April-July 2004 - 10 articles
Within the framework of the itinerant radical model, the solvated electron in liquid alcohols is understood as an itinerant alkyl-oxonium ROH2. radical. As a first step in the investigation of those radicals, this study deals with the optimization of...
Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition s...
For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiem...
In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern bioch...
This special Issue of the International Journal of Molecular Sciences contains selected papers from the US-Czech-Polish workshop on Modeling Interaction in Biomolecules that took place between 15-th and 20-th September, 2003 in Nové Hrady, Czech Repu...
We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon...
The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some famil...
In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculatio...
Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal c...
The conformational propensities of the 21-residue peptide and its Oglycosylated analogs were studied by molecular dynamics (MD) simulations. This polypeptide motif comprises the tandem repeat of the human mucin (MUC1) protein core that is differently...
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