Alternative pathway for atmospheric particles growth.

Credible climate change predictions require reliable fundamental scientific knowledge of the underlying processes. Despite extensive observational data accumulated to date, atmospheric aerosols still pose key uncertainties in the understanding of Earth's radiative balance due to direct interaction with radiation and because they modify clouds' properties. Specifically, major gaps exist in the understanding of the physicochemical pathways that lead to aerosol growth in the atmosphere and to changes in their properties while in the atmosphere. Traditionally, the driving forces for particle growth are attributed to condensation of low vapor pressure species following atmospheric oxidation of volatile compounds by gaseous oxidants. The current study presents experimental evidence of an unaccounted-for new photoinduced pathway for particle growth. We show that heterogeneous reactions activated by light can lead to fast uptake of noncondensable Volatile Organic Compounds (VOCs) at the surface of particles when only traces of a photosensitizer are present in the seed aerosol. Under such conditions, size and mass increase; changes in the chemical composition of the aerosol are also observed upon exposure to volatile organic compounds such as terpenes and near-UV irradiation. Experimentally determined growth rate values match field observations, suggesting that this photochemical process can provide a new, unaccounted-for pathway for atmospheric particle growth and should be considered by models.

Isolated gramicidin peptides probed by IR spectroscopy.

We report double-resonant IR/UV ion-dip spectroscopy of neutral gramicidin peptides in the gas phase. The IR spectra of gramicidin A and C, recorded in both the 1000 cm(-1) to 1800 cm(-1) and the 2700 to 3750 cm(-1) region, allow structural analysis. By studying this broad IR range, various local intramolecular interactions are probed, and complementary IR modes can be accessed. Ab initio quantum chemical calculations are used to support the interpretation of the experimental IR spectra. The comparison of the calculated frequencies with the experimental IR spectrum probed via the strong infrared absorptions of all the amide groups (NH stretch, C=O stretch and NH bend), shows evidence for a helical structure in the gas phase, which is similar to that in the condensed phase. Additionally, we show that to improve the spectral resolution when studying large neutral molecular structures of the size of gramicidin, the use of heavier carrier gas could be advantageous.

Changes in the optical properties of benzo[a]pyrene-coated aerosols upon heterogeneous reactions with NO2 and NO3.

Chemical reactions can alter the chemical, physical, and optical properties of aerosols. It has been postulated that nitration of aerosols can account for atmospheric absorbance over urban areas. To study this potentially important process, the change in optical properties of laboratory-generated benzo[a]pyrene (BaP)-coated aerosols following exposure to NO(2) and NO(3) was investigated at 355 nm and 532 nm by three aerosol analysis techniques. The extinction coefficient was determined at 355 nm and 532 nm from cavity ring-down aerosol spectroscopy (CRD-AS); the absorption coefficient was measured by photoacoustic spectroscopy (PAS) at 532 nm, while an on-line aerosol mass spectrometer (AMS) supplied real-time quantitative information about the chemical composition of aerosols. In this study, 240 nm polystyrene latex (PSL) spheres were thinly coated with BaP to form 300 or 310 nm aerosols that were exposed to high concentrations of NO(2) and NO(3) and measured with CRD-AS, PAS, and the AMS. The extinction efficiencies (Q(ext)) changed after exposure to NO(2) and NO(3) at both wavelengths. Prior to reaction, Q(ext) for the 355 nm and 532 nm wavelengths were 4.36 ± 0.04 and 2.39 ± 0.05, respectively, and Q(ext) increased to 5.26 ± 0.04 and 2.79 ± 0.05 after exposure. The absorption cross-section at 532 nm, determined with PAS, reached σ(abs) = (0.039 ± 0.001) × 10(-8) cm(2), indicating that absorption increased with formation of nitro-BaP, the main reaction product detected by the AMS. The single-scattering albedo (SSA), a measure of particle scattering efficiency, decreased from 1 to 0.85 ± 0.03, showing that changes in the optical properties of BaP-covered aerosols due to nitration may have implications for regional radiation budget and, hence, climate.

