Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations
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The water‐exchange mechanism of [UO2(OH2)5]2+ has been reinvestigated by using ab initio molecular orbital (MO) methods. The geometries and the vibrational frequencies were computed with CAS‐SCF(12/11)‐SCRF and CAS‐SCF(12/11)‐PCM methods, which take into a ...
A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the transfer of an e ...
We derived an orbital dependent Kohn-Sham based scheme for the correction of the self-interaction error in DFT, which is particularly suited for the study of open shell molecular systems. Our approach is based on a weighted form of the Perdew and Zunger (P ...
We characterize the superionic phase transition and the lattice and electronic structures of the archetypal type-I superionic conductor alpha-AgI using extensive first-principles molecular dynamics calculations. We find that superionicity is signaled by a ...
Recently, a novel metal Mg2+-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, ...
Geometry and energy of the reactant (UO2(OH2)(5)center dot Cl+), the transition state (UO2(OH2)(5)center dot center dot center dot Cl+ double dagger), and the product (UO2Cl(OH2)(4)center dot OH2+) of the title reaction have been computed with complete act ...
H2S adsorption and dissociation on the gallium-rich GaAs( 001)- 4 x 2 surface is investigated using hybrid density functional theory. Starting from chemisorbed H2S on the GaAs( 001)- 4 x 2 surface, two possible reaction routes have been proposed. We find 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 ...
Recently, we have introduced a scheme for optimizing atom-based nonlocal external potentials within the framework of d. functional theory (DFT) in order to systematically improve the description of mol. properties [Phys. Rev. Lett. 93, 153004 (2004); J. Ch ...
This thesis describes the application of the quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello methodology to two systems of high biological interest: (a) The potassium channel KcsA from Streptomyces lividans and (b) The DNA repair enzyme EndoIV ...
