Simulation protocols for coherent femtosecond vibrational spectra of peptides
Article Abstract:
For simulating the response of peptides to sequences of IR pulses, two algorithms are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(sub 2)O. a fluctuating vibrational-exciton for the amide 1 mode is constructed form molecular dynamics trajectories, coupling with the environment is described using a density functional theory electrostatic map, Gaussian fluctuation is adequate for NA and for isotopically labeled bands in large peptides.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
Comment about this article or add new information about this topic:
Computer simulation of Met-enkephalin using explicit atom and united atom potentials: Similarities, differences, and suggestions for improvement
Article Abstract:
The conformational dynamics of Met-enkephalin are studied using a variety of united and explicit atom force fields to compare and contrast the dynamical behavior predicted by these two types of force fields in biological systems. A comparison of these dynamical properties indicates that the explicit atom and united atom force fields produce significantly different peptide dynamical properties.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2003
User Contributions:
Comment about this article or add new information about this topic:
Molecular dynamics study of tryptophylglycine: a dipeptide nanotube with confined water
Article Abstract:
The mechanism of structural changes of a peptide and water confined inside the channel, the helical peptide tryptophylglycine monohydrate is studied by molecular dynamics simulations. The result indicates that the confined water changes its mobility at 310 K, which is close to normal human body temperature.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2004
User Contributions:
Comment about this article or add new information about this topic:
- Abstracts: CO adsorption on Pd nanoparticles: density functional and vibrational spectroscopy studies. High-pressure studies of CO adsorption on Pd(111) by X-ray photoelectron spectroscopy and sum-frequency generation
- Abstracts: Computer simulation of cosolvent effects on hydrophobic hydration. Dynamics of halide ion-water hydrogen bonds in aqueous solutions: Dependence on ion size and temperature
- Abstracts: Calculating reversible potentials for Pt-H and Pt-OH bonds formation in basic solutions. Calculating reversible potentials for elementary reactions in acid and base from model reaction energies
- Abstracts: Photoionization and photofragmentation of SF6 in Helium nanodroplets. The growth of HF polymer in helium nanodroplets: Probing the barriers to ring insertion
- Abstracts: Polarization effects of confocal Raman microspectrometry of crystal powders using interactive self-modeling analysis