Search

We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H2, D + MuH, and F + H2, and the prototypical polyatomic reaction H + CH4. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method. [ABSTRACT FROM AUTHOR]

Following our previous study of prototypical insertion reactions of energetically asymmetric type with the RPMD (Ring-Polymer Molecular Dynamics) method [Y. Li, Y. Suleimanov, and H. Guo, J. Phys. Chem. Lett. 5, 700 (2014)], we extend it to two other prototypical insertion reactions with much less exothermicity (near thermoneutral), namely, (X + H2) → HX + H(X = C(¹D), S(¹D), in order to assess the accuracy of this method for calculating thermal rate coefficients for this class of reactions. For both chemical reactions, RPMD displays remarkable accuracy and agreement with the previous quantum dynamic results that make it encouraging for the future application of the RPMD to other barrier-less, complex-forming reactions involving polyatomic reactants with any exothermicity. [ABSTRACT FROM AUTHOR]

In a recent paper, we have developed an efficient implementation of the ring polymer molecular dynamics (RPMD) method for calculating bimolecular chemical reaction rates in the gas phase, and illustrated it with applications to some benchmark atom-diatom reactions. In this paper, we show that the same methodology can readily be used to treat more complex polyatomic reactions in their full dimensionality, such as the hydrogen abstraction reaction from methane, H + CH4→ H2 + CH3. The present calculations were carried out using a modified and recalibrated version of the Jordan-Gilbert potential energy surface. The thermal rate coefficients obtained between 200 and 2000 K are presented and compared with previous results for the same potential energy surface. Throughout the temperature range that is available for comparison, the RPMD approximation gives better agreement with accurate quantum mechanical (multiconfigurational time-dependent Hartree) calculations than do either the centroid density version of quantum transition state theory (QTST) or the quantum instanton (QI) model. The RPMD rate coefficients are within a factor of 2 of the exact quantum mechanical rate coefficients at temperatures in the deep tunneling regime. These results indicate that our previous assessment of the accuracy of the RPMD approximation for atom-diatom reactions remains valid for more complex polyatomic reactions. They also suggest that the sensitivity of the QTST and QI rate coefficients to the choice of the transition state dividing surface becomes more of an issue as the dimensionality of the reaction increases. [ABSTRACT FROM AUTHOR]

Collision properties of atoms and molecules in low temperature gases can be controlled by applying an external magnetic or electric field. The external field shifts the energy levels of the colliding particles, which gives rise to Feshbach resonances modifying the scattering cross sections. The resonances occur at particular magnitudes of the external field, where a bound state of the collision complex is degenerate with a scattering state. The positions of the resonances in the external field are usually identified by computing either the scattering cross sections or the bound states of the collision complex as functions of the external field magnitude. We propose a more efficient method for locating Feshbach resonances that requires neither of these computations. In particular, we show that the positions of Feshbach resonances can be identified by computing the log-derivative of the total wave function in a classically allowed region as a function of the external field strength. This procedure is particularly useful for locating narrow Feshbach resonances that may be hard to identify with the other methods. [ABSTRACT FROM AUTHOR]

We describe an efficient procedure for calculating the rates of bimolecular chemical reactions in the gas phase within the ring polymer molecular dynamics approximation. A key feature of the procedure is that it does not require that one calculate the absolute quantum mechanical partition function of the reactants or the transition state: The rate coefficient only depends on the ratio of these two partition functions which can be obtained from a thermodynamic integration along a suitable reaction coordinate. The procedure is illustrated with applications to the three-dimensional H+H2, Cl+HCl, and F+H2 reactions, for which well-converged quantum reactive scattering results are computed for comparison. The ring polymer rate coefficients agree with these exact results at high temperatures and are within a factor of 3 of the exact results at temperatures in the deep quantum tunneling regime, where the classical rate coefficients are too small by several orders of magnitude. This is probably already good enough to encourage future applications of the ring polymer theory to more complex chemical reactions, which it is capable of treating in their full dimensionality. However, there is clearly some scope for improving on the ring polymer approximation at low temperatures, and we end by suggesting a way in which this might be accomplished. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 METASCOPA 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 metaanalysis 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions. [ABSTRACT FROM AUTHOR]

