Dorit Shemesh

Efficient excited-state deactivation of the Gly-Phe-Ala tripeptide via an electron-driven proton-transfer process.

Ab initio electronic-structure calculations indicate a mechanism for efficient excited-state deactivation of a low-energy conformer of the Gly-Phe-Ala tripeptide. The particularly short excited-state lifetime can explain the unexpected absence of this conformer in resonant two-photon ionization spectra. It is suggested that these ultrafast electronic deactivation processes provide specific conformers of peptides with a high degree of photostability.

Computational Studies of the Photophysics of Neutral and Zwitterionic Amino Acids in an Aqueous Environment: Tyrosine−(H2O)2 and Tryptophan−(H2O)2 Clusters

Tyrosine-(H(2)O)(2) and tryptophan-(H(2)O)(2) clusters have been considered as models for the study of the photochemistry of neutral and zwitterionic tyrosine and tryptophan in an aqueous environment. It has been found that the detachment of neutral NH(3) in the S(1) state of the zwitterionic clusters leads to a low-lying conical intersection of the S(1) and S(0) energy surfaces. This conical intersection can provide the mechanism for efficient radiationless deactivation of the excited state back to the ground state or, alternatively, deamination (loss of ammonia). These results provide a mechanistic explanation of the efficient fluorescence quenching and the high quantum yield of ammonia in the UV photolysis of tyrosine and tryptophan in aqueous solution.

Experimental and Theoretical Study of Aqueous cis-Pinonic Acid Photolysis

Direct aqueous photolysis of cis-pinonic acid (PA; 2-(3-acetyl-2,2-dimethylcyclobutyl)acetic acid; CAS Registry No. 473-72-3) by 280-400 nm radiation was investigated. The photolysis resulted in Norrish type II isomerization of PA leading to 3-isopropenyl-6-oxoheptanoic acid (CAS Registry No. 4436-82-2), also known as limononic acid, as the major product, confirmed by (1)H and (13)C NMR analysis, chemical ionization mass spectrometry, and electrospray ionization mass spectrometry. Several minor products resulting from Norrish type I splitting of PA were also detected. The molar extinction coefficients of aqueous PA were measured and used to calculate the photolysis quantum yield of aqueous PA as 0.5 ± 0.3 (effective average value over the 280-400 nm range). The gas-phase photolysis quantum yield of 0.53 ± 0.06 for PA methyl ester (PAMe; CAS Registry No. 16978-11-3) was also measured for comparison. These results indicate that photolysis of PA is not significantly suppressed by the presence of water. This fact was confirmed by photodissociation dynamics simulations of bare PA and of PAMe hydrated with one or five water molecules using on-the-fly dynamics simulations on a semiempirical potential energy surface. The calculations correctly predicted the occurrence of both Norrish type I and Norrish type II photolysis pathways, both driven by the dynamics on the lowest triplet excited state of PA and PAMe. The rate of removal of PA by direct aqueous photolysis in cloudwater and in aerosol water was calculated for a range of solar zenith angles and compared with rates of other removal processes such as gas-phase oxidation by OH, aqueous-phase oxidation by OH, and gas-phase photolysis. Although the direct photolysis mechanism was not the most significant sink for PA in cloud and fog droplets, direct photolysis can be expected to contribute to removal of PA and more soluble/less volatile biogenic oxidation products in wet particulate matter.

Computational Studies of Atmospherically-Relevant Chemical Reactions in Water Clusters and on Liquid Water and Ice Surfaces

CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on isolated defects where it involves formation of H3O(+)-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.

Absorption Spectra and Photolysis of Methyl Peroxide in Liquid and Frozen Water

Methyl peroxide (CH(3)OOH) is commonly found in atmospheric waters and ices in significant concentrations. It is the simplest organic peroxide and an important precursor to hydroxyl radical. Many studies have examined the photochemical behavior of gaseous CH(3)OOH; however, the photochemistry of liquid and frozen water solutions is poorly understood. We present a series of experiments and theoretical calculations designed to elucidate the photochemical behavior of CH(3)OOH dissolved in liquid water and ice over a range of temperatures. The molar extinction coefficients of aqueous CH(3)OOH are different from the gas phase, and they do not change upon freezing. Between -12 and 43 °C, the quantum yield of CH(3)OOH photolysis is described by the following equation: Φ(T) = exp((-2175 ± 448)1/T) + 7.66 ± 1.56). We use on-the-fly ab initio molecular dynamics simulations to model structures and absorption spectra of a bare CH(3)OOH molecule and a CH(3)OOH molecule immersed inside 20 water molecules at 50, 200, and 220 K. The simulations predict large sensitivity in the absorption spectrum of CH(3)OOH to temperature, with the spectrum narrowing and shifting to the blue under cryogenic conditions because of constrained dihedral motion around the O-O bond. The shift in the absorption spectrum is not observed in the experiment when the CH(3)OOH solution is frozen suggesting that CH(3)OOH remains in a liquid layer between the ice grains. Using the extinction coefficients and photolysis quantum yields obtained in this work, we show that under conditions with low temperatures, in the presence of clouds with a high liquid-water content and large solar zenith angles, the loss of CH(3)OOH by aqueous photolysis is responsible for up to 20% of the total loss of CH(3)OOH due to photolysis. Gas phase photolysis of CH(3)OOH dominates under all other conditions.

Femtosecond timescale deactivation of electronically excited peroxides at ice surfaces

Peroxides are ubiquitous in the atmosphere and their photochemistry at ice surfaces is important. Here the primary steps following photoexcitation of methyl hydroperoxide (MHP) on ice particles are investigated using the MNDO method that describes semiempirically multiple electronic states and treats non-adiabatic dynamical transitions between them by surface hopping. Results are compared with the isolated MHP. Important findings are as follows. (1) Ice catalyzes the deactivation of MHP from the excited state to the ground state. (2) The deactivation process takes place on a femtosecond timescale and is followed by dissociation into fragments. (3) Recombination of fragments occurs to a small extent on ice, but not for the isolated peroxide.

