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In lipid vesicles, the size and shape modulates the chemistry within.

Exposure to the secondary pollutant ozone in ambient air is associated with adverse health effects when inhaled. In this work we use surface pressure measurements, combined with X-ray and neutron reflection, to observe changes in a layer of lung surfactant at the air water interface when exposed to gas phase ozone. The results demonstrate that the layer reacts with ozone changing its physical characteristics. A slight loss of material, a significant thinning of the layer and increased hydration of the surfactant material is observed. The results support the hypothesis that unsaturated lipids present in lung surfactant are still susceptible to rapid reaction with ozone and the reaction changes the properties of the interfacial layer.

The use of functionalised gold nanoparticles in biomedical applications is expanding. Here we explore the interaction of gold nanoparticles with lipid membranes using readily available equipment and basic techniques to explore how the charge on the nanoparticles, and the nature of the lipid, influences the interaction. Gold nanoparticles were synthesised with two different surface functionalisations, negatively charged citrate groups and positively charged cetyltrimethylammonium groups from CTAB, to determine how surface charge affects the interaction of the nanoparticles with the Zwitterionic lipid POPC and the anionic lipid POPG. It was observed that the surface pressure/area isotherms of POPG monolayers on exposure to citrate capped nanoparticles were not shifted to higher molecular areas as much as those of POPC, suggesting that the anionic headgroups of the POPG lipid repel the anionic surface charge of the citrate capped nanoparticles to some extent limiting inclusion. In contrast, the surface pressure/area isotherms of the POPG monolayers exposed to CTAB capped nanoparticles are shifted to higher molecular areas more than for the POPC monolayers. The interaction of anionic nanoparticles with lipid bilayers was measured by the mass change of the bilayer deposited on the surface of a quartz crystal microbalance (QCM) exposed to nanoparticles in an aqueous phase flow. The QCM frequency changes show that bilayers of unsaturated phosophocholine lipids readily took up particles, whereas for the saturated lipid DPPC significant uptake was only observed when the bilayer was warmed to above its gel-to-fluid transition temperature, T

Abstrct 2-Aminopurine (2AP) is a fluorescent nucleobase analogue of the DNA nucleobase adenine and can be inserted in place of adenine into nucleic acids with minimal structural perturbation. The inserted 2-aminopurine can be selectively excited, and the fluorescence observed used as a sensitive probe for local structure, in addition selective ionization of 2-aminopurine within a nucleic acid is possible and once formed the ionized 2-aminopurine will oxidize nearby guanine bases, providing a route to study charge transfer within nucleic acids. Time resolved infrared spectroscopy is a powerful tool to study oxidation processes on picosecond, and longer timescales. There is a lack of availability of high quality IR spectra in the literature of the individual, short lived, photoproducts, required to fully elucidate the mechanism of the interaction of photoionized 2-aminopurine with guanine. Density functional theory (DFT) methods (B3LYP/6–31G+(d) and EDF1/6–31G+(d)) have been used to calculate the energies and infrared spectra of 2-aminopurine, guanine and potential photoproducts that may result from photoionization reactions between 2-aminopurine and guanine. Direct comparison can therefore be made between areas of bleaching of bands in the IR spectra of 2-aminopurine or guanine and the appearance of new transient bands of potential photoproducts. These potential photoproducts could include deprotonated neutral radical species, deprotonated anion species, radical cations and radical anions. It was found in the current work that the key intermediates in the oxidation reaction between photoionized 2-aminopurine and guanine were: 2AP•(−H,N2) (formed from deprotonation from the 2AP•+ amino group); G•(−H) (formed from deprotonation from the N1 nitrogen, or possibly the amino group, of the initially formed G•+), and 2AP−(−H,N2) (formed from the reduction of 2AP•(−H,N2) by guanine).

