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showing 10 items of 1641 documents
A Multisite Molecular Mechanism for Baeyer-Villiger Oxidations on Solid Catalysts Using Environmentally Friendly H2O2 as Oxidant
2005
The molecular mechanism of the Baeyer-Villiger oxidation of cyclohexanone with hydrogen peroxide catalyzed by the Sn-beta zeolite has been investigated by combining molecular mechanics, quantum-chemical calculations, spectroscopic, and kinetic techniques. A theoretical study of the location of Sn in zeolite beta was performed by using atomistic force-field techniques to simulate the local environment of the active site. An interatomic potential for Sn/Si zeolites, which allows the simulation of zeolites containing Sn in a tetrahedral environment, has been developed by fitting it to the experimental properties of quartz and SnO 2 (rutile). The tin active site has been modeled by means of a S…
Net charge and polarizability of zeolitic Brønsted acidic sites
2007
The interacting induced-dipoles polarization model, implemented in our program POLAR, is used for the calculation of the effective polarizability of the zeolitic bridged OH group, which results much higher than that of the free silanol group. A high polarizability is also calculated for the bridged OH group with a Si4+, in the absence of Lewis-acid promotion of silanol by Al3+. The crystal polarizability is estimated from the Clausius-Mossotti relationship. Siliceous zeolites are low-permittivity isolators. The interaction of a weak base with the zeolitic OH can be considered as a local bond. Only when cations are located in the zeolite micropore, next to tetrahedra that contain trivalent c…
Cluster and Periodic Calculations of the Ethene Protonation Reaction Catalyzed by theta-1 Zeolite: Influence of Method, Model Size, and Structural Co…
2001
The protonation of ethene by three different acid sites of theta-1 zeolite was theoretically studied to analyze the extent and relevance of the following aspects of heterogeneous catalysis: the local geometry of the Bronsted acid site in a particular zeolite, the size of the cluster used to model the catalyst, the degree of geometry relaxation around the active site, and the effects related to medium- and long-range interactions between the reaction site and its environment. It has been found that while the reaction energy is very sensitive to the local geometry of the site, the activation energy is mainly affected by the methodology used and by electrostatic effects on account of the carbo…
High resolution crystal structures of triosephosphate isomerase complexed with its suicide inhibitors: The conformational flexibility of the catalyti…
2011
The key residue of the active site of triosephosphate isomerase (TIM) is the catalytic glutamate, which is proposed to be important (i) as a catalytic base, for initiating the reaction, as well as (ii) for the subsequent proton shuttling steps. The structural properties of this glutamate in the liganded complex have been investigated by studying the high resolution crystal structures of typanosomal TIM, complexed with three suicide inhibitors: (S)-glycidol phosphate ((S)-GOP, at 0.99 A resolution), (R)-glycidol phosphate, ((R)-GOP, at 1.08 A resolution), and bromohydroxyacetone phosphate (BHAP, at 1.97 A resolution). The structures show that in the (S)-GOP active site this catalytic glutama…
BER, MGMT, and MMR in defense against alkylation-induced genotoxicity and apoptosis
2001
Methylating carcinogens and cytostatic drugs induce different methylation products in DNA. In cells not expressing the repair protein MGMT or expressing it at a low level, O6-methylguanine is the major genotoxic, recombinogenic, and apoptotic lesion. Genotoxicity and apoptosis triggered by O6-methylguanine require mismatch repair (MMR). In cells expressing O6-methylguanine-DNA methyl transferase (MGMT) at a high level or for agents producing low amounts of O6-methylguanine, N-alkylations become the major genotoxic lesions. N-Alkylations are repaired by base excision repair (BER). In mammalian cells, naturally occurring mutants of BER have not been detected, which points to the importance of…
Chromatin structure of the 5′ flanking region of the yeastLEU2 gene
1989
The chromatin structure of theLEU2 gene and its flanks has been studied by means of nuclease digestion, both with micrococcal nuclease and DNase I. The gene is organized in an array of positioned nucleosomes. Within the promoter region, the nucleosome positioning places the regulatory sequences, putative TATA box and upstream activator sequence outside the nucleosomal cores. The tRNA3 Leu gene possesses a characteristic structure and is protected against nucleases. Most of the 5′ flank is sensitive to DNase I digestion, although no clear hypersensitive sites were found. The chromatin structure is independent of either the transcriptional state of the gene or the chromosomal or episomal loca…
On Transition Structures for Hydride Transfer Step: A Theoretical Study of the Reaction Catalyzed by Dihydrofolate Reductase Enzyme
1996
Abstract A theoretical study is presented of the catalytic mechanism of dihydrofolate reductase (DHFR) enzyme based upon the characterization of the transition structure (TS) for the hydride transfer step. Analytical gradients at AM1 and PM3 semiempirical levels have been used to characterize the saddle point of index one (SPi-1) on global energy hypersurface for the hydride transfer in the active site of DHFR enzyme. The geometry, stereochemistry, electronic structure, and transition vector (TV) components associated to SPi-1 are qualitatively computational level independent. The TV amplitudes show primary and secondary isotope effects to be strongly coupled. The geometrical arrangement of…
Azide and chloride binding to carboxypeptidase A in the presence of L-phenylalanine
1990
The interaction of chloride with native and cobalt (Co)-substituted carboxypeptidase-A (CPD) has been investigated by 35Cl nuclear magnetic resonance (NMR) spectroscopy in the presence and absence of L-Phe. The affinity constants of azide and chloride toward the Co(II)CPD·L-Phe complex have been measured by electronic spectroscopy. The correlation times determining T1 and T2 for the 35Cl nuclei are related to movements inside the cavity. In the presence of L-Phe, the anions bind to the metal with a relatively high affinity at pH values below 6. Anion binding to the Co enzyme can be analyzed in terms of the three protonation state model for the enzyme (EH2 α EH α E). In the presence of L-Phe…
Modeling for the active site nitrate reductase. Oxidation of the complex [MovO(O2CC(S) CH3Ph)2]− by nitrate and nitrite in methanol
1998
Abstract Under acid conditions the [MoVIO2(O2CC(S)CH1Ph)2]2 reacts with thiols to yield the monomeric [MoVO(O2CC(S)CH3Ph)2] and disulfide. The reduced complex [MoVO(O2CC(S)CH3Ph)2]− can react with NO3− and NO2− in a one-electron step yeilding respectively NO2 and NO and the original molybdenum (VI)-dioxo complex. The experimental pseudo-first-order rate constant with respect to the Mo(V) complex at 25°C was found to be kobs=2.3×10−4s−1 for NO3− and kobs=1.0×10−2 for NO2−. Oxo transfers to and from the substrate have been coupled to produce a catalytic system which turns over the reaction RSH+(No3− or NO2−)+H+a 1 2 [ RS ] 2 +( NO ] 2 or NO )+ H 2 O , in which thiols, NO1− and NO2− serve as a…
How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study
2020
<div>In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.</div>