Theoretical study of the Cl(2P) + SiH4 reaction: global potential energy surface and product pair-correlated distributions. Comparison with experiment

For the theoretical study of the title reaction, an analytical full-dimensional potential energy surface named PES-2021 was developed for the first time, by fitting high-level explicitly-correlated ab initio data. This reaction presented high exothermicity, (298 K) = -11.6 kcal mol^-1, reproducing the experimental evidence; it is a barrierless reaction and no intermediate complexes were found. PES-2021 is a continuous and smooth potential energy surface, it includes intuitive concepts in its development and fitting, such as stretching and bending nuclear motions, and it presents analytical first energy derivatives. Based on PES-2021, kinetics and dynamics studies were carried out using quasi-classical trajectory calculations. In the kinetics study, over the temperature range 300-450 K, we observed that rate constants were practically independent of temperature, with an almost zero activation energy, as compared to 0.0 and -0.48 kcal mol^-1 experimentally reported. In this kinetics study the role of the spin-orbit effect on reactivity was analysed. In the dynamics study, different product pair-correlated dynamics properties were compared with the only experimental evidence: product energy partition, product vibrational distribution, product angular distribution and product speed distribution. We observed two mechanisms of reaction, a stripping mechanism associated with large impact parameters and forward scattering, and an indirect mechanism associated with sideways-backward scattering related with "nearly-trapped" trajectories due to the product rotation. In general, theoretical results reasonably simulate the experimental measurements when they consider some rotational and vibrational constraints as well as binning techniques to mimic a quantum-mechanical behaviour. Although the agreement is not quantitative, the present results shed light on the mechanism of this difficult polyatomic reactive system.

Serotonin signaling by maternal neurons upon stress ensures progeny survival

Germ cells are vulnerable to stress. Therefore, how organisms protect their future progeny from damage in a fluctuating environment is a fundamental question in biology. We show that in Caenorhabditis elegans, serotonin released by maternal neurons during stress ensures the viability and stress resilience of future offspring. Serotonin acts through a signal transduction pathway conserved between C. elegans and mammalian cells to enable the transcription factor HSF1 to alter chromatin in soon-to-be fertilized germ cells by recruiting the histone chaperone FACT, displacing histones, and initiating protective gene expression. Without serotonin release by maternal neurons, FACT is not recruited by HSF1 in germ cells, transcription occurs but is delayed, and progeny of stressed C. elegans mothers fail to complete development. These studies uncover a novel mechanism by which stress sensing by neurons is coupled to transcription response times of germ cells to protect future offspring.

Theoretical study of the O(3P) + C2H6 reaction based on a new ab initio-based global potential energy surface

A new analytical potential energy surface was developed for the first time for the nine-body O(3P) + C2H6 hydrogen abstraction reaction, named PES-2020, which was fitted to explicitly-correlated high-level electronic structure calculations. This surface simulates the topography of the reactive system, from reactants to products, OH(v,j) + C2H5. The adiabatic energy of reaction, ΔHr(0 K) = -2.33 kcal mol-1, reproduces the experimental evidence, and the barrier height, 10.70 kcal mol-1, agrees with the ab initio calculations used as input. In addition, an intermediate complex in the exit channel is observed, which is stabilized with respect to the products of the reaction. Based on PES-2020 a dynamics study was carried out, where quasi-classical trajectory calculations were performed for collision energies in the range of 7.0-60.0 kcal mol-1, which covers high collision energy regions. The reaction cross section increases with collision energy; the largest fraction of available energy is deposited as translational energy (44-66%), and the scattering distribution evolves from backward to forward with collision energy. These findings reproduce previous theoretical calculations using electronic structure calculations of lower levels. However, where these previous studies failed, viz. in rotational and vibrational OH(v,j) distributions, PES-2020 reproduces practically quantitatively the experimental evidence, i.e., cold vibration and rotation, the rotational distribution peaking at j = 1-3 depending on the collision energy. In sum, this behaviour is typical of gas-phase hydrogen abstraction reactions with direct mechanism and high reaction barrier.

