Study Of Reaction Dynamics Research Articles

Two-dimensional reactive scattering with transmitted quantum trajectories

A simple and easy-to-implement method is presented for the study of time-dependent reaction dynamics by propagating an ensemble of transmitted quantum trajectories. During the trajectory evolution, reflected trajectories are gradually removed and all the remaining trajectories represent the transmitted subensemble. The removal process of reflected trajectories avoids numerical instabilities arising from node formation in the reactant region, and allows stable long-time propagation of transmitted trajectories. This method is applied to a two-dimensional model chemical reaction. Excellent computational results are obtained for the time-dependent reaction probabilities evaluated by the time integration of the probability flux. © 2014 Wiley Periodicals, Inc.

Laser sculpting of atomic sp, sp(2) , and sp(3) hybrid orbitals.

Atomic sp, sp(2) , and sp(3) hybrid orbitals were introduced by Linus Pauling to explain the nature of the chemical bond. Quantum dynamics simulations show that they can be sculpted by means of a selective series of coherent laser pulses, starting from the 1s orbital of the hydrogen atom. Laser hybridization generates atoms with state-selective electric dipoles, opening up new possibilities for the study of chemical reaction dynamics and heterogeneous catalysis.

Reaction coordinates for elucidating reaction dynamics with anharmonic couplings

Saddle points can be found on the potential energy surface between the reactants and products regions in many chemical reactions. The dynamics occurring in the vicinity of a saddle point play an essential role in the study of reaction dynamics because the reactivity of a trajectory is primarily determined in the saddle region. There are many cases where a well‐defined boundary (called reactivity boundary here) between reacting and nonreacting trajectories can be located in the phase space. Locating the reactivity boundary, however, becomes challenging when anharmonic couplings between the reaction coordinate and the vibrational coordinates complicate the reaction dynamics. The aim of this article is to present a review of recent studies that use nonlinear coordinate transformations to disentangle the anharmonic couplings. The reaction coordinates constructed through such nonlinear coordinate transformations are decoupled from the other coordinates as much as possible, thus simplifying analysis of reaction dynamics. Several options are introduced for nonlinear coordinate transformations which should be appropriately chosen by examining the extent of the anharmonic couplings. Under certain conditions, special reaction coordinates constructed by a suitable nonlinear coordinate transformation reveals the existence of a clear reactivity boundary in the phase space even when there are strong anharmonic couplings. © 2014 Wiley Periodicals, Inc.

Real time study of wet-chemical reaction dynamics at beamline P02.1 @ PETRA III

The high brilliance synchrotron light source PETRA III in Hamburg, Germany, provides a dedicated X-ray powder diffraction beamline called P02.1 [1]. It is a side station to the hard X-ray diffraction beamline and runs at a fixed photon energy of 60 keV. Its dispersive monochromator produces a highly collimated photon beam of very narrow energy bandwidth and high intensity. These excellent beam characteristics turn P02.1 into an ideal instrument for many different kinds of experiments, ranging from high resolution powder diffraction of polycrystalline materials for structure solution and refinement or microstructure analysis, to the study of nanocrystalline and disordered materials to determine their local structure. In particular, it is the scope of P02.1 to study dynamic processes such as chemical and crystallographic transitions under non-ambient conditions in real time. For this purpose, the beamline is equipped with a large and fast area detector which enables sub-second time-resolution. The accessible range in reciprocal space is beyond Q = 30 Å-1. Hence, P02.1 is a powerful tool for total scattering experiments as it provides high resolution in real and reciprocal space which are determined by the max. Q and the instrumental resolution, respectively. This presentation describes some recent experiments carried out at P02.1 that relate to pair distribution function (PDF) and total scattering analysis. The focus will be on the investigation of structural changes on the atomic scale during the wet-chemical synthesis of nanoparticles, e.g. in the system ZrO2. By means of evaluating the changes of bond distances and atomic coordination on a time scale of seconds, it is possible to describe the molecular structure of intermediates and, thus, to deduce the underlying reaction mechanism. On the basis of this information, synthesis processes may be optimised with respect to tuning the properties of the product and to maximize its yield.

