Search results for "Transition state"
showing 10 items of 85 documents
Highly regio- and stereoselective iodocyclization of chiral 3-alkoxycarbonyl-4-propenyl-2,2-dimethyl-1,3-oxazolidines: a computational investigation
1999
The iodocyclization of allylic carbamates 3a and 3b proceeded with high regio- and stereoselection to give 2-oxobicyclo[4.3.0]nonane 5a as the major product. Both the regio- and diastereoselection of the reaction were investigated with the help of molecular mechanics and quantomechanical calculations. The energetic difference between the competing transition states TS-5a and TS-5b is in good agreement with the experimental results and from the calculated transition structures it appears that steric factors direct the discrimination.
Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale DFT/MM Methods
2020
<p>We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions stablished by a peptidic substrate in the active site and then we have explored the free energy landscape associated to the acylation and de-acylation steps of the proteolysis reaction, characterizing the transition states of the process. Our mechanistic proposals can explain most of the experimental observations made on the highly similar ortholog protease of SARS-CoV. We point out to some key interactions that may facilitate the acylation process and thus can be crucial in the …
Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods
2020
We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions established by a peptidic substrate in the active site, and then we have explored the free energy landscape associated with the acylation and deacylation steps of the proteolysis reaction, characterizing the transition states of the process. Our mechanistic proposals can explain most of the experimental observations made on the highly similar ortholog protease of SARS-CoV. We point to some key interactions that may facilitate the acylation process and thus can be crucial in the design of …
The 1,3-dipolar cycloaddition of 1H-pyridinium-3-olate and 1-methylpyridinium-3-olate with methyl acrylate: a density functional theory study
2010
The 1,3-dipolar cycloaddition reaction of 1-substituted pyridinium 3-olates with methyl acrylate is studied using density functional theory (DFT) method at the B3LYP/6-31G(d) level. The molecular mechanisms of the possible stereo- and regio-chemical pathways are characterized and explored. Solvent effects are also evaluated by the polarizable continuum model (PCM). Analysis of the results shows that there are relevant differences in the reaction pathways between the gas phase and with solvent. Only results in solvent phase are in accord with literature experimental results where 6-substituted 8-azabicyclo[3.2.1]oct-3-en-2-ones are formed preferentially. These polar cycloaddition reactions t…
A Three-State Model for the Photophysics of Adenine
2006
An ab initio theoretical study at the CASPT2 level is reported on minimum energy reaction paths, state minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of two tautomers of adenine: 9H- and 7H-adenine. The obtained results led to a complete interpretation of the photophysics of adenine and derivatives, both under jet-cooled conditions and in solution, within a three-state model. The ultrafast subpicosecond fluorescence decay measured in adenine is attributed to the low-lying conical intersection (gs/pipi* La)(CI), reached from the initially populated 1(pipi* La) state along a path which is found to be barrierless only in 9H-adenine…
Ab initio study on the mechanism of the atmospheric reaction OH + O3--HO2 + O2.
2003
The atmospheric reaction (1) OH + O 3 → + O 2 was investigated theoretically by using MP2, QCISD, QCISD(T), and CCSD(T) methods with various basis sets. At the highest level of theory, namely, QCISD, the reaction is direct, with only one transition state between reactants and products. However, at the MP2 level, the reaction proceeds through a two-step mechanism and shows two transition states, TS1 and TS2, separated by an intermediate, Int. The different methodologies employed in this paper consistently predict the barrier height of reaction (1) to be within the range 2.16 - 5.11 kcal mol -1 , somewhat higher than the experimental value of 2.0 kcal mol -1 .
A DFT Study of Inter- and Intramolecular Aryne Ene Reactions
2015
The molecular mechanisms of inter- and intramolecular aryne-ene reactions have been theoretically studied by DFT methods at the MPWB1K/6-311G(d,p) level. These reactions proceed through a one-step mechanism via nearly asynchronous transition states (TSs), in which the C–C single bond formation is slightly more advanced than the hydrogen transfer process. These ene reactions show very low activation enthalpies (<1 kcal/mol) and are strongly exothermic by more than 73 kcal/mol. An electron localisation function (ELF) topological analysis of the changes of electron density during these ene reactions indicates that the bonding changes are nonconcerted. ELF topological analysis of the electron d…
Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.
2013
We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is employed to find the minimum free energy paths on a multidimensional free energy surface defined in terms of interatomic distances, which is a convenient selection to study bond forming/breaking processes. Once the paths have been determined, a reaction coordinate is defined as a measure of the advance of the system along these paths. This reaction coordinate can be then used to trace the reaction Potential of Mean Force from which the activation free energy can be obtained. Th…
A theoretical study on the decomposition mechanism of β-propiolactone and β-butyrolactone
1998
Abstract The reaction mechanism associated with the decomposition of β-propiolactone and β-butyrolactone in the gas phase to form carbon dioxide and ethylene or propene, respectively, has been theoretically characterized by using analytical gradients at the B3LYP/6-31G**, B3LYP/6-31++G**, MP2/6-31G** and MP2/6-31++G** calculation levels, as well as by single point calculations at QCISD(T)/6-31++G**//MP2/6-31++G**. A detailed analysis of the results points out that the reaction pathway can be described as an asynchronous concerted process. The geometrical parameters and the components of the transition vector are weakly dependent on the computational method. By applying transition state theo…
An Ab Initio Study on the Mechanism of the Atmospheric Reaction NH2+O3→H2NO+O2
2003
The atmospheric reaction NH 2 +0 3 →H 2 NO+O 2 has been investigated theoretically by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At the MP2 level or theory, the hypersurface of the potential energy (HPES) shows a two step reaction mechanism. Therefore, the mechanism proceeds along two transition states (TS1 and TS2), seperated by an intermediate disignated as Int. However, when the single-reference higler correlated QCISD and the multiconfigurational CASSCF methodologies have been employed, the minimum structure Int and TS2 are not found on the HPES, which thus confirms a direct reaction mechanism. Single-reference high correlated and multiconfi…