Organic films that form on atmospheric particulate matter change the optical and cloud condensation nucleation properties of the particulate matter and consequently have implications for modern climate and climate models. The organic films are subject to attack from gas-phase oxidants present in ambient air. Here we revisit in greater detail the oxidation of a monolayer of oleic acid by gas-phase ozone at the air-water interface as this provides a model system for the oxidation reactions that occur at the air-water interface of aqueous atmospheric aerosol. Experiments were performed on monolayers of oleic acid at the air-liquid interface at atmospherically relevant ozone concentrations to investigate if the viscosity of the sub-phase influences the rate of the reaction and to determine the effect of the presence of a second component within the monolayer, stearic acid, which is generally considered to be non-reactive towards ozone, on the reaction kinetics as determined by neutron reflectometry measurements. Atmospheric aerosol can be extremely viscous. The kinetics of the reaction were found to be independent of the viscosity of the sub-phase below the monolayer over a range of moderate viscosities, eta/eta water = 1.0-7.2, demonstrating no involvement of aqueous sub-phase oxidants in the rate determining step. The kinetics of oxidation of monolayers of pure oleic acid were found to depend on the surface coverage with different behaviour observed above and below a surface coverage of oleic acid of similar to 1 x 10(18) molecule m(-2). Atmospheric aerosol are typically complex mixtures, and the presence of an additional compound in the monolayer that is inert to direct ozone oxidation, stearic acid, did not significantly change the reaction kinetics. It is demonstrated that oleic acid monolayers at the air-water interface do not leave any detectable material at the air-water interface, contradicting the previous work published in this journal which the authors now believe to be erroneous. The combined results presented here indicate that the kinetics, and thus the atmospheric chemical lifetime for unsaturated surface active materials at the air-water interface to loss by reaction with gas-phase ozone, can be considered to be independent of other materials present at either the air-water interface or in the aqueous sub-phase.

Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.

DPPC (dipalmitoylphosphatidylcholine) is a disaturated lipid capable of forming closely packed monolayers at the air-liquid interface of the lung and allows the surface tension within the alveoli to reduce to almost zero and thus prevent alveolar collapse. Carbon nanoparticles are formed in natural and man-made combustion events, including diesel engines, and are capable of reaching the alveolar epithelium during breathing. In this work, we have used Brewster angle microscopy and neutron reflectivity to study the effect of differing concentrations of carbon nanoparticles on the structure of DPPC monolayer as the monolayer is subject to compression and expansion. The results show that the inclusion of carbon nanoparticles within a DPPC monolayer affects the formation and structure of the lipid domains. The domains lose their circular structure and show a crenated structure as well as a reduction in overall size of the domains. This change in structure is also evident following expansion of the lipid monolayer, suggesting that some carbon nanoparticles may remain associated with the monolayer. This observation could have an important implication regarding the removal of nanosized airborne pollutants from the human lung.

Deuteration of biomolecules has a major impact on both quality and scope of neutron scattering experiments. Cholesterol is a major component of mammalian cells, where it plays a critical role in membrane permeability, rigidity and dynamics, and contributes to specific membrane structures such as lipid rafts. Cholesterol is the main cargo in low and high-density lipoprotein complexes (i.e. LDL, HDL) and is directly implicated in several pathogenic conditions such as coronary artery disease which leads to 17 million deaths annually. Neutron scattering studies on membranes or lipid-protein complexes exploiting contrast variation have been limited by the lack of availability of fully deuterated biomolecules and especially perdeuterated cholesterol. The availability of perdeuterated cholesterol provides a unique way of probing the structural and dynamical properties of the lipoprotein complexes that underly many of these disease conditions. Here we describe a procedure for in vivo production of perdeuterated recombinant cholesterol in lipid-engineered Pichia pastoris using flask and fed-batch fermenter cultures in deuterated minimal medium. Perdeuteration of the purified cholesterol was verified by mass spectrometry and its use in a neutron scattering study was demonstrated by neutron reflectometry measurements using the FIGAROO instrument at the ILL.

The presence of unsaturated lipids in lung surfactant is important for proper respiratory function. In this work, we have used neutron reflection and surface pressure measurements to study the reaction of the ubiquitous pollutant gas-phase ozone, O3, with pure and mixed phospholipid monolayers at the air-water interface. The results reveal that the reaction of the unsaturated lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, POPC, with ozone leads to the rapid loss of the terminal C9 portion of the oleoyl strand of POPC from the air-water interface. The loss of the C9 portion from the interface is accompanied by an increase in the surface pressure (decrease in surface tension) of the film at the air-water interface. The results suggest that the portion of the oxidized oleoyl strand that is still attached to the lipid headgroup rapidly reverses its orientation and penetrates the air-water interface alongside the original headgroup, thus increasing the surface pressure. The reaction of POPC with ozone also leads to a loss of material from the palmitoyl strand, but the loss of palmitoyl material occurs after the loss of the terminal C9 portion from the oleoyl strand of the molecule, suggesting that the palmitoyl material is lost in a secondary reaction step. Further experiments studying the reaction of mixed monolayers composed of unsaturated lipid POPC and saturated lipid dipalmitoyl-sn-glycero-3-phosphocholine, DPPC, revealed that no loss of DPPC from the air-water interface occurs, eliminating the possibility that a reactive species such as an OH radical is formed and is able to attack nearby lipid chains. The reaction of ozone with the mixed films does cause a significant change in the surface pressure of the air-water interface. Thus, the reaction of unsaturated lipids in lung surfactant changes and impairs the physical properties of the film at the air-water interface.