Perimetric coordinate system in potential energy surfaces, spline interpolations, and the study of triatomic reaction dynamics

Two applications of the perimetric coordinates to triatomic potential energy surfaces are explored. The first is the depiction of level surfaces, providing a global visualization of the potential energy surface. In this representation, the relation among the stationary points and the dissociation channels are easily seen. These level surfaces are shown to be the natural generalization of the well-known two-dimensional level curves of restricted potential energy surfaces; they also allow us to understand the relation of the two-dimensional graphs with the global potential energy surface. Case studies for [Cl, H2], [H, O, Cl] and [O3] potential energy surfaces are discussed in detail. The second application of the perimetric coordinates is the construction of global potential energy surfaces by means of cubic splines, thus avoiding the restrictions related to the triangular inequality. The procedure is straightforward, and a careful analysis of the influence of the interpolation knots on the quality of the potential energy surface was carried out. The potential energy surfaces constructed by such procedure were able to reproduce known dynamical features of the following chemical reactions: Cl + H2 → H + HCl, F + HD → HF(DH) + D(H) and O(1D) + HCl → Cl + OH (H + OCl).

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.

Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A0

Molecular dynamics (MD) calculations, a semi-continuum (SC) approach, and quantum chemistry (QC) calculations were employed together to investigate the molecular mechanics of ultrafast charge separation reactions in Photosystem I (PS I) of Thermosynechococcus elongatus. A molecular model of PS I was developed with the aim to relate the atomic structure with electron transfer events in the two branches of cofactors. A structural flexibility map of PS I was constructed based on MD simulations, which demonstrated its rigid hydrophobic core and more flexible peripheral regions. The MD model permitted the study of atomic movements (dielectric polarization) in response to primary and secondary charge separations, while QC calculations were used to estimate the direct chemical effect of the A0A/A0B ligands (Met or Asn in the 688/668 position) on the redox potential of chlorophylls A0A/A0B and phylloquinones A1A/A1B. A combination of MD and SC approaches was used to estimate reorganization energies λ of the primary (λ1) and secondary (λ2) charge separation reactions, which were found to be independent of the active branch of electron transfer; in PS I from the wild type, λ1 was estimated to be 390±20mV, while λ2 was estimated to be higher at 445±15mV. MD and QC approaches were used to describe the effect of substituting Met688PsaA/Met668PsaB by Asn688PsaA/Asn668PsaB on the energetics of electron transfer. Unlike Met, which has limited degrees of freedom in the site, Asn was found to switch between two relatively stable conformations depending on cofactor charge. The introduction of Asn and its conformation flexibility significantly affected the reorganization energy of charge separation and the redox potentials of chlorophylls A0A/A0B and phylloquinones A1A/A1B, which may explain the experimentally observed slowdown of secondary electron transfer in the M688NPsaA variant. This article is part of a Special Issue entitled: Photosynthesis research for sustainability: Keys to produce clean energy.

Perspective: Bimolecular chemical reaction dynamics in liquids

Bimolecular reactions in the gas phase exhibit rich and varied dynamical behaviour, but whether a profound knowledge of the mechanisms of isolated reactive collisions can usefully inform our understanding of reactions in liquid solutions remains an open question. The fluctuating environment in a liquid may significantly alter the motions of the reacting particles and the flow of energy into the reaction products after a transition state has been crossed. Recent experimental and computational studies of exothermic reactions of CN radicals with organic molecules indicate that many features of the gas-phase dynamics are retained in solution. However, observed differences may also provide information on the ways in which a solvent modifies fundamental chemical mechanisms. This perspective examines progress in the use of time-resolved infra-red spectroscopy to study reaction dynamics in liquids, discusses how existing theories can guide the interpretation of experimental data, and suggests future challenges for this field of research.

