arXiv subjects

D. Asthagiri

Publications and source records attributed to D. Asthagiri.

At least 37 records · Page 2Linked to original sources

arXiv2011

Range of ion specific effects in the hydration of ions

Within the quasichemical approach, the hydration free energy of an ion is decomposed into a chemical term accounting for ion specific ion-water interactions within the coordination sphere and nonspecific contributions accounting for packing (excluded volume) and long range interactions. The change in the chemical term with a change in the radius of the coordination sphere is the compressive force exerted by the bulk solvent medium on the surface of the coordination sphere. For the Na+, K+, F-, and Cl- ions considered here this compressive force becomes equal for similarly charged ions for coordination radii of about 0.39 nm, not much larger than a water molecule. These results show that ion specific effects are short ranged and arise primarily due to differences in the local ion-water interactions.

physics.bio-ph↗

arXiv2011

Ion-water clusters, bulk medium effects, and ion hydration

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 cluster that are usually not observed in the gas phase, while also simultaneously lowering the excess chemical potential of the ion. This effect is more pronounced for soft ions. Since the coordination number that minimizes the excess chemical potential of the ion is identified as the optimal or most probable coordination number, for such soft ions, the optimum cluster size and the hydration thermodynamics obtained without account of the bulk medium on the ion-water clustering reaction can be different from those observed in simulations of the aqueous ion. The ideas presented in this work are expected to be relevant to experimental studies that translate thermochemistry of ion-water clusters to the thermodynamics of the hydrated ion and to evolving theoretical approaches that combine high-level calculations on clusters with coarse-grained models of the medium.

physics.bio-ph↗

arXiv2011

An elastic-network based local molecular field analysis of zinc-finger proteins

We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue cluster by a molecular field represented by generalized harmonic restraints. The strength of the field is adjusted to reproduce the binding energy distribution of the metal with the cluster obtained in a reference all-atom simulation with empirical potentials. The quadratic field allows us to investigate analytically the protein restraints on the binding site in terms of its eigenmodes. Examining these eigenmodes suggests, consistent with experimental observations, the importance of the first histidine (H) in the CCHH cluster in metal binding. Further, the eigenvalues corresponding to these modes also indicate that the designed proteins form a tighter complex with the metal. We find that the bulk protein and solvent response tends to destabilize metal-binding, emphasizing that the favorable energetics of metal-residue interaction is necessary to drive folding in this system. The representation of the bulk protein and solvent response by a local field allows us to perform Monte Carlo simulations of the metal-residue cluster using quantum-chemical approaches, here using a semi-empirical Hamiltonian. For configurations sampled from this simulation, we study the free energy of replacing Zn(II) with Fe(II), Co(II), and Ni(II) using density functional theory. The calculated selectivities are in fair agreement with experimental results.

physics.bio-ph↗

arXiv2011

Water coordination structures and the excess free energy of the liquid

For a distinguished water molecule, the solute water, we assess the contribution of each coordination state to its excess chemical potential, using a molecular aufbau approach. In this approach, we define a coordination sphere, the inner-shell, and separate the excess chemical potential into packing, outer-shell, and local chemical contributions; the coordination state is defined by the number of solvent water molecules within the coordination sphere. The packing term accounts for the free energy of creating a solute-free coordination sphere in the liquid. The outer-shell term accounts for the interaction of the solute with the fluid outside the coordination sphere and it is accurately described by a Gaussian model of hydration for coordination radii greater than the minimum of the oxygen-oxygen pair correlation function. Consistent with the conventional radial cut-off used for defining hydrogen-bonds in liquid water, theory helps identify a chemically meaningful coordination radius. The local chemical contribution is recast as a sum over coordination states. The n-th term in this sum is given by the probability of observing n water molecules inside the coordination sphere in the absence of the solute water times a factor accounting for the interaction of the solute with the inner-shell solvent water molecules. Using this molecular aufbau expansion, we monitor the change in the chemical contribution due to the incremental increase in n. We find that though four water molecules are needed to fully account for the chemical term, the first added water accounts for nearly half the chemical term. Our results emphasize the need to acknowledge the intrinsic occupancy of a solute-free coordination sphere together with solute-solvent interactions in rationalizing the tetrahedral coordination of the solute water.