Fluorescence resonance energy transfer, FRET, can be used to obtain long-range distance information for macromolecules and is particularly powerful when used in single-molecule studies. The determination of accurate distances requires knowledge of the fluorophore position with respect to the macromolecule. In this study we have used NMR to determine the structure of the commonly used fluorophore indocarbocyanine-5 (Cy5) covalently attached to the 5'-terminus of double-helical DNA. We find that Cy5 is predominantly stacked onto the end of the duplex, in a manner similar to an additional base pair. This is very similar to the behavior of Cy3 terminally attached to DNA and suggests that the efficiency of energy transfer between Cy3 and Cy5, that are attached to nucleic acids in this way, will exhibit significant dependence on fluorophore orientation.

The results of an experimental study into the oxidative degradation of proxies for atmospheric aerosol are presented. We demonstrate that the laser Raman tweezers method can be used successfully to obtain uptake coeffcients for gaseous oxidants on individual aqueous and organic droplets, whilst the size and composition of the droplets is simultaneously followed. A laser tweezers system was used to trap individual droplets containing an unsaturated organic compound in either an aqueous or organic ( alkane) solvent. The droplet was exposed to gas- phase ozone and the reaction kinetics and products followed using Raman spectroscopy. The reactions of three different organic compounds with ozone were studied: fumarate anions, benzoate anions and alpha pinene. The fumarate and benzoate anions in aqueous solution were used to represent components of humic- like substances, HULIS; a alpha- pinene in an alkane solvent was studied as a proxy for biogenic aerosol. The kinetic analysis shows that for these systems the diffusive transport and mass accommodation of ozone is relatively fast, and that liquid- phase di. ffusion and reaction are the rate determining steps. Uptake coe. ffcients, g, were found to be ( 1.1 +/- 0.7) x 10(-5), ( 1.5 +/- 0.7) x 10 (-5) and ( 3.0 - 7.5) x 10 (-3) for the reactions of ozone with the fumarate, benzoate and a- pinene containing droplets, respectively. Liquid- phase bimolecular rate coe. cients for reactions of dissolved ozone molecules with fumarate, benzoate and a- pinene were also obtained: k(fumarate) = ( 2.7 +/- 2) x 10 (5), k(benzoate) = ( 3.5 +/- 3) x 10 (5) and k(alpha-pinene) = ( 1-3) x 10(7) dm(3) mol (-1) s (- 1). The droplet size was found to remain stable over the course of the oxidation process for the HULIS- proxies and for the oxidation of a- pinene in pentadecane. The study of the alpha- pinene/ ozone system is the first using organic seed particles to show that the hygroscopicity of the particle does not increase dramatically over the course of the oxidation. No products were detected by Raman spectroscopy for the reaction of benzoate ions with ozone. One product peak, consistent with aqueous carbonate anions, was observed when following the oxidation of fumarate ions by ozone. Product peaks observed in the reaction of ozone with alpha- pinene suggest the formation of new species containing carbonyl groups.

