Eric Henon

KiSThelP: A program to predict thermodynamic properties and rate constants from quantum chemistry results†

Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas‐phase molecular thermodynamic properties (offering hindered rotor treatment), thermal equilibrium constants, transition state theory rate coefficients (transition state theory (TST), variational transition state theory (VTST)) including one‐dimensional (1D) tunnelling effects (Wigner, and Eckart) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate constants, for elementary reactions with well‐defined barriers. KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front‐end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the graphical user interface and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D plots, exporting images and data files. These features make this program also well‐suited to support and enhance students learning and can serve as a very attractive courseware, taking the teaching content directly from results in molecular and kinetic modelling.

The stimulating adventure of KRN 7000

Associated with the CD1d protein, KRN 7000, a potent synthetic α-galactosylceramide, is known to activate the invariant NKT immune cells. This stimulation then leads to the production of different cytokines modulating a T(H)1/T(H)2 immune response balance involved in protection against several pathologies such as autoimmune diseases and cancers. Various efforts have been made toward the synthesis of simple and more functionalized analogues in order to selectively induce T(H)1 or T(H)2-type cytokine production. Since the discovery of KRN 7000, structure-activity relationships, crystallographic and modelling studies have pointed to the potential of several GalCer analogues in term of selective bioactivity, and have highlighted interesting elements in order to better understand the recognition and activation mechanisms of immune iNKT cells. By presenting an up-to-date library of analogues, collecting recent breakthroughs done in crystallography and molecular modelling, and relating them to the available biological results, we hope that this review will highlight and help the scientific community in their KRN research.

Tunneling in the reaction of acetone with OH

Based on recent detailed quantum mechanical computations of the mechanism of the title reaction and, this paper presents kinetics analysis of the overall rate constant and its temperature dependence, for which ample experimental data are available for comparison. The analysis confirms that the principal channel is the formation of acetonyl radical + H(2)O, while the channel leading to acetic acid is of negligible importance. It is shown that the unusual temperature dependence of the overall rate constant, as observed experimentally, is well accounted for by standard RRKM treatment that includes tunneling. This treatment is applied at the microcanonical level, with chemically activated distribution of entrance species, i.e. using a stationary rather than a thermal distribution that incorporates collisional energy transfer and competition between the redissociation and exit channel. A similar procedure is applied to the isotopic reaction acetone-d6 + OH with equally satisfying results, so that the experimental temperature dependence of the KIE (kinetic isotope effect) is perfectly reproduced. This very good agreement between calculation and experiment is obtained without any fitting to experimental values and without any adjustment of the parameters of calculation.

Features of the potential energy surface for the reaction of OH radical with acetone

The mechanism of the reaction of OH with acetone has been studied by quantum chemical computations. 21 stationary points (among them reactant complexes, reaction transition states, intermediate complexes and product complexes) have been characterised on the potential energy surface of the reaction. The MP2 method with 6-31G(d,p) basis set was employed for geometry optimisation. Electronic energies were obtained at the CCSD(T)/6-311G(d,p) level of theory. Hydrogen abstraction was found to occur through two complex mechanisms; no transition state for direct abstraction could be located. Minimum energy path analyses have revealed two distinct pathways which lead to CH3 (+CH3COOH) formation. One of them sets out the abstraction channel and proceeds via intermolecular complexes and the other one involves addition of OH to the carbonyl double bond and subsequent decomposition of the adduct hydroxy-alkoxy radical. The rate limiting steps involve large energy barriers and, consequently, these pathways do not explain the high methyl yields observed experimentally at and below room temperature. Characteristic for the reaction of OH with acetone is the existence of numerous hydrogen-bridged complexes on the potential energy surface that are stabilised by as much as 3.2–26.6 kJ mol−1 binding energy. Some properties of these complexes and their possible role in the molecular mechanism of the reaction are discussed.

Theoretical study of photochemical processes involving singlet excited states of formaldehyde carbonyl oxide in the atmosphere

Abstract We report a theoretical study on the photochemical reactivity of formaldehyde carbonyl oxide H2COO, a compound of atmospheric relevance. Calculations are carried out at the CASSCF and CASPT2 levels with extended basis sets. We are particularly interested in three important unimolecular processes: isomerization into dioxirane, syn/anti isomerization and dissociation into formaldehyde and atomic oxygen. The results suggest that the photochemical reactivity of H2COO in the troposphere is strongly linked to the properties of the second singlet excited state a 1 A ′ ( π → π * ) because it is energetically accessible from the ground state and has a large oscillator strength. Construction of potential energy curves reveals that photochemical isomerization into dioxirane is very unlikely to occur whereas syn/anti isomerization should be favorable. Besides, in the a1A′ state, carbonyl oxide spontaneously dissociates into formaldehyde H2CO and atomic oxygen O ( 1 D ) in close relationship to the excited 1 B 2 state of the isoelectronic ozone molecule occurring in Hartley’s band.

Theoretical study of the reaction OH + acetone: a possible kinetic effect of the presence of water?

