Direct versus resonances mediated F+OH collisions on a new 3A″ potential energy surface

DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*

Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O₂ at room temperature because O₂ is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.

Low temperature reaction dynamics for CH3OH + OH collisions on a new full dimensional potential energy surface

Is the rise of the rate constant measured in laval expansion experiments of OH with organic molecules at low temperatures due to the reaction between the reactants or due to the formation of complexes with the buffer gas? This question has importance for understanding the evolution of prebiotic molecules observed in different astrophysical objects. Among these molecules methanol is one of the most widely observed, and its reaction with OH has been studied by several groups showing a fast increase in the rate constant under 100 K. Transition state theory doesn't reproduce this behavior and here dynamical calculations are performed on a new full dimensional potential energy surface developed for this purpose. The calculated classical reactive cross sections show an increase at low collision energies due to a complex forming mechanism. However, the calculated rate constant at temperatures below 100 K remains lower than the observed one. Quantum effects are likely responsible for the measured behavior at low temperatures.

Full dimensional potential energy surface and low temperature dynamics of the H2CO + OH → HCO + H2O reaction

A new method is proposed to analytically represent the potential energy surface of reactions involving polyatomic molecules capable of accurately describing long-range interactions and saddle points, needed to describe low-temperature collisions. It is based on two terms, a reactive force field term and a many-body term. The reactive force field term accurately describes the fragments, long-range interactions among them and the saddle points for reactions. The many-body term increases the desired accuracy everywhere else. This method has been applied to the OH + H2CO → H2O + HCO reaction, giving a barrier of 27.4 meV. The simulated classical rate constants with this potential are in good agreement with recent experimental results [Ocaña et al., Astrophys. J., 2017, submitted], showing an important increase at temperatures below 100 K. The reaction mechanism is analyzed in detail here, and explains the observed behavior at low energy by the formation of long-lived collision complexes, with roaming trajectories, with a capture observed for very long impact parameters, >100 a.u., determined by the long-range dipole-dipole interaction.

Is the gas-phase OH+H2CO reaction a source of HCO in interstellar cold dark clouds? A kinetic, dynamic and modelling study

Chemical kinetics of neutral-neutral gas-phase reactions at ultralow temperatures is a fascinating research subject with important implications on the chemistry of complex organic molecules in the interstellar medium (T∼10-100K). Scarce kinetic information is currently available for this kind of reactions at T<200 K. In this work we use the CRESU (Cinétique de Réaction en Ecoulement Supersonique Uniforme, which means Reaction Kinetics in a Uniform Supersonic Flow) technique to measure for the first time the rate coefficients (k) of the gas-phase OH+H2CO reaction between 22 and 107 K. k values greatly increase from 2.1×10-11 cm3 s-1 at 107 K to 1.2×10-10 cm3 s-1 at 22 K. This is also confirmed by quasi-classical trajectories (QCT) at collision energies down to 0.1 meV performed using a new full dimension and ab initio potential energy surface, recently developed which generates highly accurate potential and includes long range dipole-dipole interactions. QCT calculations indicate that at low temperatures HCO is the exclusive product for the OH+H2CO reaction. In order to revisit the chemistry of HCO in cold dense clouds, k is reasonably extrapolated from the experimental results at 10K (2.6×10-10 cm3 s-1). The modeled abundances of HCO are in agreement with the observations in cold dark clouds for an evolving time of 105-106 yrs. The different sources of production of HCO are presented and the uncertainties in the chemical networks discussed. This reaction can be expected to be a competitive process in the chemistry of prestellar cores. The present reaction is shown to account for a few percent of the total HCO production rate. Extensions to photodissociation regions and diffuse clouds environments are also commented.

Quantum and quasi-classical calculations for the S⁺ + H₂(v,j) → SH⁺(v',j') + H reactive collisions

State-to-state cross-sections for the S(+) + H2(v,j) → SH(+)(v',j') + H endothermic reaction are obtained using quantum wave packet (WP) and quasi-classical (QCT) methods for different initial ro-vibrational H2(v,j) over a wide range of translation energies. The final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient that vibrational energy is the most favorable for the reaction, and rotational excitation significantly enhances the reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid to an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2. An interesting resonant behaviour found in WP calculations is also discussed and associated with the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al. for S(+) + HD and S(+) + D2 reactions exhibits a reasonably good agreement with those results.

