Evaluation of molecular radial distribution function and solvent-excluded volume with the numerical integration of the union of spheres

Vchirawongkwin, Saowapak; Vchirawongkwin, Viwat

doi:10.1016/j.comptc.2011.07.007

Cited by 7 publications

(16 citation statements)

References 29 publications

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“…The density maps show the geometry of the molecular hydration shell, corresponding to the previous proposal based on the union of spheres. 43 The density maps suggest a more ordered hydration structure of the O sites than the N site, according to a higher density around the former than the latter. This indicates a deficiency in the solitary use of atomic RDFs to interpret the boundary of the hydration shells.…”

Section: Structural and Dynamical Properties Of The Hydration Shellmentioning

confidence: 94%

“…The definition of the molecular hydration shell is the combination of all atomic hydration spheres for the coordinating sites of the nitrite ion, producing the molecular domain. 43 The coordinating site for each water molecule to the nitrite is the shortest distance between the oxygen atom of a water molecule and each atom within the ion. 29,31 We calculated all MRT values based on the direct method, 44 counting the water exchange processes between the hydration shell and the bulk.…”

Section: Methodsmentioning

confidence: 99%

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Hydration properties determining the reactivity of nitrite in aqueous solution

et al. 2014

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The knowledge of the hydration properties of the nitrite ion is key to understanding its reaction mechanism controlled by solvent effects. Here, ab initio quantum mechanical charge field molecular dynamics was performed to obtain the structural and dynamical properties of the hydration shell in an aqueous solution of nitrite ions, elucidated by data analysis using a molecular approach and an extended quantitative analysis of all superimposed trajectories with three-dimensional alignment (density map). The pattern of the power spectra corresponded to the experimental data, indicating the suitability of the Hartree-Fock method coupled with double-ζ plus polarization and diffuse functional basis sets to study this system. The density maps revealed the structure of the hydration shell, that presented a higher density in the N-O bond direction than in the axis vertical to the molecular plane, whereas the atomic and molecular radial distribution functions provided vague information. The number of actual contacts indicated 4.6 water molecules interacting with a nitrite ion, and 1.5 extra water molecules located in the molecular hydration shell, forming a H-bonding network with the bulk water. The mean residence times for the water ligands designated the strength of the hydration spheres for the oxygen sites, whilst the results for the nitrogen sites over-estimated the number of water molecules from other sites and indicated a weak structure. These results show the influence of the water molecules surrounding the nitrite ion creating an anisotropic hydration shell, suggesting that the reactive sites are situated above and below the molecular plane with a lower water density.

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Section: Structural and Dynamical Properties Of The Hydration Shellmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

Hydration properties determining the reactivity of nitrite in aqueous solution

et al. 2014

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“…The definition of the molecular hydration shell is the combination of all atomic hydration spheres for the coordinating sites of the thiosulfate ion, producing the molecular domain. 52 The coordinating site for each water molecule to the thiosulfate is the shortest distance between the oxygen atom of a water molecule and each atom within the ion. 43,45 We calculated all MRT values based on the direct method, 53 counting the water exchange processes between hydration shell and bulk water.…”

Section: Papermentioning

confidence: 99%

“…43 We applied the molecular approach to evaluate the RDFs and CN for the thiosulfate ion. The molecular RDFs provide the possibility to find water molecules within the isotropic molecular domain constructed from the union of spheres having identical radii, 52 by assigning the coordinating site with the shortest distance among the values obtained from the oxygen of water and each site within the thiosulfate ion. The evaluation of the molecular RDFs with or without the inclusion of the S(1) atom gave the same distributions, indicating it has a negligible role in the molecular hydration shell.…”

Section: Structural and Dynamical Properties Of The Hydration Shellmentioning

confidence: 99%

“…The difference between the first peak of the (molecular)⋯O water and (molecular)⋯H water RDFs (1.00 Å) corresponds to the average length of O-H bonds (0.98 ± 0.03 Å) within the water molecules located in the molecular hydration shell, indicating the orientation of water molecules utilizing one hydrogen atom to coordinate with the ion. We evaluated the molecular CND with the molecular domain, constructed by applying the boundary obtained from the atomic RDFs for each site of the thiosulfate ion 52 shown in Fig. 8b.…”

Section: Structural and Dynamical Properties Of The Hydration Shellmentioning

confidence: 99%

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Active site of the solvated thiosulfate ion characterized by hydration structures and dynamics

et al. 2013

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The reactivity of the terminated sulfur atom within the thiosulfate ion (S2O3(2-)) when it is involved in chemical reactions was investigated through the properties of the molecular hydration shell, obtained from the ab initio quantum mechanical change field molecular dynamics (QMCF MD) simulation. The average geometry indicated the significant effect of explicit water on the reduction of the S-S length, which was reflected in the splitting peaks of the spectrum for the stretching mode of this bond (ν(SS)). A further investigation on a simple model with various theoretical levels exhibited the hydrophobicity of the S-S bond. The evaluation of the molecular coordination number was sensitive to the radii of the atomic hydration spheres, which were obtained from the vague boundaries of the first peak in the atomic radial distribution functions. The number of actual contacts specified 6.8 water molecules interacting with the thiosulfate ion, and 2.4 extra waters located in the molecular hydration shell, forming a H-bonding network with the bulk water. The mean residence times for the water ligands distinguished the asymmetric strength of the hydration shell into a weaker sulfur and three stronger oxygen sites, instigating the terminated sulfur atom as the active site that is involved in chemical reactions.

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