Sundaram Balasubramanian, Subrata Pal, Biman Bagchi
Our atomistic molecular dynamics simulations reveal the existence of bound and free water molecules in the hydration layer of an aqueous micelle. The bound water molecules can be either singly or doubly hydrogen bonded to the polar head group on the surface of the micelle. The ratio of bound to free water is found to be approximately equal to 9:1 at 300 K.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
继续探索
In this paper we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium and, to a lesser extent, chloride translate into large differences in the computed radial-distribution functions. This uncertainty reflects the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity.We discuss possible implications on the computation of potential of mean force …
Hydrophobic hydration plays a crucial role in self-assembly processes over multiple length-scales, but the extrapolation of molecular-scale models to larger length-scale hydration phenomena is sometimes not warranted. Scaled-particle theories are based upon an interpolative view of that issue. We revisit the scaled-particle theory proposed thirty years ago by Stillinger, adopt a practical generalization, and consider the implications for hydrophobic hydration in light of our current understanding. The generalization is based upon identifying a molecular length, implicit in previous application…
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if those protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry view depends on understanding the hydration structure and free energies of metal ions in water to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water, and the molecula…
A theoretical treatment based upon the quasi-chemical theory of solutions predicts the most probable number of water neighbors in the inner shell of a Li+ ion in liquid water to be four. The instability of a six water molecule inner sphere complex relative to four-coordinated structures is confirmed by an `ab initio' molecular dynamics calculation. A classical Monte Carlo simulation equilibrated 26 water molecules with a rigid six-coordinated Li(H2O)6+ complex with periodic boundary conditions in aqueous solution. With that initial configuration for the molecular dynamics, the six-coordinated …
This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of so-dium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of Wo = [H2O]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At Wo = 9.1, according to the X-ray structure, con…
The HO$^-$(aq) ion participates in myriad aqueous phase chemical processes of biological and chemical interest. A molecularly valid description of its hydration state, currently poorly understood, is a natural prerequisite to modeling chemical transformations involving HO$^-$(aq). Here it is shown that the statistical mechanical quasi-chemical theory of solutions predicts that $\mathrm{HO\cdot[H_2O]_3{}^-}$ is the dominant inner shell coordination structure for HO$^-$(aq) under standard conditions. Experimental observations and other theoretical calculations are adduced to support this conclus…
The hydroxide anion plays an essential role in many chemical and biochemical reactions. But a molecular-scale description of its hydration state, and hence also its transport, in water is currently controversial. The statistical mechanical quasi-chemical theory of solutions suggests that HO[H2O]3- is the predominant species in the aqueous phase under standard conditions. This result is in close agreement with recent spectroscopic studies on hydroxide water clusters, and with the available thermodynamic hydration free energies. In contrast, a recent ab initio molecular dynamics simulation has s…
Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the solvent explain the inverse temperature signatures that have been interpreted traditionally in favor of hydrophobic mechanisms for stabilizing the structure and function of soluble proteins.
A micelle consists of monolayer of lipid molecules containing hydrophilic head and hydrophobic tail. These amphiphilic molecules in aqueous environment aggregate spontaneously into monomolecular layer held together due to hydrophobic effect by weak non-covalent forces. Micelles are flexible surfaces that show variety of shapes of different topology, but remarkably in mechanical equilibrium conditions they are spherical in shape. The shape and size of a micelle are functions of many variables such as lipid concentration, temperature, ionic strength, etc. Addressing the question, why the shape o…
Thermochemistry of gas-phase ion-water clusters together with estimates of the hydration free energy of the clusters and the water ligands are used to calculate the hydration free energy of the ion. Often the hydration calculations use a continuum model of the solvent. The primitive quasichemical approximation to the quasichemical theory provides a transparent framework to anchor such efforts. Here we evaluate the approximations inherent in the primitive quasichemical approach and elucidate the different roles of the bulk medium. We find that the bulk medium can stabilize configurations of the…
