Development of transferable interaction potentials for water. V. Extension of the flexible, polarizable, Thole-type model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water

The quest for the best nonpolarizable water model from the adaptive force matching method

The recently introduced adaptive force matching (AFM) method is used to develop a significantly improved pair-wise nonpolarizable potential for water. A rigid version of the potential is also presented to enable larger time steps for biological simulations. In this work, it is demonstrated that the AFM method can be used to systematically assess the importance of each functional term during the construction of a force field. For a water potential, it is established that a single off-atom charge center (M) in the plane of water outperforms two out-of-plane charge sites for reproducing intermolecular forces. The four-site pair-wise nonpolarizable force field developed in this work rivals some of the most sophisticated polarizable models in terms of reproducing accurate ab initio forces. The force fields are parameterized to perform best in the temperature range from 0 to 40°C. Equilibrium and dynamical properties calculated with the flexible and rigid force fields are in good agreement with experimental results. For the flexible model, the agreement improves when path integral simulation is performed. These force fields provide high-quality results at a very low computational cost and are thus well suited to atomistic scale biological simulations. The AFM method provides a mechanism for selecting important terms in force field expressions and is a very promising tool for producing accurate force fields in condensed phases.

Vertical ionization potentials of nucleobases in a fully solvated DNA environment

Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.; et al. J. Am. Chem. Soc. 2009, 131, 6460). In a first step, a high level of theory, CCSD(T)/aug-cc-pVDZ, was used to calculate the vertical IP of each of the four single bases isolated in the QM region while the remaining DNA fragment, counterions, and water solvent molecules were included in the MM region. The calculated vertical IPs show a large positive shift of 3.2-3.3 eV compared to the corresponding gas-phase values. This shift is similar for all four DNA bases. The origin of the large increase in vertical IPs of nucleobases is found to be the long-range electrostatic interactions with the solvation structure outside the DNA helix. Thermal fluctuations in the fluid can result in IP changes of roughly 1 eV on a picosecond time scale. IPs of pi-stacked and H-bonded clusters of DNA bases were also calculated using the same QM/MM model but with a lower level of theory, B3LYP/6-31G(d=0.2). An IP shift of 4.02 eV relative to the gas phase is found for a four-base-pair B-DNA duplex configuration. The primary goal of this work was to estimate the influence of long-range solvation interactions on the ionization properties of DNA bases rather than provide highly precise IP evaluations. The QM/MM model presented in this work provides an attractive method to treat the difficult problem of incorporating a detailed long-range structural model of physiological conditions into investigations of the electronic processes in DNA.

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.

Combining THz spectroscopy and MD simulations to study protein-hydration coupling

THz spectroscopy is combined with MD simulations to study the dynamical properties of water in the solvation shell of proteins. The solvation dynamics is found to be influenced on length-scales of several hydration layers which is significantly more than what is found for static properties. Our experiments show that the properties of this dynamical solvation shell depend on the folding state of the protein. Kinetic THz absorption studies allow us to observe the formation of the dynamical solvation shell of the native protein upon folding. The experimental results can be reproduced using MD simulations which helps to develop a molecular understanding in terms of retardation of water dynamics.

Heat capacity of water: A signature of nuclear quantum effects

In this note we present results for the heat capacity at constant pressure for the TIP4PQ/2005 model, as obtained from path-integral simulations. The model does a rather good job of describing both the heat capacity of ice I(h) and of liquid water. Classical simulations using the TIP4P/2005, TIP3P, TIP4P, TIP4P-Ew, simple point charge/extended, and TIP5P models are unable to reproduce the heat capacity of water. Given that classical simulations do not satisfy the third law of thermodynamics, one would expect such a failure at low temperatures. However, it seems that for water, nuclear quantum effects influence the heat capacities all the way up to room temperature. The failure of classical simulations to reproduce C(p) points to the necessity of incorporating nuclear quantum effects to describe this property accurately.

A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids

We first describe a wave-function based formalism of polarizable charge model by starting from the Hartree product ansatz for the total wave function and making the second-order expansion of individual molecular energies with the use of partial charge operators. The resulting model is shown to be formally equivalent to the charge response kernel model that starts from the linear-response approximation to partial charges, and also closely related to a family of fluctuating charge models that are based on the electronegativity equalization principle. We then apply the above model to a systematic comparison of polarization effects on qualitatively different liquids, namely, protic solvents (water and methanol), an aprotic polar solvent (acetonitrile), and imidazolium-based ionic liquids. Electronic polarization is known to decelerate molecular motions in conventional solvents while it accelerates them in ionic liquids. To obtain more insights into these phenomena, we consider an effective decomposition of total polarization energy into molecular contributions, and show that their statistical distribution is well-correlated with the acceleration/deceleration of molecular motions. In addition, we perform effective nonpolarizable simulations based on mean polarized charges, and compare them with fully polarizable simulations. The result shows that the former can reproduce structural properties of conventional solvents rather accurately, while they fail qualitatively to reproduce acceleration of molecular motions in ionic liquids.

A second generation distributed point polarizable water model

A distributed point polarizable model (DPP2) for water, with explicit terms for charge penetration, induction, and charge transfer, is introduced. The DPP2 model accurately describes the interaction energies in small and large water clusters and also gives an average internal energy per molecule and radial distribution functions of liquid water in good agreement with experiment. A key to the success of the model is its accurate description of the individual terms in the n-body expansion of the interaction energies.

Analysis of anisotropic local field in sum frequency generation spectroscopy with the charge response kernel water model

A new flexible and polarizable water model based on the charge response kernel (CRK) theory is developed for the analysis of sum frequency generation (SFG) spectroscopy. The CRK model well describes several bulk water properties and SFG spectrum by molecular dynamics (MD) calculations. While the flexible and polarizable MD simulation generally adopts the short-range damping of intermolecular interaction, it is found that the same procedure is not adequate for the calculation of transition dipole in strongly hydrogen bonding environment. Accordingly, the improved calculation of the nonlinear susceptibility of water surface results in the positive imaginary part in the 3000-3200 cm(-1) region, which is consistent with recent phase-sensitive experiments. The mechanism of the positive region is attributed to the anisotropic local field effect induced by the orientational correlation of surface water.

The properties of water: insights from quantum simulations

The properties of water play a central role in many phenomena of relevance to different areas of science, including physics, chemistry, biology, geology, and climate research. Although well studied for decades, the behavior of water under different conditions and in different environments still remains mysterious and often surprising. In this article, various efforts aimed at providing a comprehensive representation of the water properties at a molecular level through computer modeling and simulation will be described. In particular, the unique role played by the hydrogen-bond network will be examined, first in liquid water, then in the solvation of model biological compounds, and finally in ice, especially highlighting the important effects related to the quantization of the nuclear motion.