in this study, functionalized β-cyclodextrin (β-cd) by aldehyde group was investigated as an oxidase enzyme mimic for the amino phenol oxidation. all calculations were performed by gaussian 09 package using two layers oniom method at the oniom (mpw1pw91/6-311++g(d,p)/uff) level. in the first step, h2o2 is encapsulated in the hydrophobic cavity. in the second step, h2o2 molecule oxidized the ald...

X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-bod...

     In this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (R), alpha helix (α) and beta sheet (b) were investigated theoretically. These structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. Computational methods at the HF, B3LYP, X3LYP and M05-2X levels in t...

FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biol...

The performance of a variety of DFT functionals (BLYP, PBE, B3LYP, B3P86, KMLYP, B1B95, MPWPW91, MPW1B95, BB1K, MPW1K, MPWB1K, and BMK), together with the ab initio methods RHF, RMP2, and G3(MP2)-RAD, and with ONIOM methods based on combinations of these procedures, is examined for calculating the enthalpies of a range of radical reactions. The systems studied include the bond dissociation ener...

The two-layered ONIOM(B3LYP:MNDO) method has been used to investigate the hydrolytical mechanism of matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases capable of degrading a wide range of macromolecules of the extracellular matrix. Human stromelysin-1 (MMP-3) was chosen as a physiologically important member of the MMP family. As a structural reference, X-ray data ...