CD3 Reaction Research Articles

Accurate Quantum Dynamics Calculations for the Cl + CH4/CHD3/CD4 Reaction Rates.

Full-dimensional quantum dynamics simulations of the reaction of Cl with methane and its isotopomers are reported. Thermal rate constants are computed for the Cl + CH4 → HCl + CH3, Cl + CHD3 → HCl + CD3, and Cl + CD4 → DCl + CD3 reactions. Temperatures between 200 and 500 K are considered. In this temperature range, excellent agreement with the experiment is obtained. A detailed analysis of the kinetic isotope effect reveals the crucial importance of the CH3/CD3 umbrella motion. Comparison with approximate ring-polymer molecular dynamics simulations shows significant differences depending on the isotope studied.

Isotope Effect and Heavy-Light-Heavy Reactivity Oscillation in the Cl + CHD3/CHT3 Reaction.

Previous experiments and theories have shown the existence of heavy-light-heavy (HLH) reactivity oscillation in the Cl + CH4 reaction and anticipated that similar oscillations should exist in many HLH reactions involving polyatomic reagents. However, the total reaction probabilities for the Cl + CHD3 → HCl + CD3 reaction exhibit only a step-like feature, and the total reaction probabilities for Cl + CHT3 → HCl + CT3 do not show any structure at all. Here, we report seven-dimensional state-to-state quantum dynamics studies for this reaction on the FI-NN PES, and we demonstrate that HLH reactivity oscillations also exist in these two reactions, manifesting as peaks in the reaction probabilities for low product rotational states. These oscillations, however, are obscured in the total reaction probability because of the higher excitation of j ≥ 2 product rotational states. Furthermore, the isotope replacement of nonreactive hydrogen with deuterium and tritium significantly enhances reactivity at collision energies above 0.112 eV, indicating an inverse secondary isotope effect on the probabilities, which is proved to be also caused by HLH mass combination. We also demonstrate that the highly rotational excitation of CHD3 substantially enhances reactivity and the HLH oscillations, similar to HLH triatomic reactions. These observations are completely different from those in the H + CHD3 reaction, which is also a late-barrier reaction. Therefore, the HLH mass combination is very important, which affects not only the reactivity oscillation but also the amplitude and product rotational state distribution and makes the initial rotation excitation play a pivotal role in the reaction.

Показники імунітету і функціонального стану центральної нервової системи при хронічному набутому токсоплазмозі

For the first time, patterns of changes in the ratio of immunity indicators were revealed in chronic acquired toxoplasmosis — leukocyte intoxication index (LII), CD3, immunoregulatory index (IRI), total immunoglobulins, adaptive and compensatory reactions (tension coefficient) and functional state of the central nervous system (CNS) — changes in electroencephalographic research (EEG) according to the stem-diencephalic type — with the help of available informative methods, which allowed to assess the severity of the course, plan treatment and predict the outcome of the disease, without resorting to complex research methods. It has been established that the host-parasite relationship and clinical manifestations in chronic acquired toxoplasmosis largely depend on the protective and adaptive reactions and compensatory capabilities of the human body.

Feshbach resonances in the F + CHD3 → HF + CD3 reaction.

The signature of dynamics resonances was observed in the benchmark polyatomic F + CH4/CHD3 reactions more than a decade ago; however, the dynamical origin of the resonances is still not clear due to the lack of reliable quantum dynamics studies on accurate potential energy surfaces. Here, we report a six-dimensional state-to-state quantum dynamics study on the F + CHD3 → HF + CD3 reaction on a highly accurate potential energy surface. Pronounced oscillatory structures are observed in the total and product rovibrational-state-resolved reaction probabilities. Detailed analysis reveals that these oscillating features originate from the Feshbach resonance states trapped in the peculiar well on the HF(v' = 3)-CD3 vibrationally adiabatic potential caused by HF chemical bond softening. Most of the resonance structures on the reaction probabilities are washed out in the well converged integral cross sections (ICS), leaving only one distinct peak at low collision energy. The calculated HF vibrational state-resolved ICS for CD3(v = 0) agrees quantitatively with the experimental results, especially the branching ratio, but the theoretical CD3 umbrella vibration state distribution is found to be much hotter than the experiment.

