The Fast Regulation of Photosynthesis in Diatoms: an inquiry into the physiological and physical origins of non-photochemical chlorophyll fluorescence quenching.

Diatoms are renowned for their robust ability to perform NPQ (Non-Photochemical Quenching of chlorophyll fluorescence) as a dissipative response to heightened light stress on photosystem II, plausibly explaining their dominance over other algal groups in turbulent light environs. Their NPQ mechanism has been principally attributed to a xanthophyll cycle involving the lumenal pH regulated reversible de-epoxidation of diadinoxanthin. The principal goal of this dissertation is to reveal the physiological and physical origins and consequences of the NPQ response in diatoms during short-term transitions to excessive irradiation. The investigation involves diatom species from different originating light environs to highlight the diversity of diatom NPQ and to facilitate the detection of core mechanisms common among the diatoms as a group. A chiefly spectroscopic approach was used to investigate NPQ in diatom cells. Prime methodologies include: the real time monitoring of PSII excitation and de-excitation pathways via PAM fluorometry and pigment interconversion via transient absorbance measurements, the collection of cryogenic absorbance spectra to measure pigment energy levels, and the collection of cryogenic fluorescence spectra and room temperature picosecond time resolved fluorescence decay spectra to study excitation energy transfer and dissipation. Chemical inhibitors that target the trans-thylakoid pH gradient, the enzyme responsible for diadinoxanthin de-epoxidation, and photosynthetic electron flow were additionally used to experimentally manipulate the NPQ response. Multifaceted analyses of the NPQ responses from two previously un-photosynthetically characterised species, Nitzschia curvilineata and Navicula sp., were used to identify an excitation pressure relief ‘strategy’ for each species. Three key areas of NPQ were examined: (i) the NPQ activation/deactivation processes, (ii) how NPQ affects the collection, dissipation, and usage of absorbed light energy, and (iii) the interdependence of NPQ and photosynthetic electron flow. It was found that Nitzschia cells regulate excitation pressure via performing a high amplitude, reversible antenna based quenching which is dependent on the de-epoxidation of diadinoxanthin. In Navicula cells excitation pressure could be effectively regulated solely within the PSII reaction centre, whilst antenna based, diadinoxanthin de-epoxidation dependent quenching was implicated to be used as a supplemental, long-lasting source of excitation energy dissipation. These strategies for excitation balance were discussed in the context of resource partitioning under these species’ originating light climates. A more detailed investigation of the NPQ response in Nitzschia was used to develop a comprehensive model describing the mechanism for antenna centred non-photochemical quenching in this species. The experimental evidence was strongly supportive of a mechanism whereby: an acidic lumen triggers the diadinoxanthin de-epoxidation and protonation mediated aggregation of light harvesting complexes leading to the formation of quencher chlorophyll a-chlorophyll a dimers with short-lived excited states; quenching relaxes when a rise in lumen pH triggers the dispersal of light harvesting complex aggregates via deprotonation events and the input of diadinoxanthin. This model may also be applicable for describing antenna based NPQ in other diatom species.

“Synthesis and Photochemical Transformations of a few Tethered Barrelenes”

the author has designed few barrelene molecules in such a way that the structural features of these compounds will enable them to undergo intriguing triplet state mediated di- -methane rearrangement. The strategy involved the preparation of dibenzobarrelenes appended with a fused ring systems, thereby restricting the rotational freedom of the bridgehead substituent. We describe these systems as ‘tethered barrelenes’. These tethered barrelenes enabled us to examine the effect of orientation and the nature of the bridgehead-substituents in controlling the regioselectivity of di-π-methane rearrangement in a more systematic fashion. In this background, the thesis entitled “SYNTHESIS AND PHOTOCHEMICAL TRANSFORMATIONS OF A FEW TETHERED BARRELENES” reveals our attempts to explore the factors controlling the regioselectivity of di-π-methane rearrangement displayed by dibenzobarrelenes. Moreover, we have observed interesting dark reactions of suitable substituted tethered dibenzosemibullvalenes in a few cases

Evaluation of data for atmospheric models: master equation/RRKM calculations on the combination reaction, BrO+NO2 -> BrONO2, a conundrum

