with them at higher internal energy is the cleavage of the central bond to form the m/z = 102 fragment ion, with an E0 value of 3.65 ± 0.10 eV and ΔS(‡)(600 K) = 83 ± 10 J K(-1) mol(-1).
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Affiliation(s)
- Paul M Mayer
- Chemistry Department, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, K1N 6N5 Canada.
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ZHANG YAN, WANG CHANGSHENG, YANG ZHONGZHI. ESTIMATION ON THE INTRAMOLECULAR 8- AND 12-MEMBERED RING N–H…O=C HYDROGEN BONDING ENERGIES IN β-PEPTIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609004708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Computation of accurate hydrogen bonding energies in peptides is of great importance in understanding the conformational stabilities of peptides. In this paper, the intramolecular 8- and 12-membered ring N – H … O = C hydrogen bonding energies in β-peptide structures were evaluated. The optimal structures of the β-peptide conformers were obtained using MP2/6-31G(d) method. The MP2/6-311++G(d,p) calculations were then carried out to evaluate the single-point energies. The results show that the intramolecular 8-membered ring N – H … O = C hydrogen bonding energies in the five β-dipeptide structures β-di, β-di-R1, β-di-R2, β-di-R3, and β-di-R4 are -5.50, -5.40, -7.28, -4.94, and -6.84 kcal/mol with BSSE correction, respectively; the intramolecular 12-membered ring N – H … O = C hydrogen bonding energies in the nine β-tripeptide structures β-tri, β-tri-R1, β-tri-R2, β-tri-R3, β-tri-R4, β-tri-R1', β-tri-R2', β-tri-R3' and β-tri-R4' are -10.23, -10.32, -9.53, -10.30, -10.32, -10.55, -10.09, -10.51, and -9.60 kcal/mol with BSSE correction, respectively. Our calculation results further indicate that for the intramolecular 8-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "a–a" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "e–e", while for the intramolecular 12-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "e–e" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "a–a". The method is also applied to estimate the individual intermolecular hydrogen bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, 2-oxo-acetamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen bonding energies in the four dimers are calculated to be -1.71, -1.50, -4.67, and -3.22 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -4.93, and -3.26 kcal/mol predicted by the supermolecular method.
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Affiliation(s)
- YAN ZHANG
- Department of Chemistry, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - CHANG-SHENG WANG
- Department of Chemistry, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - ZHONG-ZHI YANG
- Department of Chemistry, Liaoning Normal University, Dalian 116029, People's Republic of China
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Ramalho TC, Pereira DH, Thiel W. Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug. J Phys Chem A 2011; 115:13504-12. [PMID: 21995614 DOI: 10.1021/jp201576u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.
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Affiliation(s)
- Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Minas Gerais, Brazil.
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Gong F, Wang Q, Chen J, Yang Z, Liu M, Li S, Yang G, Bai L, Liu J, Dong Y. Exploring Intertrimer Cu···Cu Interactions and Further Phosphorescent Properties of Aryl Trimer Copper(I) Pyrazolates via Substituent Changing and External Pressure. Inorg Chem 2010; 49:1658-66. [DOI: 10.1021/ic9020417] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hu Y, Bernstein ER. Vibrational and Photoionization Spectroscopy of Neutral Valine Clusters. J Phys Chem A 2009; 113:8454-61. [DOI: 10.1021/jp901208f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yongjun Hu
- MOE Key Lab of Laser Life Science & Institute of Laser Life Science, South China Normal University, Guangzhou 510631, P. R. China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872
| | - Elliot R. Bernstein
- MOE Key Lab of Laser Life Science & Institute of Laser Life Science, South China Normal University, Guangzhou 510631, P. R. China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872
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Tian SX, Sun X, Cao R, Yang J. Thermal Stabilities of the Microhydrated Zwitterionic Glycine: A Kinetics and Dynamics Study. J Phys Chem A 2008; 113:480-3. [DOI: 10.1021/jp8092594] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiang Sun
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui Cao
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Dobrowolski JC, Jamróz MH, Kołos R, Rode JE, Sadlej J. IR Low-Temperature Matrix and ab Initio Study on β-Alanine Conformers. Chemphyschem 2008; 9:2042-51. [DOI: 10.1002/cphc.200800383] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hu Y, Bernstein ER. Vibrational and photoionization spectroscopy of biomolecules: Aliphatic amino acid structures. J Chem Phys 2008; 128:164311. [DOI: 10.1063/1.2902980] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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