Quantum mechanical calculations of state-to-state cross sections and rate constants for the F + DCl → Cl + DF reaction

We present accurate state-to-state quantum wave packet calculations of integral cross sections and rate constants for the title reaction. Calculations are carried out on the best available ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged state-to-state reaction cross sections have been calculated for collision energies up to 0.5 eV and different initial rotational and vibrational excitations, DCl(v = 0, j = 0 - 1; v = 1, j = 0). Also, initial-state resolved rate constants of the title reaction have been calculated in a temperature range of 100-400 K. It is found that the initial rotational excitation of the DCl molecule does not enhance reactivity, in contract to the reaction with the isotopologue HCl in which initial rotational excitation produces an important enhancement. These differences between the isotopologue reactions are analyzed in detail and attributed to the presence of resonances for HCl(v = 0, j), absent in the case of DCl(v = 0, j). For vibrational excited DCl(v = 1, j), however, the reaction cross section increases noticeably, what is also explained by another resonance.

Stereodynamics investigation of F + HO → HF + O(1D) on the ground singlet potential energy surface by means of the quasi-classical trajectory method

The stereodynamics calculation of F + HO → HF + O(1D) was carried out using the quasi-classical trajectory method on the 11A′ potential energy surface provided by Gomez-Carrasco et al. (Chem. Phys. Lett. 2007, 435, 188). The effect of the collision energy, isotopic substitution, and different initial ro-vibrational states on the reaction is discussed. It is found that for the initial ground state of HO (v = 0, j = 0), the degree of the forward scattering and the product polarizations remarkably change as the collision energy varies. Isotopic effect leads to the increase of alignment and decrease of orientation of product rotational angular momentum. Moreover, the P(θr) distribution and P(φr) distribution change noticeably by varying the initial vibrational number. The initial vibrational excitation plays a more important role in the enhancement of alignment and orientation distribution of j′ for the title reaction. Although the influence of the initial rotational excitation effect on the aligned and oriented distribution of product is not stronger than that of the initial vibrational excitation effect, the initial rotational excitation makes the alignment of the product rotational angular momentum decrease to some extent. The probabilities show that the reactivity of the title reaction strongly depends on the initial vibrational state.

Wave packet calculations on nonadiabatic effects for the O(3P)+HF(1Σ+) reaction under hyperthermal conditions

We present wave packet calculations of total and state-to-state reaction probabilities and integral cross sections for the nonadiabatic dynamics of the O((3)P)+HF → F((2)P)+OH((2)Π) reaction at hyperthermal collision energies ranging from 1.2 to 2.4 eV. The validity of the centrifugal sudden approximation is discussed for the title reaction and a comprehensive investigation of the influence of nonadiabatic effects on the dynamics of this reactive system at high (hyperthermal) collision energies is presented. In general, nonadiabatic effects are negligible for averaged observables, such as total reaction probabilities and integral cross sections, but they are clearly observed in detailed observables such as rotationally state-resolved reaction probabilities. A critical discussion of nonadiabatic effects on the dynamics of the title reaction is carried out by comparing with the reverse reaction and the characteristics of the adiabatic and diabatic potential energy surfaces involved.

EFFECT OF THE REACTANT ALIGNMENT ON STEREODYNAMICS FOR THE REACTION F + OH

Quasi-classical trajectory (QCT) calculations are performed for the reaction F + OH → HF + O based on the adiabatic potential-energy surface (PES) of the 13A″ triplet state. The reaction probability as a function of incident angle has been presented. The differential cross sections (DCSs), the distribution of angle between k and j′, P(θr) and the distribution of dihedral angle denoting k – k′ – j′ correlation, P(ϕr) have also been calculated at the different incident angles in the center-of-mass (CM) frame, respectively. The effects of reactant alignment on stereodynamics of the reaction are firstly revealed, which provides the theoretical foundation for the related experiment and enriches the theories of the stereodynamics.

