Teresa Head-Gordon

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

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.

Current Status of the AMOEBA Polarizable Force Field

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Analytic MP2 frequencies without fifth-order storage. Theory and application to bifurcated hydrogen bonds in the water hexamer

Abstract An obstacle to obtaining vibrational frequencies of large molecules via second-order Moller—Plesset (MP2) theory has been the need to store transformed electron repulsion integral derivatives in the molecular orbital (MO) basis. A semi-direct algorithm for eliminating this fifth-order storage is described in which small batches of MO integral derivatives are made at a time, their contributions to the MP2 second derivatives are evaluated, and then they are discarded. No extra computation is required. We locate and characterize a transition structure of the water hexamer cluster which exhibits a bifurcated hydrogen bond structure, at the MP2/6–31 + G* level of theory.

What can x-ray scattering tell us about the radial distribution functions of water?

We present an analysis of the Advanced Light Source (ALS) x-ray scattering experiment on pure liquid water at ambient temperature and pressure described in the preceding article. The present study discusses the extraction of radial distribution functions from the x-ray scattering of molecular fluids. It is proposed that the atomic scattering factors used to model water be modified to include the changes in the intramolecular electron distribution caused by chemical bonding effects. Based on this analysis we present a gOO(r) for water consistent with our recent experimental data gathered at the ALS, which differs in some aspects from the gOO(r) reported by other x-ray and neutron scattering experiments. Our gOO(r) exhibits a taller and sharper first peak, and systematic shifts in all peak positions to smaller r. Based on experimental uncertainties, we discuss what features of gOO(r) should be reproduced by classical simulations of nonpolarizable and polarizable water models, as well as ab initio simulation...

A high-quality x-ray scattering experiment on liquid water at ambient conditions

We report a new, high-quality x-ray scattering experiment on pure ambient water using a synchrotron beam line at the Advanced Light Source at Lawrence Berkeley National Laboratory. Several factors contribute to the improved quality of our intensity curves including use of a highly monochromatic source, a well-characterized polarization correction, a Compton scattering correction that includes electron correlation, and more accurate intensities using a modern charge coupled device (CCD) detector. We provide a comprehensive description of the data processing that we have used for correcting systematic errors, and we provide an estimate of our remaining random errors. The resulting error estimates of our data are smaller then the discrepancies between data sets collected in past x-ray experiments. We find that the older x-ray curves support a family of gOO(r)’s that exhibit a smaller first peak (∼2.2), while the current data is better fit with a family of gOO(r)’s with a first peak height of 2.8, and systema...

Hydration dynamics near a model protein surface

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation for both the completely deuterated and completely hydrogenated leucine monomer. The NALMA-water system and the QENS data together provide a unique study for characterizing the dynamics of different hydration layers near a prototypical hydrophobic side chain and the backbone of which it is attached. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational and rotational water dynamics at the highest solute concentrations are found to be highly suppressed as characterized by long residential time and slow diffusion coefficients. The analysis of the more dilute concentration solutions models the first hydration shell with the 2.0 M spectra. We find that for outer layer hydration dynamics that the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis of the first hydration shell water dynamics shows spatially heterogeneous water dynamics, with fast water motions near the hydrophobic side chain, and much slower water motions near the hydrophilic backbone. We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition.

The structure of ambient water

We review the spectroscopic techniques and scattering experiments used to probe the structure of water, and their interpretation using empirical and ab initio models, over the last 5 years. We show that all available scientific evidence overwhelmingly favors the view of classifying water near ambient conditions as a uniform, continuous tetrahedral liquid. While there are controversial issues in our understanding of water in the supercooled state, in confinement, at interfaces, or in solution, there is no real controversy in what is understood as regards bulk liquid water under ambient conditions.

Representability problems for coarse-grained water potentials.

The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density ranges from 0.88 to 1.30 g/cm3 and temperature ranges from 235 to 310 K. Although by construction these effective potentials correctly represent the isothermal compressibility of TIP4P-Ew water, they do not accurately resolve other thermodynamic properties such as the virial pressure, the internal energy, or thermodynamic anomalies. Because at a given state point the pair potential that reproduces the pair structure is unique, we have therefore explicitly demonstrated that it is impossible to simultaneously represent the pair structure and several key equilibrium thermodynamic properties of water with state-point dependent radially symmetric pair potentials. We argue that such representability problems are related to, but different from, more widely acknowledged transferability problems and discuss in detail the implications this has for the modeling of water and other liquids by coarse-grained potentials. Nevertheless, regardless of thermodynamic inconsistencies, the state-point dependent effective potentials for water do generate structural and dynamical anomalies.

Excitation energy transfer in condensed media

We derive an expression for resonance energy transfer between a pair of chromophores embedded in a condensed medium by considering the energy splitting of the chromophores from their resonant excited states. We employ time-dependent density functional response theory in our derivation. The linear response theory treatment is rigorous within the framework of time-dependent density functional theory, while in obtaining the energy transfer coupling, the standard first-order approximation is used. The density response function for the medium, which can be replaced by the macroscopic dielectric susceptibility, enables the inclusion of the medium influence on the energy transfer coupling between the donor and acceptor. We consider the Coulomb coupling, and determine that our result is isomorphic to the Coulomb interaction between two charge densities inside a dielectric medium. The isomorphism we found not only provides a general and useful expression for applications, but additionally offers a basis for the ex...

Minimalist models for protein folding and design

Protein folding research during the past decade has emphasized the dominant role of native state topology in determining the speed and mechanism of folding for small proteins; this has been illustrated by simulations using minimalist protein models. The advantages of minimalist protein models lie in their ability to rapidly collect meaningful statistics about folding pathways and kinetics, their ease of characterization with coarse-grained order parameters and their concentration on the essential physics of the problem to connect with experimental observables for a target protein. The maturation of experimental protein folding has driven the need for more quantitative protein simulations to better understand the balance between sequence details and fold topology. In the past year, we have seen the emergence of more complex minimalist models, ranging from all-atom Gō potentials to coarse-grained bead models in which Gō interactions are replaced or supplemented by more physically motivated potentials. The reduced computational cost at the coarse-grained level of abstraction will potentially enable both folding studies on a genomic scale and systematic application in protein design.