Coriolis coupling effects in exact quantum scattering study of the isotopic reaction dynamics of [formula omitted

To study the Coriolis coupling (CC) effects on the reactions Ne+D2+/T2+, time-dependent quantum wave-packet scattering calculations are performed based on a new three-dimensional potential energy surface constructed by Lv et al. The CC and centrifugal sudden (CS) approximation reaction probabilities, the total reaction cross sections, and the rate constants are calculated over a collision energy range of 0.5–1.5eV. The CC reaction thresholds of both title reactions are lower than that of the CS reaction thresholds. Comparisons between the CC and CS cross sections for initial quantum numbers v=0 and j=0 reveal that neglecting the CC effect can significantly underestimate the reaction cross section. The thermal rate constants demonstrate that the mass difference induces the faster ion-molecular rotation of the D2+, which causes the reaction Ne+D2+ to occur easier than the reaction Ne+T2+. Initial vibrational excitation of the D2+/T2+ enhances the reactivity considerably.

Collective Autoionization in Multiply-Excited Systems: A novel ionization process observed in Helium Nanodroplets

Free electron lasers (FELs) offer the unprecedented capability to study reaction dynamics and image the structure of complex systems. When multiple photons are absorbed in complex systems, a plasma-like state is formed where many atoms are ionized on a femtosecond timescale. If multiphoton absorption is resonantly-enhanced, the system becomes electronically-excited prior to plasma formation, with subsequent decay paths which have been scarcely investigated to date. Here, we show using helium nanodroplets as an example that these systems can decay by a new type of process, named collective autoionization. In addition, we show that this process is surprisingly efficient, leading to ion abundances much greater than that of direct single-photon ionization. This novel collective ionization process is expected to be important in many other complex systems, e.g. macromolecules and nanoparticles, exposed to high intensity radiation fields.

Imaging Dynamics on the F + H 2 O → HF + OH Potential Energy Surfaces from Wells to Barriers

The study of gas-phase reaction dynamics has advanced to a point where four-atom reactions are the proving ground for detailed comparisons between experiment and theory. Here, a combined experimental and theoretical study of the dissociation dynamics of the tetra-atomic FH2O system is presented, providing snapshots of the F + H2O → HF + OH reaction. Photoelectron-photofragment coincidence measurements of the dissociative photodetachment (DPD) of the F(-)(H2O) anion revealed various dissociation pathways along different electronic states. A distinct photoelectron spectrum of stable FH-OH complexes was also measured and attributed to long-lived Feshbach resonances. Comparison to full-dimensional quantum calculations confirms the sensitivity of the DPD measurements to the subtle dynamics on the low-lying FH2O potential energy surfaces over a wide range of nuclear configurations and energies.

On the Choice of the Ab Initio Level of Theory for Potential Energy Surface Developments

We test the accuracy of various standard, explicitly correlated F12, and composite ab initio methods with different correlation consistent basis sets for high-dimensional potential energy surface (PES) developments, thereby providing a practical guidance for reaction dynamics studies. Relative potential energies are computed at 15 geometries covering the energy range and configuration space of chemical importance for each of the six prototypical polyatomic reactions, X + CH4 → HX + CH3 [X = F, O, Cl] and X(-) + CH3Y → Y(-) + CH3X [X/Y = F/F, OH/F, F/Cl]. The average accuracies of the Hartree-Fock and MP2 methods are 1500-8000 and 400-1000 cm(-1), respectively. The standard CCSD(T) method provides errors of 900-1400 and 250-450 cm(-1) with aug-cc-pVDZ and aug-cc-pVTZ basis sets, respectively. The explicitly correlated CCSD(T)-F12 method reduces the corresponding errors to about 200 and 100 cm(-1); thus, we recommend using the F12 methods for PES developments. For F12 computations, the cc-pVnZ-F12 [n = D and T] basis sets usually, but not always, perform better than the corresponding aug-cc-pVnZ bases. We do not find clear preference between the F12a and F12b methods for PES developments. Composite methods are advocated instead of standard CCSD(T) because for example, one can obtain CCSD(T)/aug-cc-pVnZ quality results on the expense of MP2/aug-cc-pVnZ [n = T and Q] computations. The post-CCSD(T), the core correlation, and the scalar relativistic effects are found to be ∼100, 80-130, and 10-50 cm(-1), respectively. The all-electron CCSD(T)/aug-cc-pCVnZ relative energies differ from the complete-basis-set limit by about 1000, 300, 100, and 50 cm(-1) for n = D, T, Q, and 5, respectively.

