Aminoacid zwitterions in solution: Geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations

Tortonda, Francisco R.; Pascual-Ahuir, Juan-Luis; Silla, Estanislao; Tuñón, Iñaki; Ramı́rez, Francisco J.

doi:10.1063/1.476596

Cited by 89 publications

(83 citation statements)

References 57 publications

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“…Indeed, these results were obtained after parameterization of the EVB method with Hartree±Fock (HF) energies, which severely overestimate the activation barrier for this process. For instance, the computed NE ® ZW activation barrier is 11.0, 2.4 and 1.9 kcal/ mol at the HF, second-order Mùller-Plesset (MP2) and density functional (DF) levels, respectively [8,9] (results in aqueous solution using the 6-31+G** basis set and a solvent continuum model). Very close values have been obtained for alanine [9].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, the computed NE ® ZW activation barrier is 11.0, 2.4 and 1.9 kcal/ mol at the HF, second-order Mùller-Plesset (MP2) and density functional (DF) levels, respectively [8,9] (results in aqueous solution using the 6-31+G** basis set and a solvent continuum model). Very close values have been obtained for alanine [9]. Combined DF molecular mechanics (MM) simulations have predicted a fast and very exothermic conversion of the NE to the ZW form of glycine [22], in consonance with a small energy barrier for proton transfer.…”

Section: Introductionmentioning

confidence: 99%

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Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Tortonda

Silla

Tuñón

et al. 2000

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-pointenergy contributions are added. Our calculations allow the dynamic aspects of the ionization mechanism to be discussed by incorporating nonequilibrium eects.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Tortonda

Silla

Tuñón

et al. 2000

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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“…10 In solids and polar liquids ␣-amino acids exist as zwitterions, presenting an interesting dilemma to the theoretician. Computational solutions to this dilemma have implemented continuum solvent models, [11][12][13] explicit hydration using water, [13][14][15][16] and hybrid methods that use molecular dynamics to modify ab initio forces and force constants. 17,18 Although such methods have provided useful insights, it is desirable to have methods that are less complicated, less time consuming, and that are applicable to large systems.…”

Section: Introductionmentioning

confidence: 99%

Molecular mechanics force‐field development for amino acid zwitterions

2002

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Understanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas-phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. Møller-Plesset second-order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly.

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“…The estimated angles are in good agreement with the previously published results. 54 The O-C=O angle presents the largest discrepancy for the zwitterionic form. The PBE/ TZVP estimated O-C=O angle is 13 degrees larger than the value estimated with DC-SCC-DFTB.…”

Section: Glycine In Aqueous Solutionmentioning

confidence: 99%

Density-functional based tight-binding: an approximate DFT method

Oliveira¹,

Seifert²,

Heine³

et al. 2009

J. Braz. Chem. Soc.

192

185

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O método DFTB, bem como a sua extensão com carga corrigida auto-consistente SCC-DFTB, tem ampliado a faixa de aplicações das ferramentas teóricas com fundamentos bem estabelecidos. Como uma aproximação do método do funcional de densidade, o método DFTB mantém aproximadamente a mesma precisão, mas com custo computacional menor, permitindo a investigação da estrutura eletrônica de sistemas grandes que não podem ser explorados com métodos ab initio convencionais. No presente artigo, os fundamentos dos métodos DFTB, SCC-DFTB e da inclusão das forças de dispersão de London são revisados. Para mostrar um exemplo da aplicabilidade do método DFTB, o equilíbrio zwitteriônico de glicina em solução aquosa é investigado. Foram realizadas simulações de dinâmica molecular usando o hamiltoniano SCC-DFTB corrigido para incluir a dispersão e uma caixa periódica contendo 129 moléculas de água, a partir de uma abordagem puramente mecânico-quântica.The DFTB method, as well as its self-consistent charge corrected variant SCC-DFTB, has widened the range of applications of fundamentally well established theoretical tools. As an approximate density-functional method, DFTB holds nearly the same accuracy, but at much lower computational costs, allowing investigation of the electronic structure of large systems which can not be exploited with conventional ab initio methods. In the present paper the fundaments of DFTB and SCC-DFTB and inclusion of London dispersion forces are reviewed. In order to show an example of the DFTB applicability, the zwitterionic equilibrium of glycine in aqueous solution is investigated by molecular-dynamics simulation using a dispersion-corrected SCC-DFTB Hamiltonian and a periodic box containing 129 water molecules, in a purely quantum-mechanical approach.

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Aminoacid zwitterions in solution: Geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations

Cited by 89 publications

References 57 publications

Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Molecular mechanics force‐field development for amino acid zwitterions

Density-functional based tight-binding: an approximate DFT method

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