Experimental data for the title reaction were modeled using master equation (ME)/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA (Sander, S. P.; Finlayson-Pitts, B. J.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Molina, M. J.; Moortgat, G. K.; Orkin, V. L.; Ravishankara, A. R. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 15; Jet Propulsion Laboratory: Pasadena, California, 2006)(1) and IUPAC (Atkinson, R.; Baulch, D. L.; Cox, R. A.: R. F. Hampson, J.; Kerr, J. A.; Rossi, M. J.; Troe, J. J. Phys. Chem. Ref. Data. 2000, 29, 167) 2 data evaluation panels, which represents the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies (Parthiban, S.; Lee, T. J. J. Chem. Phys. 2000, 113, 145)3 and a. value (Orlando, J. J.; Tyndall, G. S. J. Phys. Chem. 1996, 100,. 19398)4 of the bond dissociation energy, D-298(BrO-NO2) = 118 kJ mol(-1), corresponding to Delta H-0(circle) = 114.3 kJ mol(-1) at 0 K) and the use of RRKM/ME methods, fitting calculations to the reported data or the empirical equations was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca. 4 at, or close to, the low-pressure limit. Agreement between calculation and experiment could be achieved in two ways, either by increasing Delta H-0(circle) to an unrealistically high value (149.3 kJ mol(-1)) or by increasing , the average energy transferred in a downward collision, to an unusually large value (> 5000 cm(-1)). The discrepancy could also be reduced by making all overall rotations fully active. The system was relatively insensitive to changing the moments of inertia in the transition state to increase the centrifugal effect. The possibility of involvement of BrOONO was tested and cannot account for the difficulties of fitting the data.

Direct time-resolved study of the kinetics of the reaction of silylene with phenylsilane in the gas phase. Does SiH2 react with the aromatic ring?

Laser flash photolysis studies of silylene, SiH2, generated by the 193 nm laser flash photolysis phenylsilane, PhSiH3, have been carried out to obtain rate constants for its bimolecular reaction with PhSiH3 itself, in the gas phase. The reaction was studied in SF6 (mostly at 10 Torr total pressure) over the temperature range 298-595 K. The rate constants (also found to be pressure independent) gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-9.92 +/- 0.04) + (3.31 +/- 0.27) kJ mol(-1)/RT ln 10 Similar investigations of the reaction of silylene with benzene, C6H6, (295-410 K) gave data suggestive of the fact that SiH2 might be reacting with photochemical products of C6H6 as well as with C6H6 itself. However, in the latter system, apparent rate constants were sufficiently low to indicate that in the reaction of SiH2 with PhSiH3 addition to the aromatic ring was unlikely to be in excess of 3% of the total. Quantum chemical calculations of the energy surface for SiH2 + C6H6 indicate that 7-silanorcaradiene and 7-silacycloheptatriene are possible products but that PhSiH3 formation is unlikely. RRKM calculations suggest that 7-silanorcaradiene should be the initial product but that it cannot be collisionally stabilized under experimental conditions

Singlet oxygen generation in the reaction centers of Rhodobacter sphaeroides

Singlet oxygen ((1)O(2)) generation in the reaction centers (RCs) of Rhodobacter sphaeroides wild type was characterized by luminescent emission in the near infrared region (time resolved transients and emission spectra) and quantified to have quantum yield of 0.03 +/- 0.005. (1)O(2) emission was measured as a function of temperature, ascorbate, urea and potassium ferricyanide concentrations and as a function of incubation time in H(2)O: D(2)O mixtures. (1)O(2) was shown to be affected by the RC dynamics and to originate from the reaction of molecular oxygen with two sources of triplets: photoactive dimer formed by singlet-triplet mixing and bacteriopheophytin formed by direct photoexcitation and intersystem crossing.

Nanoparticle Platform to Modulate Reaction Mechanism of Phenothiazine Photosensitizers

Herein, we report on the synthesis of photosensitizing nanoparticles in which the generation of different oxidizing species, i.e., singlet oxygen ((1)O(2)) or radicals, was modulated. Sol gel and surface chemistry were used to obtain nanoparticles with specific ratios of dimer to monomer species of phenothiazine photosensitizers (PSs). Due to competition between the reactions involving electron transfer within dimer species and energy transfer from monomer triplets to oxygen, the efficiency of (1)O(2) generation could be controlled. Nanoparticles with an excess of dimer have an (1)O(2) generation efficiency (S(Delta)) of 0.01 while those without dimer have a S, value of 0.4. Furthermore, we demonstrate that the PS properties of the nanoparticles are not subjected to interference from the external medium as is commonly the case for free PSs, i.e., PS ground and triplet states are not reduced by NADH and ascorbate, respectively, and singlet excited states are less suppressed by bromide. The modulated (1)O(2) generation and the PS protection from external interferences make this nanoparticle platform a promising tool to aid in performing mechanistic studies in biological systems. Also, it offers potential application in technological areas in which photo-induced processes take place.

