Ring Polymer Molecular Dynamics Approach to Quantum Dissociative Chemisorption Rates.

A ring polymer molecular dynamics (RPMD) method is proposed for the calculation of the dissociative chemisorption rate coefficient on surfaces. The RPMD rate theory is capable of handling quantum effects such as the zero-point energy and tunneling in dissociative chemisorption, while it relies on classical trajectories for the simulation. Applications to H2 dissociative chemisorption are demonstrated. For the highly activated process on Ag(111), strong deviations from Arrhenius behavior are found at low temperatures and attributed to tunneling. On Pt(111), where the dissociation has a barrierless pathway, the RPMD rate coefficient is found to agree with the experimentally derived thermal sticking coefficient within a factor of 2 over a large temperature range. Significant quantum effects are also found.

Electronic Structure, Stability, and Electrical Mobility of Cationic Silver Oxide Atomic Clusters.

Silver oxide cluster cations (AgnOm+) can readily be produced by a number of methods including atmospheric-pressure spark ablation of pure silver electrodes when trace amounts of oxygen are present in the carrier gas. Here we determine the equilibrium geometries of AgnOm+ clusters (n = 1-4; m = 1-5) using accurate coupled cluster with singles and doubles (CCSD) method, while the stabilization energies are calculated with additional perturbative triples correction (CCSD(T)). Although a number of stable states have been identified, our results show that the AgnOm+ clusters with m = 1 are more stable than those with m ≥ 2 due to the absence of the terminally attached O2 molecule, corroborating recent observations by mass spectrometry. Using the computed structures, we calculate the electrical mobilities of the AgnOm+ clusters and label the values on a respective experimentally determined spectrum in an attempt to better interpret the occurrence of the peaks and troughs in the measurements.

Experimental and theoretical studies of the gas-phase reactions of O(1D) with H2O and D2O at low temperature.

Here we report the results of an experimental and theoretical study of the gas-phase reactions between O(1D) and H2O and O(1D) and D2O at room temperature and below. On the experimental side, the kinetics of these reactions have been investigated over the 50-127 K range using a continuous flow Laval nozzle apparatus, coupled with pulsed laser photolysis and pulsed laser induced fluorescence for the production and detection of O(1D) atoms respectively. Experiments were also performed at 296 K in the absence of a Laval nozzle. On the theoretical side, the existing full-dimensional ground X 1A potential energy surface for the H2O2 system involved in this process has been reinvestigated and enhanced to provide a better description of the barrierless H-atom abstraction pathway. Based on this enhanced potential energy surface, quasiclassical trajectory calculations and ring polymer molecular dynamics simulations have been performed to obtain low temperature rate constants. The measured and calculated rate constants display similar behaviour above 100 K, showing little or no variation as a function of temperature. Below 100 K, the experimental rate constants increase dramatically, in contrast to the essentially temperature independent theoretical values. The possible origins of the divergence between experiment and theory at low temperatures are discussed.

Isotopic separation of helium through graphyne membranes: a ring polymer molecular dynamics study.

Microscopic-level understanding of the separation mechanism for two-dimensional (2D) membranes is an active area of research due to potential implications of this class of membranes for various technological processes. Helium (He) purification from the natural resources is of particular interest due to the shortfall in its production. In this work, we applied the ring polymer molecular dynamics (RPMD) method to graphdiyne (Gr2) and graphtriyne (Gr3) 2D membranes having variable pore sizes for the separation of He isotopes, and compare for the first time with rigorous quantum calculations. We found that the transmission rate through Gr3 is many orders of magnitude greater than Gr2. The selectivity of either isotope at low temperatures is a consequence of a delicate balance between the zero-point energy effect and tunneling of 4He and 3He. In particular, a remarkable tunneling effect is reported on the Gr2 membrane at 10 K, leading to a much larger permeation of the lighter species as compared to the heavier isotope. RPMD provides an efficient approach for studying the separation of He isotopes, taking into account quantum effects of light nuclei motions at low temperatures, which classical methods fail to capture.

VTST and RPMD kinetics study of the nine-body X + C2H6 (X ≡ H, Cl, F) reactions based on analytical potential energy surfaces.