Kinetics and dynamics study of the OH + C2H6 → H2O + C2H5 reaction based on an analytical global potential energy surface

To describe the gas-phase hydrogen abstraction reaction between the hydroxyl radical and the ethane molecule, an analytical full-dimensional potential energy surface was developed within the Born-Oppenheimer approximation. This reactive process is a ten-body system with 24 degrees of freedom, which represents a theoretical challenge. The new surface, named PES-2020, presents low barrier, 3.76 kcal mol-1, high exothermicity, -16.20 kcal mol-1, and intermediate complexes in the entrance and exit channels. To test the quality and accuracy of the analytical surface several stringent tests were performed and, in general, PES-2020 reasonably simulates the theoretical information used as input, it is a continuous and smooth potential, without spurious minima, it presents great versatility and a reasonable description of this ten-body reaction. Based on this surface, an exhaustive kinetics and dynamics study was performed with a double objective: to analyze the capacity of the new surface to simulate the experimental evidence, and to help understand the mechanism of reaction and the role of the ethyl group in the reaction. In the kinetics study, three approaches were used: variational transition-state theory with multidimensional tunnelling (VTST/MT), ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) results, in the temperature range 200-2000 K. There is general agreement between the three approaches and they reasonably simulate the experimental behaviour, which gives confidence to the fitness of the new surface to describe the system. In the dynamics study, QCT calculations were performed at 298 K for a direct comparison with the only experimental result reported. We found that ethyl fragment presents a noticeable internal energy (∼20%) and so cannot be considered as a spectator. The water product vibrational energy is reasonably reproduced, though when a level-by-level distribution is analyzed the agreement is only qualitative.

Predictive Models of Recombination Rate Variation across the Drosophila melanogaster Genome

In all eukaryotic species examined, meiotic recombination, and crossovers in particular, occur non‐randomly along chromosomes. The cause for this non-random distribution remains poorly understood but some specific DNA sequence motifs have been shown to be enriched near crossover hotspots in a number of species. We present analyses using machine learning algorithms to investigate whether DNA motif distribution across the genome can be used to predict crossover variation in Drosophila melanogaster, a species without hotspots. Our study exposes a combinatorial non-linear influence of motif presence able to account for a significant fraction of the genome-wide variation in crossover rates at all genomic scales investigated, from 20% at 5-kb to almost 70% at 2,500-kb scale. The models are particularly predictive for regions with the highest and lowest crossover rates and remain highly informative after removing sub-telomeric and -centromeric regions known to have strongly reduced crossover rates. Transcriptional activity during early meiosis and differences in motif use between autosomes and the X chromosome add to the predictive power of the models. Moreover, we show that population-specific differences in crossover rates can be partly explained by differences in motif presence. Our results suggest that crossover distribution in Drosophila is influenced by both meiosis-specific chromatin dynamics and very local constitutive open chromatin associated with DNA motifs that prevent nucleosome stabilization. These findings provide new information on the genetic factors influencing variation in recombination rates and a baseline to study epigenetic mechanisms responsible for plastic recombination as response to different biotic and abiotic conditions and stresses.

Dynamics study of the OH + NH3 hydrogen abstraction reaction using QCT calculations based on an analytical potential energy surface

To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)]. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol(-1)) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) ≥ 6 kcal mol(-1)) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.

Product Angular Distribution for the H + CD4→ HD + CD3Reaction

Using an analytical potential energy surface previously developed by our group, namely PES-2002, we analyzed the gas-phase reaction between a hydrogen atom and perdeuterated methane. We studied the effect of quasiclassical trajectory (QCT) and reduced dimensionality quantum-scattering (QM) calculations, with their respective limitations, on CD3 product angular distributions in the collision energy range 16.1-46.1 kcal x mol(-1). It was found that at low collision energy, 16.1 kcal x mol(-1), both the QCT and QM calculations yielded forward scattered CD3 products, i.e., a rebound mechanism. However, at high energies only the QM calculations on the PES-2002 surface reproduced the angular scattering found experimentally.