STATE-TO-STATE REACTION DYNAMICS OF THE D(H) + FO → OD(OH) + F REACTIONS ON THE LOWEST TWO TRIPLET STATES

Quasiclassical trajectory (QCT) calculations have been performed to investigate the reaction dynamics of the title reactions at a state-to-state level. The recently developed adiabatic potential energy surfaces (PESs) of the two triplet electronic states of 13A″ and 13A′ (Gómez-Carrasco S. et al., J Chem Phys121:4605, 2004; J Chem Phys123:114310, 2005) are employed in the present QCT calculations. Product vibrational and rotational state distributions have been calculated at three collision energies of 0.5, 0.7 and 0.9 eV. The product vibrational state distributions are found to be Gaussian distributions. Both the vibrational and rotational state distributions depend clearly on the isotope substitution, electronic PESs and collision energies. The observed phenomena are probably attributed to the competition of direct and indirect reactions.

Vector correlations in the F + HO → HF + O reaction and its isotopic variant

The F + H(D)O → HF(DF) + O reactions have been studied using quasi-classical trajectory (QCT) calculation method, based on the three different potential energy surfaces (PESs) of Gomez-Carrasco et al. (J Chem Phys 2004, 121:4605; J Chem Phys 2005, 123:114310; Chem Phys Lett 2007, 435:188). Facilitated with the analysis of the QCT results, the pictures for product scattering and product polarizations have been presented to investigate the vector correlations in the two reactions, with effects of isotope substitution and electronic state as well as collision energy being revealed at a chemical stereodynamical level.

Quasi-classical trajectory study of the O(1D) + HF reaction dynamics on 11A′ potential energy surface

The quasi-classical trajectory (QCT) calculations for the title reaction were carried out using the recently developed, accurate potential energy surface (PES) of the [Formula: see text] singlet state of the OHF system The integral cross section and the product rotational alignment factor [Formula: see text] were calculated as a function of collision energy. In addition, I discovered the effect of isotopic substitution on stereodynamics for the title reaction, and the influence of the rotation excitation of the reagent on stereodynamics is also presented. Both the scalar and vector properties of the reaction O(1D) + HF → OH + F(2P) are studied in this paper. It was found that the reaction is mainly controlled by an indirect reaction mechanism, and that the deep noncollinear insertion HOF well has a great impact on the dynamics of the reaction. The conclusions drawn in this paper will draw from references to similar reactions, and provide a theoretical foundation for related experiments.

Nonadiabatic state-to-state reactive collisions among open shell reactants with conical intersections: the OH((2)Pi) + F((2)P) example

Accurate wave packet calculations on the OH((2)Pi) + F((2)P) → O((3)P) + HF((1)Sigma(+)) reactive collisions are performed using a recently proposed coupled diabatic states. Adiabatic and nonadiabatic dynamics are compared in detail, analyzing the final state distribution of products. It is found that with the new surfaces a significant increase of the rate constant is obtained, with noticeable nonadiabatic effects. The inclusion of the spin-orbit splittings for the calculation of the electronic partition function produces an important increase of the reaction rate constants, yielding a rather good agreement with the experimental results. It is also concluded that spin-orbit couplings are also necessary in the entrance channel to describe this reaction.

Quantum mechanics and quasiclassical study of the H/D+FO --> OH/OD+F, HF/DF+O reactions: chemical stereodynamics

The time-dependent quantum wave packet and the quasi-classical trajectory (QCT) calculations for the title reactions are carried out using three recent-developed accurate potential energy surfaces of the 1(1)A', 1(3)A', and 1(3)A'' states. The two commonly used polarization-dependent differential cross sections, dsigma(00)/domega(t), dsigma(20)/domega(t), with omega(t) being the polar coordinates of the product velocity omega', and the three angular distributions, P(theta(r)), P(Phi(r)), and P(theta(r),Phi(r)), with theta(r), Phi(r) being the polar angles of the product angular momentum, are generated in the center-of-mass frame using the QCT method to gain insight into the alignment and the orientation of the product molecules. Influences of the potential energy surface, the collision energy, and the isotope mass on the stereodynamics are shown and discussed. Validity of the QCT calculation has been examined and proved in the comparison with the quantum wave packet calculation.

