Roaming in acetaldehyde

We investigate roaming in the photodissociation of acetaldehyde (CH3CHO), providing insights into the contrasting roaming dynamics observed for this molecule compared to formaldehyde. We carry out trajectory studies for full-dimensional acetaldehyde, supplemented with an analysis of a two-degree-of-freedom restricted model and obtain evidence for two distinct roaming pathways. Trajectories exhibit roaming at both shorter (9-11.5 au) and larger (14.5-22.9 au) maximum CH3-HCO separations, characterized by differing amounts of HCO rotation. No roaming trajectories were found in the intervening gap region. The roaming dynamics near 14.5-22.9 au are well-reproduced by the restricted model and involve passage through a centrifugal barrier, analogous to formaldehyde roaming. However, the shorter-range 9-11.5 au roaming appears unique to acetaldehyde and is likely facilitated by repulsive interactions absent in the simplified models. Phase space analysis reveals that this additional roaming pathway is inaccessible in the reduced dimensionality system. The findings suggest that acetaldehyde's increased propensity for roaming compared to formaldehyde may arise from the presence of multiple distinct roaming mechanisms rather than solely the higher roaming fragment mass.

CARNOT: a Fragment-Based Direct Molecular Dynamics and Virtual-Reality Simulation Package for Reactive Systems

Traditionally, the study of reaction mechanisms of complex reaction systems such as combustion has been performed on an individual basis by optimizations of transition structure and minimum energy path or by reaction dynamics trajectory calculations for one elementary reaction at a time. It is effective, but time-consuming, whereas important and unexpected processes could have been missed. In this article, we present a direct molecular dynamics (DMD) approach and a virtual-reality simulation program, CARNOT, in which plausible chemical reactions are simulated simultaneously at finite temperature and pressure conditions. A key concept of the present ab initio molecular dynamics method is to partition a large, chemically reactive system into molecular fragments that can be adjusted on the fly of a DMD simulation. The theory represents an extension of the explicit polarization method to reactive events, called ReX-Pol. We propose a highest-and-lowest adapted-spin approximation to define the local spins of individual fragments, rather than treating the entire system by a delocalized wave function. Consequently, the present ab initio DMD can be applied to reactive systems consisting of an arbitrarily varying number of closed and open-shell fragments such as free radicals, zwitterions, and separate ions found in combustion and other reactions. A graph-data structure algorithm was incorporated in CARNOT for the analysis of reaction networks, suitable for reaction mechanism reduction. Employing the PW91 density functional theory and the 6-31+G(d) basis set, the capabilities of the CARNOT program were illustrated by a combustion reaction, consisting of 28 650 atoms, and by reaction network analysis that revealed a range of mechanistic and dynamical events. The method may be useful for applications to other types of complex reactions.

Quantum resonances and roaming dynamics in formaldehyde photodissociation

The unimolecular dissociation of formaldehyde is studied via excitation to the à band at several excitation energies from just below the ground state radical dissociation threshold to 5000 cm-1 above...

Spiers Memorial Lecture: theory of unimolecular reactions

One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our...

Quantum interference in the mechanism of H + LiH+ → H2 + Li+ reaction dynamics

In this work, the detailed reaction mechanism of the astrochemically relevant exoergic and barrierless H + LiH⁺ → H₂ + Li⁺ reaction is investigated by both time-dependent wave packet and quasi-classical trajectory (QCT) methods on the ab initio electronic ground state potential energy surface reported by Martinazzo et al. [Martinazzo et al., J. Chem. Phys., 2003, 119, 11241]. The interference terms due to the coherence between the partial waves are quantified. When plotted along the scattering angle they reveal interference of constructive or destructive nature. Significant interference was found in the differential cross-section (DCS) which is a symbolic of the non-statistical nature of the reaction. This is further complemented by calculating the lifetime of the collision complex by the QCT method. It is found that the reaction follows a direct stripping mechanism at higher collision energies and yields forward scattered products from collisions involving high total angular momentum. At low collision energies, the reaction follows a mixed direct/indirect mechanism but with a dominant indirect contribution. The product state-resolved DCSs reveal that two opposite mechanisms co-exist, both at low and high collision energies. The microscopic scattering mechanism of the reaction is found to be unaffected by the ro-vibrational excitation of the reagent diatom.