2-Aminopurine (2AP) is a widely used marker for nucleic acid structure because the fluorescence of 2AP in double-stranded DNA is approximately half that of 2AP in single-stranded DNA. The underlying photophysical mechanism responsible for the change in fluorescence with structure is not understood. We have performed CIS and TDB3LYP level calculations on double-stranded trinucleotide models, (X2APX)·(YTY), where X and Y represent the natural nucleobases. The results reveal that base stacking combined with hydrogen bonding reduces the oscillator strength for the fluorescence transition, and hence the fluorescence quantum yield. It is also shown that the electronic transitions of double-stranded trinucleotides are not simply those of the individual bases, but rather involve orbitals that are delocalized across several bases. Although the results obtained at the CIS level suffer from the neglect of electron correlation, the results obtained at the TDB3LYP level are not necessarily better because this method has problems describing long-range interactions and tends to underestimate the energies of charge-transfer states. Calculations on a full (rather than model) dinucleotide 5′-G2AP-3′ confirm that the inclusion of the sugar and phosphate groups is not necessary when studying the energetically low-lying excited states of nucleic acids containing 2AP. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Lung surfactant protein B (SP-B) is an essential protein found in the surfactant fluid at the air–water interface of the lung. Exposure to the air pollutant ozone could potentially damage SP-B and lead to respiratory distress. We have studied two peptides, one consisting of the N-terminus of SP-B [SP-B(1–25)] and the other a construct of the N- and C-termini of SP-B [SP-B(1–25,63–78)], called SMB. Exposure to dilute levels of ozone (∼2 ppm) of monolayers of each peptide at the air–water interface leads to a rapid reaction, which is evident from an increase in the surface tension. Fluorescence experiments revealed that this increase in surface tension is accompanied by a loss of fluorescence from the tryptophan residue at the interface. Neutron and X-ray reflectivity experiments show that, in contrast to suggestions in the literature, the peptides are not solubilized upon oxidation but rather remain at the interface with little change in their hydration. Analysis of the product material reveals that no cleavage of the peptides occurs, but a more hydrophobic product is slowly formed together with an increased level of oligomerization. We attributed this to partial unfolding of the peptides. Experiments conducted in the presence of phospholipids reveal that the presence of the lipids does not prevent oxidation of the peptides. Our results strongly suggest that exposure to low levels of ozone gas will damage SP-B, leading to a change in its structure. The implication is that the oxidized protein will be impaired in its ability to interact at the air–water interface with negatively charged phosphoglycerol lipids, thus compromising what is thought to be its main biological function.

Rate constants for the gas-phase reaction of NO and HO2 radicals with 33 peroxy radicals are presented. The peroxy radicals are derived from the addition of either OH, Cl, or NO3 radicals, followed by addition of O2, to a series of alkenes: tetrachloroethene, ethene, 2,3-dimethyl but-2-ene, butadiene, 2,3,4,5-tetramethyl hexa-2,4-diene, 1,1,2,3,4,4-hexachlorobutadiene, but-1-ene-3-one (methyl vinyl ketone) and 2,3-dimethylpen-2-ene-4-one. The rate constants were predicted using a correlation between the singly occupied molecular orbital (SOMO) energy of the peroxy radical and the logarithm of the rate constant for reaction with NO or HO2. A discussion of the accuracy of the method and the trends in the reactivity of the titled peroxy radicals is given. Peroxy radicals derived from halogenated alkenes have larger values of rate constants for reaction with NO relative to reaction with HO2, indicating that they are more likely to react with NO, rather than HO2, in the atmosphere. The reverse is true for peroxy radicals derived from alkylated alkenes.

The inter-conversion of nitrogen oxides and oxy acids on silica surfaces is of major atmospheric importance. As a preliminary step towards rationalising experimental observations, and understanding the mechanisms behind such reactions we have looked at the binding energies of NO2, N2O4, HNO3, HONO and H2O with simple proxies of a silica surface, namely SiH3OH and Si(OH)4 units. The geometries of these molecular clusters were optimised at both HF/6-311+G(d) and B3LYP/6-311+G(d) level of theory. The SCF energies of the species were determined at the HF/6-311++G(3df,2pd) and B3LYP/6-311++G(3df,2pd) level. The values indicate that nitric acid is by far the most strongly bound species, in agreement with experimental observations. It was also found that the dimer N2O4 is significantly more strongly bound to the Si(OH)4 and SiH3OH units than NO2 itself. The vibrational frequencies calculated for the hydrogen-bonded complexes are compared to the experimentally observed frequencies of the adsorbed species where possible.

Methyl salicylate is one of a number of semiochemicals, signal molecules, emitted by herbivore-infested plants. These signal molecules attract predators of the herbivore, and the chemicals thus act indirectly as part of the defence mechanism of the plant. Previous studies have shown that ozone damage to plants can also elicit the emission of signal molecules. The fate of these signal molecules in the atmosphere is not known. Preliminary studies have been undertaken to examine the atmospheric chemistry of methyl salicylate for the first time. Rate coefficients for the reaction of methyl salicylate with atomic chlorine and with ozone have been determined; the values are (2.8±0.3)×10−12 and ∼4×10−21 cm3 molecule−1 s−1. These results suggest that neither reaction with atomic chlorine nor reaction with ozone will provide important loss routes for methyl salicylate in the atmosphere. The possible importance of photolysis of methyl salicylate in the atmosphere is considered.