Thermal rate constants and several kinetic isotope effects were evaluated for the OH + CH4 hydrogen abstraction reaction using two kinetics approaches, ring polymer molecular dynamics (RPMD) and variational transition state theory with multidimensional tunneling (VTST/MT), based on a refined full-dimensional analytical potential energy surface, PES-2014, in the temperature range 200-2000 K. For the OH + CH4 reaction, at low temperatures, T = 200 K, where the quantum tunneling effect is more important, RPMD overestimates the experimental rate constants due to problems associated with PES-2014 in the deep tunneling regime and to the known overestimation of this method in asymmetric reactions, while VTST/MT presents a better agreement, differences about 10%, due to compensation of several factors, inaccuracy of PES-2014, and ignoring anharmonicity. In the opposite extreme, T = 1000 K, recrossing effects play the main role, and the difference between both methods is now smaller, by a factor of 1.5. Given that RPMD results are exact in the high-temperature limit, the discrepancy is due to the approaches used in the VTST/MT method, such as ignoring the anharmonicity of the lowest vibrational frequencies along the reaction path, which leads to an incorrect location of the dividing surface between reactants and products. The analysis of several kinetic isotope effects, OH + CD4, OD + CH4, and OH + 12CH4/13CH4, sheds light on these problems and confirms the previous conclusions. In general, the agreement with the available experimental data is reasonable, although discrepancies persist, and they have been analyzed as a function of the many factors affecting the theoretical calculations: limitations of the kinetics methods and of the potential energy surface, and uncertainties in the experimental measurements. Finally, in the absence of full-dimensional quantum mechanics calculations, this study represents an additional step in understanding this seven-atom hydrogen abstraction reaction. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Thermal rate coefficients and kineticisotope effect have been calculated for prototypical heavy–light–heavypolyatomic bimolecular reactions Cl + CH4/CD4→ HCl/DCl + CH3/CD3, using a recentlyproposed quantum dynamics approach: ring polymer molecular dynamics(RPMD). Agreement with experimental rate coefficients, which are quitescattered, is satisfactory. However, differences up to 50% have beenfound between the RPMD results and those obtained from the harmonicvariational transition-state theory on one of the two full-dimensionalpotential energy surfaces used in the calculations. Possible reasonsfor such discrepancy are discussed. The present work is an importantstep in a series of benchmark studies aimed at assessing accuracyfor RPMD for chemical reaction rates, which demonstrates that thisnovel method is a quite reliable alternative to previously developedtechniques based on transition-state theory. [ABSTRACT FROM AUTHOR]

A correction to the article "Bimolecular reaction rates from ring polymer molecular dynamics" is presented.

[Display omitted] • RPMD rate constants for the reaction DH + H → D + H 2 are reported. • RPMD simulation parameters should be carefully chosen at low temperatures. • Standard parameters of the RPMDrate code can be used at high temperatures. Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for the thermally activated reaction DH + H → D + H 2 , we calculate the RPMD rate constants at T = 50 , 100, and 300 K and demonstrate that for T ≥ 100 K the standard input parameters yield accurate results, but at low temperatures (e.g., 50 K) one must increase the asymptotic distance and force constant, and decrease the umbrella integration step. [ABSTRACT FROM AUTHOR]