Conformational structure of tyrosine, tyrosyl-glycine, and tyrosyl-glycyl-glycine by double resonance spectroscopy.

We investigated the variation in conformation for the amino acid tyrosine (Y), alone and in the small peptides tyrosine-glycine (YG) and tyrosine-glycine-glycine (YGG), in the gas phase by using UV-UV and IR-UV double resonance spectroscopy and density functional theory calculations. For tyrosine we found seven different conformations, for YG we found four different conformations, and for YGG we found three different conformations. As the peptides get larger, we observe fewer stable conformers, despite the increasing complexity and number of degrees of freedom. We find structural trends similar to those in phenylalanine-glycine-glycine (FGG) and tryptophan-glycine-glycine (WGG); however, the effect of dispersive forces in FGG for stabilizing a folded structure is replaced by that of hydrogen bonding in YGG.

Guanine-aspartic acid interactions probed with IR-UV resonance spectroscopy.

Double resonance spectroscopy of clusters of guanine with aspartic acid reveals geometries similar to patterns exhibited in DNA base pairs. In the spectral region of 32,800 cm(-1) to 35,500 cm(-1) we observe five isomers of guanine-aspartic acid clusters and assign their structures based on IR-UV hole-burning spectra and wave function theory calculations at the MP2/cc-pVDZ and MP2/cc-pVTZ levels. The calculations employed both harmonic and one-dimensional scan anharmonic approximations. Three of the isomers are similar, assigned to structures containing three hydrogen bonds and 9-enolguanine. We assign the fourth isomer to a structure containing a 9-keto tautomer of guanine and forming a triply bonded structure similar to a base pairing interaction. The fifth isomer dissociates with proton transfer upon excitation or ionization. This is the first set of experiments and high-level ab initio calculations of the isolated, microscopic interactions of an amino acid and a nucleobase, the building blocks of nucleic acids and proteins.

Interaction of internally mixed aerosols with light.

Atmospheric aerosols scatter and absorb solar radiation leading to variable effects on Earth's radiative balance. Aerosols individually comprising mixtures of different components ("internally mixed") interact differently with light than mixtures of aerosols, each comprising a different single component ("externally mixed"), even if the relative fractions of the different components are equal. In climate models, the optical properties of internally mixed aerosols are generally calculated by using electromagnetic "mixing rules", which average the refractive indices of the individual components in different proportions, or by using coated-sphere Mie scattering codes, which solve the full light scattering problem assuming that the components are divided into two distinct layers. Because these calculation approaches are in common use, it is important to validate them experimentally. In this article, we present a broad perspective on the optical properties of internally mixed aerosols based on a series of laboratory experiments and theoretical calculations. The optical properties of homogenously mixed aerosols comprised of non-absorbing and weakly absorbing compounds, and of coated aerosols comprised of strongly absorbing, non-absorbing, and weakly absorbing compounds in different combinations are measured using pulsed and continuous wave cavity ring down aerosol spectrometry (CRD-AS). The success of electromagnetic mixing rules and Mie scattering codes in reproducing the measured aerosol extinction values is discussed.

Isomer discrimination of polycyclic aromatic hydrocarbons in the Murchison meteorite by resonant ionization.

We have used two-color resonant two-photon ionization (2C-R2PI) mass spectrometry to discriminate between isomers of polycyclic aromatic hydrocarbons in the Murchison meteorite. We measured the 2C-R2PI spectra of chrysene and triphenylene seeded in a supersonic jet by laser desorption. Since each isomer differs in its R2PI spectrum, we can distinguish between isomers using wavelength dependent ionization and mass spectrometry. We found both chrysene and triphenylene in sublimates from carbonaceous residue obtained by acid demineralization of the Murchison meteorite. Their R2PI mass spectra show only the molecular ion, even though these samples contain a complex inventory of organic molecules.

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory.

