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Yalagi S, Tonannavar J, Yenagi J. Experimental and DFT dimer modeling studies of the H-bond induced-vibration modes of l-β-Homoserine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:109-115. [PMID: 28347921 DOI: 10.1016/j.saa.2017.03.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/03/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
The vibrational spectra for l-β-Homoserine have been measured (IR absorption: 4000-400cm-1/Raman spectra: 4000-200cm-1). Characteristic vibrational modes of ammonium (-NH3+), carboxylate (-CO2-) and hydroxyl (-OH) groups across the 3700-1400cm-1 are all identified to have originated in inter-molecular hydrogen bonding involving these functional groups. DFT calculations at B3LYP/6-311++G(d, p) level have yielded a single neutral monomer in the gas phase. Since as a member of the amino acids which are known to possess zwitterionic structure in condensed phase, the neutral monomer of l-β-Homoserine is optimized to a zwitterionic structure in a water medium. Consideration of two dimer structures, one dimer with -NH‧‧‧O bond and another -OH‧‧‧O bond, has given rise to vibrational modes that satisfactorily fit to all the observed absorption and Raman bands. It is found that the dimer with -OH‧‧‧O bond (binding energy, 8.896kcal/mol) is more tightly bound than the dimer with -NH‧‧‧O bond (8.363kcal/mol).
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Affiliation(s)
- Shashikala Yalagi
- Vibrational Spectroscopy Group, Department of Physics, Karnatak University, Dharwad 580 003, Karnataka, India
| | - J Tonannavar
- Vibrational Spectroscopy Group, Department of Physics, Karnatak University, Dharwad 580 003, Karnataka, India
| | - Jayashree Yenagi
- Vibrational Spectroscopy Group, Department of Physics, Karnatak University, Dharwad 580 003, Karnataka, India.
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2
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De Santis S, La Mesa C, Masci G. On the upper critical solution temperature of PNIPAAM in an ionic liquid: Effect of molecular weight, tacticity and water. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.05.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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Kavanoz M, Pekmez NÖ, Can M. Investigation of the behavior of hydrogen-bonded phenolic compounds and their determination by using poly(vinylferrocenium)-polyaniline composite film. J Appl Polym Sci 2016. [DOI: 10.1002/app.43596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Muammer Kavanoz
- Department of Chemistry; Recep Tayyip Erdogan University; 53100 Rize Turkey
| | | | - Muzaffer Can
- Department of Chemistry; Kırıkkale University; 71450 Kırıkkale Turkey
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4
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Kollipost F, Papendorf K, Lee YF, Lee YP, Suhm MA. Alcohol dimers – how much diagonal OH anharmonicity? Phys Chem Chem Phys 2014; 16:15948-56. [DOI: 10.1039/c4cp01418a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The massive infrared attenuation and increased anharmonicity of OH stretching overtones in alcohol dimers is experimentally quantified.
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Affiliation(s)
- Franz Kollipost
- Georg-August-Universität Göttingen
- Institut für Physikalische Chemie
- 37077 Göttingen, Germany
| | - Kim Papendorf
- Georg-August-Universität Göttingen
- Institut für Physikalische Chemie
- 37077 Göttingen, Germany
| | - Yu-Fang Lee
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao Tung University
- Hsinchu 30010, Taiwan
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao Tung University
- Hsinchu 30010, Taiwan
- Institute of Atomic and Molecular Sciences
- Academia Sinica
| | - Martin A. Suhm
- Georg-August-Universität Göttingen
- Institut für Physikalische Chemie
- 37077 Göttingen, Germany
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5
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Storz MP, Brengel C, Weidel E, Hoffmann M, Hollemeyer K, Steinbach A, Müller R, Empting M, Hartmann RW. Biochemical and biophysical analysis of a chiral PqsD inhibitor revealing tight-binding behavior and enantiomers with contrary thermodynamic signatures. ACS Chem Biol 2013; 8:2794-801. [PMID: 24099650 DOI: 10.1021/cb400530d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antivirulence strategies addressing bacterial pathogenicity without exhibiting growth inhibition effects represent a novel approach to overcome today's crisis in antibiotic development. In recent studies, we examined various inhibitors of PqsD, an enzyme involved in formation of Pseudomonas aeruginosa cell-to-cell signaling molecules, and observed desired cellular effects for 2-nitrophenyl derivatives. Herein, we investigated the binding characteristics of this interesting compound class using several biochemical and biophysical methods. The inhibitors showed time-dependent activity, tight-binding behavior, and interactions with the catalytic center. Furthermore, isothermal titration calorimetry (ITC) experiments with separated enantiomers revealed contrary thermodynamic signatures showing either enthalpy- or entropy-driven affinity. A combination of site-directed mutagenesis and thermodynamic profiling was used to identify key residues involved in inhibitor binding. This information allowed the proposal of experimentally confirmed docking poses. Although originally designed as transition state analogs, our results suggest an altered position for both enantiomers. Interestingly, the main difference between stereoisomers was found in the orientation of the hydroxyl group at the stereogenic center. The predicted binding modes are in accordance with experimental data and, thus, allow future structure-guided optimization.