Thermal rate constants of nine-atom hydrogen abstraction reactions, X + C2H6 → HX + C2H5 (X ≡ H, Cl, F) with qualitatively different reaction paths, have been investigated using two kinetics approaches - variational transition state theory with multidimensional tunnelling (VTST/MT) and ring polymer molecular dynamics (RPMD) - and full dimensional analytical potential energy surfaces. For the H + C2H6 reaction, which proceeds through a noticeable barrier height of 11.62 kcal mol-1, kinetics approaches showed excellent agreement between them (with differences less than 30%) and with the experiment (with differences less than 60%) in the wide temperature range of 200-2000 K. For X = Cl and F, however, the situation is very different. The barrier height is either low or very low, 2.44 and 0.23 kcal mol-1, respectively, and the presence of van der Waals complexes in the entrance channel leads to a very flat topography and, consequently, imposes theoretical challenges. For the Cl(2P) reaction, VTST/MT underestimates the experimental rate constants (with differences less than 86%), and RPMD demonstrates better agreement (with differences less than 47%), although the temperature dependence is opposite to the experiment at low temperatures. Finally, for the F(2P) reaction, available experimental information shows discrepancies, both in the absolute values of the rate constants and also in the temperature dependence. Unfortunately, kinetics theories did not resolve this discrepancy. Different possible causes of these theory/experiment discrepancies were analyzed.

Ring polymer molecular dynamics and active learning of moment tensor potential for gas-phase barrierless reactions: Application to S + H2.

Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying full-dimensional potential energy surfaces (PESs) and the corresponding energy gradients are required. Recently, we have proposed a fully automated procedure based on combining the original RPMDrate code with active learning for PES on-the-fly using moment tensor potential and successfully applied it to two representative thermally activated chemical reactions [I. S. Novikov et al., Phys. Chem. Chem. Phys. 20, 29503-29512 (2018)]. In this work, using a prototype insertion chemical reaction S + H2, we show that this procedure works equally well for another class of chemical reactions. We find that the corresponding PES can be generated by fitting to less than 1500 automatically generated structures, while the RPMD rate coefficients show deviation from the reference values within the typical convergence error of the RPMDrate. We note that more structures are accumulated during the real-time propagation of the dynamic factor (the recrossing factor) as opposed to the previous study. We also observe that a relatively flat free energy profile along the reaction coordinate before entering the complex-formation well can cause issues with locating the maximum of the free energy surface for less converged PESs. However, the final RPMD rate coefficient is independent of the position of the dividing surface that makes it invulnerable to this problem, keeping the total number of necessary structures within a few thousand. Our work concludes that, in the future, the proposed methodology can be applied to realistic complex chemical reactions with various energy profiles.

Dynamics of H + HeH+(v = 0, j = 0) → H2+ + He: Insight on the Possible Complex-Forming Behavior of the Reaction.

The H + HeH+→ He + H2+ reaction has been studied by means of a combination of theoretical approaches: a statistical quantum method (SQM), ring polymer molecular dynamics (RPMD), and the quasiclassical trajectory (QCT) method. Cross sections and rate constants have been calculated in an attempt to investigate the dynamics of the process. The comparison with previous calculations and experimental results reveals that despite the fact that statistical predictions seem to reproduce some of the overall observed features, the analysis at a more detailed state-to-state level shows noticeable deviations from a complex-forming dynamics. We find some differences in cross sections and rate constants obtained in the QCT calculation with a Gaussian binning procedure with respect to previous works in which the standard histogram binning was employed.

Zero- and high-pressure mechanisms in the complex forming reactions of OH with methanol and formaldehyde at low temperatures.

