QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations.

Amide I bands of terminally blocked alanine in solutions investigated by infrared spectroscopy and density functional theory calculation: hydrogen-bonding interactions and solvent effects.

Structural aspects of terminally blocked alanine trans-N-acetyl-L-alanyl-trans-N'-methylamide (Ac-Ala-NHMe) in several different solvents were compared by attenuated total reflection infrared (ATR-IR) spectroscopy and density functional theory (DFT) calculations. The amide I bands between 1600 and 1700 cm(-1) appeared to change depending on media, indicating dissimilar hydrogen-bonding interactions among the peptides and solvent molecules. The minimum energy geometry in the isolated gas phase and aqueous environments were calculated at the B3LYP/6-311++G** theoretical level.

Molecular Thermodynamics of Methane Solvation in tert-Butanol-Water Mixtures.

We studied solvation structure and thermodynamics of methane in mixtures of tert-butanol and water using computer simulations. We show that for alcohol mole fractions below 20%, methane is preferentially solvated by hydrated alcohol clusters. Because methane expels water molecules from these clusters, a large endothermic solvent reorganization enthalpy occurs.

Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions.

By comparison of neopentane pair potentials of mean force (PMFs) in room temperature water and 6.9 molar aqueous urea, it was recently shown that urea molecules affect the PMF minima in an unexpected way (Lee, M.-E.

Does urea denature hydrophobic interactions?

It is generally accepted that clusters of hydrophobic moieties in water fall apart when urea is added in substantial amounts. We performed atomistic molecular dynamics simulations of hydrophobic solute pairs and found evidence that urea molecules act as "glue" bridging these pairs thereby holding them together. The picture is quite general as it applies to aliphatic-aliphatic as well as aromatic-aromatic interactions.

A new force field for atomistic simulations of aqueous tertiary butanol solutions.

We present a new tert-butanol force field parametrized to reproduce the mixture thermodynamics of tert-butanol/water over a wide range of solution compositions at room temperature and atmospheric pressure. The experimental Kirkwood-Buff integrals, which quantify preferential solvation of solution components by the same species or by the other components, were used as target values to be reproduced. Water was modeled using the simple point charge model.