Andrew Pohorille

Surface potential of the water liquid–vapor interface

The surface potential of the water liquid-vapor interface is studied by molecular dynamics using the TIP4P model. The surface potential predicted by this empirical model is -(130 +/- 50) mV. This value for the surface potential is of reasonable magnitude but of opposite sign to the expectations derived from laboratory experiments. The electrostatic potential displays a nonmonotonic variation with depth into the liquid. This nonmonotonic variation is explained on the basis of the nondipolar charge distribution of the H2O molecule and the observation that the more probable molecular orientations in the interfacial region place the molecular symmetry axis near the plane of the interface. It is shown that minor changes in the assumed molecular charge distribution can bring the computed surface potential into agreement with experimental expectations without qualitatively altering the nonmonotonic variation of the electrostatic potential through the interfacial region. Computed quantum mechanical descriptions of the electron distribution of the isolated H2O molecule are not compatible with the surface structure predicted by the TIP4P model and the experimental expectation that the surface potential of the water liquid-vapor interface is small, roughly of the of order of 10-100 mV. The surface potential is sensitive to details in the large distance wings of the molecular electron distribution. It is hypothesized that the surface environment qualitatively alters the wings of the distribution from the result obtained by a superposition of the isolated molecule electron densities.

Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

Results of molecular dynamics studies on the ions Na+, F-, and Cl- near the water liquid-vapor interface are reported. The free energies required to move the ions to the interface are presented and shown to depend on the sign of the ionic charge, and not the size of the ion. F- and Cl- can approach to within 2 molecular layers of the interface without incurring a significant change in free energy, while it costs about 2.5 kcal/mole to move Na+ this same distance. The free energy differences between the cation and the anions arise from the interaction of the ions with the water molecules in the interfacial region. These water molecules are oriented with a slight preference for their molecular dipoles to point toward the liquid. Thus, the anions approaching the interface disrupt the water structure less than does the cation. The calculated free energy curves are compared with predictions of simple dielectric models. It is shown that these models do not provide a good description of ions at the water surface. The ions are found to retain their first solvation shells at the interface. The anions also retain part of their second solvation shells, while Na+ does not. As a result, a larger bulge in the water surface is observed above the anions than above Na+. The lateral mobilities of the ions increase at the interface, in qualitative agreement with predictions of hydrodynamic models.

Comment on ‘‘Study on the liquid–vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure’’

This comment on the article by Matsumoto and Kataoka [J. Chem. Phys. 88, 3233 (1988)] identifies a discrepancy between recent calculations of the surface potential of the water liquid–vapor interface. The cited work assumes that the field of a water molecule in the interfacial region is strictly the field of a point molecular dipole, whereas other works have made more detailed assumptions about the molecular charge distributions. The difference between the values for the surface potential obtained from these different assumptions is large compared to the surface potential value in question. It is shown that the numerical difference is associated with the densities of molecular quadrupole moment in the coexisting bulk phases. The correction can be evaluated analytically and applied to the molecular dynamics results after the fact.

Comparison of the structure of harmonic aqueous glasses and liquid water

Glassy structures of water were generated by rapidly quenching configurations of 64 and 343 molecules of liquid water. The potential energy was then expanded through quadratic order around local minima generated this way and properties of the resulting harmonic system were calculated. The results were used to test the extent to which the structure of liquid water is similar to that of a harmonic aqueous glass. The radial distribution functions for the glass are remarkably similar to those of the liquid. The vibrational density of states for the glassy water exhibits a gap between 300 and 400 cm-1. The normal modes below 300 cm-1 correspond to molecular translations while the modes above 400 cm-1 are ascribed to molecular librations. Translational modes are almost entirely responsible for the broadening of oxygen-oxygen radial distribution function of the quenched configuration. They are also primarily responsible for the broadening of other radial distribution functions. Vibrational density of states leads to classical and quantum free energies for the harmonic system equal -9.62 +/- 0.12 and -8.89 +/- 0.12 kcal/mol, respectively, at T = 300 K. Both free energies were found to be insensitive to sample size and to the configurational differences between the quenched structures.