Orbiting resonances in formaldehyde reveal coupling of roaming, radical, and molecular channels

[Figure: see text].

Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories

In this paper, we report how graph theory can be used to analyze an ensemble of independent molecular trajectories, which can react during the simulation time-length, and obtain structural and kinetic information. This method is totally general and here is applied to the prototypical case of gas phase fragmentation of protonated cyclo-di-glycine. This methodology allows us to analyze the whole set of trajectories in an automatic computer-based way without the need of visual inspection but by getting all the needed information. In particular, we not only determine the appearance of different products and intermediates but also characterize the corresponding kinetics. The use of colored graph and canonical labeling allows for the correct characterization of the chemical species involved. In the present case, the simulations consist of an ensemble of unimolecular fragmentation trajectories at constant energy such that from the rate constants at different energies, the threshold energy can also be obtained for both global and specific pathways. This approach allows for the characterization of ion-molecule complexes, likely through a roaming mechanism, by properly taking into account the elusive nature of such species. Finally, it is possible to directly obtain the theoretical mass spectrum of the fragmenting species if the reacting system is an ion as in the specific example.

Application of Reaction Path Search Calculations to Potential Energy Surface Fits

There has been significant progress in recent years in the use of machine learning techniques to model high-dimensional reactive potential energy surfaces using large-scale data obtained from ab initio electronic structure calculations. In these methods, the strategy used to gather data becomes a key issue as the molecular size increases. In this work, we examine the applicability of the reaction path search algorithm implemented in the Global Reaction Route Mapping (GRRM) code as a data-gathering approach. The electronic energies and gradients sampled by using the GRRM calculation are directly used in potential energy surface fitting to a permutationally invariant polynomial function. This simple approach was applied to the HNS and HCNO reaction systems, and we found that the fitted potential energy surfaces reasonably reproduce the features of the electronic structure calculations used in the GRRM calculations. This suggests that the GRRM sampling scheme can be used to construct an initial potential energy surface.

Photodissociation Dynamics of CO-Forming Channels on the Ground-State Surface of Methyl Formate at 248 nm: Direct Dynamics Study and Assessment of Generalized Multicenter Impulsive Models

The photodissociation dynamics of methyl formate in the electronic ground state S₀, initiated by a 248 nm-wavelength laser, is studied by direct dynamics simulations. We analyze five channels, where four of them have as products CH₃OH + CO, one leading to the formation of three fragments, H₂CO + H₂ + CO, and a channel characterized by a roaming transition state. The analysis of energy distribution among the degrees of freedom of the product and the comparison with experimental results previously published by other groups provide the ingredients to distinguish the examined dissociation pathways. The interpretation of the results proves that the characterization of dissociation mechanisms must rely on a dynamics approach involving multiple electronic states, including considerations on the features of the S₁/S₀ conical intersection. Here, we also assess the generalized multicenter impulsive model, GMCIM, that has been designed for dissociation processes with exit barriers, and the energy distribution in the products is predicted on the basis of information from the saddle points and the intrinsic reaction coordinates. Main features, advantages, limits, and future perspectives of the method are reported and discussed.

Reactions in Tirapazamine Induced by the Attachment of Low-Energy Electrons: Dissociation Versus Roaming of OH

Tirapazamine (TPZ) has been tested in clinical trials on radio-chemotherapy due to its potential highly selective toxicity towards hypoxic tumor cells. It was suggested that either the hydroxyl radical or benzotriazinyl radical may form as bioactive radical after the initial reduction of TPZ in solution. In the present work, we studied low-energy electron attachment to TPZ in the gas phase and investigated the decomposition of the formed TPZ- anion by mass spectrometry. We observed the formation of the (TPZ-OH)- anion accompanied by the dissociation of the hydroxyl radical as by far the most abundant reaction pathway upon attachment of a low-energy electron. Quantum chemical calculations suggest that NH2 pyramidalization is the key reaction coordinate for the reaction dynamics upon electron attachment. We propose an OH roaming mechanism for other reaction channels observed, in competition with the OH dissociation.

