Steven W. Rick

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

The five-site transferable interaction potential (TIP5P) for water is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like potential can be made which is very accurate for liquid water when used with Ewald sums, a more physical and increasingly more commonly used method for treating long-ranged electrostatic interactions. The new model demonstrates a density maximum near 4 degrees C, like the TIP5P model, and otherwise is similar to the TIP5P model for thermodynamic, dielectric, and dynamical properties of liquid water over a range of temperatures and densities. An analysis of this and other commonly used water models reveals how the quadrupole moment of a model can influence the dielectric response of liquid water.

Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model

The temperature dependence of the thermodynamic and dynamical properties of liquid water using the polarizable fluctuating charge (FQ) model is presented. The properties of ice Ih, both for a perfect lattice with no thermal disorder and at a temperature of 273 K, are also presented. In contrast to nonpolarizable models, the FQ model has a density maximum of water near 277 K. For ice, the model has a dipole moment of the perfect lattice of 3.05 Debye, in good agreement with a recent induction model calculation. The simulations at 273 K and the correct density find that thermal motion decreases the average dipole moment to 2.96 D. The liquid state dipole moment is less than the ice value and decreases with temperature.

Kinetic resolution of constitutional isomers controlled by selective protection inside a supramolecular nanocapsule

The concept of self-assembling container molecules as yocto-litre reaction flasks is gaining prominence. However, the idea of using such containers as a means of protection is not well developed. Here, we illustrate this idea in the context of kinetic resolutions. Specifically, we report on the use of a water-soluble, deep-cavity cavitand to bring about kinetic resolutions within pairs of esters that otherwise cannot be resolved because they react at very similar rates. Resolution occurs because the presence of the cavitand leads to a competitive binding equilibrium in which the stronger binder primarily resides inside the host and the weaker binding ester primarily resides in the bulk hydrolytic medium. For the two families of ester examined, the observed kinetic resolutions were highest within the optimally fitting smaller esters.

The effects of charge transfer on the properties of liquid water

A method for treating charge transfer interactions in classical potential models is developed and applied to water. In this method, a discrete amount of charge is transferred for each hydrogen bond formed. It is designed to be simple to implement, to be applicable to a variety of potential models, and to satisfy various physical requirements. The method does not transfer charge at large intramolecular distances, it does not result in a conductive liquid, and it can be easily parameterized to give the correct amount of charge transfer. Two charge transfer models are developed for a polarizable and a non-polarizable potential. The models reproduce many of the properties of liquid water, including the structure, the diffusion constant, and thermodynamic properties over a range of temperatures.

Dielectric constant and proton order and disorder in ice Ih: Monte Carlo computer simulations

The dielectric properties of ice Ih are studied using a Monte Carlo algorithm for sampling over proton configurations. The algorithm makes possible the calculation of the dielectric constant and other properties of the proton-disordered crystal. Results are presented for three classical models of water, two commonly used nonpolarizable models (SPC/E and TIP4P) and a polarizable model (TIP4P-FQ).

The effects of charge transfer on the aqueous solvation of ions

Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na(+), K(+), and Cl(-), respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.

The quantum dynamics of hydrogen and deuterium on the Pd(111) surface : a path integral transition state theory study

The surface diffusion constant for hydrogen and deuterium on the palladium(111) surface is calculated using quantum mechanical transition state theory. The rate constants for diffusion into the subsurface layer are also calculated. Quantum effects are seen to be most important for the surface/subsurface transition and cause an inverse isotope effect in which the rate for deuterium is greater than the rate for hydrogen. The results of ground and excited state wave function calculations show localized hydrogenic states, despite large zero point energies, and that the preferred binding site can vary with isotope between surface and subsurface sites. In addition, estimates of the tunneling rate between the surface and subsurface are in qualitative agreement with the low temperature transition state results.

Water inside a hydrophobic cavitand molecule.

The structure and dynamics of water inside a water-soluble, bowl-shaped cavitand molecule with a hydrophobic interior are studied using molecular dynamics computer simulations. The simulations find that the number of inside water molecules is about 4.5, but it fluctuates from being completely empty to full on a time scale of tens of nanoseconds. The transition from empty to full is energetically favorable and entropically unfavorable. The water molecules inside have fewer hydrogen bonds than the bulk and in general weaker interactions; the lower energy results from the nearest-neighbor interactions with the cavitand atoms and the water molecules at the entrance of the cavitand, interactions that are lost upon dewetting. An analysis of translational and rotational motion suggests that the lower entropy of the inside water molecules is due to decreased translational entropy, which outweighs an increased orientational entropy. The cavitand molecule acts as a host binding hydrophobic guests, and dewetting can be induced by the presence of a hydrophobic guest molecule about 3 A above the entrance. At this position, the guest displaces the water molecules which stabilize the inside water molecules and the empty cavitand becomes more stable than the full.

Simulations of proton order and disorder in ice Ih.

Computer simulations of ice Ih with different proton orientations are presented. Simulations of proton disordered ice are carried out using a Monte Carlo method which samples over proton degree of freedom, allowing for the calculation of the dielectric constant and for the examination of the degree of proton disorder. Simulations are also presented for two proton ordered structures of ice Ih, the ferroelectric Cmc2(1) structure or ice XI and the antiferroelectric Pna2(1) structure. These simulations indicate that a transition to a proton ordered phase occurs at low temperatures (below 80 K). The symmetry of the ordered phase is found to be dependent on the water potential. The stability of the two proton ordered structures is due to a balance of short-ranged interactions which tend to stabilize the Pna2(1) structure and longer-range interactions which stabilize the Cmc2(1) structure.

Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase

Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistant to novobiocin as well as those with a decreased affinity for novobiocin over clorobiocin both involve a less favorable entropy of binding, which more than compensates for a more favorable enthalpy, and additional water molecules at the protein-ligand interface. Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamic integration computer simulations. The calculations show that addition of the water molecules is entropically unfavorable, with values that are comparable to the measured entropy differences. The free energies and entropies correlate with the change in the number of hydrogen bonds due to the addition of water molecules.