An `ab initio' molecular dynamics simulation of a Na+ ion in aqueous solution is presented and discussed. The calculation treats a Na+ ion and 32 water molecules with periodic boundary conditions on a cubic volume determined by an estimate of zero partial molar volume for this solute in water at normal density and at a temperature of 344+/-24 K. Analysis of the last half of the 12 ps trajectory shows 4.6 water molecules occupying the inner hydration shell of the Na+ ion on average, with 5 being the most probable occupancy. The self-diffusion coefficient observed for the Na+ is 1.0 x 10$^{-5}$ …
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus crucial to uncover the mystery of hydration structure and dynamics as well as their coupling to collective motions of proteins in aqueous solutions. Here we report dielectric properties of aqueous bovine serum albumin protein solutions as a model system using an extremely sensitive dielectric spectrometer with frequencies spanning from megahertz to terahertz. The …
We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and hydroxyectoine are able to accumulate more water molecules than urea by a pronounced ordering due to hydrogen bonds. We have validated that the charging of the molecules is of main importance resulting in a well defined hydration sphere. The influence of a varying salt concentration is also investigated. Finally we present experimental results of a DPPC monolayer ph…
Water offers a large temperature domain of stable liquid, and the characteristic hydrophobic effects are first a consequence of the temperature insensitivity of equation-of-state features of the aqueous medium, compared to other liquids. On this basis, the known aqueous media and conditions offer low risk compared to alternatives as a matrix to which familiar molecular biological structures and processes have adapted. The current molecular-scale understanding of hydrophobic hydration is not conformant in detail with a standard structural entropy rationalization. That classic pictorial explanat…
Transport properties of concentrated electrolytes have been analyzed using classical molecular dynamics simulations with the algorithms and parameters typical of simulations describing complex electrokinetic phenomena. The electrical conductivity and transport numbers of electrolytes containing monovalent (KCl), divalent (MgCl$_2$), a mixture of both (KCl + MgCl$_2$), and trivalent (LaCl$_3$) cations have been obtained from simulations of the electrolytes in electric fields of different magnitude. The results obtained for different simulation parameters have been discussed and compared with ex…
Recent progress on molecular theories of hydration of nonpolar solutes in aqueous solution has led to new ways of thinking about the old issue of free, or "available," volume in liquids. This article surveys the principal new results with particular attention to general issues of packing in liquids.
The S$_2$ site of the KcsA K$^+$ channel has eight carbonyl ligands in the ion-binding site. A recent study suggests that the K$^+$-over-Na$^+$ selectivity of the S$_2$ site can be understood by noting the larger free energy change involved in enforcing an eight water coordination state around Na$^+$ relative to K$^+$. The free energies were obtained from the probabilities of observing eight water molecules within a coordination sphere whose radius ($λ_{\rm Na^+} \approx 3.1$ Å and $λ_{\rm K^+} \approx 3.5$ Å) extends to the first minimum of the ion-water oxygen pair correlation function. Curi…
The small r variation of the probability density P(r) for end-to-end separations of a -CH2CH3 capped (-OCH2CH2-)n oligomer in water is computed to be closely similar to the CH4 ... CH4 potential of mean force under the same circumstances. Since the aqueous solution CH4 ... CH4 potential of mean force is the natural physical definition of a primitive hydrophobic bond, the present result identifies an experimentally accessible circumstance for direct observation of a hydrophobic bond which has not been observed previously because of the low solubility of CH4 in water. The physical picture is tha…
Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water
本研究通过实验与理论分析揭示了吲哚在水中特异性氢键与非特异性溶剂相互作用的微观细节，利用最大重叠方法等建模技术定量解释了其光电子能谱和Auger谱。
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1 MHz to 40 GHz and for temperatures from 275 to 330 K. We analyze the three dispersion regions, commonly found in protein solutions, usually termed beta-, gamma-, and delta-relaxation. The beta-relaxation, occurring in the frequency range around 10 MHz and the gamma-relaxation around 20 GHz (at room temperature) can be attributed to the rotation of the polar protein molecules in their aqueous medium and the reorientational motion of the free water molecules…
Urea-Mediated Solvent Reorganization of Bovine Serum Albumin in an Acid-Induced Expanded Conformation at pH 3.7
研究尿素如何通过分子动力学模拟影响牛血清白蛋白的结构稳定性，揭示尿素在不同浓度下对蛋白质水合壳层的脱水/再水合机制及二级结构的保护作用。
扫码添加微信好友，提出您的宝贵建议 👇
💡 备注请填写：网站反馈
发表机构由 AI 从论文文本抽取，如发现错误，欢迎反馈修正建议。