The effect of water on the molecular mechanism of the reaction of the OH radical with acetone in the homogeneous gas-phase has been studied by quantum chemical computations. The three-molecular reaction system of OH + acetone + H2O has been characterised using molecular parameters, electronic energies and Gibbs free energies computed for the stationary points of the potential energy surface. The MP2 method with a 6-31G(d,p) basis set was employed for geometry optimisation. The electronic energies were obtained at the MP4 and the CCSD(T) level of theory using the 6-311G(d,p) basis set. We have found that the presence of a water molecule changes significantly both the energy profile and free energy profiles of the reaction. A “water-assisted” reaction mechanism has been established in which both the H-abstraction channel and the CO-addition channel occur via intermolecular complexes and transition state structures that involve the water molecule. The activation free energy for the out-of-plane abstraction channel at low temperatures has been found to be significantly smaller than that for the “water-free” system indicating a possible catalytic rate enhancement effect. Abstraction is the predominant reaction route also for the water-assisted reaction as shown by the much larger activation free energy computed for the addition channel. In order to estimate atmospheric concentrations of some intermolecular complexes, we have validated our employed level of theory by computing the equilibrium constant of HO2 + H2O ⇄ HO2⋯H2O at three temperatures and compared them to the values derived from experiments available in the literature. Then, using our theoretical results, we have estimated the tropospheric concentration of OH⋯acetone⋯H2O complexes to be very small, but they are probably detectable under laboratory conditions.

Degradation of three oxygenated alkoxy radicals of atmospheric interest: HOCH2O˙, CH3OCH2O˙, CH3OCH2OCH2O˙. RRKM theoretical study of the β-C–H bond scission and the 1,6-isomerisation kinetics

A detailed theoretical study on the pressure and temperature dependence of the rate constants k1, k2, k3 for the thermal β-C–H dissociation of the three radicals: HOCH2O˙, CH3OCH2O˙, CH3OCH2OCH2O˙ is presented. This investigation is extended to the rate constant k4 for the 1,6-H-shift isomerisation of CH3OCH2OCH2O˙. High-level ab initio computations (CCSD(T)//MP2) have been performed and combined with RRKM theory to obtain rate constants. The β-C–H scission pathway is predicted to occur with an activation energy of 10–13 kcal mol−1. Estimation of the competition between the β-C–H and β-C–O decompositions, the isomerisation process, and the reaction with oxygen has been done. At 760 Torr and 298 K, k1, k2, k3, k4 are 4.4 × 104 s−1, 5.2 × 104 s−1, 4.2 × 103 s−1 and 5.6 × 103 s−1 respectively. An interesting result is that the isomerisation through a seven-membered transition state may compete with the H-atom elimination from the CH3OCH2OCH2O˙ radical.

Molecular properties affecting the adsorption coefficient of pesticides from various chemical families

Forty pesticides were selected in function of their chemical families and their physico-chemical properties to represent a wide range of pesticide properties. Adsorption of these pesticides was studied on two soils by batch experiments. The two soils differed largely in organic matter and calcite contents. Distribution coefficient Kd was determined for each pesticide on the two soils. Adsorption was higher for the soil having the highest organic matter content and the lowest calcite content. In order to identify pesticide properties governing retention, eight molecular descriptors were determined from three-dimensional (3D) structure of molecules. Class-specific quantitative structure properties relationship (QSPR) soil adsorption models using one and two parameters were developed from experimental Kd. Three properties seemed to influence most retention of pesticides: hydrophobicity, solubility, and polarisability. Models combining these properties were suggested and discussed.

Use of the NEO strategy (Nucleophilic addition/Epoxide Opening) for the synthesis of a new C-galactoside ester analogue of KRN 7000

Our goal in the search for potentially bioactive analogues of KRN 7000 was to design an easy synthetic approach to a library of analogues using a strategy recently developed in our laboratory based on a Nucleophilic addition followed by an Epoxide Opening (the NEO strategy). Through the use of a common pivotal structure, a new C-galactoside ester analogue (23) was synthesized which showed an encouraging T(H)2 biased response during preliminary biological tests.

Molecular properties affecting the adsorption coefficient of phenylurea herbicides

The adsorption of 12 pesticides of the phenylurea family was studied by batch experiments in order to determine the adsorption coefficient, Kd. The study was conducted in two soils chosen for their differences in organic matter and calcite contents. Kd pesticide adsorption coefficients were higher for soil S1 than for soil S2 due to the presence of a higher organic matter content and a lower calcite content in soil S1. To identify pesticide properties governing retention, 18 molecular descriptors were considered. Class-specific quantitative structure–property relationship (QSPR) soil sorption models using one, two, and three descriptors were developed from our experimental data using linear regressions. One of the aims of this work was to check whether QSPR models that did not include literature values of Kow were able to predict Kd coefficients in satisfactory agreement with our experimental data. The influence of the level of theory in determining Kow and polarisability predictors on the predictive performance of the model was also examined by comparing quantum chemistry and empirical (QikProp) approaches. The one-descriptor model using “quantum” polarisability α was found to perform almost as well as or better than the other models.