Molecular dynamics of phenol at the liquid–vapor interface of water

Molecular dynamics results are presented for phenol at the water liquid-vapor interface at 300 K. The calculated excess free energy of phenol at the interface is -2.8 +/- 0.4 kcal/mol, in good agreement with the recent experimental results of Eisenthal and co-workers. The most probable orientation of the phenol molecule at the surface is such that the aromatic ring is perpendicular to the interface and the OH group is fully immersed in water. The hydroxyl substituent has a preferred orientation which is similar to the orientation of OH bonds of water at the pure water liquid-vapor interface. The transition between interfacial and bulk-like behavior of phenol is abrupt and occurs when the center of mass of the solute is located about 6 angstroms from the Gibbs surface of water. In this region the para carbon atom of the hydrophobic benzene ring can reach the interface and become partially dehydrated. This result suggests that the width of the interfacial region in which the behavior of a simple amphiphilic solute in water is influenced by the presence of the surface depends primarily on the size of its hydrophobic part. The role of the OH substituent was investigated by comparing phenol at the interface with two model systems: benzene with and without partial charges on carbon and hydrogen atoms. It is shown that in the absence of the hydrophilic substituent the solute is located further away from the liquid phase and is more likely to be oriented parallel to the interface. However, when the center of mass of the solute is moved into the interfacial region where the density of water approaches that of the bulk solvent, all three molecules become oriented perpendicularly to the surface. In this orientation the work of cavity formation needed to accommodate the hydrophobic ring in aqueous solvent is minimized.

Molecular dynamics test of the Brownian description of Na(+) motion in water

The autocorrelation function of the velocity of an infinitely dilute Na+ ion in aqueous solution, and the autocorrelation function of the force exerted on a stationary Na+ under the same conditions are evaluated by molecular dynamics calculations. The results are used to test the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dynamics in solution. The self‐diffusion coefficient of the Na+ ion predicted by Brownian motion theory is (0.65±0.1)×10−5cm2/s. This value is about 60% greater than the one obtained for the proper dynamics of the finite mass ion, (0.4±0.1)×10−5cm2/s. The numerically correct velocity autocorrelation function is nonexponential, and the autocorrelation of the force on the stationary ion does not decay faster than the ion velocity autocorrelation function. Motivated by previous hydrodynamic modeling of friction kernels, we examine the approximation in which the memory function for the velocity autocorrelation function is identified with the autocor...

Interaction of a sodium ion with the water liquid-vapor interface

Molecular dynamics results are presented for the density profile of a sodium ion near the water liquid-vapor interface at 320 K. These results are compared with the predictions of a simple dielectric model for the interaction of a monovalent ion with this interface. The interfacial region described by the model profile is too narrow and the profile decreases too abruptly near the solution interface. Thus, the simple model does not provide a satisfactory description of the molecular dynamics results for ion positions within two molecular diameters from the solution interface where appreciable ion concentrations are observed. These results suggest that surfaces associated with dielectric models of ionic processes at aqueous solution interfaces should be located at least two molecular diameters inside the liquid phase. A free energy expense of about 2 kcal/mol is required to move the ion within two molecular layers of the free water liquid-vapor interface.

Solution influence on biomolecular equilibria - Nucleic acid base associations

This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimental data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.

DNA dynamics in aqueous solution: opening the double helix

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the mo lecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest re action in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dy namics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water mol ecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environ ment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

Base-pairing properties of O-methylated bases of nucleic acids energetic and steric considerations

Base-pairing properties of O-methylated nucleic-acid bases have been systematically investigated using both semi-empirical quantum-mechanical methods and a second-order perturbation formalism. The energetic, steric and electronic properties of (a) the individual methylated bases, (b) possible base-pairs formed between O-methylated and normal bases, and (c) mini-helices incorporating O-methylated bases were calculated. Two types of base-paired complexes were obtained: Those involving classical linear hydrogen bonds, and those involving bifurcated hydrogen-donor-hydrogen-acceptor interactions. In most complexes the presence of mispairs in the helical structure of nucleic acids is expected to create a local perturbation in the structure of the helix. Even though the most stable planar configurations of the mispairs may deviate markedly from those in the regular double helix, the induced deformations in the structure of the backbone are relatively small. Internal energies and geometries of mispairs are strongly affected by the conformation of the exocyclic group of the methylated bases. Another important contribution to the stability of various base-pairing schemes comes from stacking interactions.