physics.chem-ph↗

arXiv2010

Thermodynamics of water modeled using ab initio simulations

We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena.

physics.chem-ph↗

arXiv2010

Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals

In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create the solute-free coordination sphere (the observation volume) in bulk water. With the SPC/E water model as a reference, we examine the chemical and packing contributions in the free energy of water simulated using different electron density functionals. The density is fixed at a value corresponding to that for SPC/E water at a pressure of 1 bar. The chemical contribution shows that water simulated at 300 K with BLYP is somewhat more tightly bound than water simulated at 300 K with the revPBE functional or at 350 K with the BLYP and BLYP-D functionals. The packing contribution for various radii of the observation volume is studied. In the size range where the distribution of water molecules in the observation volume is expected to be Gaussian, the packing contribution is expected to scale with the volume of the observation sphere. Water simulated at 300 K with the revPBE and at 350 K with BLYP-D or BLYP conforms to this expectation, but the results suggest an earlier onset of system size effects in the BLYP 350 K and revPBE 300 K systems than that observed for either BLYP-D 350 K or SPC/E. The implication of this observation for constant pressure simulations is indicated. For water simulated at 300 K with BLYP, in the size range where Gaussian distribution of occupation is expected, we instead find non-Gaussian behavior, and the packing contribution scales with surface area of the observation volume, suggesting the presence of heterogeneities in the system.

physics.chem-ph↗

arXiv2009

On inferring the ion selectivity of the KcsA potassium channel using the distribution of coordination states of the aqueous ions

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. Curiously, using the same coordination radius led to results that question the very idea of using coordination states in water to understand selectivity in the channel. We show that density fluctuations in neat water at the length scale of the coordination volume enter the description of the hydration thermodynamics of the ion expressed in terms of its coordination states. Density fluctuations explain the sensitivity to the choice of radius. After accounting for this effect, the results lead to the conclusion that free energy changes involved in the transition between coordination states in water are inadequate to explain selectivity in the ion-channel.

physics.bio-ph↗

arXiv2008

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

On the basis of a gaussian quasi-chemical model of hydration, a model of non van der Waals character, we explore the role of attractive methane-water interactions in the hydration of methane and in the potential of mean force between two methane molecules in water. We find that the hydration of methane is dominated by packing and a mean-field energetic contribution. Contributions beyond the mean-field term are unimportant in the hydration phenomena for a hydrophobic solute such as methane. Attractive solute-water interactions make a net repulsive contribution to these pair potentials of mean force. With no conditioning, the observed distributions of binding energies are super-gaussian and can be effectively modeled by a Gumbel (extreme value) distribution. This further supports the view that the characteristic form of the unconditioned distribution in the high-e tail is due to energetic interactions with a small number of molecules. Generalized extreme value distributions also effectively model the results with minimal conditioning, but in those cases the distributions are sufficiently narrow that details of their shape aren't significant.

physics.bio-ph↗

arXiv2007

Balancing Local Order and Long-Ranged Interactions in the Molecular Theory of Liquid Water

A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish outside a finite spatial range, and therefore provides a precise analysis tool for investigating the effects of longer-ranged intermolecular interactions. We show how local order can be introduced through quasi-chemical theory. Long-ranged interactions are characterized generally by a conditional distribution of binding energies, and this formulation is interpreted as a regularization of the primitive statistical thermodynamic problem. These binding-energy distributions for liquid water are observed to be unimodal. The gaussian approximation proposed is remarkably successful in predicting the Gibbs free energy and the molar entropy of liquid water, as judged by comparison with numerically exact results. The remaining discrepancies are subtle quantitative problems that do have significant consequences for the thermodynamic properties that distinguish water from many other liquids. The basic subtlety of liquid water is found then in the competition of several effects which must be quantitatively balanced for realistic results.

physics.chem-ph↗

arXiv2007

What is special about water as a matrix of life?

