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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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Plekan O, Feyer V, Richter R, Coreno M, Vall-llosera G, Prince KC, Trofimov AB, Zaytseva IL, Moskovskaya TE, Gromov EV, Schirmer J. An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine. J Phys Chem A 2009; 113:9376-85. [DOI: 10.1021/jp903209t] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oksana Plekan
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Vitaliy Feyer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Robert Richter
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Marcello Coreno
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Gemma Vall-llosera
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Kevin C. Prince
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Alexander B. Trofimov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Irina L. Zaytseva
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Tatyana E. Moskovskaya
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Evgeniy V. Gromov
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
| | - Jochen Schirmer
- Sincrotrone Trieste, in Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, I-00016 Montelibretti (Rome), Italy, Department of Physics, School of Engineering Science, Royal Institute of Technology, 10691 Stockholm, Sweden, Laboratorio Nazionale TASC, INFM-CNR, 34012 Trieste, Italy, Laboratory of Quantum Chemistry, Irkutsk State University, 664003 Irkutsk, Russia, Favorsky Institute of Chemistry, SB RAS, 664033 Irkutsk, Russia, and Theoretische Chemie, Physikalisch-Chemisches Institut,
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Feyer V, Plekan O, Richter R, Coreno M, Prince KC, Carravetta V. Core Level Study of Alanine and Threonine. J Phys Chem A 2008; 112:7806-15. [DOI: 10.1021/jp803017y] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitaliy Feyer
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Oksana Plekan
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Marcello Coreno
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Kevin C. Prince
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
| | - Vincenzo Carravetta
- Sincrotrone Trieste, Area Science Park, I-34012 Basovizza (Trieste), Italy, CNR-IMIP, Montelibretti, Rome, I-00016 Italy, Laboratorio Nazionale TASC, CNR-INFM, 34012 Trieste, Italy, and CNR-Institute of Chemical Physical Processes, Via Moruzzi 1, 56124 Pisa, Italy
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