Vibrational control of the reaction pathway in the H + CHD3 → H2 + CD3 reaction.

An accurate full-dimensional quantum state-to-state simulation of the six-atom title reaction based on first-principles theory is reported. Counterintuitive effects are found: Increasing the energy in the reactant’s CD3 umbrella vibration reduces the energy in the corresponding product vibration. An in-depth analysis reveals the crucial role of the effective dynamical transition state: Its geometry is controlled by the vibrational states of the reactants and subsequently controls the quantum state distribution of the products. This finding enables generalizing the concept of transition state control of chemical reactions to the quantum state–specific level.

The symmetric C-D stretching spectator mode in the H + CHD3 → H2 + CD3 reaction and its effect on dynamical modeling.

The symmetric C-D stretching mode is a spectator mode in the H + CHD3 → H2 + CD3 reaction. Effects of multiple vibrational excitations of the CHD3 reactant are studied with the quantum transition-state (QTS) framework and an eight-dimensional (8D) model Hamiltonian developed by Palma and Clary. By including many thermal flux eigenstates, results have been obtained up to high energies, allowing the study of the symmetric C-D stretching spectator mode. A new concept of a state-specific thermal flux operator is proposed to analyze the C-D stretching spectator mode in detail, providing a new and insightful venue for studying transition-state control of chemical reactions. Furthermore, as a spectator mode, whether the C-D stretching motion can be excluded in a seven-dimensional (7D) model has not been fully interrogated, although the 7D model is a reasonable approximation and has provided accurate theoretical predictions. By comparing with available results of full-dimensional calculations, both the 7D and 8D models predict reasonably accurate results. However, the 7D model underestimates the mixing of two vibrational states that are in Fermi resonance. Despite its spectator nature, the C-D stretch is important in the dynamical modeling of chemical reaction systems affected by state mixing.

Non-adiabatic transitions in the reaction of fluorine with methane.

Reactions of methane with different atoms are benchmark examples of elementary reaction processes intensively studied by theory and experiment. Due to the presence of conical intersections and spin-orbit coupling, non-adiabatic transitions can occur in reactions with F, Cl, or O atoms. Extending detailed quantum theory beyond the Born-Oppenheimer approximation for polyatomic reaction processes, non-adiabatic wave packet dynamics calculations studying the F(2P3/2)/F*(2P1/2) + CHD3 → HF + CD3 reaction on accurate vibronically and spin-orbit coupled diabatic potential energy surfaces are presented. Non-adiabatic transitions are found to increase the reactivity compared to Born-Oppenheimer theory and are more prominent than in triatomic reactions previously studied. Furthermore, the lifetimes of reactive resonances are reduced. The reactivity of F(2P3/2) is found to exceed the one of F*(2P1/2) even at low collision energies.

Full-dimensional quantum dynamics calculations for H + CHD3 → H2 + CD3: The effect of multiple vibrational excitations

Initial state-selected reaction probabilities for the H + CHD3 → H2 + CD3 reaction starting from various different ro-vibrational states of CHD3 are studied by accurate full-dimensional (12D) quantum dynamics calculation for vanishing total angular momentum (J = 0). The calculations employ the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach. First results focusing on fundamental excitations and the reactivity borrowing effect were communicated recently [R. Ellerbrock and U. Manthe, J. Chem. Phys. 147, 241104 (2017)]. In the present work, all vibrational states of the methane reactant are considered. It is found that energy deposited in overtones and combination bands is less efficient in promoting reactivity than expected from separable or sudden models. Furthermore, the effects of rotational excitation on the reactivity are studied in detail.

Decellularized and Secured Porcine Arteries with NaOH-based Process: Proof of Concept

There is a need for small caliber vascular prosthesis. Synthetic grafts are hindered by thrombogenicity and rapid occlusion. Decellularized matrices could be an alternative. We assessed invitro and invivo the biocompatibility of porcine artery treated with a chemical/physical process for decellularization and graft securitization with non/conventional pathogens inactivation. Porcine carotid arteries (PCA) were treated. First, biopsies (n=4/tissue) were performed before/after treatment to assess decellularization (hematoxylin and eosin/-4',6-diamidino-2-phenylindole/DNA/Miller). Second, 5 rats received an abdominal aortic patchof decellularized PCA (DPCA). Four pigs received subcutaneous DPCA implants (n=2/pig). Half were explanted at day 15 and half at day 30. Finally, 2 pigs received DPCA (n=2) and polytetrafluoroethylene prosthesis (n=1), respectively, as carotid interposition. Implants were removed at day 30. Inflammation (CD3 and CD68 immunostaining) calcifications (von Kossa staining), remodeling (hematoxylin and eosin), and vascular characterization (CD31 and alpha-smooth muscle actin immunofluorescent staining) were investigated. Ninety-five percentage of decellularization was obtained without structural deterioration. No death occurred. Low inflammatory reaction was found in the 2 models for DPCA. Acquisition of vascular identity was confirmed in the rodent and porcine models. Similarity between native PCA and DPCA was observed after 30days. In contrast, polytetrafluoroethylene graft showed severe calcifications, higher CD3 reaction, and higher intimal hyperplasia (P<0.05). The physical and chemical process ensures decellularization of carotid porcinearteries and their invivo remodeling with the presence of an endothelium and smooth-muscle-like cells as well as a low level of inflammatory cells.

Communication: Reactivity borrowing in the mode selective chemistry of H + CHD3 → H2 + CD3.

Quantum state-resolved reaction probabilities for the H + CHD3 → H2 + CD3 reaction are calculated by accurate full-dimensional quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree approach and the quantum transition state concept. Reaction probabilities of various ro-vibrational states of the CHD3 reactant are investigated for vanishing total angular momentum. While the reactivity of the different vibrational states of CHD3 mostly follows intuitive patterns, an unusually large reaction probability is found for CHD3 molecules triply excited in the CD3 umbrella-bending vibration. This surprising reactivity can be explained by a Fermi resonance-type mixing of the single CH-stretch excited and the triple CD3 umbrella-bend excited vibrational states of CHD3. These findings show that resonant energy transfer can significantly affect the mode-selective chemistry of CHD3 and result in counter-intuitive reactivity patterns.

Non-adiabatic effects in F + CHD3 reactive scattering.

The effect of non-adiabatic transitions on the F(2P) + CHD3(ν1) → DF + CHD2 and F(2P) + CHD3(ν1) → HF + CD3 reactions is investigated. The dynamics of the nuclei was simulated using trajectory surface hopping and a vibronically and spin-orbit coupled diabatic potential energy matrix. To facilitate the calculations, the fewest switching algorithm of Tully was adapted to the use of a complex diabatic potential energy matrix. For reactions of CHD3 with ground state fluorine atoms, F(2P3/2), the ratio between the previously computed adiabatic cross sections and the non-adiabatic ones was found to range from 1.4 to 2.1. The actual ratio depends on the translational energy and the initial vibrational state of CHD3. The total reactivity of CHD3(ν1 = 1) was found to be always larger than that of CHD3(ν1=0) mainly because of the increase in the cross sections for the HF + CD3 channel. Thus, the inclusion of non-adiabatic transitions in the theoretical treatment cannot resolve the existing disagreement between theory and experiment. Cross sections for the reaction of CHD3 with spin-orbit excited fluorine atoms, F(2P1/2), were found to be significantly smaller than the ones for reaction with F(2P3/2).

CH stretching excitation promotes its cleavage in the F + CHD3(ν1 = 1) → HF + CD3 reaction at low collision energies.

The effects of CH stretching excitation on the reactivity of the F + CHD3 → HF + CD3 reaction were studied experimentally using crossed-beam and time-sliced velocity map imaging techniques over the collision energy range of 1.21 to 9.00 kcal mol-1. The experimental results showed that the CH stretching excitation promoted its cleavage and enhanced the title reaction at low collision energies. This enhancement dropped with an increase of the collision energy. And at high collision energies, CH stretching excitation appeared to lower the reactivity of the above reaction, in contrast to the case at low collision energies. This decreasing trend in the enhancement of reactivity was in agreement with previous theoretical studies. The vibrationally excited reaction was further compared with the ground-state reaction at a same total reagent energy of 9.80 kcal mol-1, and similar reactivities were derived.

Communication: Mode specific quantum dynamics of the F + CHD3 → HF + CD3 reaction.

The mode specific reactivity of the F + CHD3 → HF + CD3 reaction is investigated using an eight-dimensional quantum dynamical model on a recently developed ab initio based full-dimensional potential energy surface. Our results indicate prominent resonance structures at low collision energies and absence of an energy threshold in reaction probabilities. It was also found that excitation of the C-D stretching or CD3 umbrella mode has a relatively small impact on reactivity. On the other hand, the excitation of the C-H vibration (v1) in CHD3 is shown to significantly increase the reactivity, which, like several recent quasi-classical trajectory studies, is at odds with the available experimental data. Possible sources of the disagreement are discussed.

A Quasiclassical Study of the F((2)P) + CHD3 (ν1 = 0,1) Reactive System on an Accurate Potential Energy Surface.

Quasiclassical trajectories (QCT) have been employed to elucidate the effect of exciting the C-H bond in F + CHD3 collisions. The calculations were performed on a new potential energy surface that accurately describes the van der Waals complexes in the entrance channel of the reaction. It was found that exciting the C-H bond significantly enhances the yield of HF + CD3, whereas it has a minor effect on the production of DF + CHD2. Therefore, the net effect is that the total reactivity increases upon excitation. This result strongly contradicts recent experimental findings. Significant differences in regard to the yield of each product channel were also found between QCT results calculated with the new surface and those obtained with the surface previously developed by Czakó et al. This shows that relatively small variations in the topography of the entrance channel can result in huge discrepancies in the predicted DF/HF branching ratio. However, in regard to other attributes of the reaction, the agreement between QCT results computed with different surfaces, and between them and experimental results, is good. For the F + CHD3 → HF + CD3 reaction, at a collisional energy of 9.0 kcal/mol, experiments and QCT calculations agree, indicating that the extra energy deposited in the C-H bond is channelled into the HF product. In addition, the angular distribution of CD3 is backward oriented and is not sensitive to the excitation of the C-H bond.

Quasiclassical trajectory study of the rotational mode specificity in the O((3)P) + CHD3(v1 = 0, 1, JK) → OH + CD3 reactions.

Quasiclassical trajectory computations on an ab initio potential energy surface reveal that rotational excitation can significantly enhance the reactivity of the ground-state and CH stretching-excited O((3)P) + CHD3(v1 = 0,1, JK) → OH + CD3 reactions. The state-specific rotational effects investigated up to J = 8 show that the K = 0 (tumbling rotation) enhancement factors can be as large as 1.5-3.5 depending on J and the collision energy, whereas the K = J (spinning rotation about the CH axis) excitations do not have any significant effect on the reactivity. The shapes of the opacity functions and scattering angle distributions depend on the initial vibrational state, but show virtually no JK dependence. The origin of the K = 0 rotational enhancements is that the tumbling rotation enlarges the range of the reactive initial attack angles, thereby increasing the reactivity.

Effects of reagent rotational excitation on the H + CHD₃ → H₂ + CD₃ reaction: a seven dimensional time-dependent wave packet study.

Seven-dimensional time-dependent wave packet calculations have been carried out for the title reaction to obtain reaction probabilities and cross sections for CHD3 in J0 = 1, 2 rotationally excited initial states with k0 = 0 - J0 (the projection of CHD3 rotational angular momentum on its C3 axis). Under the centrifugal sudden (CS) approximation, the initial states with the projection of the total angular momentum on the body fixed axis (K0) equal to k0 are found to be much more reactive, indicating strong dependence of reactivity on the orientation of the reagent CHD3 with respect to the relative velocity between the reagents H and CHD3. However, at the coupled-channel (CC) level this dependence becomes much weak although in general the K0 specified cross sections for the K0 = k0 initial states remain primary to the overall cross sections, implying the Coriolis coupling is important to the dynamics of the reaction. The calculated CS and CC integral cross sections obtained after K0 averaging for the J0 = 1, 2 initial states with all different k0 are essentially identical to the corresponding CS and CC results for the J0 = 0 initial state, meaning that the initial rotational excitation of CHD3 up to J0 = 2, regardless of its initial k0, does not have any effect on the total cross sections for the title reaction, and the errors introduced by the CS approximation on integral cross sections for the rotationally excited J0 = 1, 2 initial states are the same as those for the J0 = 0 initial state.

Rotational mode specificity in the Cl + CHD3 → HCl + CD3 reaction.

By exciting the rotational modes of vibrationally excited CHD3(v1 = 1, JK), the reactivity for the Cl + CHD3 → HCl + CD3 reaction is observed enhanced by as much as a factor of two relative to the rotationless reactant. To understand the mode specificity, the reaction dynamics was studied using both a reduced-dimensional quantum dynamical model and the conventional quasi-classical trajectory method, both of which reproduced qualitatively the measured enhancements. The mechanism of enhancement was analyzed using a Franck-Condon model and by inspecting trajectories. It is shown that the higher reactivity for higher J states of CHD3 with K = 0 can be attributed to the enlargement of the cone of acceptance. On the other hand, the less pronounced enhancement for the higher J = K states is apparently due to the fact that the rotation along the C-H bond is less effective in opening up the cone of acceptance.

How Is C-H Vibrational Energy Redistributed in F + CHD3(ν1 = 1) → HF + CD3?

The effects of CH stretching excitation on the F + CHD3 → HF + CD3 reaction are studied experimentally using crossed-beam and time-sliced velocity map imaging techniques at the collision energy of 9.0 kcal/mol. The fraction of the vibrationally excited CHD3 reagent in the crossed-beam region was determined accurately, allowing us to investigate quantitatively the effects of CH stretching excitation on the title reaction. Experimental data show that the vibrational energy in the excited CH bond of CHD3 is almost exclusively deposited into the HF product vibration, and hence, the HF products from the excited-state reaction are about one vibrational quantum hotter than those of the ground-state reaction, while the vibrational state distribution of the CD3 products is only slightly affected. The reaction is suppressed by the CH stretching excitation, and the overall reactivity of the vibrationally excited reaction is 74 ± 4% of that of the ground-state reaction for CD3(ν2 = 0, 1, 2, 3) product channels.

Quantum reaction dynamics study of vibrational excitation effects on the Cl + CHD3/CD4 → HCl/DCl + CD3 reactions

Energy efficiency in surmounting the reaction energy barrier and vibrational enhancement on reactivity of the Cl+CHD3/CD4→HCl/DCl+CD3 reactions have been studied using the reduced dimensional, time-dependent wavepacket method in six degrees of freedom. All the vibrational excitations of CHD3/CD4 enhance the reactivity and the C–H/C–D stretching motions have the biggest impact on the reactivity. Both reactions’ vibrational energies raise the reactivity more effectively than the translational energies except at very low collision energies. In other words, except at very low collision energies, the Polanyi rules hold for these two late-barrier polyatomic reactions.

Effect of antisymmetric C–H stretching excitation on the dynamics of O(1D) + CH4 → OH + CH3

The effect of antisymmetric C–H stretching excitation of CH4 on the dynamics and reactivity of the O(1D) + CH4 → OH + CD3 reaction at the collision energy of 6.10 kcal/mol has been investigated using the crossed-beam and time-sliced velocity map imaging techniques. The antisymmetric C–H stretching mode excited CH4 molecule was prepared by direct infrared excitation. From the measured images of the CH3 products with the infrared laser on and off, the product translational energy and angular distributions were derived for both the ground and vibrationally excited reactions. Experimental results show that the vibrational energy of the antisymmetric stretching excited CH4 reagent is channeled exclusively into the vibrational energy of the OH co-products and, hence, the OH products from the excited-state reaction are about one vibrational quantum hotter than those from the ground-state reaction, and the product angular distributions are barely affected by the vibrational excitation of the CH4 reagent. The reactivity was found to be suppressed by the antisymmetric stretching excitation of CH4 for all observed CH3 vibrational states. The degree of suppression is different for different CH3 vibrational states: the suppression is about 40%–60% for the ground state and the umbrella mode excited CH3 products, while for the CH3 products with one quantum symmetric stretching mode excitation, the suppression is much less pronounced. In consequence, the vibrational state distribution of the CH3 product from the excited-state reaction is considerably different from that of the ground-state reaction.