Nonstatistical dynamics on potentials exhibiting reaction path bifurcations and valley-ridge inflection points

We study reaction dynamics on a model potential energy surface exhibiting post-transition state bifurcation in the vicinity of a valley ridge inflection (VRI) point. We compute fractional yields of products reached after the VRI region is traversed, both with and without dissipation. It is found that apparently minor variations in the potential lead to significant changes in the reaction dynamics. Moreover, when dissipative effects are incorporated, the product ratio depends in a complicated and highly non-monotonic fashion on the dissipation parameter. Dynamics in the vicinity of the VRI point itself play essentially no role in determining the product ratio, except in the highly dissipative regime.

The application of reed-vibration mechanical spectroscopy for liquids to detect chemical reactions of an acrylic structural adhesive

There remain a number of unsolved problems about chemical reactions, and it is significant to explore new detection methods because they always offer some unique information about reactions from new points of view. For the first time, the solidification course of a modified two-component acrylic structural adhesive is measured by using reed-vibration mechanical spectroscopy for liquids (RMS-L) in this work, and results show that there are four sequential processes of mechanical spectra with time. The in-depth analyses indicate that RMS-L can detect in real-time the generation and disappearance of active free radicals, as well as the chemical cross-link processes in the adhesive. This kind of real-time detection will undoubtedly facilitate the study of the chemical reaction dynamics controlled by free radicals.

Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space

The ability to characterise and control matter far away from equilibrium is a frontier challenge facing modern science. In this article, we sketch out a heuristic structure for thinking about the different ways in which non-equilibrium phenomena can impact molecular reaction dynamics. Our analytical schema includes three different regimes, organised according to increasing dynamical resolution: at the lowest resolution, we have conformer phase space, at an intermediate resolution, we have energy space; and at the highest resolution, we have mode space. Within each regime, we discuss practical definitions of non-equilibrium phenomena, mostly in terms of the corresponding relaxation timescales. Using this analytical framework, we discuss some recent non-equilibrium reaction dynamics studies spanning isolated small-molecule ensembles, gas-phase ensembles and solution-phase ensembles. This includes new results that provide insight into how non-equilibrium phenomena impact the solution-phase alkene–hydroboration reaction. We emphasise that interesting non-equilibrium dynamical phenomena often occur when the relaxation timescales characterising each regime are similar. In closing, we reflect on outstanding challenges and future research directions to guide our understanding of how non-equilibrium phenomena impact reaction dynamics.

Communication: A six-dimensional state-to-state quantum dynamics study of the H + CH4 → H2 + CH3 reaction (J = 0)

We report a quantum state-to-state reaction dynamics study for the title reaction. The calculation was based on an approximation that we introduced to the eight-dimensional model for the X + YCZ(3) → XY + CZ(3) type of reactions that restricts the non-reacting CZ(3) group in C(3V) symmetry proposed by Palma and Clary [J. Chem. Phys. 112, 1859 (2000)], by assuming that the CZ(3) group can rotate freely with respect to its C(3V) symmetry axis. With the CH bond length in group fixed at its equilibrium distance, the degree of freedom included in the calculation was reduced to six. Our calculation shows that the six-dimensional treatment can produce reaction probabilities essentially indistinguishable from the seven-dimensional (with CH bond length fixed in the original eight-dimensional model) results. The product vibrational/rotational state distributions and product energy partitioning information are presented for ground initial rovibrational state with the total angular momentum J = 0.

