Comparison of software for molecular mechanics modeling
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Within the Born-Oppenheimer picture of the electronic Schrödinger equation the external potential due to the nuclei influences the resulting expectation values during the self consistent field procedure. In this thesis, the optimization and the benefit of ...
EPFL2005
The energetics of dissocn. reactions of S82+ into stoichiometric mixts. of Sn+, n = 2-7, and Sm2+, m = 3, 4, 6, 10, were investigated by the B3PW91 method [6-311+G(3df)//6-311+G*] in the gas phase and in soln., with solvation energies calcd. using the SCIP ...
2004
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme is implicated in replication initiation and DNA topology ...
2008
Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative ...
We report a systematic density functional theory (DFT) computational investigation of Ru(II) sensitizer/TiO2 systems relevant to dye-sensitized solar cells (DSSCs). Focusing on the prototypical N719 and the recently introduced YE05 sensitizers, and conside ...
The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in e ...
The adsorption of terephthalic acid [C6H4(COOH)(2), TPA] on a Pd(111) surface has been investigated by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure spectroscopy under ultrahig ...
The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization ...
Redox potentials measure the free energy required to transfer a mol. species (ion) between two states of different total charge. In soln. a major contribution to the redox potential is the hydration free energy difference of the ion in the two oxidn. state ...
The conformational analysis of a series of configurational isomers of 2-(hydroxymethyl)azepan-3,4,5,6-tetrols 1-4 has been carried out. H-1 NMR spectroscopic data, especially vicinal J couplings and nuclear Overhauser enhancements (NOE), assisted by molecu ...