An investigation into the reactions between Cl atoms and acrolein (1), methacrolein (2) and methyl vinyl ketone (3) is presented. Values of the rate constants for the reactions have been determined by an absolute technique for the first time. At a pressure of 1.6 Torr, the rate constants obtained were: k1 = 1.1 ± 0.2, k2 = 3.3 ± 0.6 and k3 = 0.99 ± 0.20 in units of 10−10 cm3 molecule−1 s−1. k1 was also determined at atmospheric pressure using a relative-rate technique. The rate constant obtained was (2.2 ± 0.3) × 10−10 cm3 molecule−1 s−1; the larger value compared with that for 1.6 Torr is thought to reflect a true dependence of the reaction rate on pressure. The final products of the reactions performed under an atmosphere of synthetic air were investigated using FTIR spectroscopy. The only chlorinated organic species identified as products of the reactions were chloroacetaldehyde in the case of reaction of Cl atoms with acrolein; chloroacetone with methacrolein; and chloroacetaldehyde with methyl vinyl ketone. Branching ratios for abstraction (the fraction of reactions occurring by abstraction relative to the sum of addition and abstraction processes) were found to be 0.22 ± 0.13 for acrolein, 0.18 ± 0.02 for methacrolein and

Absolute and relative-rate techniques have been used to obtain rate coefficients for the reactions: NO3+CH3C(O)CHCH2→products (1), NO3+CH2C(CH3)CHO→products (2), NO3+CH2CHCHO→ products (3), and NO3+CH2CHC(O)OCH3→products (4). The reaction NO3+CH2C(CH3)C(O)OCH3→ products (5), has been investigated by a relative-rate method only. The rate coefficients obtained by the relative-rate method at T=296±2 K and P=760 Torr are k1=(4.7±1.7)×10-16 cm3 molecule-1 s-1, k2=(3.7±1.0)×10-15 cm3 molecule-1 s-1, k3=(1.1±0.4)×10-15 cm3 molecule-1 s-1, k4=(1.0±0.6)×10-16 cm3 molecule-1 s-1 and k5=(3.6±1.3)×10-15 cm3 molecule-1 s-1. The rate coefficients determined by the discharge-flow technique at low pressure (P=1–10 Torr) and at T=293–303 K are k1=(3.2±0.6)×10-16 cm3 molecule-1 s-1, k2=(9.6±2.0)×10-15 cm3 molecule-1 s-1, k3=(8.9±2.8)×10-15 cm3 molecule-1 s-1, k4=(1.9±0.4)×10-16 cm3 molecule-1 s-1. The discrepancy between the values obtained from the relative-rate technique and the absolute technique are discussed and explained in terms of interference in the absolute study caused by secondary chemistry and fast-reacting impurities. Product studies reveal that methyl glyoxal is a product of reactions (1) and (2) along with peroxymethacryloyl nitrate (MPAN) for reaction (2) in air. A diurnally varying boundary-layer model suggests that reaction (2) is an important loss process for methacrolein and that it can lead to the generation of OH at night.

The rate coefficients for the reaction between atomic chlorine and a number of naturally occurring species have been measured at ambient temperature and atmospheric pressure using the relative rate technique. The values obtained were (4.0 ± 0.8) × 10-10, (2.1 ± 0.5) × 10-10, (3.2 ± 0.5) × 10-10, and (4.9 ± 0.5) × 10-10 cm3 molecule-1 s-1, for reactions with isoprene, methyl vinyl ketone, methacrolein and δ3-carene, respectively. The value obtained for isoprene compares favourably with previously reported values. No values have been reported to date for the rate constants of the other reactions.

