R-matrix calculation of differential cross sections for low-energy electron collisions with ground and electronically excited state O2 molecules

Differential cross sections for electron collisions with the O$_2$ molecule in its ground ${X}^{3}\Sigma_g^-$ state, as well as excited ${a}^{1}\Delta_g$ and ${b}^{1}\Sigma_g^+$ states are calculated. As previously, the fixed-bond R-matrix method based on state-averaged complete active space SCF orbitals is employed. In additions to elastic scattering of electron with the O$_2$ ${X}^{3}\Sigma_g^-$, ${a}^{1}\Delta_g$ and ${b}^{1}\Sigma_g^+$ states, electron impact excitation from the ${X}^{3}\Sigma_g^-$ state to the ${a}^{1}\Delta_g$ and ${b}^{1}\Sigma_g^+$ states as well as '6 eV states' of ${c}^{1}\Sigma_u^{-}$, ${A'}^{3}\Delta_u$ and ${A}^{3}\Sigma_u^{+}$ states is studied. Differential cross sections for excitation to the '6 eV states' have not been calculated previously. Electron impact excitation to the ${b}^{1}\Sigma_g^+$ state from the metastable ${a}^{1}\Delta_g$ state is also studied. For electron impact excitation from the O$_2$ ${X}^{3}\Sigma_g^-$ state to the ${b}^{1}\Sigma_g^+$ state, our results agree better with the experimental measurements than previous theoretical calculations. Our cross sections show angular behaviour similar to the experimental ones for transitions from the ${X}^{3}\Sigma_g^-$ state to the '6 eV states', although the calculated cross sections are up to a factor two larger at large scattering angles. For the excitation from the ${a}^{1}\Delta_g$ state to the ${b}^{1}\Sigma_g^+$ state, our results marginally agree with the experimental data except for the forward scattering direction

R-matrix calculation of electron collisions with electronically excited O2 molecules

Low-energy electron collisions with O$_2$ molecules are studied using the fixed-bond R-matrix method. In addition to the O$_2$ ${X}^3\Sigma_{g}^-$ ground state, integrated cross sections are calculated for elecron collisions with the ${a}^1\Delta_{g}$ and ${b}^1\Sigma_{g}^+$ excited states of O$_2$ molecules. 13 target electronic states of O$_2$ are included in the model within a valence configuration interaction representations of the target states. Elastic cross sections for the ${a}^1\Delta_{g}$ and ${b}^1\Sigma_{g}^+$ excited states are similar to the cross sections for the ${X}^3\Sigma_{g}^-$ ground state. As in case of excitation from the ${X}^3\Sigma_{g}^-$ state, the O$_2^-$ $\Pi_u$ resonance makes the dominant contribution to excitation cross sections from the ${a}^1\Delta_{g}$ and ${b}^1\Sigma_{g}^+$ states. The magnitude of excitation cross sections from the ${a}^1\Delta_{g}$ state to the ${b}^1\Sigma_{g}^+$ state is about 10 time larger than the corresponding cross sections from the ${X}^3\Sigma_{g}^-$ to the ${b}^1\Sigma_{g}^+$ state. For this ${a}^1\Delta_{g}$ $\to$ ${b}^1\Sigma_{g}^+$ transition, our cross section at 4.5 eV agrees well with the available experimental value. These results should be important for models of plasma discharge chemistry which often requires cross sections between the excited electronic states of O$_2$.Comment: 26 pages, 10 figure

Palladium-catalyzed regioselective and stereo-invertive ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: Experimental and computational studies

A palladium catalyzed regioselective borylative ring opening reaction of 2-arylaziridines to give β-amino-β-arylethylborates was developed. The reaction reported herein represents the first example of ring-opening borylation of non-vinylic aziridines and direct borylative C(sp3)-N bond cleavage of neutral organic substrates. NMR studies and density functional theory (DFT) calculations suggested that the active intermediate for the reaction is a PdL2 complex [L = P(t-Bu)2Me]. The multi-component artificial force-induced reaction method (MC-AFIR) located the transition states for the regioselectivity-determining aziridine ring opening that proceeds in an SN2 fashion, and explained the selectivity of the reaction. The full catalytic cycle consists of a selectivity-determining aziridine ring opening (oxidative addition), a proton transfer, phosphine ligand dissociation from the catalyst, boron-boron bond cleavage, and reductive elimination. Water is important to the drive the transmetalation step. The calculated overall mechanism and selectivity are consistent with the experimental results

