Search results for "Transition state"
showing 10 items of 85 documents
A theoretical study on NHC-catalysed enantioselective cycloaddition of ketenes and 3-aroylcoumarins: mechanism and enantioselectivity.
2018
NHC-catalysed enantioselective cycloaddition of ketenes to 3-aroylcoumarins to yield dihydrocoumarin-fused dihydropyranones has been investigated using DFT methods at the B3LYP/6-31G* and MPWB1K/6-311G** computational levels. Two plausible mechanisms have been studied: the “ketene-first” mechanism A and the “coumarin-first” mechanism B. An analysis of the activation Gibbs free energies involved in the two competitive pathways makes it possible to rule out the pathway associated with the “coumarin-first” mechanism B. The first step of the “ketene-first” mechanism A is the formation of zwitterionic intermediate IN1-Zvia a nucleophilic attack of NHC 1 on ketene 2. A [4 + 2] cycloaddition throu…
[3+2] Cycloaddition reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl acrylate: A DFT study
2016
Abstract A density functional theory study was performed on the [3+2] cycloaddition (32CA) reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl acrylate. The thermodynamic and kinetic parameters were analysed by considering the regio- and stereoisomeric pathways in gas phase and solvents. The geometries indicate that the transition states are slightly more advanced and asynchronous in ethanol. Electron localisation function topological analysis of the bonding changes along the most favourable reaction pathway associated with the 32CA reaction of 1H-phosphorinium-3-olate with methyl acrylate indicates that the reaction takes place through a two-stage one-step me…
Heavy enzymes—experimental and computational insights in enzyme dynamics
2014
The role of protein motions in the chemical step of enzyme-catalyzed reactions is the subject of an open debate in the scientific literature. The systematic use of isotopically substituted enzymes has been revealed as a useful tool to quantify the role of these motions. According to the Born-Oppenheimer approximation, changing the mass of the protein does not change the forces acting on the system but alters the frequencies of the protein motions, which in turn can affect the rate constant. Experimental and theoretical studies carried out in this field are presented in this article and discussed in the framework of Transition State Theory.
Theoretical study of spiropyran-merocyanine thermal isomerization.
2004
Abstract Quantum mechanical computations at DFT level were carried out on the processes involved in the thermal reaction SP ⇆ ME, where SP is the nitro-substituted spirobenzopyran (1 ′ ,3 ′ -dihydro-1 ′ ,3 ′ ,3 ′ -trimethyl-6-nitro-spiro[2H-1-benzopyran-2,2 ′ - [2H]indole]) in the closed form and ME is the corresponding open form. A detailed theoretical description of the overall reaction is reported along with the thermodynamic parameters for all intermediates and transition states. The obtained activation energy value is in agreement with the available experimental data in solution.
Ziegler–Natta catalysts based on vanadium halides: a DFT study
2003
Abstract Ziegler–Natta ethylene insertion into the carbon–metal bond for a number of fragments containing vanadium on different oxidation states as well as the halogen ligands has been studied by means of DFT. It is shown that the complexation and insertion energies are strongly influenced by the charge on the transition metal atom and, to some extent, by the electronegativity of the halogen atom. Complexation energy varies in the range −129 to −159 kJ/mol for charged species and −64 to −77 kJ/mol for neutral ones. Insertion energy follows a similar pattern and ranges from −28 to −62 and −82 to −100 kJ/mol, respectively. The calculated values are compared with the experimental results and d…
ChemInform Abstract: LOCATION OF TRANSITION STATES AND STABLE INTERMEDIATES BY MINIMAX/MINIMI OPTIMIZATION OF SYNCHRONOUS TRANSIT PATHWAYS
1983
The MINIMAX/MINIMI concept for the location of transition states and/or stable intermediates of chemical reactions is introduced, based on the synchronous transit method. According to this strategy, minimization of quadratic synchronous transit path maxima or minima is achieved by constrained exhaustive optimization of internal coordinates. The method and its efficiency are demonstrated for two-dimensional model surfaces as well as for thermally allowed electrocyclic interconversions of cyclopropyl-/allyl-cation and cyclobutene-/butadiene (gauche) within the framework of MNDO-SCF calculations. Thus, in both cases a direct comparison with the exact solution determined by minimization of the …
Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1
2017
Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics. These constructs were found to be potent CARM1 inhibitors and also formed stable complexes with the enzyme. High-resolution crystal structures of CARM1 in complex with these compounds co…
Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study
2019
AbstractCyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results show that the base-assisted mechanism is preferred over the substrat…
Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects
2013
Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from dif…
On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study
2012
The mechanism of the intramolecular Diels#8211;Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition stat…