The oxidation of organic films on cloud condensation nuclei has the potential to affect climate and precipitation events. In this work we present a study of the oxidation of a monolayer of deuterated oleic acid (cis-9-octadecenoic acid) at the air-water interface by ozone to determine if oxidation removes the organic film or replaces it with a product film. A range of different aqueous sub-phases were studied. The surface excess of deuterated material was followed by neutron reflection whilst the surface pressure was followed using a Wilhelmy plate. The neutron reflection data reveal that approximately half the organic material remains at the air-water interface following the oxidation of oleic acid by ozone, thus cleavage of the double bond by ozone creates one surface active species and one species that partitions to the bulk (or gas) phase. The most probable products, produced with a yield of approximately (87 +/- 14)%, are nonanoic acid, which remains at the interface, and azelaic acid (nonanedioic acid), which dissolves into the bulk solution. We also report a surface bimolecular rate constant for the reaction between ozone and oleic acid of (7.3 +/- 0.9) x 10(-11) cm2 molecule s(-1). The rate constant and product yield are not affected by the solution sub-phase. An uptake coefficient of ozone on the oleic acid monolayer of approximately 4 x 10(-6) is estimated from our results. A simple Kohler analysis demonstrates that the oxidation of oleic acid by ozone on an atmospheric aerosol will lower the critical supersaturation needed for cloud droplet formation. We calculate an atmospheric chemical lifetime of oleic acid of 1.3 hours, significantly longer than laboratory studies on pure oleic acid particles suggest, but more consistent with field studies reporting oleic acid present in aged atmospheric aerosol.

Pyrrolocytosine (PC), is a highly fluorescent analog of the natural nucleobase cytosine. The fluorescence of PC is quenched upon helix formation but the origin of the quenching is not known. We investigated the effects of base stacking in the aqueous phase by following the fluorescence of dinucleotides and trinucleotides containing PC. The quantum yields and lifetimes (ns) (in parenthesis) obtained at 25 degrees C were: PC-T, 0.026 (2.0), PC-C, 0.033 (2.5), PC-A, 0.032 (2.7), PC-G, 0.021 (2.0), T-PC-T, 0.044 (3.0) and G-PC-G, 0.036 (0.65 and 2.6), compared with 0.038 (2.9) for PC and 0.028 (2.1) for the nucleoside triphosphate. The results show that base stacking does not, except in the case of guanine, quench the fluorescence of PC; indeed the increased solvent shielding can enhance the emitted fluorescence. In the case of G-PC-G the guanines do shield the fluorescent base from the solvent but a particular environment of PC between two guanines also appears to allow a rapid nonradiative pathway, suggested to be electron transfer to the excited PC, to depopulate the excited state leading to the shorter fluorescence lifetime.

Fluorescent nucleobase analogues are used extensively to probe the structure and dynamics of nucleic acids. The fluorescence of the adenine analogue 2-aminopurine and the cytosine analogue pyrrolocytosine is significantly quenched when the bases are located in regions of double-stranded nucleic acids. To allow more detailed structural information to be obtained from fluorescence studies using these bases, we have studied the excited-state properties of the bases at the CIS and TDB3LYP level in hydrogen-bonded and base-stacked complexes. The results reveal that the first excited state (the fluorescent state) of a hydrogen-bonded complex containing 2-aminopurine and thymine is just the first excited state of 2-aminopurine alone. However, the same cannot be said for structures in which 2-aminopurine is base stacked with other nucleobases. Stacking causes the molecular orbitals involved in the fluorescence transition to spread over more than one base. The predicted rate for the fluorescence transition is reduced, thus reducing the fluorescence quantum yield. The decrease in radiative rate varies with the stacking arrangement (e.g., A- or B-form DNA) and with the identity of the nucleobase with which 2-aminopurine is stacked. Stacking 2-aminopurine between two guanine moieties is shown to significantly decrease the energy gap between the first and second excited states. We do not find reliable evidence for a low-energy charge-transfer state in any of the systems that were studied. In the case of pyrrolocytosine, base stacking was found to reduce the oscillator strength for the fluorescence transition, but very little spreading of molecular orbitals across more than one base was observed.

