A new mechanism for ethanol oxidation mediated by cytochrome P450 2E1: bulk polarity of the active site makes a difference.
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Binding Sites↗
Biomedical subjects
Chuanlu Yang
Publications and source records attributed to Chuanlu Yang.
Density functional theory investigation of product distribution following reaction of acrylonitrile on diamond (001)-2 x 1 surface.
The reaction of acrylonitrile with the C(001)-2 x 1 surface has been investigated by employing density functional cluster model calculations. The calculations revealed eight possible reaction pathways for acrylonitrile with the surface dimer. Full geometry optimized structures were obtained for all adducts, including intra- and interdimer reaction products. These results were analyzed in terms of both the total energy values and the detailed optimized geometries. We find that the reaction of acrylonitrile with the diamond (001) surface occurs primarily through its nonpolar C=C group and the intradimer [2+2](cc) product is the dominant product. All these results are in good agreement with the experimental work by Schwartz. It is noteworthy that the isomerization process plays an important role in the chemisorption process. Both intradimer [4+2] product and interdimer [2+2](cc) product can isomerize to the intradimer [2+2](cc) product. The present study shows that the isomerization between intradimer [4+2] product and intradimer [2+2](cc) product is slightly favorable over the direct path to formation of the intradimer [2+2](cc) product.
Journal Article↗
Ordering spatiotemporal chaos in complex thermosensitive neuron networks.
We have studied the effect of random long-range connections in chaotic thermosensitive neuron networks with each neuron being capable of exhibiting diverse bursting behaviors, and found stochastic synchronization and optimal spatiotemporal patterns. For a given coupling strength, the chaotic burst-firings of the neurons become more and more synchronized as the number of random connections (or randomness) is increased and, rather, the most pronounced spatiotemporal pattern appears for an optimal randomness. As the coupling strength is increased, the optimal randomness shifts towards a smaller strength. This result shows that random long-range connections can tame the chaos in the neural networks and make the neurons more effectively reach synchronization. Since the model studied can be used to account for hypothalamic neurons of dogfish, catfish, etc., this result may reflect the significant role of random connections in transferring biological information.
Journal Article↗
Theoretical study of the mechanism of acetaldehyde hydroxylation by compound I of CYP2E1.
Recent experimental studies revealed that cytochrome P450 2E1 (CYP2E1) could metabolize not only ethanol but also its primary product, acetaldehyde, accompanying the well-known acetaldehyde dehydrogenases (ALDH) in the metabolism of acetaldehyde. Mechanistic aspects of acetaldehyde hydroxylation by Compound I model active species of CYP2E1 were investigated by means of B3LYP DFT calculations in the present paper. Our study results demonstrate that acetaldehyde hydroxylation by CYP2E1 is in accord with the effectively concerted mechanisms both on the high quartet spin state (HS) and on the low doublet spin state (LS). The rate-limiting step is H-abstraction, and the activation energy is about 11.7 approximately 14.0 kcal/mol on the quartet (doublet) reaction route, which is about one-half to one-third of that needed by methane hydroxylation. The phenomenon that the HS and LS reaction routes are both effectively concerted was shown for the first time to occur in trans-2-phenyl-iso-propylcyclopropane hydroxylation by Kumar et al. (see Figure 7 in the paper of Kumar, D.; de Visser, S. P.; Sharma, P. K.; Cohen, S.; Shaik, S. J. Am. Chem. Soc. 2004, 126, 1907) and was confirmed in our work of acetaldehyde hydroxylation by cytochrome P450. Theoretical exploration of the HS O-rebound barrier degradation is also presented in the present paper on the basis of Shaik's valence bond (VB) model.
Acetaldehyde↗
A density functional theory study on the role of His-107 in arylamine N-acetyltransferase 2 acetylation.
Arylamine N-acetyltransferases (NATs, EC 2.3.1.5) catalyze an acetyl group transfer from acetyl coenzyme A (AcCoA) to primary arylamines, and are responsible for the biotransformation and metabolism of drugs, carcinogens, etc. Structure analysis revealed that His-107 was likely the residue accountable for mediating acetyl transfer. We have examined the full catalytic mechanism of this system by means of DFT method. The results indicate that if the acetyl group directly transferred from the donor, p-nitrophenyl acetate, to the acceptor, cysteine, the high activation energy will be a great hindrance. These energies have dropped a little in a range of 20-25 kJ/mol when His-107 is assisting the transfer process. However, when protonated His-107 is mediating the reaction, the activation energies have dropped about 70-85 kJ/mol. Our calculations strongly support an enzymatic acetylation mechanism that experiences a thiolate-imidazolium pair, which have verified the presumption from experiments.
Acetyl Coenzyme A↗
The molecular structure and vibrational spectra of corrolazine metal complexes (CzM) by density functional theory.
The ground-state geometries, electronic structures and vibrational frequencies of metal corrolazine complexes, CzM (M=Mn, Co, Ni and Fe) have been studied using B3LYP/6-311 g(d) method. The molecular geometries are sensitive to the species of the metal, and the bond length of the MN is increase with the metal atom radii. The ground-state electronic structures indicate that there are strong interactions between dx2-y2 of the metal fragments and the corrolazine fragments. The calculations also indicate that the CzNi is the stabilest among the four metal corrolazine complexes. Vibrational frequencies of these metal corrolazine complexes were also calculated and were assigned to the local coordinates of the corrolazine ring, which reveals the some common feature of the molecular vibrations of the metal corrolazine complexes as four-coordination metallocorrolazines.
Metals, Heavy↗
A quantum chemical study on the mechanism of glycinamide ribonucleotide transformylase inhibitor: 10-Formyl-5,8,10-trideazafolic acid.
A density functional theory (DFT) study is presented on the reaction mechanism of glycinamide ribonucleotide (GAR) with 10-formyl-5,8,10-trideazafolic acid (10f-TDAF), which is an inhibitor designed for GAR transformylase (GAR Tfase). There are three different paths for this system and the results indicate that inhibitor 10f-TDAF can form a very stable intermediate with the substrate GAR or generate an imine bond with GAR by elimination of water. The results have verified the presumption from available experiments and implied that 10f-TDAF would be an important target for anti-neoplastic intervention.
Catalysis↗