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Rapid prediction of interaction energies for nucleoside-containing hydrogen-bonded complexes: Lone-pair dipole moment treatment for adenine, cytosine and guanine. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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2
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Adamski A, Bogucki A, Świetlik R, Wróbel RJ, Klapiszewski Ł, Jesionowski T, Tylkowski B, Kubicki M, Patroniak V. Supramolecular synthons and pattern recognition in adenine amides – synthesis, structures and thermal properties. Supramol Chem 2015. [DOI: 10.1080/10610278.2015.1034125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ariel Adamski
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Andrzej Bogucki
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan, Poland
| | - Roman Świetlik
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznan, Poland
| | - Rafał J. Wróbel
- Institute of Chemical and Environment Engineering, West Pomeranian University of Technology, Pułaskiego 10, 70-310 Szczecin, Poland
| | - Łukasz Klapiszewski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Bartosz Tylkowski
- Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Maciej Kubicki
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
| | - Violetta Patroniak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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Deshmukh MM, Gadre SR, Cocinero EJ. Stability of conformationally locked free fructose: theoretical and computational insights. NEW J CHEM 2015. [DOI: 10.1039/c5nj02106e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Total stabilization is governed by three predominant factors viz. the sum of energy of all H-bonds, ring strain and anomeric stabilization.
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Affiliation(s)
- Milind M. Deshmukh
- Department of Chemistry
- Dr. Harisingh Gour Central University
- Sagar, 470003
- India
| | - Shridhar R. Gadre
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur 208 016
- India
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
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4
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Oliveira BG. The covalence and infrared spectra of cationic hydrogen bonds and dihydrogen bonds. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical study of hydrogen bonds and dihydrogen bonds formed by ethyl cation, hydrocarbons and magnesium hydride is presented with calculations performed at the BHandHLYP/6-31G(d,p) level of theory. The structural results and IR analyses demonstrated great insights, mainly the strengthening and weakness of the CC bond of the ethyl cation and π or pseudo-π bonds, respectively. The interaction strength was measured through the supermolecule as well as by means of additional approaches. The QTAIM calculations were applied to characterize not only the intermolecular interactions but specifically the covalent character in the H + ⋯ π, H + ⋯ pseudo-π and H + ⋯ H contacts. The NBO calculations were useful to interpret the polarization on the CC bond and whether this effect is related with the bond length reduction as well as increase of charge density and frequency shifts.
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Affiliation(s)
- Boaz G. Oliveira
- Institute of Environmental Sciences and Sustainable Development (ICADS), Federal University of Bahia, 47801-100, Barreiras – BA, Brazil
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5
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Hao J, Li S, Jiang X, Huang C, Wang C. Rapid evaluation of individual hydrogen bonding energies in linear water chains. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-4047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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6
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Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Sun CL, Ding F, Ding YL, Li Y. The effect of water molecules upon the hydrogen-bonding cooperativity of three-stranded antiparallel β-sheet models. RSC Adv 2014. [DOI: 10.1039/c3ra45892j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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8
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Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- 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
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Wang D, Ámundadóttir ML, van Gunsteren WF, Hünenberger PH. Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:521-37. [DOI: 10.1007/s00249-013-0901-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/19/2013] [Accepted: 03/28/2013] [Indexed: 10/26/2022]
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10
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Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Li Y, Wang C. Rapid evaluation of the binding energies between peptide amide and DNA base. J Comput Chem 2011; 32:2765-73. [DOI: 10.1002/jcc.21856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/03/2011] [Accepted: 05/13/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Yang Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Chang‐Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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