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH...OC intramolecular H-bond (families CO(2)H(free) and CO(2)H(bonded)). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentally the CO(2)H(bonded) family (also predicted by metadynamics), although its stability is comparable to that of the CO(2)H(free) structures. This fact was explained by the former's short excited-state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilising peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.

IR-UV double resonance spectroscopy of xanthine.

We present resonant two-photon ionization (R2PI), UV-UV, and IR-UV double resonance spectra of xanthine seeded in a supersonic jet by laser desorption. We show that there is only one tautomer of xanthine which absorbs in the wavelength range of 36 700 to 37 700 cm(-1). The IR-UV double resonance spectrum shows three strong bands at 3444, 3485, and 3501 cm(-1), all of which we assign as N-H stretching vibrations. Comparison of the IR-UV double resonance spectrum with frequencies and intensities obtained from density functional theory (DFT) and second order Møller Plesset (MP2) calculations suggests that the observed xanthine is the diketo N(7)H tautomer.

The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine.

We present the mid-IR (400-1800 cm(-1)) spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine measured by IR-UV double-resonance spectroscopy. We compare the recorded mid-IR spectra with the spectra of the most stable structures obtained from RI-MP2 and RI-DFT-D calculations. The results confirm the enol form for all structures and demonstrate the efficacy of a new approach to DFT calculations that includes dispersion interactions.

IR-UV double resonance spectroscopy of guanine-H2O clusters.

We present the IR-UV double resonance spectrum of guanine monohydrate in the region 3100 cm(-1) to 3800 cm(-1) along with the energies and frequencies of these structures calculated at the non-empirical correlated ab initio RI-MP2/cc-pVDZ level. We assign the structures of guanine-water clusters by comparing the experimental spectra with the ab initio calculations and with the IR spectra of the bare guanine monomer. We find two clusters with guanine in the enol-amino tautomeric form and one structure with guanine in the keto-amino form.

An in situ silver cationization method for hydrocarbon mass spectrometry.

We have developed a novel cationization method for the analysis of long-chain hydrocarbons via UV laser desorption mass spectrometry. In this technique we electrospray a thin coating of AgNO3 over a sample and perform UV laser desorption to produce Ag+ cationization of sample molecules. Use of this technique in our microscope/TOF-MS allows us to determine the spatial distribution of the species we detect in the sample. We demonstrate 8-mu spatial resolution, and submicron resolution is possible in principle. In mixed samples containing aromatic and aliphatic compounds, the aromatic compounds ionize directly and do not form adducts, and thus give single peaks as opposed to doublets from silver cations. This enables distinction between aromatic and aliphatic compounds that are in the same sample.

Microhydration of Guanine base pairs.

We report spectroscopy of clusters of guanine base pairs with one and two water molecules. We recorded the vibronic spectra of the mass-selected GG(H2O) and GG(H2O)2 clusters using resonant two photon ionization (R2PI) and we used IR-UV double resonance spectroscopy to obtain ground state IR spectra of these clusters. We found that a single water molecule stabilizes one of two structures we had previously found for guanine dimers. Addition of a second water molecule causes no further structural change.

Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings.

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.

Photochemical selectivity in guanine-cytosine base-pair structures.

Prebiotic chemistry presumably took place before formation of an oxygen-rich atmosphere and thus under conditions of intense short wavelength UV irradiation. Therefore, the UV photochemical stability of the molecular building blocks of life may have been an important selective factor in determining the eventual chemical makeup of critical biomolecules. To investigate the role of UV irradiation in base-pairing we have studied guanine (G) and cytosine (C) base pairs in the absence of the RNA backbone. We distinguished base-pair structures by IR-UV hole-burning spectroscopy as well as by high-level correlated ab initio calculations. The Watson-Crick structure exhibits broad UV absorption, in stark contrast to other GC structures and other base-pair structures. This broad absorption may be explained by a rapid internal conversion that makes this specific base pair arrangement uniquely photochemically stable.