Effect of Ionic Solutes on the Hydrogen Bond Network Dynamics of Water:  Power Spectral Analysis of Aqueous NaCl Solutions

Mudi, Anirban; Chakravarty, Charusita

doi:10.1021/jp056003l

Cited by 35 publications

(33 citation statements)

References 46 publications

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“…In a series of recent papers, we showed that power spectral analysis could be used to understand the connections between the local order, hydrogen bond network dynamics and the kinetic anomalies in water 14,15,16,17,18,19 . The power spectral density of an observable A(t) as a function of time t is defined as follows 20 :…”

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confidence: 99%

Diffusional anomaly and network dynamics in liquid silica

Sharma

Mudi

Chakravarty

2006

The Journal of Chemical Physics

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The present study applies the power spectral analysis technique to understand the diffusional anomaly in liquid silica, modeled using the BKS potential. Molecular dynamics simulations have been carried out to show that power spectrum of tagged particle potential energy of silica shows a regime with 1/f α dependence on frequency f which is the characteristic signature of multiple time-scale behaviour in networks. As demonstrated earlier in the case of water (J. Chem. Phys., 122, 104507 (2005)), the variations in the mobility associated with the diffusional anomaly are mirrored in the scaling exponent α associated with this multiple time-scale behaviour. Our results indicate that in the anomalous regime, as the local tetrahedral order decreases with temperature or pressure, the coupling of local modes to network reorganisations increases and so does the diffusivity. This symmetry-dependence of the vibrational couplings is responsible for the connection between the structural and diffusional anomalies.

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confidence: 99%

Diffusional anomaly and network dynamics in liquid silica

Sharma

Mudi

Chakravarty

2006

The Journal of Chemical Physics

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“…It is possible to build mixtures of several components, solvate proteins, and build ordered arrangements as double layers or micelles. [20][21][22][23][24][25][26][27] Further improvements of the package may include macro-input keywords to build the most common systems and more complex unit cells, the parallelization of tasks other than function and gradient evaluation, the improvement of global convergence heuristics, and the development of a graphical user interface, or its incorporation as a plugin into some graphical molecular viewer.…”

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confidence: 99%

PACKMOL: A package for building initial configurations for molecular dynamics simulations

et al. 2009

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Abstract:Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from

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“…This definition of binding energy is identical to the tagged potential energy (TPE) of the molecule, u, where the sum is over interactions of the tagged species with all others. 11,21,22,24 When the interactions in the system are pairadditive, then one can write that U ) (0.5/N)∑ i u i , where the index i runs over all atoms in the system. The molecular tagged potential energy requires a summation over all constituent atoms of a molecule.…”

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Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides

2009

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The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.

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Effect of Ionic Solutes on the Hydrogen Bond Network Dynamics of Water: Power Spectral Analysis of Aqueous NaCl Solutions

Cited by 35 publications

References 46 publications

Diffusional anomaly and network dynamics in liquid silica

Diffusional anomaly and network dynamics in liquid silica

PACKMOL: A package for building initial configurations for molecular dynamics simulations

Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides

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