A recent Ring Polymer Molecular Dynamics study of the reactions of OH with methanol and formaldehyde, at zero pressure and below 100 K, has shown the formation of long lived complexes, with long lifetimes, longer than 100 ns for the lower temperatures studied, 20-100 K (del Mazo-Sevillano et al., 2019). These long lifetimes support the existence of multi collision events with the He buffer-gas atoms under experimental conditions, as suggested by several transition state theory studies of these reactions. In this work we study these secondary collisions, as a dynamical approach to study pressure effects on these reactions. For this purpose, the potential energy surfaces of He with H2CO, OH, H2O and HCO are calculated at highly accurate ab initio level. The stability of some of the complexes is studied using Path Integral Molecular dynamics techniques, determining that OH-H2CO complexes can be formed up to 100 K or higher temperatures, while the weaker He-H2CO complexes dissociate at approximately 50 K. The predicted IR intensity spectra shows new features which could help the identification of the OH-H2CO complex. Finally, the He-H2CO + OH and OH-H2CO + He collisions are studied using quassi-classical trajectories, finding that the cross section to produce HCO + H2O products increases with decreasing collision energy, and that it is ten times higher in the He-H2CO + OH case.

Experimental and Theoretical Study of the O(1D) + HD Reaction.

This work addresses the kinetics and dynamics of the gas-phase reaction between O(1D) and HD molecules down to low temperature. Here, measurements were performed by using a supersonic flow (Laval nozzle) reactor coupled with pulsed laser photolysis for O(1D) production and pulsed-laser-induced fluorescence for O(1D) detection to obtain rate constants over the 50-300 K range. Additionally, temperature-dependent branching ratios (OD + H/OH + D) were obtained experimentally by comparison of the H/D atom atom yields with those of a reference reaction. In parallel, theoretical rate constants and branching ratios were calculated by using three different techniques; mean potential phase space theory (MPPST), the statistical quantum mechanical method (SQM), and ring polymer molecular dynamics (RPMD). Although the agreement between experimental and theoretical rate constants is reasonably good, with differences not exceeding 30% over the entire temperature range, the theoretical branching ratios derived by the MPPST and SQM methods are as much as 50% larger than the experimental ones. These results are presented in the context of earlier work, while the possible origins of the discrepancies between experiment and theory are discussed.

Quantum Roaming in the Complex-Forming Mechanism of the Reactions of OH with Formaldehyde and Methanol at Low Temperature and Zero Pressure: A Ring Polymer Molecular Dynamics Approach.

The quantum dynamics of the title reactions are studied using the ring polymer molecular dynamics (RPMD) method from 20 to 1200 K using recently proposed full dimensional potential energy surfaces which include long-range dipole-dipole interactions. A V-shaped dependence of the reaction rate constants is found with a minimum at 200-300 K, in rather good agreement with the current experimental data. For temperatures above 300 K the reaction proceeds following a direct H-abstraction mechanism. However, below 100 K the reaction proceeds via organic-molecule···OH collision complexes, with very long lifetimes, longer than 10-7 s, associated with quantum roaming arising from the inclusion of quantum effects by the use of RPMD. The long lifetimes of these complexes are comparable to the time scale of the tunnelling to form reaction products. These complexes are formed at zero pressure because of quantum effects and not only at high pressure as suggested by transition state theory (TST) calculations for OH + methanol and other OH reactions. The zero-pressure rate constants reproduce quite well measured ones below 200 K, and this agreement opens the question of how important the pressure effects on the reaction rate constants are, as implied in TST-like formalisms. The zero-pressure mechanism is applicable only to very low gas density environments, such as the interstellar medium, which are not repeatable by experiments.

The low temperature D+ + H2→ HD + H+ reaction rate coefficient: a ring polymer molecular dynamics and quasi-classical trajectory study.

The reaction between D+ and H2 plays an important role in astrochemistry at low temperatures and also serves as a prototype for a simple ion-molecule reaction. Its ground X[combining tilde]1A' state has a very small thermodynamic barrier (up to 1.8 × 10-2 eV) and the reaction proceeds through the formation of an intermediate complex lying within the potential well with a depth of at least 0.2 eV, thus representing a challenge for dynamical studies. In the present work, we analyze the title reaction within the temperature range of 20-100 K by means of ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) methods over the full-dimensional global potential energy surface developed by Aguado et al. [A. Aguado, O. Roncero, C. Tablero, C. Sanz and M. Paniagua, J. Chem. Phys., 2000, 112, 1240]. The computed thermal RPMD and QCT rate coefficients are found to be almost independent of temperature and fall within the range of 1.34-2.01 × 10-9 cm3 s-1. They are also in very good agreement with previous time-independent quantum mechanical and statistical quantum method calculations. Furthermore, we observe that the choice of asymptotic separation distance between the reactants can markedly alter the rate coefficient in the low temperature regime (20-50 K). Therefore it is of utmost importance to correctly assign the value of this parameter for dynamical studies, particularly at very low temperatures of astrochemical importance. We finally conclude that the experimental rate measurements for the title reaction are highly desirable in future.

