Prediction of Kinetic Product Ratios: Investigation of a Dynamically Controlled Case.

Of the various factors influencing kinetically controlled product ratios, the role of nonstatistical dynamics is arguably the least well understood. In this paper, reactions were chosen in which dynamics played a dominant role in product selection, by design. Specifically, the reactions studied were the ring openings of cyclopropylidene to allene and tetramethylcyclopropylidene to tetramethylallene (2,4-dimethylpenta-2,3-diene).

A Conical Intersection Influences the Ground State Rearrangement of Fulvene to Benzene.

The rearrangement of fulvene to benzene is believed to play an important role in the formation of soot during hydrocarbon combustion. Previous work has identified two possible mechanisms for the rearrangement─a unimolecular path and a hydrogen-atom-assisted, bimolecular path. Computational results to date have suggested that the unimolecular mechanism faces a barrier of about 74 kcal/mol, which makes it unable to compete with the bimolecular mechanism under typical combustion conditions.

Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices.

Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (, a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called , which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization.

Environmental Processing of Lipids Driven by Aqueous Photochemistry of α-Keto Acids.

Sunlight can initiate photochemical reactions of organic molecules though direct photolysis, photosensitization, and indirect processes, often leading to complex radical chemistry that can increase molecular complexity in the environment. α-Keto acids act as photoinitiators for organic species that are not themselves photoactive. Here, we demonstrate this capability through the reaction of two α-keto acids, pyruvic acid and 2-oxooctanoic acid, with a series of fatty acids and fatty alcohols.

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.

Mechanistic Description of Photochemical Oligomer Formation from Aqueous Pyruvic Acid.

The aqueous phase photochemistry of pyruvic acid, an important oxidation product of isoprene, is known to generate larger oligomeric species that may contribute to the formation of secondary organic aerosol in the atmosphere. Using high resolution negative mode electrospray ionization mass spectrometry, the aqueous photochemistry of dilute solutions of pyruvic acid (10, 1, and 0.5 mM) under anaerobic conditions was investigated.

Photochemical Synthesis of Oligomeric Amphiphiles from Alkyl Oxoacids in Aqueous Environments.

The aqueous phase photochemistry of a series of amphiphilic α-keto acids with differing linear alkyl chain lengths was investigated, demonstrating the ability of sunlight-initiated reactions to build molecular complexity under environmentally relevant conditions. We show that the photochemical reaction mechanisms for α-keto acids in aqueous solution are robust and generalizable across alkyl chain lengths. The organic radicals generated during photolysis are indiscriminate, leading to a large mixture of photoproducts that are observed using high-resolution electrospray ionization mass spectrometry, but these products are identifiable following literature photochemical mechanisms.

Roaming: A Phase Space Perspective.

In this review we discuss the recently described roaming mechanism for chemical reactions from the point of view of nonlinear dynamical systems in phase space. The recognition of the roaming phenomenon shows the need for further developments in our fundamental understanding of basic reaction dynamics, as is made clear by considering some questions that cut across most studies of roaming: Is the dynamics statistical? Can transition state theory be applied to estimate roaming reaction rates? What role do saddle points on the potential energy surface play in explaining the behavior of roaming trajectories? How do we construct a dividing surface that is appropriate for describing the transformation from reactants to products for roaming trajectories? How should we define the roaming region? We show that the phase space perspective on reaction dynamics provides the setting in which these questions can be properly framed and answered. We illustrate these ideas by considering photodissociation of formaldehyde.

Gas-Phase Photolysis of Pyruvic Acid: The Effect of Pressure on Reaction Rates and Products.

In this work, we investigate the impact of pressure and oxygen on the kinetics of and products from the gas-phase photolysis of pyruvic acid. The results reveal a decrease in the photolysis quantum yield as pressure of air or nitrogen is increased, a trend not yet documented in the literature. A Stern-Volmer analysis demonstrates this effect is due to deactivation of the singlet state of pyruvic acid when the photolysis is performed in nitrogen, and from quenching of both the singlet and triplet state in air.

Chemical Equilibria and Kinetics in Aqueous Solutions of Zymonic Acid.

The chemistry of pyruvic acid is of great interest due to its essential role in metabolism for all life and its role in atmospheric chemistry. Pyruvic acid under a wide range of conditions, including normal storage conditions, will spontaneously dimerize to form zymonic acid. We isolated zymonic acid and, using a variety of 1D and 2D NMR techniques, identified it as a single structure as a solid or dissolved in DMSO.

The Study of Reactive Intermediates in Condensed Phases.

Novel experimental techniques and computational methods have provided new insight into the behavior of reactive intermediates in solution. The results of these studies show that some of the earlier ideas about how reactive intermediates ought to behave in solution were incomplete or even incorrect. This Perspective summarizes the new experimental and computational methods and draws attention to the shortcomings that their application has brought to light in previous models.

Toward Understanding the Roaming Mechanism in H + MgH → Mg + HH Reaction.

The roaming mechanism in the reaction H + MgH →Mg + HH is investigated by classical and quantum dynamics employing an accurate ab initio three-dimensional ground electronic state potential energy surface. The reaction dynamics are explored by running trajectories initialized on a four-dimensional dividing surface anchored on three-dimensional normally hyperbolic invariant manifold associated with a family of unstable orbiting periodic orbits in the entrance channel of the reaction (H + MgH). By locating periodic orbits localized in the HMgH well or involving H orbiting around the MgH diatom, and following their continuation with the total energy, regions in phase space where reactive or nonreactive trajectories may be trapped are found.

Phase space barriers and dividing surfaces in the absence of critical points of the potential energy: Application to roaming in ozone.

We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori, it is possible to define phase space dividing surfaces that are analogous to the dividing surfaces governing transition from reactants to products near a critical point of the potential energy surface. We investigate the problem of capture of an atom by a diatomic molecule and show that a normally hyperbolic invariant manifold exists at large atom-diatom distances, away from any critical points on the potential.

Phase Space Structures Explain Hydrogen Atom Roaming in Formaldehyde Decomposition.

We re-examine the prototypical roaming reaction--hydrogen atom roaming in formaldehyde decomposition--from a phase space perspective. Specifically, we address the question "why do trajectories roam, rather than dissociate through the radical channel?" We describe and compute the phase space structures that define and control all possible reactive events for this reaction, as well as provide a dynamically exact description of the roaming region in phase space. Using these phase space constructs, we show that in the roaming region, there is an unstable periodic orbit whose stable and unstable manifolds define a conduit that both encompasses all roaming trajectories exiting the formaldehyde well and shepherds them toward the H2···CO well.

Reaction Path Bifurcation in an Electrocyclic Reaction: Ring-Opening of the Cyclopropyl Radical.

Following previous work [J. Chem. Phys.

Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path.

Classical molecular dynamics simulations are reported for the deazetisation and ring opening of meso-2,3-difluoro-2,3-dimethyldiazocyclopropane in three solvents: CHCl3, CHFClBr and CH3CH(OH)CF3 (TFIPA). The achiral reactant leads to enantiomeric allene products, and the question addressed in the study is whether either of the chiral, enantiomerically pure solvents can induce significant enantiomeric excess in the products. The direct dynamics calculations use an empirical valence bond potential for the solute, with empirical parameters optimised against M06-2X/cc-pVTZ density functional results.

Nonstatistical dynamics on the caldera.

We explore both classical and quantum dynamics of a model potential exhibiting a caldera: that is, a shallow potential well with two pairs of symmetry related index one saddles associated with entrance/exit channels. Classical trajectory simulations at several different energies confirm the existence of the "dynamical matching" phenomenon originally proposed by Carpenter, where the momentum direction associated with an incoming trajectory initiated at a high energy saddle point determines to a considerable extent the outcome of the reaction (passage through the diametrically opposing exit channel). By studying a "stretched" version of the caldera model, we have uncovered a generalized dynamical matching: bundles of trajectories can reflect off a hard potential wall so as to end up exiting predominantly through the transition state opposite the reflection point.

Photoinitiated synthesis of self-assembled vesicles.

The aqueous photochemistry of 2-oxooctanoic acid (a single-tailed surfactant) results in the synthesis of a double-tailed surfactant product followed by spontaneous self-assembly into vesicles. The photochemical mechanism is detailed here, and the reaction products are identified using mass spectrometry. Then, the self-assembled vesicles are characterized using dynamic light scattering, fluorescence microscopy, and NMR.

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.

Photochemistry of aqueous pyruvic acid.

The study of organic chemistry in atmospheric aerosols and cloud formation is of interest in predictions of air quality and climate change. It is now known that aqueous phase chemistry is important in the formation of secondary organic aerosols. Here, the photoreactivity of pyruvic acid (PA; CH3COCOOH) is investigated in aqueous environments characteristic of atmospheric aerosols.