Pyrrolocytosine is a novel, environment sensitive, fluorescent base that can be used in place of cytosine as a fluorescent marker in nucleic acids. In this work the results of a detailed computational investigation into the hybridization and photochemical properties of the base are reported. The interaction energy of the base pair formed between pyrrolocytosine and guanine, calculated at the MP2/6-31G(d,0.25)//HF/6-31G(d,p) level, was found to be -27.2 kcal mol(-1), comparing very favorably with the value calculated for the cytosine and guanine base pair, -25.8 kcal mol(-1). The wavelengths for the vertical transitions of pyrrolocytosine and cytosine were determined using both the configuration interaction technique, with singly excited configurations (CIS) and time-dependent density functional theory using the B3LYP functional (TDB3LYP). It was found that the spacing between the first pipi state and the first npi state was significantly larger in the case of pyrrolocytosine than cytosine, providing a rationale for the higher fluorescence quantum yield of the former. Hydrogen bonding of pyrrolocytosine to guanine did not affect the predicted fluorescence properties of pyrrolocytosine whereas stacking guanine above pyrrolocytosine, in a manner appropriate to B-form DNA, significantly reduced the predicted fluorescence. Calculations on the two base systems using the TDB3LYP method produced low-lying charge-transfer states which are not predicted when the CIS method is used and are not thought to be physically meaningful.

In this communication we report the first use of the Raman laser tweezers technique to trap and hold a mixed droplet of oleic acid and water at atmospheric pressure for 30 min, oxidize the oleic acid on the droplet, follow the decay of reactants and the growth of chemical products using Raman spectroscopy, and monitor the growth in size of the droplet as it becomes more hydrophilic. We demonstrate that the oxidation of organic films on water droplets could have large climatic effects in the atmosphere. We show that cloud-droplet growth and activation of cloud condensation nuclei (to become cloud droplets) is retarded by the presence of an organic film and that chemical oxidation of this film would allow a cloud droplet to grow, reducing cloud albedo by inducing precipitation, and would allow a cloud condensation nucleus to grow to a cloud droplet, thus forming a cloud and increasing the albedo of the Earth.

An aerosol time-of-flight mass spectrometer (ATOFMS) was used to determine, in real time, the size and chemical composition of individual particles in the atmosphere at the remote inland site of Eskdalemuir, Scotland. A total of 51,980 particles, in the size range 0.3-7.4 microm, were detected between the 25th and 30th June 2001. Rapid changes in the number density, size and chemical composition of the atmospheric aerosol were observed. These changes are attributed to two distinct types of air mass; a polluted air mass that had passed over the British mainland before reaching Eskdalemuir, interposed between two cleaner air masses that had arrived directly from the sea. Such changes in the background aerosol could clearly be very important to studies of urban aerosols and attempts at source apportionment. The results of an objective method of data analysis are presented. Correlations were sought between the occurrence of: lithium, potassium, rubidium, caesium, beryllium, strontium, barium, ammonium, amines, nitrate, nitrite, boron, mercury, sulfate, phosphate, fluorine, chlorine, bromine, iodine and carbon (both elemental and organic hydrocarbon) in both fine (d2.5 microm) and coarse (d2.5 microm) particle fractions. Several previously unreported correlations were observed, for instance between the elements lithium, beryllium and boron. The results suggest that about 2 in 3 of all fine particles (by number rather than by mass), and 1 in 2 of all coarse particles containing carbon, consisted of elemental carbon rather than organic hydrocarbon (although a bias in the sensitivity of the ATOFMS could have affected these numbers). The ratio of the number of coarse particles containing nitrate anions to the number of particles containing chloride anions exceeded unity when the air mass had travelled over the British mainland. The analysis also illustrates that an air mass of marine origin that had travelled slowly over agricultural land can accumulate amines and ammonium.

Dimethyl selenide is the most abundant gaseous selenium species in marine environments. In this work, the value of the rate coefficient for the gas-phase reaction between dimethyl selenide and Cl atoms has been determined for the first time. The value of the second-order rate coefficient obtained was (5.0 ± 1.4) × 10−10 cm3 molecule−1 s−1. The very fast nature of the reaction means that, when estimating the lifetime of dimethyl selenide in the atmosphere, loss due to reaction with Cl atoms should be considered along with loss due to reaction with O3 and with OH and NO3 radicals. Analysis of the available kinetic data suggests that at 760 Torr the dominant reaction pathway for the reaction of Cl atoms with dimethyl selenide will be the addition of Cl to the Se atom forming an adduct of the type CH3Se(Cl)CH3. Theoretical calculations, at the B3LYP/6-311++G(2df,p)//B3LYP/6-311++G(d,p) level of theory, show that at 298 K the value of ΔrH for the formation of the adduct is −111.4 kJ mol−1. This value may be compared to −97.0 kJ mol−1, the value calculated for ΔrH for the formation of the analogous sulfur adduct, CH3S(Cl)CH3, following the reaction between Cl atoms and dimethyl sulfide. Variational RRKM theory was used to predict the thermal decomposition rates of the two adducts back to starting materials. The estimated rate constant for the decomposition of the selenium adduct to the reactants is 5 × 10−5 s−1, compared to 0.02 s−1 in the case of the sulfur adduct. However, our calculations suggest that the CH3Se(Cl)CH3 adduct, which is initially formed highly excited, will not be stabilised under atmospheric conditions, but rather will decompose to yield CH3SeCl and CH3, a process that is calculated to be exothermic with respect to the initial reactants by 5.8 kJ mol−1. The formation of CH3SCl and CH3 from the sulfur adduct, on the other hand, is endothermic by 20.8 kJ mol−1 with respect to the initial reactants, and is thus not expected to occur.