Low temperature rates for key steps of interstellar gas-phase water formation.

The gas-phase formation of water molecules in the diffuse interstellar medium (ISM) proceeds mainly via a series of reactions involving the molecular ions OH+, H2O+, and H3O+ and molecular hydrogen. These reactions form the backbone for the chemistry leading to the formation of several complex molecular species in space. A comprehensive understanding of the mechanisms involved in these reactions in the ISM necessitates an accurate knowledge of the rate coefficients at the relevant temperatures (10 to 100 K). We present measurements of the rate coefficients for two key reactions below 100 K, which, in both cases, are significantly higher than the values used in astronomical models thus far. The experimental rate coefficients show excellent agreement with dedicated theoretical calculations using a novel ring-polymer molecular dynamics approach that offers a first-principles treatment of low-temperature barrierless gas-phase reactions, which are prevalent in interstellar chemical networks.

A Ring Polymer Molecular Dynamics Approach to Study the Transition between Statistical and Direct Mechanisms in the H2 + H3+ → H3+ + H2 Reaction.

Because of its fundamental importance in astrochemistry, the H2 + H3+ → H3+ + H2 reaction has been studied experimentally in a wide temperature range. Theoretical studies of the title reaction significantly lag primarily because of the challenges associated with the proper treatment of the zero-point energy (ZPE). As a result, all previous theoretical estimates for the ratio between a direct proton-hop and indirect exchange (via the H5+ complex) channels deviate from the experiment, in particular, at lower temperatures where the quantum effects dominate. In this work, the ring polymer molecular dynamics (RPMD) method is applied to study this reaction, providing very good agreement with the experiment. RPMD is immune to the shortcomings associated with the ZPE leakage and is able to describe the transition from direct to indirect mechanisms below room temperature. We argue that RPMD represents a useful tool for further studies of numerous ZPE-sensitive chemical reactions that are of high interest in astrochemistry.

A combined theoretical and experimental investigation of the kinetics and dynamics of the O(1D) + D2 reaction at low temperature.

The O(1D) + H2 reaction is a prototype for simple atom-diatom insertion type mechanisms considered to involve deep potential wells. While exact quantum mechanical methods can be applied to describe the dynamics, such calculations are challenging given the numerous bound quantum states involved. Consequently, efforts have been made to develop alternative theoretical strategies to portray accurately the reactive process. Here we report an experimental and theoretical investigation of the O(1D) + D2 reaction over the 50-296 K range. The calculations employ three conceptually different approaches - mean potential phase space theory, the statistical quantum mechanical method and ring polymer molecular dynamics. The calculated rate constants are in excellent agreement over the entire temperature range, exhibiting only weak temperature dependence. The agreement between experiment and theory is also very good, with discrepancies smaller than 26%. Taken together, the present and previous theoretical results validate the hypothesis that long-lived complex formation dominates the reaction dynamics at low temperature.

Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods.

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The present joint approach significantly outperforms previous manual and automated transition-state searches - 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Overall, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).

Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface.

We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300-1500 K, both theories agree within a factor of <2, reproducing the experimental behaviour taking into account the experimental uncertainties. At high temperatures, where the recrossing effects dominate and the RPMD theory is exact, both theories differ by a factor of about 20%; while at low temperatures this difference is larger, 45%. Note that in this temperature regime, the tunnelling effect is negligible. The CN + CH4/CD4 kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.

Low-Temperature Experimental and Theoretical Rate Constants for the O(1D) + H2 Reaction.

