Dynamics of bound and free water in an aqueous micellar solution: Analysis of the lifetime and vibrational frequencies of hydrogen bonds at a complex interface

Pal, Subrata; Balasubramanian, Sundaram; Bagchi, Biman

doi:10.1103/physreve.67.061502

Cited by 90 publications

(129 citation statements)

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“…Such blue shift of the water libration is also observed by Pal et al in their simulation study of water near a micelle of cesium perfluorooctanoate surfactant. 25 The numerical values of translational diffusion coefficients of water in different domains are listed in Table 5. The reductions of D T from the bulk to surface and buried water are 19% and 89%, respectively, for high pH solution.…”

Section: Change Of Water Translation and Rotation Dynamics Under Diffmentioning

confidence: 99%

“…It is interesting to note that our finding of the small alteration in water energetics (0.1 kcal/mol) due to the presence of a macromolecule despite a dramatic change in the water dynamics is similar to that reported by Pal et al in an aqueous micelle system. 25 The entropy of water molecules in different environments around the PAMAM dendrimer can be determined by using the 2PT method recently developed by Lin et al 35 The 2PT method is a modification of the quasiharmonic approximation methods [36][37][38][39] where the entropy is determined by treating each mode in the vibrational spectrum S(υ) as a harmonic oscillator. The fluidicity problems, including the singularity in entropy at zero frequency due to diffusion and the anharmonicities at lowfrequency regime, are resolved by decomposing the liquid S(υ) into a solid S s (υ) and a gas S g (υ) component, and treating each component with appropriate statistics.…”

Section: Change Of Water Translation and Rotation Dynamics Under Diffmentioning

confidence: 99%

“…Such phenomena have been widely investigated by experiments [13][14][15][16][17][18] and by molecular simulations [19][20][21][22][23][24][25][26] for water in biological systems such as proteins and DNA.…”

Section: Introductionmentioning

confidence: 99%

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Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

2005

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Atomistic molecular dynamics simulations are used to study generation 5 polyamidoamine (PAMAM) dendrimers immersed in a bath of water. We interpret the results in terms of three classes of water: buried water well inside of the dendrimer surface, surface water associated with the dendrimer-water interface, and bulk water well outside of the dendrimer. We studied the dynamic and thermodynamic properties of the water at three pH values: high pH with none of the primary or tertiary amines protonated, intermediate pH with only the primary amines protonated, and low pH with all amines protonated. For all pH values we find that both buried and surface water exhibit two relaxation times: a fast relaxation (∼1 ps) corresponding to the libration motion of the water and a slow (∼20 ps) diffusional component related to the escaping of water from one domain to another. In contrast for bulk water the fast relaxation is ∼0.4 ps while the slow relaxation is ∼14 ps. These results are similar to those found in biological systems, where the fast relaxation is found to be ∼1 ps while the slow relaxation ranges from 20 to 1000 ps. We used the 2PT MD method to extract the vibrational (power) spectrum and found substantial differences for the three classes of water. The translational diffusion coefficient for buried water is 11-33% (depending on pH) of the bulk value while the surface water is about 80%. The change in rotational diffusion is quite similar: 21-45% of the bulk value for buried water and 80% for surface water. This shows that translational and rotational dynamics of water are affected by the PAMAM-water interactions as well as due to the confinement in the interior of the dendrimer. We find that the reduction of translational or rotational diffusion is accompanied by a blue shift of the corresponding libration motions (∼10 cm -1 for translation, ∼35 cm -1 for rotation), indicating higher local force constants for these motions. These effects are most pronounced for the lowest pH, probably because of the increased rigidity caused by the internal charges. From the vibrational density of states we also calculate the enthalpies and entropies of the various waters. We find that water molecules are enthalpically favored near the PAMAM dendrimer: energy for surface water is ∼0.1 kcal/mol lower to that in the bulk, and ∼0.5-0.9 kcal/mol lower for buried water. In contrast, we find that both the buried and surface water are entropically unfavored: buried water is 0.9-2.2 kcal/mol lower than the bulk while the surface water is 0.1-0.2 kcal/mol lower. The net result is a thermodynamically unfavored state of the water surrounding the PAMAM dendrimer: 0.4-1.3 kcal/mol higher for buried water and 0.1-0.2 kcal/mol for surface water. This excess free energy of the surface and buried waters is released when the PAMAM dendrimer binds to DNA or metal ions, providing an extra driving force.

