Using molecular dynamics based free energy simulations, we computed relative solvation
free energies for pairs of N-acetyl-methylamide amino acids (Ala-Ser, Val-Thr, Phe-Tyr, Val …

Including solvation effects (in the Poisson− Boltzmann continuum solvent approximation) we
report ab initio quantum mechanical calculations (HF/6-31G**) on the conformational …

Analysis of a series of molecular dynamics simulations reveals that the kinetics of breaking
and forming water− water hydrogen bonds is slower in the first solvation shell of a 16 …

The formation of monohydrates of capped phenylalanine model peptides, CH3-CO-Phe-
NH2 and CH3-CO-Phe-NH-CH3, in a supersonic expansion has been investigated using …

We compute the potential of mean force (PMF) around the ϕ and ψ torsions of alanine
dipeptide with a Poisson− Boltzmann (PB) method and compare these results to simulations …

In protein crystal structures, orderedwater molecules have been frequently observed at
instances where a-helices bend or fold. A series of molecular dynamics (MD) simulations …

The solvation free energies of amino acids and their side-chain analogues in water and
cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are …

The β-hairpin fold mechanism of a nine-residue peptide, which is modified from the β-hairpin
of α-amylase inhibitor tendamistat (residues 15–23), is studied through direct folding …

The folding free energy landscape of the C-terminal β-hairpin of protein G is explored using
the surface-generalized Born (SGB) implicit solvent model, and the results are compared …

Recent work has shown that the nature of hydration of pure hydrophobic surfaces changes
with the length scale considered: water hydrogen-bonding networks adapt to small exposed …