Dynamics of Triplet-State Photochemistry of Pentanal: Mechanisms of Norrish I, Norrish II, and H Abstraction Reactions

The photochemistry of aldehydes in the gas phase has been the topic of extensive studies over the years. However, for all but the smallest aldehydes the dynamics of the processes is largely unknown, and key issues of the mechanisms are open. In this article, the photochemistry of pentanal is studied by dynamics simulation using a semiempirical MRCI code for the singlet and triplet potential energy surfaces involved. The simulations explore the processes on the triplet state following intersystem crossing from the initially excited singlet. Test simulations show that the photochemistry takes place on the adiabatic triplet surface only and that no nonadiabatic transitions occur to the other triplets. The main findings include the following: (1) Norrish type I and type II reactions and H detachment have been observed. (2) The time scales of Norrish type I and Norrish type II reactions are determined: Norrish type I reaction tends to occur in the time scale below 10 ps, whereas the Norrish type II reaction is mostly pronounced after 20 ps. The factors affecting the time scales are analyzed. (3) The relative yield for Norrish type I and type II reactions is 34% and 66%, which is close to the experimental observed ones. Bond orders and Mulliken partial charges are computed along the trajectories and provide mechanistic insights. The results throw light on the time scales and mechanisms and competition between different channels in aldehyde photochemistry. It is suggested that direct dynamics simulations using semiempirical potentials can be a very useful tool for exploring the photochemistry of large aldehydes, ketones, and related species.

Effect of the Chirality of Residues and γ-Turns on the Electronic Excitation Spectra, Excited-State Reaction Paths and Conical Intersections of Capped Phenylalanine–Alanine Dipeptides

The capped dipeptides Ac-L-Phe-Xxx-NH(2) , Xxx=L-Ala, D-Ala, Aib, where Aib (aminoisobutyric acid) is a non-chiral amino acid, have been investigated by means of UV/IR double-resonance spectroscopy in supersonic jets and density functional theory calculations by Gloaguen et al. [Phys. Chem. Chem. Phys. 2007, 9, 4491]. The UV and IR spectra of five different species were observed and their structures assigned by comparison with calculated vibrational frequencies in the NH-stretching region. The peptides with two chiral residues can form homochiral or heterochiral species. In addition, γ-turns exist as two helical forms (γ(D), γ(L)) of opposite handedness. Herein, we explore the excited-state potential-energy surfaces of these dipeptides with ab initio calculations. Vertical and adiabatic excitation energies, excited-state reaction paths and conical intersections are characterized with the ADC(2) propagator method. It is shown that electron/proton transfer along the hydrogen bond of the γ-turn gives rise to efficient radiationless deactivation of the (1)ππ* state of the chromophore via several conical intersections. While the homo/hetero chirality of the residues appears to have a negligible effect on the photophysical dynamics, we found evidence that the γ(L) conformers may have shorter excited-state lifetimes (and thus higher photostability) than the γ(D) conformers.

Absorption spectra and aqueous photochemistry of β-hydroxyalkyl nitrates of atmospheric interest

Molar absorption coefficients were measured for select alkyl nitrates and β-hydroxyalkyl nitrates in methanol. The presence of the β-hydroxyl group has a relatively minor effect on the absorption spectrum in the vicinity of the weak n → π* transition, which is responsible for photolysis of organic nitrates in the atmosphere. For both alkyl nitrates and β-hydroxyalkyl nitrates, there is an enhancement in the absorption coefficients in solution compared to the gas-phase values. The effect of the β-hydroxyl group on the spectra was modelled with molecular dynamics simulations using an OM2/GUGA-CI Hamiltonian for ethyl nitrate and β-hydroxyethyl nitrate. The simulation provided a qualitatively correct shape of the low energy tail of the absorption spectrum, which is important for atmospheric photochemistry. The role of direct aqueous photolysis in removal of β-hydroxyalkyl nitrates in cloud and fog water was modelled using a relative rate approach, and shown to be insignificant relative to gas-phase photochemical processes and aqueous OH oxidation under typical atmospheric conditions.

Photochemistry of Thin Solid Films of the Neonicotinoid Imidacloprid on Surfaces

Imidacloprid (IMD) is the most widely used neonicotinoid insecticide found on environmental surfaces and in water. Analysis of surface-bound IMD photolysis products was performed using attenuated total reflectance Fourier transfer infrared (ATR-FTIR) analysis, electrospray ionization (ESI-MS), direct analysis in real time mass spectrometry (DART-MS), and transmission FTIR for gas-phase products. Photolysis quantum yields (ϕ) for loss of IMD were determined to be (1.6 ± 0.6) × 10-3 (1s) at 305 nm and (8.5 ± 2.1) × 10-3 (1s) at 254 nm. The major product is the imidacloprid urea derivative (IMD-UR, 84% yield), with smaller amounts of the desnitro-imidacloprid (DN-IMD, 16% yield) product, and gaseous nitrous oxide (N2O). Theoretical calculations show that the first step of the main mechanism is the photodissociation of NO2, which then recombines with the ground electronic state of IMD radical to form IMD-UR and N2O in a thermally driven process. The photolytic lifetime of IMD at a solar zenith angle of 35° is calculated to be 16 h, indicating the significant reaction of IMD over the course of a day. Desnitro-imidacloprid has been identified by others as having increased binding to target receptors compared to IMD, suggesting that photolysis on environmental surfaces increases toxicity.