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.

Analysis, Spectra, Vibrational spectra

---

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.

---

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.

Structure

Similar abstracts:

• 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

This website is not affiliated with document authors or copyright owners. This page is provided for informational purposes only. Unintentional errors are possible.