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Affiliation(s)
- Michael P. Storz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Christian Brengel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Elisabeth Weidel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Michael Hoffmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Microbial Natural Products, Campus C2.3, 66123 Saarbrücken, Germany
| | - Klaus Hollemeyer
- Biochemical
Engineering, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
| | - Anke Steinbach
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Microbial Natural Products, Campus C2.3, 66123 Saarbrücken, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Campus C2.3, 66123 Saarbrücken, Germany
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
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6
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Bouabdallah I, Rahal M, Harit T, El Hajbi A, Malek F, Eddike D, Tillard M, Ramdani A. Hartree–Fock and density functional theory studies on tautomerism of 5,5′-diisopropyl-3,3′-bipyrazole in gas phase and solution. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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8
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A DFT study on the mechanisms of three-component reaction between imidazoles, isocyanates and cyanophenylacetylene. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.021] [Citation(s) in RCA: 6] [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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9
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Vega-Hissi EG, Estrada MR, Lavecchia MJ, Pis Diez R. Computational chemical analysis of unconjugated bilirubin anions and insights into pKa values clarification. J Chem Phys 2013; 138:035101. [PMID: 23343304 DOI: 10.1063/1.4773586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The pKa, the negative logarithm of the acid dissociation equilibrium constant, of the carboxylic acid groups of unconjugated bilirubin in water is a discussed issue because there are quite different experimental values reported. Using quantum mechanical calculations we have studied the conformational behavior of unconjugated bilirubin species (in gas phase and in solution modeled implicitly and explicitly) to provide evidence that may clarify pKa values because of its pathophysiological relevance. Our results show that rotation of carboxylate group, which is not restricted, settles it in a suitable place to establish stronger interactions that stabilizes the monoanion and the dianion to be properly solvated, demonstrating that the rationalization used to justify the high pKa values of unconjugated bilirubin is inappropriate. Furthermore, low unconjugated bilirubin (UCB) pKa values were estimated from a linear regression analysis.
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Affiliation(s)
- Esteban G Vega-Hissi
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia, Universidad Nac. de San Luis, Chacabuco 917, (5700) San Luis, Argentina.
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10
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Poly(vinylferrocenium) perchlorate–polyaniline composite film-coated electrode for amperometric determination of hydroquinone. J Solid State Electrochem 2011. [DOI: 10.1007/s10008-011-1505-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Bodo E, Caminiti R. The structure of geminal imidazolium bis(trifluoromethylsulfonyl)amide ionic liquids: a theoretical study of the gas phase ionic complexes. J Phys Chem A 2010; 114:12506-12. [PMID: 21049958 DOI: 10.1021/jp107023b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this work we report molecular mechanics and ab initio calculations on the geminal di-imidazolium bis(trifluoromethylsulfonyl)amide ionic liquid in the gas phase. We report the likely energetically preferred geometries of the ionic complex and its main features in terms of charge distribution, electronic density, structure, and energetics. We find that the gas phase structure of the ionic complex is quite compact and that the alkyl chain connecting the two imidazolium charged rings is strongly bent in order to maximize their electrostatic interactions with the two anions.