Identifying reaction pathways in phase space via asymptotic trajectories

In this paper, we revisit the concepts of the reactivity map and the reactivity bands as an alternative to the use of perturbation theory for the determination of the phase space geometry of chemical reactions. We introduce a reformulated metric, called the asymptotic trajectory indicator, and an efficient algorithm to obtain reactivity boundaries. We demonstrate that this method has sufficient accuracy to reproduce phase space structures such as turnstiles for a 1D model of the isomerization of ketene in an external field. The asymptotic trajectory indicator can be applied to higher dimensional systems coupled to Langevin baths as we demonstrate for a 3D model of the isomerization of ketene.

Roaming Reactions and Dynamics in the van der Waals Region

Roaming reactions were first clearly identified in photodissociation of formaldehyde 15 years ago, and roaming dynamics are now recognized as a universal aspect of chemical reactivity. These reactions typically involve frustrated near-dissociation of a quasibound system to radical fragments, followed by reorientation at long range and intramolecular abstraction. The consequences can be unexpected formation of molecular products, depletion of the radical pool in chemical systems, and formation of products with unusual internal state distributions. In this review, I examine some current aspects of roaming reactions with an emphasis on experimental results, focusing on possible quantum effects in roaming and roaming dynamics in bimolecular systems. These considerations lead to a more inclusive definition of roaming reactions as those for which key dynamics take place at long range.

Strong inverse kinetic isotope effect observed in ammonia charge exchange reactions

Isotopic substitution has long been used to understand the detailed mechanisms of chemical reactions; normally the substitution of hydrogen by deuterium leads to a slower reaction. Here, we report our findings on the charge transfer collisions of cold [Formula: see text] ions and two isotopologues of ammonia, [Formula: see text] and [Formula: see text]. Deuterated ammonia is found to react more than three times faster than hydrogenated ammonia. Classical capture models are unable to account for this pronounced inverse kinetic isotope effect. Moreover, detailed ab initio calculations cannot identify any (energetically accessible) crossing points between the reactant and product potential energy surfaces, indicating that electron transfer is likely to be slow. The higher reactivity of [Formula: see text] is attributed to the greater density of states (and therefore lifetime) of the deuterated reaction complex compared to the hydrogenated system. Our observations could provide valuable insight into possible mechanisms contributing to deuterium fractionation in the interstellar medium.

Intramolecular vibrational energy redistribution and the quantum ergodicity transition: a phase space perspective

The onset of facile intramolecular vibrational energy flow can be related to features in the connected network of anharmonic resonances in the classical phase space.

The separation of the reaction coordinate in transition state theory: Regularity and dimensionality reduction resulting from local symmetry

Local symmetry in a transition state is defined as the absence of cross terms involving the reaction coordinate in the Taylor expansion about a saddle point of a potential energy surface (i.e., by the assumption ∂²V/∂R∂q_j|_* = 0). Then, the plane R = R_* is, but in the immediate neighborhood of the saddle point only, a local plane of symmetry of the potential energy surface. When this decisive condition is met, together with a second requirement that the kinetic energy be diagonal, the reaction dynamics becomes extremely simple, even in a multidimensional system, because it is determined solely by the harmonic part of the potential, at least during the early stages of the evolution. The dimensionality of the system is then reduced, with the reaction coordinate neatly separated from the vibrational degrees of freedom. The latter are then spectators that can only interact among themselves. As a result of this local symmetry, the subset of reactive trajectories is, during an appreciable period of time, observed to form a bundle grouped around an average trajectory. The distance separating the centers of mass of the two dissociating fragments is the appropriate reaction coordinate. The dynamical reaction path, defined as the central curve of a reactive cylinder in phase space, can be derived in closed form as a surprisingly simple one-dimensional law of motion and can be said to derive from a 1D effective Hamiltonian. An alternative formulation of the problem is possible, in which bond lengths are adopted as internal coordinates, although the expression of the kinetic energy becomes much more complicated. Explicit conditions under which the reaction coordinate decouples from spectator modes can be stipulated.

Imaging the infrared multiphoton excitation and dissociation of propargyl chloride

Infrared multiphoton excitation is combined with UV excitation and state-resolved probes of Cl(²P_3/2), Cl*(²P_1/2), and HCl to study the photochemistry of propargyl chloride. The results show evidence both of infrared multiphoton dissociation on the ground electronic state and infrared multiphoton excitation followed by UV dissociation. The results are interpreted with the aid of a full characterization of the stationary points on the ground state using ab initio methods, as well as our recent experimental and theoretical characterization of the UV photochemistry of the molecule. The data suggest elimination of HCl on the ground electronic state produces linear propadienylidene as a coproduct over a roaming-like transition state that accesses the Cl-H-C abstraction geometry. This identification is supported by separate chirped-pulse microwave studies in a quasi-uniform flow also reported here.

UV photofragmentation dynamics of acetaldehyde cations prepared by single-photon VUV ionization

UV excitation of cold acetaldehyde cations prepared by single-photon VUV ionization results in remarkably rich photochemistry.

Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions

A post-transition state bifurcation (PTSB) involved in a Pummerer-type rearrangement is characterized using density functional theory (DFT) calculations on potential energy stationary points and direct dynamics simulations. A sensitivity of the ratio of products produced via this PTSB to solvent dielectric constant is revealed and implications of such a dependence for selectivity control of organic reactions are discussed.

Sampling Phase Space Dividing Surfaces Constructed from Normally Hyperbolic Invariant Manifolds (NHIMs)

In this paper, we further investigate the construction of a phase space dividing surface (DS) from a normally hyperbolic invariant manifold (NHIM) and the sampling procedure for the resulting dividing surface described in earlier work ( Wiggins , S. ; J. Chem. Phys. 2016 , 144 , 054107 ). Our discussion centers on the relationship between geometrical structures and dynamics for 2 and 3 degree of freedom (DoF) systems, specifically, the construction of a DS from a NHIM. We show that if the equation for the NHIM and associated DS is known (e.g., as obtained from Poincaré-Birkhoff normal form theory), then the numerical procedure described in Wiggins et al. ( J. Chem. Phys. 2016 , 144 , 054107 ) gives the same result as a sampling method based upon the explicit form of the NHIM. After describing the sampling procedure in a general context, it is applied to a quadratic Hamiltonian normal form near an index-one saddle where explicit formulas exist for both the NHIM and the DS. It is shown for both 2 and 3 DoF systems that a version of the general sampling procedure provides points on the analytically defined DS with the correct microcanonical density on the constant-energy DS. Excellent agreement is obtained between analytical and numerical averages of quadratic energy terms over the DS for a range of energies.

A generalized unimolecular impulsive model for curved reaction path

This work aims to introduce a generalized impulsive model for unimolecular dissociation processes. This model allows us to take into account the curvature of the reaction path explicitly. It is a generalization of the previously developed multi-center impulsive model [P.-Y. Tsai and K.-C. Lin, J. Phys. Chem. A 119, 29 (2015)]. Several limitations of conventional impulsive models are eliminated by this study: (1) Unlike conventional impulsive models, in which a single molecular geometry is responsible for the impulse determination, the gradients on the whole dissociation path are taken into account. The model can treat dissociation pathways with large curvatures and loose saddle points. (2) The method can describe the vibrational excitation of polyatomic fragments due to the bond formation by multi-center impulse. (3) The available energy in conventional impulsive models is separated into uncoupled statistical and impulsive energy reservoirs, while the interplay between these reservoirs is allowed in the new model. (4) The quantum state correlation between fragments can be preserved in analysis. Dissociations of several molecular systems including the roaming pathways of formaldehyde, nitrate radical, acetaldehyde, and glyoxal are chosen as benchmarks. The predicted photofragment energy and vector distributions are consistent with the experimental results reported previously. In these examples, the capability of the new model to treat the curved dissociation path, loose saddle points, polyatomic fragments, and multiple-body dissociation is verified. As a cheaper computational tool with respect to ab initio on-the-fly direct dynamic simulations, this model can provide detailed information on the energy disposal, quantum state correlation, and stereodynamics in unimolecular dissociation processes.

Structurally Flexible Oxocarbenium/Borohydride Ion Pair: Dynamics of Hydride Transfer on the Background of Conformational Roaming

We apply Born-Oppenheimer molecular dynamics to the practically significant [dioxane-H⁽⁺⁾-acetone][(C₆F₅)₃B-H^(-)] and [Et₂O-H⁽⁺⁾-OCPr₂][(C₆F₅)₃B-H^(-)] ion pair intermediates. Dynamics of hydride transfer in cation/anion ion pair takes place on the background of large-amplitude configurational changes. Geometry of oxocarbenium/borohydride ion pairs is flexible, meaning that we uncover significant actual structural disorder at a finite temperature. Therefore, although the starting structure can be fairly close to the configurational area of the hydride transfer transition state (TS) and despite a low potential energy barrier (ca. 1.5 kcal/mol, according to the literature), already at T ≈ 325 K the system can remain ignorant of the TS region and move round and about ("roam") in the configurational space for a period of time in the range between 10 and 100 ps. This indicates structural flexibility of oxocarbenium/borohydride ion pair on apparently a flat potential energy "landscape" of cation/anion interaction, and this has not been taken into consideration by the free energy estimations in static considerations made thus far. The difference between the dynamics-based representation of the system versus the static representation amounts to the difference between quasi-bimolecular versus unimolecular descriptions of the hydride transfer step.

Hamiltonian flow over saddles for exploring molecular phase space structures

Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective.This article is part of the theme issue 'Modern theoretical chemistry'.

Theories and simulations of roaming

The phenomenon of roaming in chemical reactions has now become both commonly observed in experiment and extensively supported by theory and simulations. Roaming occurs in highly-excited molecules when the trajectories of atomic motion often bypass the minimum energy pathway and produce reaction in unexpected ways from unlikely geometries. The prototypical example is the unimolecular dissociation of formaldehyde (H₂CO), in which the "normal" reaction proceeds through a tight transition state to yield H₂ + CO but for which a high fraction of dissociations take place via a "roaming" mechanism in which one H atom moves far from the HCO, almost to dissociation, and then returns to abstract the second H atom. We review below the theories and simulations that have recently been developed to address and understand this new reaction phenomenon.

Empirical Classification of Trajectory Data: An Opportunity for the Use of Machine Learning in Molecular Dynamics

Classical Hamiltonian trajectories are initiated at random points in phase space on a fixed energy shell of a model two degrees of freedom potential, consisting of two interacting minima in an otherwise flat energy plane of infinite extent. Below the energy of the plane, the dynamics are demonstrably chaotic. However, most of the work in this paper involves trajectories at a fixed energy that is 1% above that of the plane, in which regime the dynamics exhibit behavior characteristic of chaotic scattering. The trajectories are analyzed without reference to the potential, as if they had been generated in a typical direct molecular dynamics simulation. The questions addressed are whether one can recover useful information about the structures controlling the dynamics in phase space from the trajectory data alone, and whether, despite the at least partially chaotic nature of the dynamics, one can make statistically meaningful predictions of trajectory outcomes from initial conditions. It is found that key unstable periodic orbits, which can be identified on the analytical potential, appear by simple classification of the trajectories, and that the specific roles of these periodic orbits in controlling the dynamics are also readily discerned from the trajectory data alone. Two different approaches to predicting trajectory outcomes from initial conditions are evaluated, and it is shown that the more successful of them has ∼90% success. The results are compared with those from a simple neural network, which has higher predictive success (97%) but requires the information obtained from the "by-hand" analysis to achieve that level. Finally, the dynamics, which occur partly on the very flat region of the potential, show characteristics of the much-studied phenomenon called "roaming." On this potential, it is found that roaming trajectories are effectively "failed" periodic orbits and that angular momentum can be identified as a key controlling factor, despite the fact that it is not a strictly conserved quantity. It is also noteworthy that roaming on this potential occurs in the absence of a "roaming saddle," which has previously been hypothesized to be a necessary feature for roaming to occur.