Quasi-classical Trajectory Calculations Analyzing the Role of Bending Mode Excitations of Methane in the Cl + CH4 Reaction

The effects of the methane torsional (nu(2)), umbrella (nu(4)), and the combination nu(2)+nu(4) bending mode excitations on the reactivity and dynamics of the gas-phase Cl + CH(4) --> HCl + CH(3) reaction were analyzed. Quasi-classical trajectory (QCT) calculations, including corrections to avoid zero-point energy leakage along the trajectories, were used on an analytical potential energy surface previously developed by our group. With respect to the reactivity, we found that excitation of either bending mode independently gave similar increases in the reactivity, while the increase observed upon excitation of both modes was larger than the sum of the effect of exciting them independently. Both results agree with recent experimental measures. With respect to the dynamics (rotovibrational and angular distributions of the products), the two bending modes and their combination gave very similar pictures, reproducing the experimental behavior. The satisfactory agreement obtained with a great variety of experimental data (always qualitatively acceptable and sometimes even quantitatively) of the present QCT study lends confidence to the potential energy surface constructed by our group.

Quasiclassical trajectory calculations comparing the reactivity and dynamics of symmetric and asymmetric stretch and the role of the bending mode excitations of methane in the Cl+CH4 reaction

To analyze the effects of the symmetric (nu(1)) and asymmetric (nu(3)) stretch mode excitations and the role played by the "umbrella" bending (nu(4)) mode excitation in the reactivity and the dynamics of the gas-phase Cl+CH(4) reaction, an exhaustive dynamics study was performed. Quasiclassical trajectory (QCT) calculations, including corrections to avoid zero-point energy leakage along the trajectories, were used in this work on an analytical potential energy surface previously developed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)]. First, with respect to the reactivity, we found that the nu(1) mode excitation is more reactive than the nu(3) mode by a factor of 1.20, in agreement with the experimental tendency between these modes. The inclusion of the nu(4) bending mode practically does not affect this relative reactivity, (nu(1+)nu(4))(nu(3+)nu(4)) = 1.16. Second, with respect to the dynamics (rotovibrational and angular distributions of the products), the two stretch modes, nu(1) and nu(3), give very similar pictures, reproducing the experimental behavior, and the nu(4) "umbrella" mode does not affect the dynamics. The satisfactory reproduction (always qualitatively acceptable and sometimes even quantitatively) of a great variety of experimental data by the QCT study presented here lends confidence to the potential energy surface constructed by Espinosa-Garcia et al. [J. Chem. Phys. (to be published)].

Trapping of the OH radical by alpha-tocopherol: a theoretical study

The antioxidant activity of alpha-tocopherol against the damaging hydroxyl radical was analyzed theoretically by hybrid density functional theory, following the direct dynamics method, where the thermal rate constants were calculated using variational transition-state theory with multidimensional tunneling. We found that the OH radical is only slightly or not at all selective, attacking by different mechanisms at several positions of the alpha-tocopherol molecule, giving competitive reactions. The most favorable pathways are the hydrogen abstraction reaction from the phenolic hydrogen and the electrophilic addition onto the aromatic ring. We propose a final rate constant, the sum of the competitive hydrogen abstraction and addition reactions, > or =2.7 x 10(8) M(-1) s(-1) at 298 K, where the hydrogen abstraction reaction represents only 20% of the total OH radical reaction. This result indicates that, molecule by molecule, in an apolar environment, alpha-tocopherol is less effective than coenzyme Q (which presents a rate constant of 6.2 x 10(10) M(-1) s(-1) at 298 K) as a scavenger of OH radicals. It was also found that both mechanisms are not direct but pass through intermediates in the entry channel, with little or no influence on the dynamics of the reactions. The hydrogen abstraction reaction also presents another intermediate in the exit channel, which may have a significant role in preventing the pro-oxidant effects of alpha-tocopherol, although less important than with free radicals other than OH.