Search results for "action"
showing 10 items of 25852 documents
Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase
2017
Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we study the mechanism of the hPNP enzyme and the dynamic effects by means of the calculation of the recrossing transmission coefficient. A free energy surface (FES), as a function of both a chemical and an environmental coordinate, is obtained to show the role of the environment on the chemical reaction. Analysis of reactive and nonreactive trajectories allows us …
Quantum dynamics of 16O in collision with ortho- and para-17O17O
2017
Abstract We report full quantum dynamical observables, such as integral and differential cross sections and rate constants, for the 16 O + 17 O 17 O reactive collision process. We particularly emphasize the effect coming from the nonzero nuclear spin of 17 O, leading to two nuclear spin isomers of 34 O 2 , ortho- and para- 34 O 2 which can be studied independently and behave differently. A comparison with the 16 O + 18 O 18 O collision is given. We find that processes involving 17 O 17 O are always faster than with 18 O 18 O.
Adaptive Finite Temperature String Method in Collective Variables.
2017
Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane…
Introduction to the special issue on molecular spectroscopy, atmospheric composition and climate change
2018
International audience
Unravelling the kinetics and molecular mechanism of the degenerate Cope rearrangement of bullvalene
2020
The kinetics and molecular mechanism of the gas phase degenerate Cope rearrangement (DCR) of bullvalene have been investigated by applying quantum mechanical calculations. Highly accurate energies (CBS-QB3 and CBS-APNO) and RRKM calculations were employed to study the kinetics and ‘fall-off’ behavior. It was found that the DCR of bullvalene (C3v) occurs through a bishomoaromatic transition structure (C2v) with an energy barrier of ∼49 kJ mol−1. The calculated activation energy and enthalpy were in good agreement with the available values in the literature, but lower than those of common Cope rearrangement; this result is related to the high stabilization energy due to the interaction of the…
High excitations in coupled-cluster series: vibrational energy levels of ammonia
2004
The ammonia molecule containing large amplitude inversion motion is a revealing system in examining high-order correlation effects on potential energy surfaces. Correlation contributions to the equilibrium and saddle point geometries, inversion barrier height and vibrational energy levels, including inversion splittings, have been investigated. A six-dimensional Taylor-type series expansion of the Born–Oppenheimer potential energy surface, which is scaled to different levels of theory, is used to determine vibrational energy levels and inversion splittings variationally. The electronic energies are calculated by coupled-cluster methods, combining explicitly correlated R12 theory (which incl…
Gas-Phase Synthesis of the Elusive Trisilicontetrahydride Species (Si3H4)
2016
The bimolecular gas-phase reaction of ground-state atomic silicon (Si; 3P) with disilane (Si2H6; 1A1g) was explored under single-collision conditions in a crossed molecular beam machine at a collision energy of 21 kJ mol–1. Combined with electronic structure calculations, the results suggest the formation of Si3H4 isomer(s) along with molecular hydrogen via indirect scattering dynamics through Si3H6 collision complex(es) and intersystem crossing from the triplet to the singlet surface. The nonadiabatic reaction dynamics can synthesize the energetically accessible singlet Si3H4 isomers in overall exoergic reaction(s) (−93 ± 21 kJ mol–1). All reasonable reaction products are either cyclic or …
Carbonyl compounds of Tc, Re, and Bh: Electronic structure, bonding, and volatility.
2018
Calculations of molecular properties of M(CO)5 and MH(CO)5, where M = Tc, Re, and Bh, and of the products of their decomposition, M(CO)4 and MH(CO)4, were performed using density functional theory and coupled-cluster methods implemented in the relativistic program suits such as ADF, DIRAC, and ReSpect. The calculated first M—CO bond dissociation energies (FBDEs) of Bh(CO)5 and BhH(CO)5 turned out to be significantly weaker than those of the corresponding Re homologs. The reason for that is the relativistic destabilization and expansion of the 6d AOs, responsible for weaker σ-forth and π-back donations in the Bh compounds. The relativistic FBDEs of M(CO)5 have, therefore, a Λ-shape behavior …
Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study
2019
The adsorption of gas-phase pyruvic acid (CH3COCOOH) on hydroxylated silica particles has been investigated at 296 K using transmission Fourier transform infrared (FTIR) spectroscopy and theoretical simulations. Under dry conditions (<1% relative humidity, RH), both the trans-cis (Tc) and trans-trans (Tt) pyruvic acid conformers are observed on the surface as well as the (hydrogen bonded) pyruvic acid dimer. The detailed surface interactions were further understood through ab initio molecular dynamics simulations. Under higher relative humidity conditions (above 10% RH), adsorbed water competes for surface adsorption sites. Adsorbed water is also observed to change the relative populations …
Quantum Dynamics of the 17O + 32O2 Collision Process
2016
We report full quantum integral and differential cross sections and rate constants for the 17O + 32O2 reactive process. This constitutes the first quantum scattering study of the 17O16O16O system. We emphasize the comparison with the 18O + 32O2 collision in close connection to the mass-independent fractionation (hereafter referred to as MIF) puzzle for ozone in atmospheric chemistry. We find similar general trends in the cross sections and rate constants for both rare isotopes, but we note some singular behaviors peculiar to the use of 17O isotope, particularly at the lowest collision energies.