Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies

Yogeswari, Balasubramaniam; Kanakaraju, R.; Boopathi, Subramanian; Kolandaivel, P.

doi:10.1016/j.jmgm.2012.02.002

Cited by 29 publications

(9 citation statements)

References 51 publications

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“…[3][4][5] So far, amino acids (AAs) hydration, due to their small size, has been exhaustively studied by a wide variety of experimental and theoretical techniques. [6][7][8][9][10] On the other hand, oligopeptideswhich are considered promising in tissue engineering, drug delivery, as well as anticancer therapeutics [11][12][13][14] -interactions with water molecules (H 2 Os) are investigated in aqueous solution, mainly by theoretical studies 4,[15][16][17][18] without further experimental support. To the best of our knowledge, there are no experimental results clarifying the first hydration shell or predicting the number of directly interacting H 2 Os with oligopeptides.…”

Section: Introductionmentioning

confidence: 99%

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Takis

Papavasileiou

Peristeras

et al. 2013

Phys. Chem. Chem. Phys.

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How many solvent molecules and in what way do they interact directly with biomolecules? This is one of the most challenging questions regarding a deep understanding of biomolecular functionalism and solvation. We herein present a novel NMR spectroscopic study, achieving for the first time the quantification of the directly interacting water molecules with several neutral dipeptides. Our proposed method is supported by both molecular dynamics simulations and density functional theory calculations, advanced analysis of which allowed the identification of the direct interactions between solute-solvent molecules in the zwitterionic L-alanyl-L-alanine dipeptide-water system. Beyond the quantification of dipeptide-water molecule direct interactions, this NMR technique could be useful for the determination and elucidation of small to moderate bio-organic molecular groups' direct interactions with various polar solvent molecules, shedding light on the biomolecular micro-solvation processes and behaviour in various solvents.

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Section: Introductionmentioning

confidence: 99%

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Takis

Papavasileiou

Peristeras

et al. 2013

Phys. Chem. Chem. Phys.

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“…Quantum mechanical calculations using density functional theory − were performed to estimate internuclear distances between the interacting atoms in molecular entities I–X in the pure states and XI–XIV in mixed states. These distances were estimated to confirm the presence of molecular entities in pure and mixed states.…”

Section: Graph Theorymentioning

confidence: 99%

Thermodynamic Studies of Molecular Interactions in Mixtures Containing Tetrahydropyran, 1,4-Dioxane, and Cyclic Ketones

2017

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The densities ρ, speeds of sound u, and molar heat capacities C P of tetrahydropyran or 1,4-dioxane (1) + cyclohexanone or cycloheptanone (2) mixtures at 293.15, 298.15, 303.15, and 308.15 K, and excess molar enthalpies, H E at 308.15 K and atmospheric pressure 0.1 MPa have been measured over the entire composition range. The excess molar volumes V E, excess isentropic compressibilities κS E, and excess heat capacities, C P E of the studied mixtures have been determined using the measured experimental data. The observed V E, κS E, H E, and C P E data have been tested in terms of graph theory. The analyses of V E data by graph theory suggest that while tetrahydropyran or 1,4-dioxane exists as a mixture of monomer and dimer; cyclohexanone or cycloheptanone exists as a mixture of open and cyclic dimer. Further, (1 + 2) mixtures are characterized by interactions between oxygen atom/s and hydrogen atom of tetrahydropyran or 1,4-dioxane with hydrogen atom/s and oxygen atom of cyclohexanone or cycloheptanone. The quantum mechanical calculations and analysis of IR spectral data of (1 + 2) mixtures also support this viewpoint. It has been observed that graph theory correctly predicts the V E, κS E, H E, and C p E data of the present mixtures.

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“…Results of such studies revealed the big difference in the hydration of hydrophilic and hydrophobic functional groups. For instance, Yogeswari et al carried out the quantum chemical calculations of the aqueous complexes of glycine and diglycine by gradually increasing the number of water molecules. , Water molecules primarily form hydrogen bonds with the hydrophilic parts of a solute molecule. The aqueous environment around hydrophobic fragments starts when the hydration shells of hydrophilic functional groups are filled.…”

Section: The Problem Of Hydration Of Amphiphilic Moleculesmentioning

confidence: 99%

“Hydration Shells” of CH₂ Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation

et al. 2015

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Hydration phenomena play a very important role in various processes, in particular in biological systems. Water molecules in aqueous solutions of organic compounds can be distributed among the following substructures: (i) hydration shells of hydrophilic functional groups of molecules, (ii) water in the environment of nonpolar moieties, and (iii) bulk water. Up to now, the values of hydration parameters suggested for the description of various solutions of organic compounds were not thoroughly analyzed in the aspect of the consideration of the total molecular composition. The temperature and concentration dependences of relaxation rates of water deuterons were studied in a wide range of concentration and temperature in aqueous (D2O) solutions of a set of ω-amino acids. Assuming the coordination number of the CH2 group equal to 7, which was determined from quantum-chemical calculations, it was found that the rotational correlation times of water molecules near the methylene group is 1.5-2 times greater than one for pure water. The average rotational mobility of water molecules in the hydration shells of hydrophilic groups of ω-amino acids is a bit slower than that in pure solvent at temperatures higher that 60 °C, but at lower temperatures, it is 0.8-1.0 of values of correlation times for bulk water. The technique suggested provides the basis for the characterization of different hydrophobic and hydrophilic species in the convenient terms of the rotational correlation times for the nearest water molecules.

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Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies

Cited by 29 publications

References 51 publications

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Thermodynamic Studies of Molecular Interactions in Mixtures Containing Tetrahydropyran, 1,4-Dioxane, and Cyclic Ketones

“Hydration Shells” of CH₂ Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation

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Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies

Cited by 29 publications

References 51 publications

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water

Thermodynamic Studies of Molecular Interactions in Mixtures Containing Tetrahydropyran, 1,4-Dioxane, and Cyclic Ketones

“Hydration Shells” of CH2 Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation

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Product

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About

“Hydration Shells” of CH₂ Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation