Juliana Palma

Quantum dynamics of the Walden inversion reaction Cl−+CH3Cl→ClCH3+Cl−

Quantum scattering calculations on the SN2 reaction Cl−+CH3Cl→ClCH3+Cl− are reported. The rotating bond approximation (RBA) has been adapted so that three degrees of freedom including the C–Cl stretching vibration and the CH3 umbrella mode are treated explicitly. The calculations have been done with minor modifications of a potential due to Vande Linde and Hase. It is found that initial excitation of the C–Cl vibration has a large effect on the reaction probabilities, while excitation of the CH3 umbrella vibration is less significant. The reaction is dominated by scattering resonances with lifetimes ranging from 0.1 to 10 ps. It is found that the length of the C–Cl bond at the transition state of the reaction has a particularly pronounced effect on the reaction probabilities. The magnitude of the quantum reaction probabilities compares quite well with those calculated using the quasiclassical trajectory method.

Resonances in the Entrance Channel of the Elementary Chemical Reaction of Fluorine and Methane

Extending the fully quantum-state-resolved description of elementary chemical reactions beyond three or four atom systems is a crucial issue in fundamental chemical research. Reactions of methane with F, Cl, H or O are key examples that have been studied prominently. In particular, reactive resonances and nonintuitive mode-selective chemistry have been reported in experimental studies for the F+CH4 →HF+CH3 reaction. By investigating this reaction using transition-state spectroscopy, this joint theoretical and experimental study provides a clear picture of resonances in the F+CH4 system. This picture is deduced from high-resolution slow electron velocity-map imaging (SEVI) spectra and accurate full-dimensional (12D) quantum dynamics simulations in the picosecond regime.

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.

Jump in depletion rates of highly excited O2: reaction or enhanced vibrational relaxation?

Abstract A simple model is used to calculate vibrational self-relaxation rates of highly excited oxygen. In contrast to previous theoretical treatments, the model reproduces the experimental observation of a sharp increase in depletion rates above a critical value of v . It is proposed that the observed jump in O ‡ 2 (v) depletion rates is partially due to inelastic collisions, rather than to ozone formation. It is also shown that the presence of the reactive transition state region in the potential energy surface is the key for the enhancement of the relaxation rates.

Vibrational dynamics of the CH4·F- complex.

Motivated by recent photodetachment experiments studying resonance structures in the transition-state region of the F + CH(4) → HF + CH(3) reaction, the vibrational dynamics of the precursor complex CH(4)·F(-) is investigated. Delocalized vibrational eigenstates of CH(4)·F(-) are computed in full dimensionality employing the multiconfigurational time-dependent Hartree (MCTDH) approach and a recently developed iterative diagonalization approach for general multiwell systems. Different types of stereographic coordinates are used, and a corresponding general N-body kinetic energy operator is given. The calculated tunneling splittings of the ground and the lower vibrational excited states of the CH(4)·F(-) complex do not significantly exceed 1 cm(-1). Comparing the converged MCTDH results for localized vibrational excitations with existing results obtained by normal-mode-based (truncated) vibrational configuration interaction calculations, significantly lower frequencies are found for excitations in the intermolecular modes.

The effect of the symmetric and asymmetric stretching vibrations on the CH3D+O(3P)→CH3+OD reaction

Abstract We report calculations on the CH 3 D + O ( 3 P )→ CH 3 + OD reaction using a reduced dimensionality model with four degrees of freedom. The model has already been used to evaluate the effect of the symmetric and asymmetric stretching vibrations of methane on the CH 4 + O ( 3 P ) and CH4+H reactions. Unfortunately, it is not easy to establish a direct comparison between these previous calculations and experimental results. As the difficulties disappear when CH4 is replaced with CH3D we decided to try our model on the title reaction. The results of these new calculations are presented in this Letter.

A Quasiclassical Study of the F(2P) + 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.

The effect of the symmetric and asymmetric stretching vibrations of CH4 on the O(3P)+CH4→OH+CH3 reaction

We present a four-dimensional quantum scattering model to treat reactions of the type CH4+X→CH3+XH. The most important feature of the model is that it allows the effect of the symmetric and asymmetric stretching vibrations of CH4 on reactivity to be studied. We used the model to study the CH4+O(3P)→CH3+OH reaction. We found that the symmetric stretch vibration is more efficient in promoting reaction than the asymmetric stretch. We also found that exciting any of these stretching modes produces an inverted population in the umbrella vibration of product CH3 while, for the reactants in the ground state, the population is non-inverted.

A full-dimensional wave packet dynamics study of the photodetachment spectra of FCH 4−

The low-resolution photodetachment spectrum of FCH(4)(-) is studied in full dimensionality employing the multi-configurational time-dependent Hartree approach and potential energy surfaces recently developed by Bowman and co-workers. The computed spectrum qualitatively agrees with the low-resolution spectrum measured by Neumark and co-workers. It displays two peaks which can be assigned to different vibrational states of methane in the quasi-bound F·CH(4) van der Waals complex. The first intense peak correlates to methane in its vibrational ground state while the second much smaller peak results from methane where one of the bending modes is excited. The present simulations consider only a single potential energy surface for the neutral FCH(4) system and thus do not include spectral contributions arising from transitions to excited electronic states correlating to the F((2)P) + CH(4) asymptote. Considering the quantitative differences between the computed and the experimental spectra, one cannot decide whether beside the vibrational excitation of the methane fragment also electronic excitation of FCH(4) contributes to the second peak in the experimental photodetachment spectrum.

Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase.

Trypanosoma rangelis sialidase (TrSA) and Trypanosoma cruzis trans‐sialidase (TcTS) are members of the glycoside hydrolase family 33 (GH‐33). They share 70% of sequence identity and their crystallographic Cα RMSD is 0.59 Å. Despite these similarities they catalyze different reactions. TcTS transfers sialic acid between glycoconjugates while TrSA can only cleave sialic acid from sialyl‐glyconjugates. Significant effort has been invested into unraveling the differences between TrSA and TcTS, and into conferring TrSA with trans‐sialidase activity through appropriate point mutations. Recently, we calculated the free‐energy change for the formation of the covalent intermediate (CI) in TcTS and performed an energy decomposition analysis of that process. In this article we present a similar study for the formation of the CI in TrSA, as well as in a quintuple mutant (TrSA5mut), which has faint trans‐sialidase activity. The comparison of these new results with those previously obtained for TcTS allowed identifying five extra mutations to be introduced in TrSA5mut that should create a mutant (TrSA10mut) with high trans‐sialidase activity. Proteins 2014; 82:424–435.