Michael P. Grubb

No Straight Path: Roaming in Both Ground- and Excited-State Photolytic Channels of NO3 → NO + O2

Exclusive Roaming How do polyatomic molecules fall apart? The basic model, supported by centuries of chemical theory and experiment, invokes a series of internal rearrangements that lead to a fleeting high-energy transition-state geometry from which lower-energy products emerge. Over the past decade, several molecules have been shown to manifest a competing dissociation mechanism such that alongside trajectories that pass through the transition state, there are energetically accessible pathways that roam around it. Grubb et al. (p. 1075; see the Perspective by Jordan and Kable) showed that the light-induced reaction of NO3 to form NO and O2 proceeded exclusively by roaming. Although there are distinct pathways to the products in two different electronic states, neither one passes through a conventional transition state. A chemical reaction proceeds exclusively by mechanisms that do not pass through a conventional transition state. Roaming mechanisms have recently been observed in several chemical reactions alongside trajectories that pass through a traditional transition state. Here, we demonstrate that the visible light–induced reaction NO3 → NO + O2 proceeds exclusively by roaming. High-level ab initio calculations predict specific NO Λ doublet propensities (orientations of the unpaired electron with respect to the molecular rotation plane) for this mechanism, which we discern experimentally by ion imaging. The data provide direct evidence for roaming pathways in two different electronic states, corresponding to both previously documented photolysis channels that produce NO + O2. More broadly, the results raise intriguing questions about the overall prevalence of this unusual reaction mechanism.

Comparing molecular photofragmentation dynamics in the gas and liquid phases

This article explores the extent to which insights gleaned from detailed studies of molecular photodissociations in the gas phase (i.e. under isolated molecule conditions) can inform our understanding of the corresponding photofragmentation processes in solution. Systems selected for comparison include a thiophenol (p-methylthiophenol), a thioanisole (p-methylthioanisole) and phenol, in vacuum and in cyclohexane solution. UV excitation in the gas phase results in RX-Y (X = O, S; Y = H, CH3) bond fission in all cases, but over timescales that vary by ~4 orders of magnitude - all of which behaviours can be rationalised on the basis of the relevant bound and dissociative excited state potential energy surfaces (PESs) accessed by UV photoexcitation, and of the conical intersections that facilitate radiationless transfer between these PESs. Time-resolved UV pump-broadband UV/visible probe and/or UV pump-broadband IR probe studies of the corresponding systems in cyclohexane solution reveal additional processes that are unique to the condensed phase. Thus, for example, the data clearly reveal evidence of (i) vibrational relaxation of the photoexcited molecules prior to their dissociation and of the radical fragments formed upon X-Y bond fission, and (ii) geminate recombination of the RX and Y products (leading to reformation of the ground state parent and/or isomeric adducts). Nonetheless, the data also show that, in each case, the characteristics (and the timescale) of the initial bond fission process that occurs under isolated molecule conditions are barely changed by the presence of a weakly interacting solvent like cyclohexane. These condensed phase studies are then extended to an ether analogue of phenol (allyl phenyl ether), wherein UV photo-induced RO-allyl bond fission constitutes the first step of a photo-Claisen rearrangement.

Application of the accelerated molecular dynamics simulations to the folding of a small protein

In this paper, we further explore the applicability of the accelerated molecular dynamics simulation method using a bias potential. The method is applied to both simple model systems and real multidimensional systems. The method is also compared to replica exchange simulations in folding a small protein, Trp cage, using an all atom potential for the protein and an implicit model for the solvent. We show that the bias potential method allows quick searches of folding pathways. We also show that the choice of the bias potential has significant influence on the efficiency of the bias potential method.

On the Participation of Photoinduced N−H Bond Fission in Aqueous Adenine at 266 and 220 nm: A Combined Ultrafast Transient Electronic and Vibrational Absorption Spectroscopy Study

A combination of ultrafast transient electronic absorption spectroscopy (TEAS) and transient vibrational absorption spectroscopy (TVAS) is used to investigate whether photoinduced N–H bond fission, mediated by a dissociative 1πσ(*) state, is active in aqueous adenine (Ade) at 266 and 220 nm. In order to isolate UV/visible and IR spectral signatures of the adeninyl radical (Ade[-H]), formed as a result of N–H bond fission, TEAS and TVAS are performed on Ade in D2O under basic conditions (pD = 12.5), which forms Ade[-H](-) anions via deprotonation at the N7 or N9 sites of Ades 7H and 9H tautomers. At 220 nm we observe one-photon detachment of an electron from Ade[-H](-), which generates solvated electrons (eaq(-)) together with Ade[-H] radicals, with clear signatures in both TEAS and TVAS. Additional wavelength dependent TEAS measurements between 240–260 nm identify a threshold of 4.9 ± 0.1 eV (∼250 nm) for this photodetachment process in D2O. Analogous TEAS experiments on aqueous Ade at pD = 7.4 generate a similar photoproduct signal together with eaq(-) after excitation at 266 and 220 nm. These eaq(-) are born from ionization of Ade, together with Ade(+) cations, which are indistinguishable from Ade[-H] radicals in TEAS. Ade(+) and Ade[-H] are found to have different signatures in TVAS and we verify that the pD = 7.4 photoproduct signal observed in TEAS following 220 nm excitation is solely due to Ade(+) cations. Based on these observations, we conclude that: (i) N–H bond fission in aqueous Ade is inactive at wavelengths ≥220 nm; and (ii) if such a channel exists in aqueous solution, its threshold is strongly blue-shifted relative to the onset of the same process in gas phase 9H-Ade (≤233 nm). In addition, we extract excited state lifetimes and vibrational cooling dynamics for 9H-Ade and Ade[-H](-). In both cases, excited state lifetimes of <500 fs are identified, while vibrational cooling occurs within a time frame of 4–5 ps. In contrast, 7H-Ade is confirmed to have a longer excited state lifetime of ∼5–10 ps through both TEAS and TVAS.

KOALA: A program for the processing and decomposition of transient spectra

Extracting meaningful kinetic traces from time-resolved absorption spectra is a non-trivial task, particularly for solution phase spectra where solvent interactions can substantially broaden and shift the transition frequencies. Typically, each spectrum is composed of signal from a number of molecular species (e.g., excited states, intermediate complexes, product species) with overlapping spectral features. Additionally, the profiles of these spectral features may evolve in time (i.e., signal nonlinearity), further complicating the decomposition process. Here, we present a new program for decomposing mixed transient spectra into their individual component spectra and extracting the corresponding kinetic traces: KOALA (Kinetics Observed After Light Absorption). The software combines spectral target analysis with brute-force linear least squares fitting, which is computationally efficient because of the small nonlinear parameter space of most spectral features. Within, we demonstrate the application of KOALA to two sets of experimental transient absorption spectra with multiple mixed spectral components. Although designed for decomposing solution-phase transient absorption data, KOALA may in principle be applied to any time-evolving spectra with multiple components.

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson-Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine-cytosine (G⋅C) Watson-Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[-H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson-Crick pairs, but up to 10% of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

A method for the determination of speed-dependent semi-classical vector correlations from sliced image anisotropies

We present analytical expressions relating the bipolar moment β(Q)(K)(k(1)k(2)) parameters of Dixon to the measured anisotropy parameters of different pump/probe geometry sliced ion images. In the semi-classical limit, when there is no significant coherent contribution from multiple excited states to fragment angular momentum polarization, the anisotropy of the images alone is sufficient to extract the β(Q)(K)(k(1)k(2)) parameters with no need to reference relative image intensities. The analysis of sliced images is advantageous since the anisotropy can be directly obtained from the image at any radius without the need for 3D-deconvolution, which is not applicable for most pump/probe geometries. This method is therefore ideally suited for systems which result in a broad distribution of fragment velocities. The bipolar moment parameters are obtained for NO(2) dissociation at 355 nm using these equations, and are compared to the bipolar moment parameters obtained from a proven iterative fitting technique for crushed ion images. Additionally, the utility of these equations in extracting speed-dependent bipolar moments is demonstrated on the recently investigated NO(3) system.

Recombination, Solvation and Reaction of CN Radicals Following Ultraviolet Photolysis of ICN in Organic Solvents

The fates of CN radicals produced by ultraviolet (UV) photolysis of ICN in various organic solvents have been examined by transient electronic and vibrational absorption spectroscopy (TEAS and TVAS). Near-UV and visible bands in the TEAS measurement enable direct observation of the CN radicals and their complexes with the solvent molecules. Complementary TVAS measurements probe the products of CN-radical reactions. Geminate recombination to form ICN and INC is a minor pathway on the 150 fs -1300 ps time scales of our experiments in the chosen organic solvents; nonetheless, large infrared transition dipole moments permit direct observation of INC that is vibrationally excited in the C≡N stretching mode. The time constants for INC vibrational cooling range from 30 ps in tetrahydrofuran (THF) to 1400 ps in more weakly interacting solvents such as chloroform. The major channel for CN removal in the organic solvents is reaction with solvent molecules, as revealed by depletion of solvent absorption bands and growth of product bands in the TVA spectra. HCN is a reaction product of hydrogen atom abstraction in most of the photoexcited solutions, and forms with vibrational excitation in both the C-H and C≡N stretching modes. The vibrational cooling rate of the C≡N stretch in HCN depends on the solvent, and follows the same trend as the cooling rate of the C≡N stretch in INC. However, in acetonitrile solution an additional reaction pathway produces C3H3N2(•) radicals, which release HCN on a much longer time scale.

Reaction Dynamics of CN Radicals in Acetonitrile Solutions

The bimolecular reactions that follow 267 nm ultraviolet photolysis of ICN in acetonitrile solution have been studied using transient absorption spectroscopy on the picosecond time scale. Time-resolved electronic absorption spectroscopy (TEAS) in the ultraviolet and visible spectral regions observes rapid production and loss (with a decay time constant of 0.6 ± 0.1 ps) of the photolytically generated free CN radicals. Some of these radicals convert to a solvated form which decays with a lifetime of 8.5 ± 2.1 ps. Time-resolved vibrational absorption spectroscopy (TVAS) reveals that the free and solvated CN-radicals undergo geminate recombination with I atoms to make ICN and INC, H atom abstraction reactions, and addition reactions to solvent molecules to make C3H3N2 radical species. These radical products have a characteristic absorption band at 2036 cm(-1) that shifts to 2010 cm(-1) when ICN is photolyzed in CD3CN. The HCN yield is low, suggesting the addition pathway competes effectively with H atom abstraction from CH3CN, but the delayed growth of the C3H3N2 radical band is best described by reaction of solvated CN radicals through an unobserved intermediate species. Addition of methanol or tetrahydrofuran as a cosolute promotes H atom abstraction reactions that produce vibrationally hot HCN. The combination of TEAS and TVAS measurements shows that the rate-limiting process for production of ground-state HCN is vibrational cooling, the rate of which is accelerated by the presence of methanol or tetrahydrofuran.

Transient electronic and vibrational absorption studies of the photo-Claisen and photo-Fries rearrangements

The liquid-phase photo-Claisen and photo-Fries rearrangement dynamics of allyl phenyl ether and phenyl acetate in cyclohexane solution have been interrogated via ultrafast transient absorption spectroscopy. Following excitation at 267 nm, the reaction progress is monitored on a picosecond time-scale by electronic and vibrational absorption spectra obtained from broadband UV/Visible and mid-infrared probe pulses. The evolution of the ground and excited electronic states of the parent molecule, the radicals produced by photo-induced homolytic bond fission, and intermediate cyclohexadienones formed via recombination of the produced radical pair are followed, providing new insight and detail on the reaction mechanisms. Subsequent kinetic analysis allows determination of rate coefficients as well as quantum yields for the processes involved. These examples serve to highlight the utility of employing broadband UV-Visible and infrared probe spectroscopies, in conjunction, to unravel the mechanisms of photochemical reactions in solution. The underlying photo-physics that initiates bond fission in this class of molecules is also addressed in the context of the role of dissociative (n/π)σ* excited states.