Search results for "40"
showing 10 items of 17345 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 …
A quantum dynamics study of the benzopyran ring opening guided by laser pulses
2014
Abstract The ring-opening photoisomerization of benzopyran, which occurs via a photochemical route involving a conical intersection, has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method (MCTDH). We introduce a mechanistic strategy to control the conversion of benzopyran to merocyanine with laser pulses. We use a six-dimensional model developed in a previous work for the potential energy surfaces (PES) based on an extension of the vibronic-coupling Hamiltonian model (diabatization method by ansatz), which depends on the most active degrees of freedom. The main objective of these quantum dynamics simulations is to provide a set of str…
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.
Hexacarbonyls of Mo, W, and Sg: Metal–CO Bonding Revisited
2017
Calculations of the first bond dissociation energies (FBDEs) and other molecular properties of M(CO)6, where M = Mo, W, and Sg, have been performed using a variety of nonrelativistic and relativistic methods, such as ZORA-DFT, X2c+AMFI-CCSD(T), and Dirac–Coulomb density functional theory. The aim of the study is to assist experiments on the measurements of the FBDE of Sg(CO)6. We have found that, different from the results published earlier, the metal–CO bond in Sg(CO)6 should be weaker than that in W(CO)6. A comparison of the relativistic and nonrelativistic FBDE values, as well as molecular orbital and vibrational frequency analyses within both the nonrelativistic and relativistic approac…
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…
Full-dimensional control of the radiationless decay in pyrazine using the dynamic Stark effect
2014
We present a full quantum-mechanical study of the laser control of the radiationless decay between the B3u(nπ(*)) and B2u(ππ(*)) states of pyrazine using the dynamic Stark effect. In contrast to our previous study [Sala et al., J. Chem. Phys. 140, 194309 (2014)], where a four-dimensional model was used, all the 24 degrees of freedom are now included in order to test the robustness of the strategy of control. Using a vibronic coupling Hamiltonian model in a diabatic representation, the multi-layer version of the multi-configuration time-dependent Hartree method is exploited to propagate the corresponding wave packets. We still observe a trapping of the wavepacket on the B2u(ππ(*)) potential …
Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness.
2017
We present a detailed study of the parameter dependence of force probe molecular dynamics (FPMD) simulations. Using a well studied calix[4]arene catenane dimer as a model system, we systematically vary the pulling velocity and the stiffness of the applied external potential. This allows us to investigate how the results of pulling simulations operating in the constant velocity mode (force-ramp mode) depend on the details of the simulation setup. The system studied has the further advantage of showing reversible rebinding meaning that we can monitor the opening and the rebinding transition. Many models designed to extract kinetic information from rupture force distributions work in the limit…
Introduction to the special issue on molecular spectroscopy, atmospheric composition and climate change
2018
International audience
Introducing Memory in Coarse-Grained Molecular Simulations
2021
[Image: see text] Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori–Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In…
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…