Search results for "reaction mechanisms"
showing 10 items of 21 documents
A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme?
2018
Cytochrome P450 (CYP450) enzymes are involved in the metabolism of exogenous compounds and in the synthesis of signaling molecules. Among the latter, human aromatase (HA) promotes estrogen biosynthesis, which is a key pharmacological target against breast cancers. After decades of debate, interest in gaining a comprehensive picture of HA catalysis has been renewed by the recent discovery that compound I (Cpd I) is the reactive species of the peculiar aromatization step. Herein, for the first time, a complete atomic-level picture of all controversial steps of estrogen biosynthesis is presented. By performing cumulative quantum-classical molecular dynamics and metadynamics simulations of abou…
Experimental and Theoretical Studies of Nonclassical d 0 Cyclopentadienyl Polyhydride Complexes of Molybdenum and Tungsten
1998
Low-temperature protonation of compounds Cp{sup *}MH{sub 5}(PMe{sub 3}) (M = Mo, 1; W, 2) by HBF{sub 4}{center_dot}Et{sub 2}O in CD{sub 2}Cl{sub 2} or CDFCl{sub 2} affords the thermally unstable hexahydride derivatives [Cp{sup *}MH{sub 6}(PMe{sub 3})]{sup +} (M = Mo, 3; W, 4). The corresponding protonation of 1- and 2-d{sup 5} affords 3- and 4-d{sup 5}, respectively. The {Delta}{delta} on going from H{sub 6} to HD{sub 5} is small for both compounds, but positive for 3 and negative for 4, and no isotopic perturbation of resonance (IPR) is observed. The T{sub 1min} at 400 MHz for [Cp{sup *}MH{sub 6}(PMe{sub 3})]{sup +} apparently doubles on going from Mo to W (52 ms for 3 and approximately 10…
Molecular Basis of the Chemiluminescence Mechanism of Luminol
2019
Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminopho…
Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
2021
AbstractRibozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries…
Multiple Roles of Isocyanides in Palladium-Catalyzed Imidoylative Couplings: A Mechanistic Study
2016
International audience; Kinetic, spectroscopic and computational studies examining a palladium-catalyzed imidoylative coupling highlight the dual role of isocyanides as both substrates and ligands for this class of transformations. The synthesis of secondary amides from aryl halides and water is presented as a case study. The kinetics of the oxidative addition of ArI with RNC-ligated Pd-0 species have been studied and the resulting imidoyl complex [(ArC=NR)Pd(CNR)(2)I] (Ar=4-F-C6H4, R = tBu) has been isolated and characterized by X-ray diffraction. The unprecedented ability of this RNC-ligated imidoyl-Pd complex to undergo reductive elimination at room temperature to give the amide in the p…
Scalable Constant pH Molecular Dynamics in GROMACS
2022
Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to…
Copper‐Promoted Formation of Vinylsiloxanes
2020
The metathesis reactions of chlorovinylsilanes with copper(I) oxide are reported. The process is catalyzed by HCl which can be in situ generated via hydrolysis of chlorosilanes by traces of water present in the system. An appearance of olefin/CuCl π‐intermediates can provide a stereoselectivity of the process and alter the pathway of siloxanes formation employing Cu2O as the source of oxygen. It was also shown that acetonitrile may be available as a solvent for construction of the systems with large preparative capabilities, including those based on the use atmospheric oxygen in siloxane synthesis.
High Turnover Catalase Activity of a Mixed‐Valence Mn II Mn III Complex with Terminal Carboxylate Donors
2015
The neutral dimanganese(II,III) complex [Mn-2(BCPMP)-(OAc)(2)] [1; BCPMP3- = 2,6-bis({(carboxymethyl)[(1-pyridyl)-methyl] amino} methyl)-4-methylphenolato] has been synthesized and characterized. The complex contains two terminal carboxylate donors. Complex 1 was found to be an effective catalyst for the disproportionation of H2O2 with high catalytic rate and a turnover number of 7500, the highest turnover reported to date for a catalase mimic. The rates and TON were significantly higher than recorded for a dicationic dimanganese( II,III) counterpart ([Mn-2(BPBP)(OAc)(2)]center dot(ClO4)(2), 2; BPBP- = 2,6-bis{[bis(2-pyridylmethyl)amino]methyl}-4-butylphen-olato), which lacks the terminal c…
Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 …
2016
M.HhaI is a DNA methyltransferase from Haemophilus hemolyticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C5 position of a cytosine. This enzyme is a paradigmatic model for C5 DNA methyltransferases due to its major homology to mammalian enzymes and to the availability of high-resolution structures of the DNA–enzyme complex. In spite of the number of experimental and theoretical analyses carried out for this system, many mechanistic details remain unraveled. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex, where the target cytosine base is flipped out into the active site for bot…
Synthesis of Densely Functionalised 5-Halogen-1,3-oxazin-2-ones byHalogen-Mediated Regioselective Cyclisation of N-Cbz-ProtectedPropargylic Amines: A…
2013
A very efficient synthesis of 5-halogen-1,3-oxazin-2-ones has been accomplished by the halocyclisation reaction of chiral nonracemic N-carbobenzyloxy (N-Cbz)-protected propargylic amines by using I-2, Br-2 and Cl-2 as electrophile sources. The nature of the halogen influences the reaction time and yield. However, in all cases the reaction is totally regioselective taking place through a 6-endo-dig process regardless of the nature of the halogen and of the substituents in the starting material. To rationalise the experimental results, theoretical studies at the B3LYP/6-311G* level have been performed.