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Takahashi M, Ishikawa Y, Ito H. The dispersion correction and weak-hydrogen-bond network in low-frequency vibration of solid-state salicylic acid. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.02.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Structure and intermolecular vibrations of 7-azaindole-water 2:1 complex in a supersonic jet expansion: Laser-induced fluorescence spectroscopy and quantum chemistry calculation#. J CHEM SCI 2012. [DOI: 10.1007/s12039-011-0200-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Qiu Z, Xia Y, Wang H, Diao K. Hydrogen-bonding interaction of urea with DNA bases: A density functional theory study. J STRUCT CHEM+ 2011. [DOI: 10.1134/s0022476611030036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Garcia JC, Justo JF, Machado WVM, Assali LVC. Structural, Electronic, and Vibrational Properties of Amino-adamantane and Rimantadine Isomers. J Phys Chem A 2010; 114:11977-83. [DOI: 10.1021/jp107496b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. C. Garcia
- Escola Politécnica, Universidade de São Paulo, CP 61548, CEP 05424-970, São Paulo, SP, Brazil, and Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970, São Paulo, SP, Brazil
| | - J. F. Justo
- Escola Politécnica, Universidade de São Paulo, CP 61548, CEP 05424-970, São Paulo, SP, Brazil, and Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970, São Paulo, SP, Brazil
| | - W. V. M. Machado
- Escola Politécnica, Universidade de São Paulo, CP 61548, CEP 05424-970, São Paulo, SP, Brazil, and Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970, São Paulo, SP, Brazil
| | - L. V. C. Assali
- Escola Politécnica, Universidade de São Paulo, CP 61548, CEP 05424-970, São Paulo, SP, Brazil, and Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970, São Paulo, SP, Brazil
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Peral F, Troitiño D. Hydrogen-bonded dimers in self-association of 5-substituted uracil derivatives and hetero-association with l-cysteine. A density functional theory study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.12.007] [Citation(s) in RCA: 12] [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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The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci U S A 2010; 107:1888-93. [PMID: 20080677 DOI: 10.1073/pnas.0914192107] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered "double proton shuttle" mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.
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Takahashi M, Kawazoe Y, Ishikawa Y, Ito H. Interpretation of temperature-dependent low frequency vibrational spectrum of solid-state benzoic acid dimer. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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