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Affiliation(s)
- E Bodo
- Department of Chemistry, University of Rome La Sapienza, Italy.
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12
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Wang SH, Liu FF, Dong XY, Sun Y. Thermodynamic Analysis of the Molecular Interactions between Amyloid β-Peptide 42 and (−)-Epigallocatechin-3-gallate. J Phys Chem B 2010; 114:11576-83. [DOI: 10.1021/jp1001435] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shi-Hui Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fu-Feng Liu
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiao-Yan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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13
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Theoretical and spectroscopic study of hydrogen bond vibrations in imidazole and its deuterated derivative. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.04.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Wu XH, Zhang H, Wu YD. Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: a statistical and theoretical study. Proteins 2010; 78:1186-94. [PMID: 19927323 DOI: 10.1002/prot.22638] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
WD40-repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven beta-sheet propeller with each beta-sheet in a four-strand structure. An analysis of 20 available WD40-repeat proteins in Protein Data Bank reveals that each protein has at least one Asp-His-Ser/Thr-Trp (D-H-S/T-W) hydrogen-bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40-repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40-repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen-bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins.
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Affiliation(s)
- Xian-Hui Wu
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China
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15
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Klähn M, Stüber C, Seduraman A, Wu P. What Determines the Miscibility of Ionic Liquids with Water? Identification of the Underlying Factors to Enable a Straightforward Prediction. J Phys Chem B 2010; 114:2856-68. [DOI: 10.1021/jp1000557] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Klähn
- Institute of High Performance Computing, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Claudia Stüber
- Institute of High Performance Computing, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Abirami Seduraman
- Institute of High Performance Computing, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Ping Wu
- Institute of High Performance Computing, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
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16
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Rungrotmongkol T, Decha P, Sompornpisut P, Malaisree M, Intharathep P, Nunthaboot N, Udommaneethanakit T, Aruksakunwong O, Hannongbua S. Combined QM/MM mechanistic study of the acylation process in furin complexed with the H5N1 avian influenza virus hemagglutinin's cleavage site. Proteins 2009; 76:62-71. [PMID: 19089976 DOI: 10.1002/prot.22318] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Combined quantum mechanical/molecular mechanical (QM/MM) techniques have been applied to investigate the detailed reaction mechanism of the first step of the acylation process by furin in which the cleavage site of the highly pathogenic avian influenza virus subtype H5N1 (HPH5) acts as its substrate. The energy profile shows a simultaneous mechanism, known as a concerted reaction, of the two subprocesses: the proton transfer from Ser368 to His194 and the nucleophilic attack on the carbonyl carbon of the scissile peptide of the HPH5 cleavage site with a formation of tetrahedral intermediate (INT). The calculated energy barrier for this reaction is 16.2 kcal.mol(-1) at QM/MM B3LYP/6-31+G*//PM3-CHARMM22 level of theory. Once the reaction proceeds, the ordering of the electrostatic stabilization by protein environment is of the enzyme-substrate < transition state < INT complexes. Asp153 was found to play the most important role in the enzymatic reaction by providing the highest degree of intermediate complex stabilization. In addition, the negatively charged carbonyl oxygen of INT is well stabilized by the oxyanion hole constructed by Asn295's carboxamide and Ser368's backbone.
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Affiliation(s)
- Thanyada Rungrotmongkol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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17
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Sun XM, Wang HJ, Feng DC. Binding Properties of CO, NO, and O2 to P450 Heme: a Density Functional Study. CHINESE J CHEM PHYS 2007. [DOI: 10.1088/1674-0068/20/05/552-556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Kovacević B, Rozman M, Klasinc L, Srzić D, Maksić ZB, Yañez M. Gas-Phase Structure of Protonated Histidine and Histidine Methyl Ester: Combined Experimental Mass Spectrometry and Theoretical ab Initio Study. J Phys Chem A 2005; 109:8329-35. [PMID: 16834223 DOI: 10.1021/jp053288t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.
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Affiliation(s)
- Borislav Kovacević
- Quantum Organic Chemistry Group and Laboratory for Chemical Kinetics and Atmospheric Chemistry, Rudjer Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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