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 explanation may serve as a mnemonic, but isn't necessary. A more defensible view is that peculiar hydrophobic effects can be comprehended by examination of engineering parameters characterizing liquid water.

physics.bio-ph↗

arXiv2007

Water adsorption and dissociation on BeO (001) and (100) surfaces

Plateaus in water adsorption isotherms on hydroxylated BeO surfaces suggest significant differences between the hydroxylated (100) and (001) surface structures and reactivities. Density functional theory structures and energies clarify these differences. Using relaxed surface energies, a Wulff construction yields a prism crystal shape exposing long (100) sides and much smaller (001) faces. This is consistent with the BeO prisms observed when beryllium metal is oxidized. A water oxygen atom binds to a single surface beryllium ion in the preferred adsorption geometry on either surface. The water oxygen/beryllium bonding is stronger on the surface with greater beryllium atom exposure, namely the less-stable (001) surface. Water/beryllium coordination facilitates water dissociation. On the (001) surface, the dissociation products are a hydroxide bridging two beryllium ions and a metal coordinated hydride with some surface charge depletion. On the (100) surface, water dissociates into a hydroxide ligating a Be atom and a proton coordinated to a surface oxygen but the lowest energy water state on the (100) surface is the undissociated metal-coordinated water. The (100) fully hydroxylated surface structure has a hydrogen bonding network which facilitates rapid proton shuffling within the network. The corresponding (001) hydroxylated surface is fairly open and lacks internal hydrogen bonding. This supports previous experimental interpretations of the step in water adsorption isotherms. Further, when the (100) surface is heated to 1000 K, hydroxides and protons associate and water desorbs. The more open (001) hydroxylated surface is stable at 1000 K. This is consistent with the experimental disappearance of the isotherm step when heating to 973 K.

physics.chem-ph↗

arXiv2006

Gaussian Models for the Statistical Thermodynamics of Liquid Water

A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly realistic, and surprisingly accurate. Neglect of fluctuation contributions to this gaussian model yields a mean-field theory that produces useless results. A refinement that accounts for sharper-than-gaussian behavior at high binding energies recognizes contributions from a discrete number of water molecules and permits a natural matching of numerically exact results. These gaussian models, which can be understood as vigorous simplifications of quasi-chemical theories, are applicable to aqueous environments where the utility of structural models based on geometrical considerations of water hydrogen bonding have not been established.

physics.bio-ph↗

arXiv2005

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity

The KcsA potassium channel belongs to a class of K+ channels that is selective for K+ over Na+ at rates of K+ transport approaching the diffusion limit. This selectivity is explained thermodynamically in terms of favorable partitioning of K+ relative to Na+ in a narrow selectivity filter in the channel. One mechanism for selectivity based on the atomic structure of the KcsA channel invokes the size difference between K+ and Na+, and the molecular complementarity of the selectivity filter with the larger K+ ion. An alternative view holds that size-based selectivity is precluded because atomic structural fluctuations are greater than the size difference between these two ions. We examine these hypotheses by calculating the distribution of binding energies for Na+ and K+ in a simplified model of the selectivity filter of the KcsA channel. We find that Na+ binds strongly to the selectivity filter with a mean binding energy substantially lower than that for K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average filter binding energies do not discriminate Na+ from K+ when measured from the baseline of the difference in bulk hydration free energies. Instead, Na+/K+ discrimination can be attributed to scarcity of good binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, and is consistent with predicted relative constriction of the filter by Na+.

physics.bio-ph↗

arXiv2003

Inner Shell Definition and Absolute Hydration Free Energy of K+(aq) on the Basis of Quasi-chemical Theory and Ab Initio Molecular Dynamics