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Section: Change Of Water Translation and Rotation Dynamics Under Diffmentioning

confidence: 99%

Section: Change Of Water Translation and Rotation Dynamics Under Diffmentioning

confidence: 99%

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Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

2005

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“…In this context, the study of water dynamics in hydrogels is part of an increasing number of investigations concerning the study of nonreactive processes in the wider class of systems where water is confined in cages with different chemical and structural features. [13][14][15][16] Many experimental approaches are adopted in the study of macroscopic equilibrium and dynamic properties of hydrogel systems. Swelling and viscoelastic properties and the selective absorption of permeants provide information on structural features such as the mesh size and the average molecular weight of a strand between two cross links.…”

Section: Introductionmentioning

confidence: 99%

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

2005

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Molecular dynamics (MD) simulations were carried out to elucidate the dynamic behavior of water confined in poly(vinyl alcohol), PVA, hydrogels. Model topology is supported by experimental network parameters, and simulation results are compared to an incoherent quasielastic neutron scattering (QENS) investigation carried out on PVA hydrogels.1 From the QENS dynamic scattering law (part I), 1 a random jump model was adopted for the description of water diffusion to extract a microscopic diffusion coefficient and a residence time between two "jumps". In the present work, consistently with this framework, water diffusion parameters as diffusion coefficients and residence times have been evaluated using the mean square displacement of water in a time window of 10 ps and the time autocorrelation function of water hydrogen bonds. The calculated parameters are in good agreement with the experimental ones, giving confidence to this approach. Further developments are in progress to take into account a more realistic description of hydrogel structure in the molecular dynamics simulations.

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“…Many groups have discussed the fluctuations in micelles such as phase transition in simple models of rod-like and disk-like [5], behavior of water near micelles [6,7], anomalous behavior of water [8], free energy analysis of the solubilization [9], temperature dependence [10], the solvation dynamics [11], and vibration at complex interface [12,13]. Interestingly, in experiment using atomic force microscopy (AFM), the lipids show three stable states: globule-like (sphere-like), stripe-like (rod-like), and spaghettilike micelles (irregular shapes resembling spaghetti) [14].…”

Section: Introduction Bmentioning

confidence: 99%

Synchronization patterns in spaghetti‐like nanoclusters

Purqon

Nagao

Nishikawa

2008

Int J of Quantum Chemistry

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Spaghetti-like nanoclusters concern disordered shapes and irregular shape fluctuations in few correlated biological lipids. We evaluate the shape fluctuations by introducing Symmetry-S as a physical parameter for measuring symmetry degrees and detecting shape transitions. From numerical simulation of few correlated lipids of POPC and POPE at 300 K and 340 K by using molecular dynamics, we investigate the symmetry dynamics for each individual cluster by analyzing both spatiotemporal and frequency. From spatiotemporal analysis, we find several jump motions in S-dynamics and non-Gaussian distributions in S-distribution. Interestingly, the jump motions likely contribute on the existence of transitions in the non-Gaussian distributions. Additionally, even number of lipids show more symmetric than the odd number of lipids and the symmetry distributions shift at higher temperature, while, from three dimension of actual position of symmetry dynamics, they are not easy to configure high symmetry as well as showing certain patterns. From power spectra density analysis, each individual cluster shows nearly random fluctuation. Besides individual clusters, we also investigate mutual clusters. Surprisingly, although individual clusters show fluctuations randomly, mutual clusters show certain direction correlations. Moreover, they show certain patterns in delayed time analysis such as mutual fluctuations periodically occur for same number of lipids. It indicates that an existence of synchronization patterns occur in shape fluctuations of spaghetti-like nanoclusters.

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Dynamics of bound and free water in an aqueous micellar solution: Analysis of the lifetime and vibrational frequencies of hydrogen bonds at a complex interface

Cited by 90 publications

References 69 publications

Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

Dynamics and Thermodynamics of Water in PAMAM Dendrimers at Subnanosecond Time Scales

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

Synchronization patterns in spaghetti‐like nanoclusters

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