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5
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Adesokan AA, Fredj E, Brown EC, Gerber * RB. Anharmonic vibrational frequency calculations of 5,6-dihydrouracil and its complex with water: testing improved semiempirical potentials for biological molecules. Mol Phys 2005. [DOI: 10.1080/00268970500105201] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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6
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Williams RW, Bone I, Weir AF. A scaled quantum mechanical force field for the alanine–alanine zwitterions in water based on scale factors for alanine, glycine, N-methylacetamide, acetate, formate, and methylamine. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.03.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Yamabe S, Tsuchida N. A computational study of interactions between acetic acid and water molecules. J Comput Chem 2003; 24:939-47. [PMID: 12720314 DOI: 10.1002/jcc.10178] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Density functional theory calculations were performed for the title reactions to elucidate the difference between the strong cyclic hydrogen bond of (Me-COOH)(2) and the electrolytic dissociation, MeCOOH <==> Me-COO(-) + H(+), as a weak acid. The association of water clusters with acetic acid dimers strengthens the cyclic hydrogen bond. A nucleophilic attack of the carboxylic carbon by a water cluster leads to a first zwitterionic intermediate, MeCOO(-) + H(3)O(+) + (HO)(3)C-Me. The intermediate is unstable and is isomerized to a neutral interacting system, MeCOOH...(HO)(3)C-Me + H(2)O. The ethanetriol, (HO)(3)-CMe is transformed to an acetic acid monomer. The monomer may be dissociated to give a second zwitterionic intermediate with reasonable proton-relay patterns and energy changes. In proton relay reaction channels, H in MeCOOH is not an acidic proton but is always a hydroxy proton.
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Affiliation(s)
- Shinichi Yamabe
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
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9
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Abstract
We have obtained ab initio scale factors and assigned frequencies for the alanine-alanine peptide in water. Calculations were performed on the isolated acidic and basic Ala-Ala structures, two one-water basic Ala-Ala supermolecules, and one two-water acidic and one two-water basic Ala-Ala supermolecules. Force constants were scaled using the experimentally determined Raman and Fourier transform infrared vibrational frequencies of four isotopic species of Ala-Ala in water at pH 13 and pH 1. Most of the 4-31G scale factors were transferable from smaller molecules. All but one scale factor were directly transferable between the pH 1 and pH 13 species for coordinates unchanged by protonation in both the isolated and two-water supermolecule structures. Scale factors for nonpolar coordinates were transferable between all Ala-Ala species with only a few small changes. Good agreement was obtained between the calculated and experimental frequencies for all isotopic species and structures.
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Affiliation(s)
- A F Weir
- Department of Bioinformatics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA
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11
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Liao DW, Mebel AM, Chen YT, Lin SH. Theoretical Study of the Structure, Energetics, and the n−π* Electronic Transition of the Acetone + nH2O (n = 1−3) Complexes. J Phys Chem A 1997. [DOI: 10.1021/jp972102q] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dai-Wei Liao
- Institute of Physical Chemistry, Department of Chemistry and State Key Lab of Physical Chemistry on Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10764, Taiwan, ROC, Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, ROC, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Alexander M. Mebel
- Institute of Physical Chemistry, Department of Chemistry and State Key Lab of Physical Chemistry on Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10764, Taiwan, ROC, Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, ROC, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Yit-Tsong Chen
- Institute of Physical Chemistry, Department of Chemistry and State Key Lab of Physical Chemistry on Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10764, Taiwan, ROC, Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, ROC, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
| | - Sheng-Hsien Lin
- Institute of Physical Chemistry, Department of Chemistry and State Key Lab of Physical Chemistry on Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China, Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10764, Taiwan, ROC, Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, ROC, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604
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14
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Markham LM, Hudson BS. Ab Initio Analysis of the Effects of Aqueous Solvation on the Resonance Raman Intensities of N-Methylacetamide. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952729d] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura M. Markham
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403
| | - Bruce S. Hudson
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403
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