In the present joint experimental and theoretical study, we report thermal rate constants for the O(1D) + H2 reaction within the 50-300 K temperature range. Experimental kinetics measurements were performed using a continuous supersonic flow reactor coupled with pulsed laser photolysis for O(1D) production and pulsed laser-induced fluorescence in the vacuum ultraviolet wavelength range (VUV LIF) for O(1D) detection. Theoretical rate constants were obtained using the ring polymer molecular dynamics (RPMD) approach over the two lowest potential energy surfaces 11A' and 11A″, which possess barrierless and thermally activated energy profiles, respectively. Both the experimental and theoretical rate constants exhibit a weak temperature dependence. The theoretical results show the dominant role of the 11A' ground state and that contribution of the 11A″ excited state to the total thermal rate decreases dramatically at lower temperature. Agreement between the experimental and theoretical results is good, and the discrepancy does not exceed 25%. It is argued that these differences are likely to be due to nonadiabatic couplings between the 11A' and 21A' surfaces.

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes.

BACKGROUND: Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits. RESULTS: We have developed the SCOPA software to enable GWAS analysis of multiple correlated phenotypes. The software implements "reverse regression" methodology, which treats the genotype of an individual at a SNP as the outcome and the phenotypes as predictors in a general linear model. SCOPA can be applied to quantitative traits and categorical phenotypes, and can accommodate imputed genotypes under a dosage model. The accompanying META-SCOPA software enables meta-analysis of association summary statistics from SCOPA across GWAS. Application of SCOPA to two GWAS of high-and low-density lipoprotein cholesterol, triglycerides and body mass index, and subsequent meta-analysis with META-SCOPA, highlighted stronger association signals than univariate phenotype analysis at established lipid and obesity loci. The META-SCOPA meta-analysis also revealed a novel signal of association at genome-wide significance for triglycerides mapping to GPC5 (lead SNP rs71427535, p = 1.1x10-8), which has not been reported in previous large-scale GWAS of lipid traits. CONCLUSIONS: The SCOPA and META-SCOPA software enable discovery and dissection of multiple phenotype association signals through implementation of a powerful reverse regression approach.

An experimental and theoretical investigation of the C(1D) + D2 reaction.

In a previous joint experimental and theoretical study of the barrierless chemical reaction C(1D) + H2 at low temperatures (300-50 K) [K. M. Hickson, J.-C. Loison, H. Guo and Y. V. Suleimanov, J. Phys. Chem. Lett., 2015, 6, 4194], excellent agreement was found between experimental thermal rate constants and theoretical estimates based on ring polymer molecular dynamics (RPMD) over the two lowest singlet potential energy surfaces (PESs). Here, we extend this work to one of its isotopologues, C(1D) + D2, over the same temperature range. Experimental and RPMD results are in good agreement when contributions from both PESs to this chemical reaction are included in the RPMD simulations. The deviation between experiment and the RPMD calculations does not exceed 25% and both results exhibit a slight negative temperature dependence. The first excited 1A'' PES plays a more important role than the ground 1A' PES as the temperature is decreased, similar to our previous studies of the C(1D) + H2 reaction but with a more pronounced effect. The small differences in temperature dependence between the earlier and present experimental studies of C(1D) + H2/D2 reactions are discussed in terms of the use of non-equilibrium populations of ortho/para-H2/D2. We argue that RPMD provides a very convenient and reliable tool to study low-temperature chemical reactions.

Thermal Rate Coefficients for the Astrochemical Process C + CH+ → C2+ + H by Ring Polymer Molecular Dynamics.

Thermal rate coefficients for the astrochemical reaction C + CH+ → C2+ + H were computed in the temperature range 20-300 K by using novel rate theory based on ring polymer molecular dynamics (RPMD) on a recently published bond-order based potential energy surface and compared with previous Langevin capture model (LCM) and quasi-classical trajectory (QCT) calculations. Results show that there is a significant discrepancy between the RPMD rate coefficients and the previous theoretical results that can lead to overestimation of the rate coefficients for the title reaction by several orders of magnitude at very low temperatures. We argue that this can be attributed to a very challenging energy profile along the reaction coordinate for the title reaction, not taken into account in extenso by either the LCM or QCT approximation. In the absence of any rigorous quantum mechanical or experimental results, the computed RPMD rate coefficients represent state-of-the-art estimates to be included in astrochemical databases and kinetic networks.