Photochemical N-demethylation of Alkaloids

Certain alkaloids were observed to undergo N-demethylation processes under photochemical conditions. Tropine, acetyltropine, tropinone, and atropine were cleanly N-demethylated upon treatment with tetraphenylporphin, oxygen, and light. Dextromethorphan also underwent a N-demethylation reaction, but reacted further to afford an imine. In contrast, 14-acyloxycodeinones underwent a photochemically induced tandem N-demethylation–acyl migration.

Photochemical Production of MicromolarSuperoxideStandards in Aqueous SolutionT

Superoxide(O2-) is a reactive free radical that rapidly undergoes disproportionation to hydrogen peroxide and oxygen. This property makes preparation of superoxide standard for instrument calibration difficult. McDowell et al. (1983) showed photolysis of ketone and alcohol as a convenient method to generate superoxide through triplet and radical intermediates reacting with molecular oxygen. This study expands on this past work and investigates detailed mechanism of the reaction.

Thermal and photochemical stability of poly(vinyl alcohol)/modified lignin blends

A kraft lignin derivative (KLD) obtained by reaction with p-aminobenzoic acid/phthalic anhydride was blended with poly(vinyl alcohol) (PVA) by solution casting from DMSO. PVA and PVA/KLD films were exposed to ultraviolet radiation (24, 48, and 96 h) and analyzed by thermogravimetry (TG), differential scanning calorimetry (DSC), infrared spectroscopy (FTIR), hydrogen nuclear magnetic resonance (H-1 NMR) spectroscopy, and scanning electron microscopy (SEM). PVA films show a loss of thermal stability due to irradiation. PVA/KLD reveals greater thermal stability than PVA and an increase in thermal stability after irradiation. These results suggest that the incorporation of KLD into PVA provides a gain in thermal and photochemical stability. FTIR, H-1 NMR, DSC, and TG results obtained for the blends suggest that intermolecular interactions between PVA and KLD chains are present. SEM micrographs revealed blend miscibility for a KLD blend content of up to 15 wt%, as observed at magnification of 1000 times. (c) 2005 Elsevier Ltd. All rights reserved.

Design, synthesis and photochemical studies of stilbenoid dendrimers

Stilbenoid dendrimers with stilbene in the periphery and stilbene in periphery as well as core were synthesized by convergent approach except 2nd generation dendrimer with stilbene in the periphery as well as in core (D-5). All dendrimers were characterized by standard techniques such as 1H NMR, 13C NMR, MS and IR spectroscopy. The MALDI-TOF technique proved to be very helpful in the identification of the 2nd generation dendrimer (D-5) with a mass of 3231 a.m.u. The dendrimers were designed in such a way that an intramolecular photochemical CC bond formation was favored. As two stilbene units of the same molecule were close enough so they preferred an intramolecular cyclic process except for zero generation dendrimers. Apart from the cycloaddition, some E/Z isomerization and oligomer formation was also observed on irradiation. These processes were observed by 1H NMR and MALDI-TOF MS. The photochemical behavior was also studied by UV absorption spectroscopy. Irradiating by monochromatic light led to an initial E/Z isomerization and by prolonged irradiation, an irreversible cyclic structure was formed. The choice of the wavelength of incident light is very important as irradiation at 320 nm leads to a reversible E/Z isomerization and a non-reversible cyclobutane formation, but irradiation at 340 nm favors the one-way process E Z. The [2+2] cycloaddition of molecule Tm2De was also studied by irradiating thin films on a quartz surface. An AFM image was taken before irradiation, after 3 sec irradiation and after long irradiation (1 hour). AFM studies show that a short irradiation leads to a cyclic structure as formation of hills of about 20-30 nm on the surface. A prolonged irradiation leads to a CC cross linking which can be monitored on AFM images as disappearance of hills. The roughness goes back to an almost smooth surface. These results prove a very complex material transport, which accompanies the reaction in the surface region.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

Fipronil insecticide: Novel photochemical desulfinylation with retention of neurotoxicity

Fipronil is an outstanding new insecticide for crop protection with good selectivity between insects and mammals. The insecticidal action involves blocking the γ-aminobutyric acid-gated chloride channel with much greater sensitivity of this target in insects than in mammals. Fipronil contains a trifluoromethylsulfinyl moiety that is unique among the agrochemicals and therefore presumably important in its outstanding performance. We find that this substituent unexpectedly undergoes a novel and facile photoextrusion reaction on plants upon exposure to sunlight, yielding the corresponding trifluoromethylpyrazole, i.e., the desulfinyl derivative. The persistence of this photoproduct and its high neuroactivity, resulting from blocking the γ-aminobutyric acid-gated chloride channel, suggest that it may be a significant contributor to the effectiveness of fipronil. In addition, desulfinylfipronil is not a metabolite in mammals, so the safety evaluations must take into account not only the parent compound but also this completely new environmental product.