Studies of bimolecular reaction dynamics using pulsed high-intensity vacuum-ultraviolet lasers for photoionization detection

This article describes recent progress on the development and application of pulsed high-intensity (~0.1 mJ per pulse) vacuum-ultraviolet (VUV) radiation produced by commercial tabletop lasers for studies of gas phase chemical reaction dynamics involving polyatomic free radicals. Our approach employs near-triply resonant four-wave mixing of unfocussed nanosecond dye lasers in an atomic gas as an alternative to the use of synchrotron light sources for sensitive universal soft photoionization detection of reaction products using a rotatable source crossed molecular beams apparatus with fixed detector. We illustrate this approach in studies of the reactions of phenyl radicals with molecular oxygen and with propene. Future prospects for the use of tabletop laser-based VUV sources for studies of chemical reaction dynamics are discussed.

Probing Quantum Dynamics of Elementary Chemical Reactions via Accurate Potential Energy Surfaces

Probing reaction potential energy surfaces is crucial for understanding chemical reaction dynamics and kinetics. The fundamental importance of the potential energy surface in understanding chemical reactivity was pointed out in the pioneering paper by Eyring and Polanyi in 1931 [1]. Accurate potential energy surfaces, however, are difficult to obtain. In the last few decades, more accurate quantum chemistry methods to calculate potential energy surfaces became available. In addition, quantum dynamics methods were also developed and allow us to study simple chemical reactions from first principles. Furthermore, modern crossed molecular beams studies provide an excellent testing ground for developing an accurate physical picture of elementary chemical reactions, through interplay between theory and experiment. In this paper, we review recent developments in the study of reaction dynamics of elementary chemical reactions through combined experimental and theoretical efforts. We will provide two examples to demonstrate the importance of accurate potential energy surfaces in understanding the essentials of reaction dynamics. One is the simplest chemical reaction: the H + H2 reaction, the other is the benchmark system for chemical reaction resonance: the F + H2 reaction. Through these studies, dynamics of chemical reactions can be understood at the most fundamental level.

Accelerating modified Shepard interpolated potential energy calculations using graphics processing units

The potential energy surfaces constructed with the modified Shepard interpolation scheme have been widely used in studies of chemical reaction dynamics. However, computational costs of interpolation increase rapidly with the size of the system and the number of data points needed to achieve a given accuracy. In this work, we present a naive Graphics Processing Unit (GPU)-accelerated algorithm for modified Shepard interpolated potential energy calculations and its implementation with the PGI CUDA Fortran language. The benchmark tests on a NVIDIA Tesla C2050 using four interpolated potential energy surfaces (one for H+H2O↔H2+OH, two for H+NH3↔H2+NH2 and one for H+CH4↔H2+CH3) demonstrated a speedup of 50-fold over the original CPU implementation on an Intel E5620 processor and the speedup increases with the system size and the number of data points. This work presents a promising GPU application in the field of chemical reaction dynamics.

Ion imaging study of reaction dynamics in the N+ + CH4 system

The velocity map ion imaging method is applied to the ion-molecule reactions of N(+) with CH(4). The velocity space images are collected at collision energies of 0.5 and 1.8 eV, providing both product kinetic energy and angular distributions for the reaction products CH(4)(+), CH(3)(+), and HCNH(+). The charge transfer process is energy resonant and occurs by long-range electron transfer that results in minimal deflection of the products. The formation of the most abundant product, CH(3)(+), proceeds by dissociative charge transfer rather than hydride transfer, as reported in earlier publications. The formation of HCNH(+) by C-N bond formation appears to proceed by two different routes. The triplet state intermediates CH(3)NH(+) and CH(2)NH(2)(+) that are formed as N(+)((3)P) approaches CH(4) may undergo sequential loss of two hydrogen atoms to form ground state HCNH(+) products on a spin-allowed pathway. However, the kinetic energy distributions for formation of HCNH(+) extend past the thermochemical limit to form HCNH(+) + 2H, implying that HCNH(+) may also be formed in concert with molecular hydrogen, and requiring that intersystem crossing to the singlet manifold must occur in a significant (~25%) fraction of reactive collisions. We also report GAUSSIAN G2 calculations of the energies and structures of important singlet and triplet [CNH(4)(+)] complexes that serve as precursors to product formation.