We combined Moment Tensor Potential (MTP) and Ring Polymer Molecular Dynamics (RPMD) for calculating the thermal rate constants of the OH + HBr system. We used the active learning (AL) algorithm for constructing a training set during RPMD. We compared the obtained RPMD-AL-MTP rate constants with the ones previously calculated using the quasi-classical trajectories (QCT) and the POTLIB potential energy surface, and with the experimental ones. We demonstrated that the RPMD rate constants were systematically closer to the experimental rate constants than the QCT ones at 200 K, 300 K, and 500 K. [Display omitted] • AL-MTP and RPMD were used for automatic calculation of the rate constants for OH+HBr. • The rate constants were calculated with RPMD-AL-MTP at 200 K, 300 K, and 500 K. • RPMD rate constants are closer to the experimental ones than the QCT rate constants. [ABSTRACT FROM AUTHOR]

The thermal rate coefficients and kinetic isotope effects have been calculated using ring polymer molecular dynamics (RPMD) for the prototypical reactions between methane and several hydrogen isotopes (H, D, and Mu). The excellent agreement with the theoretical rate coefficients of the H + CH4 reaction obtained previously from a multi-configuration time-dependent Hartree calculation on the same potential energy surface provides strong evidence for the accuracy of the RPMD approach. These quantum mechanical rate coefficients are also in good agreement with the results obtained previously using the transition-state theory with semi-classical tunneling corrections for the H/D + CH4 reactions. However, it is shown that the RPMD rate coefficients for the ultralight Mu reaction with CH4 are significantly smaller than the experimental data, presumably suggesting inaccuracies in the potential energy surface and/or experimental errors. Significant discrepancies between the RPMD and transition-state theory results have also been found for this challenging system. [ABSTRACT FROM AUTHOR]

A correction to the article "Bimolecular reaction rates from ring polymer molecular dynamics" that was published in the May 7, 2009 issue is presented.

Review: 109 refs. [ABSTRACT FROM AUTHOR]

The article cites a research study that examines the gas-phase formation of water molecules in the diffuse interstellar medium (ISM). It is said that the process proceeds mainly through a series of reactions involving the molecular ions and molecular hydrogen. The researchers measure the rate coefficients for two key reactions below 100 Kelvin.

Nonadiabatic transitions among the first-tier ion-pair states of the iodine molecule in collisions with CF4 and SF6 partners are investigated by detecting the luminescence following the optical-optical double resonance excitation of the E0g+-state to the vibrational levels vE=8, 13, and 19. Total and partial rate constants, as well as vibrational product state distributions, are determined. It is found that electronic energy transfer in all channels is predominantly assisted by excitation of the dipole-allowed ν3 and ν4 modes of the partner. The measurements are accompanied by quantum scattering calculations that implement a close coupling treatment for the electronic and vibrational degrees of freedom and combine diatomics-in-molecule and long-range models for diabatic potential energy surfaces and coupling matrix elements. The analysis of experimental and theoretical data shows that the transitions without excitation of the partner are due to short-range couplings, whereas the vibrational excitation of the partner in the D0u+ channel originates from the long-range coupling of two transition dipole moments: electronic of the iodine molecule and vibrational of the partner. Unexpectedly efficient excitations of the partner in the other ion-pair states, which are not coupled to the initial E0g+-state by the transition dipole, are interpreted within the postcollision mechanism. Qualitatively, this implies that during a single collision the long-range nonadiabatic transitions to D, ν3 and D, ν4 channels are followed by secondary short-range transitions without changing the state of the partner. [ABSTRACT FROM AUTHOR]

Collisions of Br2, prepared in the E(0g+) ion-pair (IP) electronic state, with He or Ar result in electronic energy transfer to the D, D′, and β IP states. These events have been examined in experimental and theoretical investigations. Experimentally, analysis of the wavelength resolved emission spectra reveals the distribution of population in the vibrational levels of the final electronic states and the relative efficiencies of He and Ar collisions in promoting a specific electronic energy transfer channel. Theoretically, semiempirical rare gas-Br2 potential energy surfaces and diabatic couplings are used in quantum scattering calculations of the state-to-state rate constants for electronic energy transfer and distributions of population in the final electronic state vibrational levels. Agreement between theory and experiment is excellent. Comparison of the results with those obtained for similar processes in the IP excited I2 molecule points to the general importance of Franck–Condon effects in determining vibrational populations, although this effect is more important for He collisions than for Ar collisions. [ABSTRACT FROM AUTHOR]