Photochemical protease: Site-specific photocleavage of hen egg lysozyme and bovine serum albumin

Site-specific photocleavage of hen egg lysozyme and bovine serum albumin (BSA) by N-(l-phenylalanine)-4-(1-pyrene)butyramide (Py-Phe) is reported. Py-Phe binds to lysozyme and BSA with binding constants 2.2 ± 0.3 × 105 M−1 and 6.5 ± 0.4 × 107 M−1, respectively. Photocleavage of lysozyme and BSA was achieved with high specificity when a mixture of protein, Py-Phe, and an electron acceptor, cobalt(III) hexammine (CoHA), was irradiated at 344 nm. Quantum yields of photocleavage of lysozyme and BSA were 0.26 and 0.0021, respectively. No protein cleavage was observed in the absence of Py-Phe, CoHA, or light. N-terminal sequencing of the protein fragments indicated a single cleavage site of lysozyme between Trp-108 and Val-109, whereas the cleavage of BSA was found to be between Leu-346 and Arg-347. Laser flash photolysis studies of a mixture of protein, Py-Phe, and CoHA showed a strong transient with absorption centered at ≈460 nm, corresponding to pyrene cation radical. Quenching of the singlet excited state of Py-Phe by CoHA followed by the reaction of the resulting pyrenyl cation radical with the protein backbone may be responsible for the protein cleavage. The high specificity of photocleavage may be valuable in targeting specific sites of proteins with small molecules.

Novel Photochemical Methodologies For Diversity Oriented Synthesis And Screening Of Combinatorial Libraries

The main goal of this project was to develop an efficient methodology allowing rapid access to structurally diverse scaffolds decorated with various functional groups. Initially, we discovered and subsequently developed an experimentally straightforward, high-yielding photoinduced conversion of readily accessible diverse starting materials into polycyclic aldehydes and their (hemi)acetals decorated by various pendants. The two step sequence, involving the Diels-Alder addition of heterocyclic chalcones and other benzoyl ethylenes to a variety of dienes, followed by the Paternò-Büchi reaction, was described as an alkene-carbonyl oxametathesis. This methodology offers a rapid increase in molecular complexity and diversity of the target scaffolds. To develop this novel methodology further and explore its generality, we directed our attention to the Diels-Alder adducts based on various chromones. We discovered that the Diels-Alder adducts of chromones are capable of photoinduced alkene-arene [2+2] cycloaddition producing different dienes, which can either dimerize or be introduced into a double-tandem [4π+2π]·[2π+2π]·[4π+2π]·[2π+2π] synthetic sequence, followed by an acid-catalyzed oxametathesis, leading to a rapid expansion of molecular complexity over a few experimentally simple steps. In view of the fact that oxametathesis previously was primarily observed in aromatic oxetanes, we decided to prepare model aliphatic oxetanes with a conformationally unconstrained or "flexible" methyl group based on the Diels-Alder adducts of cyclohexadiene or cyclopentadiene with methyl vinyl ketone. Upon addition of an acid, the expected oxametathesis occurred with results similar to those observed in the aromatic series proving the generality of this approach. Also we synthesized polycyclic oxetanes resulting from the Diels-Alder adducts of cyclic ketones. This not only gave us access to remarkably strained oxetane systems, but also the mechanism for their protolytic ring opening provided a great deal of insight to how the strain affects the reactivity. Additionally, we discovered that although the model Hetero-Diels-Alder adducts did not undergo [2+2] cycloaddition, both exo- and endo-Sulfa-Diels-Alder products, nonetheless, were photochemically active and various products with defined stereochemistry could be produced upon photolysis. In conclusion, we have developed an approach to the encoding and screening of solution phase libraries based on the photorelease of externally sensitized photolabile tags. The encoding tags can be released into solution only when a binding event occurs between the ligand and the receptor, equipped with an electron transfer sensitizer. The released tags are analyzed in solution revealing the identity of the lead ligand or narrowing the range of potential leads.

Unprecedented photochemical induced cascading rearrangement of the 3-azabicyclo[3.3.1] nonane skeleton

Certain 3-azabicyclo[3.3.1] nonane derivatives undergo unprecedented stereospecific skeletal cleavage when subjected to light affording a novel heterotricyclic skeleton.