K+(aq) ion is an integral component of many cellular processes, amongst which the most important, perhaps, is its role in transmitting electrical impulses along the nerve. Understanding its hydration structure and thermodynamics is crucial in dissecting its role in such processes. Her we address these questions using both the statistical mechanical quasi-chemical theory of solutions and ab initio molecular dynamics simulations. Simulations predict an interesting hydration structure for K+(aq): the population of about six (6) water molecules within the initial minimum of the observed g_{KO}(r) at infinite dilution involves four (4) inner-most molecules that the quasi-chemical theory suggests should be taken as the theoretical inner shell. The contribution of the 5th and 6th closest water molecules is observable as a distinct shoulder on the principal maximum of the g_{KO}(r). The quasi-chemical estimate of solvation free energy for the neutral pair KOH is also in good agreement with experiments.

physics.chem-ph↗

arXiv2003

Hydration and mobility of HO-(aq)

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 suggested that HO[H_2O]4- is the only dominant aqueous solution species. We apply adiabatic ab initio molecular dynamics simulations, and find good agreement with both the quasi-chemical theoretical predictions and experimental results. The present results suggest a picture that is simpler, more traditional, but with additional subtlety. These coordination structures are labile but the tri-coordinate species is the prominent case. This conclusion is unaltered with changes in the electronic density functional. No evidence is found for rate-determining activated inter-conversion of a HO[H2O]4- trap structure to HO[H2O]3-, mediating hydroxide transport. The view of HO- diffusion as the hopping of a proton hole has substantial validity, the rate depending largely on the dynamic disorder of the water hydrogen-bond network.

physics.chem-ph↗

arXiv2003

Free energy of liquid water on the basis of quasi-chemical theory and ab initio molecular dynamics

We use ab initio molecular dynamics as a basis for quasi-chemical theory evaluation of the free energy of water near conventional liquid thermodynamic states. The PW91, PBE, and revised PBE (rPBE) functionals are employed. The oxygen radial density distribution, gOO(r), using the rPBE functional is in reasonable agreement with current experiments, whereas the PW91 and PBE functionals predict a more structured gOO(r). The diffusion coefficient with the rPBE functional is in reasonable accord with experiments. Using a maximum entropy procedure, we obtain x_0 from the coordination number distribution x_n for oxygen atoms having n neighbors. Likewise, we obtain p_0 from p_n, the probability of observing cavities of specified radius containing n water molecules. The probability x_0 is a measure of the local chemical interactions and is central to the quasi-chemical theory of solutions. The probability p_0, central to the theory of liquids, is a measure of the free energy required to open cavities of defined sizes in the solvent. Using these values and a reasonable model for electrostatic and dispersion effects, the hydration free energy of water in water at 314K is calculated to be -5.1kcal/mole with the rPBE functional, in encouraging agreement with the experimental value of -6.1kcal/mole.

physics.chem-ph↗

arXiv2003

The hydration state of HO$^-$(aq)

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 conclusion. Hydration free energies of neutral combinations of simple cations with HO$^-$(aq) are evaluated and agree well with experimental values.

physics.chem-ph↗

arXiv2003

Absolute Hydration Free Energies of Ions, Ion-Water Clusters, and Quasi-chemical Theory

Experimental studies on ion-water clusters have provided insights into the microscopic aspects of hydration phenomena. One common view is that extending those experimental studies to larger cluster sizes would give the single ion absolute hydration free energies not obtainable by classical thermodynamic methods. This issue is reanalyzed in the context of recent computations and molecular theories on ion hydration, particularly considering the hydration of H$^+$, Li$^+$, Na$^+$, and HO$^-$ ions and thence the hydration of neutral ion pairs. The hydration free energies of neutral pairs computed here are in good agreement with experimental results, whereas the calculated absolute hydration free energies, and the excess chemical potentials, deviate consistently from some recently tabulated hydration free energies based on ion-water cluster data. We show how the single ion absolute hydration free energies are not separated from the potential of the phase in recent analyses of ion-water cluster data, even in the limit of large cluster sizes. We conclude that naive calculations on ion-water clusters ought to agree with results obtained from experimental studies of ion-water clusters because both values include the contribution, somewhat extraneous to the local environment of the ion, from the potential of the phase.

physics.chem-ph↗