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). [ABSTRACT FROM AUTHOR]

The rate constant for the H atom abstraction reaction from methane by the muonic helium atom, Heμ + CH4 → HeμH + CH3, is reported at 500 K and compared with theory, providing an important test of both the potential energy surface (PES) and reaction rate theory for the prototypical polyatomic CH5 reaction system. The theory used to characterize this reaction includes both variational transition-state (CVT/μOMT) theory (VTST) and ring polymer molecular dynamics (RPMD) calculations on a recently developed PES, which are compared as well with earlier calculations on different PESs for the H, D, and Mu + CH4 reactions, the latter, in particular, providing for a variation in atomic mass by a factor of 36. Though rigorous quantum calculations have been carried out for the H + CH4 reaction, these have not yet been extended to the isotopologues of this reaction (in contrast to H3), so it is important to provide tests of less rigorous theories in comparison with kinetic isotope effects measured by experiment. In this regard, the agreement between the VTST and RPMD calculations and experiment for the rate constant of the Heμ + CH4 reaction at 500 K is excellent, within 10% in both cases, which overlaps with experimental error. [ABSTRACT FROM AUTHOR]

Comprehensive mechanistic studies on the enantioselective aldol reaction between isatin ( 1 a) and acetone, catalyzed by L-leucinol ( 3 a), unraveled that isatin, apart from being a substrate, also plays an active catalytic role. Conversion of the intermediate oxazolidine 4 into the reactive syn-enamine 6, catalyzed by isatin, was identified as the rate-determining step by both the calculations (Δ G≠=26.1 kcal mol−1 for the analogous L-alaninol, 3 b) and the kinetic isotope effect ( kH/ kD=2.7 observed for the reaction using [D6]acetone). The subsequent reaction of the syn-enamine 6 with isatin produces ( S)- 2 a (calculated Δ G≠=11.6 kcal mol−1). The calculations suggest that the overall stereochemistry is controlled by two key events: 1) the isatin-catalyzed formation of the syn-enamine 6, which is thermodynamically favored over its anti-rotamer 7 by 2.3 kcal mol−1; and 2) the high preference of the syn-enamine 6 to produce ( S)- 2 a on reaction with isatin ( 1 a) rather than its enantiomer (ΔΔ G≠=2.6 kcal mol−1). [ABSTRACT FROM AUTHOR]

The kinetic isotope effect (KIE) of the seven-atom reactions OH + CH4 → CH3 + H2O and OH + CD4 → CD3 + HDO over the temperature range 200-1000 K is investigated using ring polymer molecular dynamics (RPMD) on a full-dimensional potential energy surface. A comparison of RPMD with previous theoretical results obtained using transition state theory shows that RPMD is a more reliable theoretical approach for systems with more than 6 atoms, which provides a predictable level of accuracy. We show that the success of RPMD is a direct result of its independence of the choice of transition state dividing surface, a feature that is not shared by any of the transition state theory-based methods. Our results demonstrate that RPMD is a prospective method for studies of KIEs for polyatomic reactions for which rigorous quantum mechanical calculations are currently impossible. [ABSTRACT FROM AUTHOR]

A catalyst's catalyst Investigation of the leucinol ‐ catalyzed aldol reaction of isatin with acetone revealed an intriguing and unusual mechanistic concept: apart from being a substrate, isatin also acts as a dichotomous co ‐ catalyst that accelerates the turnover ‐ limiting step: the formation of the reactive syn ‐ enamine. This concept resembles that of a wind turbine: only when the wind is blowing, that is, when the starting material is present, rotation commences and gives rise to the desired product. For more details, see the Full Paper by M. A. Kabeshov, A. V. Malkov, P. Kočovský, and co ‐ workers on page 12026 ff. [ABSTRACT FROM AUTHOR]