150 research outputs found
Secondary structure of Ac-Ala-LysH polyalanine peptides (=5,10,15) in vacuo: Helical or not?
The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime
example that a secondary structure motif which is well-known from the solution
phase (here: helices) can be formed in vacuo. We here revisit this conclusion
for n=5,10,15, using density-functional theory (van der Waals corrected
generalized gradient approximation), and gas-phase infrared vibrational
spectroscopy. For the longer molecules (n=10,15) \alpha-helical models provide
good qualitative agreement (theory vs. experiment) already in the harmonic
approximation. For n=5, the lowest energy conformer is not a simple helix, but
competes closely with \alpha-helical motifs at 300K. Close agreement between
infrared spectra from experiment and ab initio molecular dynamics (including
anharmonic effects) supports our findings.Comment: 4 pages, 4 figures, Submitted to JPC Letter
Water-peptide dynamics during conformational transitions
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecular system during the conformational changes, in contrast to the metastable periods when water and peptide dynamics are essentially decoupled
Liquid–solid interfaces: structure and dynamics from spectroscopy and simulations
International audienc
Density functional theory across chemistry, physics and biology
International audienceThe past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT
Generating approximate Wigner distributions using Gaussian phase packets propagation in imaginary time.
Infrared spectroscopy of N-Methyl-Acetamide revisited by ab initio molecular dynamics simulations
Density-functional theory-based molecular simulation study of liquid methanol
We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials
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