Rate constants for the reaction of OH radicals with trans-1,2-dichloroethene and 1,1-dichloroethene have been determined at a pressure of 1.6 Torr and at T = 298 ± 2 K using the discharge-flow technique. The same method was used to study for the first time the kinetics of the reactions of atomic Cl with trans-1,2-dichloroethene and with 1,1-dichloroethene at low pressure. The values obtained for the rate constants for the Cl-atom reactions are significantly lower than those published previously, which refer to atmospheric pressure. The rate coefficients are therefore likely to be strongly pressure dependent over the range 1.6–760 Torr. The value obtained at low pressure may be considered as the upper limit of the rate constant for the abstraction channel. The kinetic data obtained are summarised below. The release of atomic chlorine following the reaction of OH radicals with trans-1,2-dichloroethene, 1,1-dichloroethene and vinyl chloride has been observed by a direct method for the first time. The reaction of trans-1,2-dichloroethene with OH radicals gives a yield of Cl atoms that is essentially unity. The yield is independent of the presence of molecular oxygen, suggesting that Cl is released promptly after the addition of OH. Some release of Cl following the reaction of OH with 1,1-dichloroethene occurs in the absence of oxygen, although the release is enhanced by the presence of NO2 in the system. The dominant channel leading to the formation of Cl appears not to be the initial reaction with OH, but rather the decomposition of an alkoxy radical that is formed in a secondary process. The presence of molecular oxygen increases the yield of Cl atoms, probably as a result of increased formation of the alkoxy radical. The lower limit of the yield in the absence of O2 and NO2 is estimated to be 0.03; the corresponding limit when O2 is present is 0.05. Roughly 0.09 Cl atoms are released from vinyl chloride for each OH radical consumed. The release is due to the initial reaction of OH radicals, and the yield appears to correspond to the branching ratio for addition of OH to the more substituted end of the carbon–carbon double bond. FTIR spectroscopic studies were made of the products of reaction of Cl with 2-chloroethanol in the presence of O2. This reaction provides a mimic of the reaction of OH with vinyl chloride in that the same peroxy radical species, CH2(OH)CHClO2, is formed. The only organic products observed are formyl chloride and chloroacetaldehyde. The formyl chloride results from the abstraction of an H atom from the carbon atom bearing the Cl substituent. Formaldehyde formed in the system is photolysed to produce CO, an observed product. Chloroacetaldehyde is formed following the abstraction of a hydrogen from the carbon atom bearing the OH group. The oxidation of vinyl chloride by OH in the atmosphere proceeds ia the formation of CH2(OH)CH2ClO2. In the absence of NOx, the peroxy radical reacts with RO2 to yield the corresponding alkoxy radical. This alkoxy radical appears to decompose in exactly the same way as it does when it has been formed by the reaction of CH2(OH)CH2ClO2 with NO.

The reactions between atmospheric oxidants and organic amphiphiles at the air–water interface of an aerosol droplet may affect the size and critical supersaturation required for cloud droplet formation. We demonstrate that no reaction occurs between gaseous nitrogen dioxide (1000 ppm in air) and a monolayer of an insoluble amphiphile, oleic acid (cis-9-octadecenoic acid), at the air–water interface which removes material from the air–water interface. We present evidence that the NO2 isomerises the cis-9-octadecenoic (oleic) acid to trans-9-octadecenoic (elaidic) acid. The study presented here is important for future and previous studies of (1) the reaction between the nitrate radical, NO3, and thin organic films as NO2 is usually present in high concentrations in these experimental systems and (2) the effect of NO2 air pollution on the unsaturated fatty acids and lipids found at the air–liquid surface of human lung lining fluid.