Search results for "MOLECULE"
showing 10 items of 5162 documents
On the N1-H and N3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study.
2015
The dissociative electron-attachment (DEA) phenomena at the N1-H and N3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence-bound π(-) and two dissociative σ(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the π(-) and σ(-) are established as the structures which activate the DEA processes. The N1-H and N3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of …
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 …
Bond Dissociation Energies for Diatomic Molecules Containing 3d Transition Metals: Benchmark Scalar-Relativistic Coupled-Cluster Calculations for 20 …
2017
Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the 20 diatomic molecules containing 3d transition metals in the 3dMLBE20 database ( J. Chem. Theory Comput. 2015 , 11 , 2036 ) are reported. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of 16 molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol. The discrepancies between theory and experiment remain substantial (more than 20 kJ/mol) for VH, CrH, CoH, and FeH. To explore the source of the latter discrepancies, the …
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 …
MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor
2019
Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of thre…
Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA
2018
Multiscale molecular dynamics simulations reveal out-of-plane distortions that favour DNA photostability. A novel photostability mechanism involving four proton transfers and triggered by a nearby Na+ ion is also unveiled.
Infrared Spectroscopy of Disilicon-Carbide, Si2C: The ν3 Fundamental Band
2019
The ν3 antisymmetric stretching mode of disilicon-carbide, Si2C, was studied using a narrow line width infrared quantum cascade laser spectrometer operating at 8.3 μm. The Si2C molecules were produ...
A solvent-directed stereoselective and electrocatalytic synthesis of diisoeugenol.
2018
A stereoselective and electrocatalytic coupling reaction of isoeugenol has been reported for the first time in a 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)/boron-doped diamond (BDD) electrode system. This particular C-C bond formation and diastereoselectivity is driven by a solvate interaction between the radical species and another isoeugenol molecule. Due to an electrocatalytic cycle, only understoichiometric amounts of charge are necessary. Since electric current is directly employed as the oxidant, the reaction is metal and reagent-free. In addition, the electrolysis can be conducted in a very simple undivided beaker-type cell under constant current conditions. Therefore, the protocol is …
Gold/Isophorone Interaction Driven by Keto/Enol Tautomerization
2016
The binding behavior of isophorone (C9H14O) to Au adatoms and clusters deposited on MgO/Ag(001) thin films is investigated by scanning tunneling microscopy (STM) and density functional theory (DFT). The STM data reveal the formation of various metal/organic complexes, ranging from Au1/isophorone pairs to larger Au aggregates with molecules bound to their perimeter. DFT calculations find the energetically preferred keto-isophorone to be unreactive toward gold, while the enol-tautomer readily binds to Au monomers and clusters. The interaction is governed by electrostatic forces between the hydroxyl group of the enol and negative excess charges residing on the ad-gold. The activation barrier b…
Elucidating the Influence of the Activation Energy on Reaction Rates by Simulations Based on a Simple Particle Model
2020
An application for visualizing the dynamic properties of an equimolar binary mixture of isotropic reactive particles is presented. By introducing a user selectable choice for the activation energy, the application is useful to demonstrate qualitatively that the reaction rate depends on the above choice and on temperature. The application is based on a 2D realistic dynamic model where atoms move because of their thermal energies and the trajectories are determined by solving numerically Newton’s laws according to a Molecular Dynamics (MD) scheme. Collisions are monitored as time progresses, and every time the collision energy is larger than the selected activation energy, a reactive event oc…