Coupled diabatic potential energy surfaces for studying the nonadiabatic dynamics at conical intersections in angular resolved photodetachment simulations of OHF--->OHF+e-

An energy-based method is proposed for the diabatization of the OH(2Pi)+F(2P)-->O(3P)+HF(1Sigma+) reaction. It is demonstrated that the diabatic representation obtained is regularized, i.e., the residual derivative couplings do not present singularities at the conical intersections appearing along the reaction path. This method only requires the knowledge of the 1,2 3A" and 1 3A' eigenvalues and does not require any adjustable parameter. Thus, many convergence problems arising in other derivative-based diabatization methods are avoided, and the description of the configuration space along the reaction path is enormously simplified. Three-dimensional coupled diabatic energy surfaces are obtained by an interpolation procedure using approximately 4000 accurate ab initio points. The angular resolved photodetachment cross sections are obtained in the diabatic and adiabatic representations using a wave packet method. An excellent agreement is obtained with recent experimental data [D. M. Neumark, Phys. Chem. Chem. Phys. 7, 433 (2005)] for high electron kinetic energies where only the triplet electronic states contribute.

Coordinate transformation methods to calculate state-to-state reaction probabilities with wave packet treatments

A procedure for the transformation from reactant to product Jacobi coordinates is proposed, which is designed for the extraction of state-to-state reaction probabilities using a time-dependent method in a body-fixed frame. The method consists of several steps which involve a negligible extra computational time as compared with the propagation. Several intermediate coordinates are used, in which the efficiency depends on the masses of the atoms involved in the reaction. A detailed study of the relative efficiency of using reactant and product Jacobi coordinates is presented for several systems, and simple arguments are found depending on the masses of the atoms involved in the reaction. It is found that the proposed method is, in general, more efficient than the use of product Jacobi coordinates, specially for nonzero total angular momentum. State-to-state reaction probabilities are obtained for Li+FH-->LiF+H and F+HO-->FH+O collisions for several total angular momenta.

F+OH reactive collisions on new excited A″3 and A′3 potential-energy surfaces

Global three-dimensional adiabatic potential-energy surfaces for the excited 2(3)A" and 1(3)A' triplet states of OHF are obtained to study the F(2P)+OH(2pi)-->O(3P)+HF(1sigma+) reaction. Highly accurate ab initio calculations are obtained for the two excited electronic states and fitted to analytical functions with small deviations. The reaction dynamics is studied using a wave-packet treatment within a centrifugal sudden approach, which is justified by the linear transition state of the two electronic states studied. The reaction efficiency presents a marked preference for perpendicular orientation of the initial relative velocity vector and the angular momentum of the OH reagent, consistent in the body-fixed frame used with an initial collinear geometry which facilitates the access to the transition state. It is also found that the reaction cross section presents a rather high threshold so that, in an adiabatic picture, the two excited triplet states do not contribute to the rate constant at room temperature. Thus, only the lowest triplet state leads to reaction under these conditions and the simulated rate constants are too low as compared with the experimental ones. Such disagreement is likely to be due to nonadiabatic transitions occurring at the conical intersections near the transition state for this reaction.

Transition state dynamics of OHF on several electronic states: photodetachment spectrum of OHF- and conical intersections

Wave packet simulations of the photodetachment spectrum of OHF(-) are performed on several electronic adiabatic states, two triplets and four singlets of neutral OHF. The transition moments to these six states have been approximated using the ab initio electronic wave functions of OHF(-) and OHF calculated at the equilibrium configuration of the parent anion. In a first step, two-dimensional simulations of the spectrum are performed on new two-dimensional potential energy surfaces (PESs) of the neutral in a OHF collinear geometry. The resulting simulated spectrum is in rather good agreement with the experimental one, reproducing all the structures from 0 to 2.5 eV electron kinetic energies. At energies below 0.5 eV, all calculated states, singlets and triplets, contribute to the total spectrum. At higher energies, however, only the triplet states participate. In a second step, to improve the description of the spectrum, three-dimensional wave packet simulations of the spectrum are performed, getting an excellent agreement with the experiment. The collinear (3)Sigma(-) and (3)Pi states split in two (3)A(") and one (3)A('). New adiabatic PESs are used in this work for the 2 (3)A(") and 1 (3)A(') states, while the one recently proposed was used for the ground 1 (3)A("). It is found that the minimum energy paths of the (3)Sigma(-) and (3)Pi states cross twice at collinear geometry, so that at the transition state the ground state corresponds to (3)Pi, while (3)Sigma(-) is the lowest state otherwise. Such conical intersections are expected to give rise to important Sigma-Pi vibronic effects, requiring a complete three-dimensional model of coupled diabatic states to improve our understanding of the reaction dynamics in this kind of systems.