A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy
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The structural and dynamical properties of the four a-helix bundle Due Ferri 1, which is a generic mimic of diiron proteins, have been explored using d. functional theory (DFT) based and hybrid quantum/classical mol. dynamics (QM/MM) simulations. Four quan ...
A simplified formulation of the harmonic reaction path Hamiltonian (RPH) approach is used to calculate mode specific tunneling splittings and stereomutation times in (CH3OH)-C-12 and (CH3OH)-C-13. The experimental torsional spectrum is very well reproduced ...
We modeled liquid oxygen using ab initio molecular dynamics in which both the atomic structure and the noncollinear magnetic structure evolve without constraints. The atomic structure shows preference for parallel alignment of first-neighbor molecules and ...
Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. In this work, we represent the chaotropic agent as a factor ...
Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello mol. dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The ...
To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG-H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel ...
If vibrationally excited molecules are discretised into individual species and proper account is taken of the toroidal geometry in simulating neutrals, some improvement can be made in simulating the anomalous detachment behaviour seen at the outer target o ...
We used classical molecular mechanics (MM) simulations and quantum mechanical (QM) structural relaxations to examine the active site of myosin when bound to ATP. Two conformations of myosin have been determined by x-ray crystallography. In one, there is no ...
We report rotationally resolved spectra of jet-cooled methanol for the OH stretch overtones, 2v(1) and 3v(1), and for the torsional combinations, 2v(1)+v(12), 2v(1)+2v(12), 3v(1)+v(12), and 3v(1)+2v(12). The spectra are obtained by direct excitation from t ...
The combination of time-dependent d. functional theory (TDDFT) for the description of excited states with a hybrid quantum mechanics/mol. mechanics (QM/MM) approach enables the study of photochem. processes in complex environments. Here, we present a short ...