Effects of metal ion and solute conformation change on hydration of small amino acid

Deeying, Natthiya; Sagarik, Kritsana

doi:10.1016/j.bpc.2006.06.016

Cited by 7 publications

(10 citation statements)

References 66 publications

(136 reference statements)

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“…Our previous experience on strong H-bond clusters [30][31][32][33][34] showed that some structural and energetic information in the gas phase could provide the basis for discussion in aqueous solutions. Therefore, it was our strategy to explore proton transfer reactions at low hydration levels.…”

Section: Methodsmentioning

confidence: 99%

Mechanisms of proton transfer in Nafion®: elementary reactions at the sulfonic acid groups

Sagarik

Phonyiem

Lao-ngam

et al. 2008

Phys. Chem. Chem. Phys.

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Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

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Section: Methodsmentioning

confidence: 99%

Mechanisms of proton transfer in Nafion®: elementary reactions at the sulfonic acid groups

Sagarik

Phonyiem

Lao-ngam

et al. 2008

Phys. Chem. Chem. Phys.

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“…Other M (M = Na + , Mg 2+ , Al 3+ , Ca 2+ , Co 2+ , Sc 3+ and La 3+ ) are used to testify the linear relationship. The interacted structures of multiple glycines are based on their respective MGly structures . For Na + , the canonical binding isomers predominate, and glycines are all in the canonical form when n equals 2, 3 or 4 (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Metal ions (M) play a significant role in a wide range of chemical and biological processes, through the regulation of protein folding, stabilization of protein structures, mediation of protein‐ligand interactions and acting as electrophilic centers in catalysis . Remarkable progress has recently been made in the interactions of M with amino acids (AA), especially glycine of the simplest structure . As AA are the building blocks of peptides and proteins, these studies contribute greatly to the understanding of metal‐mediated biological activities.…”

Section: Introductionmentioning

confidence: 99%

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Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

et al. 2012

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Calculations were performed to study the interactions of metal ions (M) with (multiple) amino acids (AA) and fill the gap between single AA and proteins. A complete conformational search results in nine and eleven ZnGly isomers at B3P86 and MP2 levels, respectively, and four populated conformers of glycine are responsible for production of these isomers. For all M, the isomers via the OO and NO binding modes are the main constituents, and the OO mode is favored by stronger electrostatic interactions. Binding with more glycines causes larger structural distortions, improves relative stabilities of monodentate binding isomers and generates new binding modes (e.g. ZnB(III) via only the hydroxyl group). The scaling factor of Zn(Gly)(n) structures, the ratio of its binding affinity versus the sum of comprising ZnGly isomers, is linear with glycine number (n), and the linear relationship may not be altered by mutations of glycines and M. It thus allows to estimate M(AA)(n) binding affinities (n ≥ 2) from the comprising MAA structures and analyze their structures with kinetic methods. The DFT and MP2 results become comparable by increasing metal coordination, e.g. the ZnB(III) versus ZnA(I) (zwitterionic) relative energy differs by 41.9 kcal mol(-1) at B3P86 and MP2 levels and is close by addition of three water molecules (4.1 kcal mol(-1)). The presence of water solvent improves the relative stabilities of monodentate binding isomers and results in a broader conformational distribution.

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“…En este trabajo se estudian, las propiedades volumétricas, debido a que estas son útiles para determinar el efecto que causa la adición de una sal sobre el comportamiento de los aminoácidos; siendo esta información de gran importancia para el estudio de la hidratación de péptidos y proteínas en medios salinos (Deeying et al, 2009;. Por tal motivo, aquí se reportan las densidades ρ/(g/cm 3 ) de DLalanina en función de la molalidad del líquido iónico [BMIm][OTF] a la presión de 1.011 bar, y a las temperaturas de (283.15; 288.15; 293.15; 298.15, 303.15; 308.15 y 313,15) K. Los valores experimentales de ρ se usaron para calcular los volúmenes molares aparentes V ϕ /(cm 3 .…”

Section: Introductionunclassified

Interacciones de la DL-Alanina en Soluciones Acuosas de Trifluorometanosulfonato de 1-Butil, 3-Metilimidazolio a Diferentes Temperaturas

2015

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Se determinó la densidad de DL-alanina en soluciones acuosas del líquido iónico trifluorometanosulfonato de 1-Butil-3-metil imidazolio en el intervalo de temperaturas de 283.15 a 313.15 K utilizando un densímetro de tubo vibratorio Anton Paar DMA 5000. Se calcularon los volúmenes molares aparentes, volúmenes molares aparentes a dilución infinita, la segunda derivada del volumen molar parcial a dilución infinita con respecto a la temperatura, el volumen molar parcial de transferencia a dilución infinita y los números de hidratación. Se encontró que los valores de la segunda derivada del volumen molar aparente límite con temperatura son negativos a todas las concentraciones del solvente mixto. Esto indica que se favorecen las interacciones soluto-solvente y que la DL-alanina actúa como un desestabilizador de la estructura del solvente. Palabras clave: propiedades volumétricas, volúmenes molares aparentes, DL-alanina en soluciones acuosas del líquido iónico

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Effects of metal ion and solute conformation change on hydration of small amino acid

Cited by 7 publications

References 66 publications

Mechanisms of proton transfer in Nafion®: elementary reactions at the sulfonic acid groups

Mechanisms of proton transfer in Nafion®: elementary reactions at the sulfonic acid groups

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

Interacciones de la DL-Alanina en Soluciones Acuosas de Trifluorometanosulfonato de 1-Butil, 3-Metilimidazolio a Diferentes Temperaturas

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