Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant difference...

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

The ability of simple potential functions to reproduce accurately the density of liquid water from −37 to 100 °C at 1 to 10 000 atm has been further explored. The result is the five-site TIP5P model, which yields significantly improved results; the average error in the density over the 100° temperature range from −37.5 to 62.5 °C at 1 atm is only 0.006 g cm−3. Classical Monte Carlo statistical mechanics calculations have been performed to optimize the parameters, especially the position of the negative charges along the lone-pair directions. Initial calculations with 216 molecules in the NPT ensemble at 1 atm focused on finding a model that reproduced the shape of the liquid density curve as a function of temperature. Calculations performed for 512 molecules with the final TIP5P model demonstrate that the density maximum near 4 °C at 1 atm is reproduced, while high-quality structural and thermodynamic results are maintained. Attainment of high precision for the low-temperature runs required sampling for more than 1 billion Monte Carlo configurations. In addition, the dielectric constant was computed from the response to an applied electric field; the result is 81.5±1.5 at 25 °C and the experimental curve is mirrored from 0–100 °C at 1 atm. The TIP5P model is also found to perform well as a function of pressure; the density of liquid water at 25 °C is reproduced with an average error of ∼2% over the range from 1 to 10 000 atm, and the shift of the temperature of maximum density to lower temperature with increasing pressure is also obtained.

/pdf/a-five-site-model-for-liquid-water-and-the-reproduction-of-4waghhehgx.pdf

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.

/pdf/development-of-an-improved-four-site-water-model-for-10rw432kke.pdf

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

https://www.pnas.org/content/pnas/102/19/6665.full.pdf

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

A reappraisal of what we have learnt during three decades of computer simulations on water

Monte Carlo statistical mechanics simulations have been carried out with the TIP3P, SPC, and TIP4P models for liquid water at 13 temperatures from −50°C to 100°C at 1 atm. Long runs with 512 water molecules provided definitive results for densities. Although the TIP4P model yields a flat region in the density profile and a temperature of maximum density near −15°C, the SPC and TIP3P models show monotonically increasing density with decreasing temperature. Results for heats of vaporization, isothermal compressibilities, and coefficients of thermal expansion and their convergence characteristics are also reported. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1179–1186, 1998

Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density

Computational studies of carbenium ions relevant to sterol biosynthesis via lanosterol synthase were undertaken to determine fundamental energetics underlying cyclization steps. Ab initio B3LYP/6-31G*//B3LYP/6-31G* calculations were performed for the addition of 2-methyl-2-propyl cation and 2-methylpropene to represent a tertiary cation → tertiary cation cyclization. Solvent effects were included by Monte Carlo (MC) simulations in methylene chloride, methanol, and THF. The picture that emerges for a cation−olefin cyclization is one of barrierless collapse at short distance, while desolvation and conformational barriers are expected for initial separations beyond ca. 5 A. Thus, the cyclization that forms the sterol B ring likely proceeds in barrierless concert with A-ring formation in the preorganized environment of a cyclase enzyme. However, C-ring formation appears to involve a tertiary → secondary cation rearrangement. This was modeled by ab initio and MC calculations for the interconversion of the C11 ...

Corky Jenson

Papers

Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density

Computational Investigations of Carbenium Ion Reactions Relevant to Sterol Biosynthesis

Energetics of Cation-Olefin Addition in the Gas Phase and in Solution

Solvent as Catalyst: Computational Studies of Organic Reactions in Solution