Ab Initio Study of the Molecular and Electronic Structure of CoCH2+ and of the Reaction Mechanism of CoCH2+ + H2

Both CASSCF and MR-SDCI-CASSCF methods have been used with two different effective core potentials to investigate the molecular and electronic structures of CoCH2+, as well as the mechanism for the reaction CoCH2+ + H2. Four electronic states of CoCH2+ are very low lying: the ground state is a nearly degenerate pair (3A2 and 3A1), and the 3B1 and 3B2 states are only 4-8 kcal/mol higher in energy. The binding energy of C O C H ~ + ( ~ Are~la)t,iv e to that of C ~ + ( ~ F , s l d+~ C)H 2(3B1), is estimated to be 70-80 kcal/mol. A similar hydrogenolysis reaction mechanism holds for the 3A2 and 3A1 states of the CoCH2+ + H2 reactants: In the first step, the reactants yield an ion-molecule complex, (H2)CoCH2+, stabilized by 8-9 kcal/mol. Subsequently, the H-H bond is activated, leading to a four-center transition state with an energy barrier of about 31-34 kcal/mol. An intermediate complex, HCoCH3+, is predicted to be a minimum at the CASSCF level, but MR-SDCI-CASSCF single-point calculations suggest that this minimum disappears at the higher level of theory. Following H-H bond cleavage, a CoCH4+ ion-molecule complex is formed, with a stabilization energy of 19-22 kcal/mol. The CoCH2+ hydrogenolysis reaction is predicted to be exothermic by 20-30 kcal/mol. The channels leading to formation of CoH+ + CH3 and CoCH3+ + H are endothermic by about 5-1 2 kcal/mol. The reverse reaction Co+ + CH4 may give only one product, the ion-molecule complex CoCH4+ at moderate temperatures. An increase in the available kinetic energy would make it possible to form dissociation products: CoH+ + CH3 and CoCH3+ + H. Although the channel leading to CoCH2+ + H2 is thermodynamically more favorable, a large barrier prevents it from taking place. Hay-Wadt and Stevens-Krauss-Basch-Jasien pseudopotentials give qualitatively the same results

An unexpected Ireland–Claisen rearrangement cascade during the synthesis of the tricyclic core of Curcusone C: Mechanistic elucidation by trial-and-error and automatic artificial force-induced reaction (AFIR) computations

In the course of a total synthesis effort directed toward the natural product curcusone C, the Stoltz group discovered an unexpected thermal rearrangement of a divinylcyclopropane to the product of a formal Cope/1,3-sigmatropic shift sequence. Since the involvement of a thermally forbidden 1,3-shift seemed unlikely, theoretical studies involving two approaches, the “trial-and-error” testing of various conceivable mechanisms (Houk group) and an “automatic” approach using the Maeda–Morokuma AFIR method (Morokuma group) were applied to explore the mechanism. Eventually, both approaches converged on a cascade mechanism shown to have some partial literature precedent: Cope rearrangement/1,5-sigmatropic silyl shift/Claisen rearrangement/retro-Claisen rearrangement/1,5-sigmatropic silyl shift, comprising a quintet of five sequential thermally allowed pericyclic rearrangements

Crystalline Ni3C as both carbon source and catalyst for graphene nucleation: A QM/MD study

Graphene nucleation from crystalline Ni3C has been investigated using quantum chemical molecular dynamics (QM/MD) simulations based on the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. It was observed that the lattice of Ni3C was quickly relaxed upon thermal annealing at high temperature, resulting in an amorphous Ni3C catalyst structure. With the aid of the mobile nickel atoms, inner layer carbon atoms precipitated rapidly out of the surface and then formed polyyne chains and Y-junctions. The frequent sinusoidal-like vibration of the branched carbon configurations led to the formation of nascent graphene precursors. In light of the rapid decomposition of the crystalline Ni3C, it is proposed that the crystalline Ni3C is unlikely to be a reaction intermediate in the CVD-growth of graphene at high temperatures. However, results present here indicate that Ni3C films can be employed as precursors in the synthesis of graphene with exciting possibility

Mapping behavioral specifications to model parameters in synthetic biology

With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology