Rates and Yields of Unimolecular Reactions Producing Highly Oxidized Peroxy Radicals in the OH-Induced Autoxidation of α-Pinene, ß-Pinene, and Limonene.

Recent ambient atmospheric measurements have detected highly oxygenated organic molecules (HOMs) at many sites and are a consequence of autoxidation processes occurring at ambient temperatures. Monoterpenes in particular have a propensity to autoxidize although they exhibit a wide range of HOM yields, which may be due to a variety of reasons including reactions with different oxidants like OH and O3, differing hydrogen (H) atom transfer or peroxy radical cyclization rates, numbers of available reaction pathways, and/or energy loss processes for activated HO-monoterpene or O3-monoterpene adducts. In this work, the autoxidation mechanisms of (+)-α-pinene, (+)-ß-pinene, and (+)-limonene following initial OH oxidation and three successive O2 additions are examined using density functional theory (DFT) to understand what accounts for the disparity. Rates of different potential autoxidation pathways initiated by OH addition or abstraction reactions are quantified using transition-state theory (TST) and master equation approaches using the lowest-energy conformers. OH abstraction reactions do not appreciably influence HOM production in the pinenes and limit autoxidation for limonene because the subsequent autoxidation reactions are slow while OH addition reactions are found to be the main route to HOMs for all three monoterpenes. Generally, faster autoxidation rates are computed in later unimolecular reactions that produce RO7 radicals after OH addition (∼10 s-1 or greater) than rates for RO5 peroxy radical production (0.2-7 s-1). Mechanistic pathways that form RO7 peroxy radicals are similar for all three monoterpenes with a particular bicyclo RO7 radical involving a five-membered peroxide ring being favored for all three monoterpenes. The molar yields of RO7 radicals are 4.6% (+10.0/-2.4), 3.8% (+9.1/-2.6), and 7.6% (+13.1/-4.9) for α-pinene, ß-pinene, and limonene, respectively, at 298 K and 1 ppb of NO and only significantly decline at NO concentrations exceeding 10 ppb. The higher yield for limonene relative to the pinenes is predominantly a consequence of the initial oxidation step: OH adducts of the bicyclic pinenes have to use the excess energy after OH addition to break one of the rings and make the molecule more flexible for autoxidation although this process is inefficient, while one of the prominent OH adducts for monocyclic limonene does not have to do this and may add O2 immediately before autoxidizing further. These insights may be used to guide a better representation of these processes in atmospheric models because they affect particulate matter (PM), NOx, and ozone concentrations via enhanced production of low-volatility species, less early-generation NOx cycling, and altered organic nitrate production.

Synthesis and Hydrolysis of Atmospherically Relevant Monoterpene-Derived Organic Nitrates.

The partition of gas-phase organic nitrates (ONs) to aerosols and subsequent hydrolysis are regarded as important loss mechanisms for ON species. However, the hydrolysis mechanisms and the major factors controlling the hydrolysis lifetime are not fully understood. In this work, we synthesized seven monoterpene-derived ONs and systematically investigated their hydrolysis in bulk solutions at different pH values. The hydrolysis lifetimes ranged from 12.9 min to 8.5 h for allylic primary ON and tertiary ONs, but secondary ONs were stable at neutral pH. The alkyl substitution numbers, functional groups, and carbon skeletons were three important factors controlling hydrolysis rates. Tertiary and secondary ONs were found to hydrolyze via the acid-catalyzed unimolecular (SN1) mechanism, while a competition of SN1 and bimolecular (SN2) mechanisms accounted for the hydrolysis of primary ONs. The consistency of experimental and theoretical hydrolysis rates calculated by density functional theory further supported the proposed mechanisms. Reversible reactions including hydrolysis and nitration were first reported to explain the hydrolysis of ONs, highlighting the possibility that particulate nitric acid can participate in nitration to generate new nitrogen-containing compounds. These findings demonstrate that ON hydrolysis is a complex reaction that proceeds via different mechanisms and is controlled by various parameters.

Rapid production of highly oxidized molecules in isoprene aerosol via peroxy and alkoxy radical isomerization pathways in low and high NOx environments: Combined laboratory, computational and field studies.

Recently, we identified seven novel hydroxy-carboxylic acids resulting from gas-phase reactions of isoprene in the presence of nitrogen oxides (NOx), ozone (O3), and/or hydroxyl radicals (OH). In the present study, we provide evidence that hydroxy-carboxylic acids, namely methyltartaric acids (MTA) are: (1) reliable isoprene tracers, (2) likely produced via rapid peroxy radical hydrogen atom (H) shift reactions (autoxidation mechanism) and analogous alkoxy radical H shifts in low and high NOx environments respectively and (3) representative of aged ambient aerosol in the low NOx regime. Firstly, MTA are reliable tracers of isoprene aerosol because they have been identified in numerous chamber experiments involving isoprene conducted under a wide range of conditions and are absent in the oxidation of mono- and sesquiterpenes. They are also present in numerous samples of ambient aerosol collected during the past 20 years at several locations in the U.S. and Europe. Furthermore, MTA concentrations measured during a year-long field study in Research Triangle Park (RTP), NC in 2003 show a seasonal trend consistent with isoprene emissions and photochemical activity. Secondly, an analysis of chemical ionization mass spectrometer (CIMS) data of several chamber experiments in low and high NOx environments show that highly oxidized molecules (HOMs) derived from isoprene that lead to MTAs may be produced rapidly and considered as early generation isoprene oxidation products in the gas phase. Density functional theory calculations show that rapid intramolecular H shifts involving peroxy and alkoxy radicals possess low barriers for methyl-hydroxy-butenals (MHBs) that may represent precursors for MTA. From these results, a viable rapid H shift mechanism is proposed to occur that produces isoprene derived HOMs like MTA. Finally, an analysis of the mechanism shows that autoxidation-like pathways in low and high NOx may produce HOMs in a few OH oxidation steps like commonly detected methyl tetrol (MT) isoprene tracers. The ratio of MTA/MT in isoprene aerosol is also shown to be significantly greater in field versus chamber samples indicating the importance of such pathways in the atmosphere even for smaller hydrocarbons like isoprene.

Multigenerational Theoretical Study of Isoprene Peroxy Radical 1-5-Hydrogen Shift Reactions that Regenerate HO x Radicals and Produce Highly Oxidized Molecules.

A computational protocol is employed to glean new insight into the kinetics of several 1,5-hydrogen atom (H) shift reactions subsequent to first- and second-generation OH/O2 additions to isoprene. The M06-2X density functional was initially used with the Nudged Elastic Band (NEB) method to determine the potential energy surface of OH/O2 addition reactions, the 1,5-H shift reactions, and the fragmentation exit channels. The Master Equation Solver for Multi-Energy Well Reactions (MESMER) was applied to determine the rate constants for OH addition and the 1,5-H shifts. M06-2X was capable of quantifying the rate constants of OH addition to the first and second double bonds of isoprene with deviations less than 17% from the experimentally determined values. However, M06-2X underestimated the 1,5-H shift rate constants of second-generation isoprene peroxy radicals. Consequently, MN15, ωB97X-D, and CBS-QB3 methods were employed to compute average barrier heights to first- and second-generation 1,5-H shifts. In the first generation, the rate constants of H abstraction by ß-(1,2) and (4,3) isoprene hydroxy-peroxy radicals from the neighboring hydroxyl group are 1.1 × 10-3 and 2.4 × 10-3 s-1, respectively. These values are determined primarily by the barrier of the H shift reaction and, to a smaller albeit nonnegligible extent, by the stability of the resulting alkoxy radical and the exit barrier leading to C-C bond dissociation. In contrast, the average second-generation rate constant of 1,5-H shifts from H-R-OH sites to the peroxy radical is 1.8 × 10-1 s-1, with tunneling playing the significant role of increasing this value relative to first-generation 1,5-H shifts. Under low NO x conditions, first-generation isoprene oxidation reactions may recycle HO x at levels ranging from 10 to 30% due in large part to 1,5-H shifts, with the recycling efficiency being sensitive to HO2 concentrations and temperature. HO x recycling is expected to increase to levels beyond 80% in second-generation reactions of oxidized isoprene species because of isoprene epoxydiol (IEPOX) formation and further 1,5-H shifts that are kinetically favorable.

Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.

The chemical reaction mechanism of NO addition to two ß and δ isoprene hydroxy-peroxy radical isomers is examined in detail using density functional theory, coupled cluster methods, and the energy resolved master equation formalism to provide estimates of rate constants and organic nitrate yields. At the M06-2x/aug-cc-pVTZ level, the potential energy surfaces of NO reacting with ß-(1,2)-HO-IsopOO• and δ-Z-(1,4)-HO-IsopOO• possess barrierless reactions that produce alkoxy radicals/NO2 and organic nitrates. The nudged elastic band method was used to discover a loosely bound van der Waals (vdW) complex between NO2 and the alkoxy radical that is present in both exit reaction channels. Semiempirical master equation calculations show that the ß organic nitrate yield is 8.5 ± 3.7%. Additionally, a relatively low barrier to C-C bond scission was discovered in the ß-vdW complex that leads to direct HONO formation in the gas phase with a yield of 3.1 ± 1.3%. The δ isomer produces a looser vdW complex with a smaller dissociation barrier and a larger isomerization barrier, giving a 2.4 ± 0.8% organic nitrate yield that is relatively pressure and temperature insensitive. By considering all of these pathways, the first-generation NOx recycling efficiency from isoprene organic nitrates is estimated to be 21% and is expected to increase with decreasing NOx concentration.

Epoxide pathways improve model predictions of isoprene markers and reveal key role of acidity in aerosol formation.

Isoprene significantly contributes to organic aerosol in the southeastern United States where biogenic hydrocarbons mix with anthropogenic emissions. In this work, the Community Multiscale Air Quality model is updated to predict isoprene aerosol from epoxides produced under both high- and low-NOx conditions. The new aqueous aerosol pathways allow for explicit predictions of two key isoprene-derived species, 2-methyltetrols and 2-methylglyceric acid, that are more consistent with observations than estimates based on semivolatile partitioning. The new mechanism represents a significant source of organic carbon in the lower 2 km of the atmosphere and captures the abundance of 2-methyltetrols relative to organosulfates during the simulation period. For the parametrization considered here, a 25% reduction in SOx emissions effectively reduces isoprene aerosol, while a similar reduction in NOx leads to small increases in isoprene aerosol.

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (ß-IEPOX--an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE--methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX.

Epoxide as a precursor to secondary organic aerosol formation from isoprene photooxidation in the presence of nitrogen oxides.

Isoprene is a substantial contributor to the global secondary organic aerosol (SOA) burden, with implications for public health and the climate system. The mechanism by which isoprene-derived SOA is formed and the influence of environmental conditions, however, remain unclear. We present evidence from controlled smog chamber experiments and field measurements that in the presence of high levels of nitrogen oxides (NO(x) = NO + NO2) typical of urban atmospheres, 2-methyloxirane-2-carboxylic acid (methacrylic acid epoxide, MAE) is a precursor to known isoprene-derived SOA tracers, and ultimately to SOA. We propose that MAE arises from decomposition of the OH adduct of methacryloylperoxynitrate (MPAN). This hypothesis is supported by the similarity of SOA constituents derived from MAE to those from photooxidation of isoprene, methacrolein, and MPAN under high-NOx conditions. Strong support is further derived from computational chemistry calculations and Community Multiscale Air Quality model simulations, yielding predictions consistent with field observations. Field measurements taken in Chapel Hill, North Carolina, considered along with the modeling results indicate the atmospheric significance and relevance of MAE chemistry across the United States, especially in urban areas heavily impacted by isoprene emissions. Identification of MAE implies a major role of atmospheric epoxides in forming SOA from isoprene photooxidation. Updating current atmospheric modeling frameworks with MAE chemistry could improve the way that SOA has been attributed to isoprene based on ambient tracer measurements, and lead to SOA parameterizations that better capture the dependency of yield on NO(x).

Pump-probe imaging differentiates melanoma from melanocytic nevi.

Melanoma diagnosis is clinically challenging: the accuracy of visual inspection by dermatologists is highly variable and heavily weighted toward false positives. Even the current gold standard of biopsy results in varying diagnoses among pathologists. We have developed a multiphoton technique (based on pump-probe spectroscopy) that directly determines the microscopic distribution of eumelanin and pheomelanin in pigmented lesions of human skin. Our initial results showed a marked difference in the chemical variety of melanin between nonmalignant nevi and melanoma, as well as a number of substantial architectural differences. We examined slices from 42 pigmented lesions and found that melanomas had an increased eumelanin content compared to nonmalignant nevi. When used as a diagnostic criterion, the ratio of eumelanin to pheomelanin captured all investigated melanomas but excluded three-quarters of dysplastic nevi and all benign dermal nevi. Additional evaluation of architectural and cytological features revealed by multiphoton imaging, including the maturation of melanocytes, presence of pigmented melanocytes in the dermis, number and location of melanocytic nests, and confluency of pigmented cells in the epidermis, further increased specificity, allowing rejection of more than half of the remaining false-positive results. We then adapted this multiphoton imaging technique to hematoxylin and eosin (H&E)-stained slides. By adding melanin chemical contrast to H&E-stained slides, pathologists will gain complementary information to increase the ease and accuracy of melanoma diagnosis.

Probing near-infrared photorelaxation pathways in eumelanins and pheomelanins.

Ultraviolet-visible spectroscopy readily discerns the two types of melanin pigments (eumelanin and pheomelanin), although fundamental details regarding the optical properties and pigment heterogeneity are more difficult to disentangle via analysis of the broad featureless absorption spectrum alone. We employed nonlinear transient absorption spectroscopy to study different melanin pigments at near-infrared wavelengths. Excited-state absorption, ground-state depletion, and stimulated emission signal contributions were distinguished for natural and synthetic eumelanins and pheomelanins. A starker contrast among the pigments is observed in the nonlinear excitation regime because they all exhibit distinct transient absorptive amplitudes, phase shifts, and nonexponential population dynamics spanning the femtosecond-nanosecond range. In this manner, different pigments within the pheomelanin subclass were distinguished in synthetic and human hair samples. These results highlight the potential of nonlinear spectroscopies to deliver an in situ analysis of natural melanins in tissue that are otherwise difficult to extract and purify.

Estimation of molar absorptivities and pigment sizes for eumelanin and pheomelanin using femtosecond transient absorption spectroscopy.

Fundamental optical and structural properties of melanins are not well understood due to their poor solubility characteristics and the chemical disorder present during biomolecular synthesis. We apply nonlinear transient absorption spectroscopy to quantify molar absorptivities for eumelanin and pheomelanin and thereby get an estimate for their average pigment sizes. We determine that pheomelanin exhibits a larger molar absorptivity at near IR wavelengths (750 nm), which may be extended to shorter wavelengths. Using the molar absorptivities, we estimate that melanin pigments contain approximately 46 and 28 monomer units for eumelanin and pheomelanin, respectively. This is considerably larger than the oligomeric species that have been recently proposed to account for the absorption spectrum of eumelanin and illustrates that larger pigments comprise a significant fraction of the pigment distribution.

Label-free in vivo optical imaging of microvasculature and oxygenation level.

The ability to perform high-resolution imaging of microvasculature and its oxygenation is very important in studying early tumor development. Toward this goal, we improved upon our excited state absorption (ESA)-based imaging technique to allow us to not only image hemoglobin directly but also differentiate between oxy- and deoxyhemoglobin in tissue. We demonstrate the separation of arterioles from venules in a live nude mouse ear using our imaging technique.

Rapid pulse shaping with homodyne detection for measuring nonlinear optical signals.

We have designed a common-mode interferometric acousto-optic pulse shaper that is capable of shaping individual pulses differently from a mode-locked laser. The design enables the measurement of weak nonlinear optical signals such as two-photon absorption and self-phase modulation at megahertz rates. The experimental apparatus incorporates homodyne detection as a means of resolving the phase of the detected signals. The fast data acquisition rate and the ability to perform measurements in scattering media make this experimental apparatus amenable to imaging applications analogous to measurements of two-photon fluorescence using a mode-locked laser.

Simultaneous self-phase modulation and two-photon absorption measurement by a spectral homodyne Z-scan method.

We developed a technique to simultaneously measure self-phase modulation and two-photon absorption using shaped femtosecond laser pulses. In the conventional Z-scan measurement technique the amount of nonlinearity is determined by measuring the change in shape and intensity of a transmitted laser beam. In contrast, our method sensitively measures nonlinearity-induced changes in the pulse spectrum. In this work we demonstrate the technique in nonlinear absorptive and dispersive samples, quantify the obtained signal, and compare the measurements with traditional Z-scans. This technique is capable of measuring these nonlinearities in highly scattering samples.

Self-phase modulation signatures of neuronal activity.

We use phase-sensitive detection of spectral hole refilling to demonstrate strong novel intrinsic nonlinear signatures of neuronal activation in hippocampal brain slices. The ability to gain access to this fundamentally new intrinsic contrast with modest power levels suggests a new approach to in vivo neural imaging. We expect that we can extrapolate our method to high spatial and temporal resolution in deep tissue while retaining the noninvasive character.

Water Dynamics in Nafion Fuel Cell Membranes: the Effects of Confinement and Structural Changes on the Hydrogen Bond Network.

The complex environments experienced by water molecules in the hydrophilic channels of Nafion membranes are studied by ultrafast infrared pump-probe spectroscopy. A wavelength dependent study of the vibrational lifetime of the O-D stretch of dilute HOD in H(2)O confined in Nafion membranes provides evidence of two distinct ensembles of water molecules. While only two ensembles are present at each level of membrane hydration studied, the characteristics of the two ensembles change as the water content of the membrane changes. Time dependent anisotropy measurements show that the orientational motions of water molecules in Nafion membranes are significantly slower than in bulk water and that lower hydration levels result in slower orientational relaxation. Initial wavelength dependent results for the anisotropy show no clear variation in the time scale for orientational motion across a broad range of frequencies. The anisotropy decay is analyzed using a model based on restricted orientational diffusion within a hydrogen bond configuration followed by total reorientation through jump diffusion.

What nonlinear-IR experiments can tell you about water that the IR spectrum cannot.

Frequently, the IR spectrum of water is used to characterize the structure and strength of the associated hydrogen bond network. Here, we use nonlinear-IR spectroscopy to investigate the dynamics of four aqueous systems that have very similar absorption spectra. We address the question: to what extent can the dynamics of water vary in systems with very similar absorption spectra? The results illustrate that the vibrational lifetimes and orientational relaxation time scales vary dramatically between the four samples and do not correlate with the amount of water relative to surfactant or solute in solution. Nonlinear-IR spectroscopies are therefore important for providing detailed information necessary to understand hydrogen bonded systems.

Tracking water's response to structural changes in Nafion membranes.

As the water content of Nafion membranes increases, the local environments of water molecules change due to reorganization of the pendant side chains in the hydrophilic domains. Changes in local structure as a function of water content are studied by measuring the IR spectra and the vibrational lifetimes of the hydroxyl stretch of dilute HOD in H(2)O. The main features of the IR spectra are fit well by a weighted sum of the spectra of bulk water and almost dry Nafion, suggesting a two-environment model. An additional small peak on the high frequency side of the main band associated with non-hydrogen-bonded water embedded in the polymer near the interface is analyzed quantitatively as a function of the membrane water content. The spectra of this peak show that a significant reorganization of the interfacial region occurs when the water content of the membrane exceeds the threshold for ion conduction. Vibrational excited state population relaxation times (lifetimes) of the main band lengthen substantially as the water content of the membrane is decreased. The population decays are not single exponentials and indicate that multiple ensembles of water molecules exist, and the characteristics of the individual ensembles change with water content. This is in contrast to the spectra of the main water absorption band, which is only sensitive to two classes of water molecules.

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy.

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.

Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time.

In general, the formation and dissociation of solute-solvent complexes have been too rapid to measure without disturbing the thermal equilibrium. We were able to do so with the use of two-dimensional infrared vibrational echo spectroscopy, an ultrafast vibrational analog of two-dimensional nuclear magnetic resonance spectroscopy. The equilibrium dynamics of phenol complexation to benzene in a benzene-carbon tetrachloride solvent mixture were measured in real time by the appearance of off-diagonal peaks in the two-dimensional vibrational echo spectrum of the phenol hydroxyl stretch. The dissociation time constant tau(d) for the phenol-benzene complex was 8 picoseconds. Adding two electron-donating methyl groups to the benzene nearly tripled the value of tau(d) and stabilized the complex, whereas bromobenzene, with an electron-withdrawing bromo group, formed a slightly weaker complex with a slightly lower tau(d). The spectroscopic method holds promise for studying a wide variety of other fast chemical exchange processes.