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References
The last 25 references for the LKS-series are listed below. A complete searchable database with all known laser-flash, flow-flash and stopped-flow references can be accessed by logging into the APL members area.
| Authors | Title | Year | Keywords | Journal/Proceedings | |
|---|---|---|---|---|---|
| Iñigo X. García-Zubiri, Hugh D. Burrows, J. Sérgio Seixas de Melo, Joao Pina, María Monteserín, María J. Tapia | Effects of the Interaction Between β-Carboline-3-carboxylic acid N-Methylamide and Polynucleotides on Singlet Oxygen Quantum Yield and DNA Oxidative Damage | 2008 | singlet oxygen, dna damage, dna degradation | PHOTOCHEM PHOTOBIOL, 2008 | |
| Abstract: The complexation of β-carboline-3-carboxylic acid N-methylamide (βCMAM) with the sodium salts of the nucleotides polyadenylic (Poly A), polycytidylic (Poly C), polyguanylic (Poly G), polythymidylic (Poly T) and polyuridylic (Poly U) acids, and with double stranded (dsDNA) and single stranded deoxyribonucleic acids (ssDNA) was studied at pH 4, 6 and 9. Predominant 1:1 complex formation is indicated from Job plots. Association constants were determined using the Benesi–Hildebrand equation. βCMAM-sensitized singlet oxygen quantum yields were determined at pH 4, 6 and 9, and the effects on this of adding oligonucleotides, dsDNA and ssDNA were studied at the three pH values. With dsDNA, the effect on βCMAM triplet state formation was also determined through triplet–triplet transient absorption spectra. To evaluate possible oxidative damage of DNA following singlet oxygen βCMAM photosensitization, we used thiobarbituric acid-reactivity assays and electrophoretic separation of DNA assays. The results showed no oxidative damage at the level of DNA degradation or strand break. | |||||
| J. Seixas de Melo, J. Pina, L.M. Rodrigues and R.S. Becker | A comprehensive study of the spectral and photophysical properties of arylthiophenes | 2008 | Photochemistry; Photophysics; Arylthiophene; Fluorescence; Phosphorescence; Quantum yields; OLEDs; Oligomer; Laser flash photolysis; Thiophene; Phenanthrene | J PHOTOCHEM PHOTOBIOL A-CHEM, 2008, Vol 194, Iss 1, pp 67-75 | |
| Abstract: A series of conjugated oligomers with rigid (fused-ring) structure, consisting in different polycyclic aromatic hydrocarbons (PAHs) possessing a single thiophene unit, here designated as arylthiophenes, were investigated in solution. For presentation clarity, the compounds were organized in two different groups. The first group includes the compounds where one, two, three and four benzene rings are added to a thiophene unit (a compound with two dibenzothiophene units was also investigated) and the second group includes those compounds where a single thiophene ring is located at different positions in a skeletal-type polyaromatic hydrocarbon (in the present case phenanthrene). The study includes a complete spectroscopic evaluation (including singlet–singlet and triplet–triplet absorption, fluorescence and phosphorescence spectra) as well as a photophysical evaluation (fluorescence, phosphorescence and triplet lifetimes together with fluorescence and triplet occupation quantum yields. With all the above, a complete set of deactivation rate constants (kF, kIC and kISC) was determined. From the fluorescence and phosphorescence spectra the energy of the lowest lying singlet and triplet states (S1 and T1) and the energy of splitting between the two states (?ES1–T1) was obtained. Semi-empirical ZINDO/S-CI calculations were performed and corroborated the nature and state order experimentally obtained. | |||||
| Yannick H. Ouellet, Richard Daigle, Patrick Lagüe, David Dantsker, Mario Milani, Martino Bolognesi, Joel M. Friedman, and Michel Guertin | Ligand Binding to Truncated Hemoglobin N from Mycobacterium tuberculosis Is Strongly Modulated by the Interplay between the Distal Heme Pocket Residues and Internal Water | 2008 | Nitric oxide, laser flash photolysis, hemoglobin, binding | J. Biol. Chem., Vol. 283, Issue 40, 27270-27278, October 3. | |
| Abstract: The survival of Mycobacterium tuberculosis requires detoxification of host ·NO. Oxygenated Mycobacterium tuberculosis truncated hemoglobin N catalyzes the rapid oxidation of nitric oxide to innocuous nitrate with a second-order rate constant (Formula {approx} 745 x 106 M-1·s-1), which is ~15-fold faster than the reaction of horse heart myoglobin. We ask what aspects of structure and/or dynamics give rise to this enhanced reactivity. A first step is to expose what controls ligand/substrate binding to the heme. We present evidence that the main barrier to ligand binding to deoxy-truncated hemoglobin N (deoxy-trHbN) is the displacement of a distal cavity water molecule, which is mainly stabilized by residue Tyr(B10) but not coordinated to the heme iron. As observed in the Tyr(B10)/Gln(E11) apolar mutants, once this kinetic barrier is lowered, CO and O2 binding is very rapid with rates approaching 1-2 x 109 M-1·s-1. These large values almost certainly represent the upper limit for ligand binding to a heme protein and also indicate that the iron atom in trHbN is highly reactive. Kinetic measurements on the photoproduct of the ·NO derivative of met-trHbN, where both the ·NO and water can be directly followed, revealed that water rebinding is quite fast (~1.49 x 108 s-1) and is responsible for the low geminate yield in trHbN. Molecular dynamics simulations, performed with trHbN and its distal mutants, indicated that in the absence of a distal water molecule, ligand access to the heme iron is not hindered. They also showed that a water molecule is stabilized next to the heme iron through hydrogen-bonding with Tyr(B10) and Gln(E11). | |||||
| Ulrika Flock, Faye H. Thorndycroft, Andrey D. Matorin, David J. Richardson, Nicholas J. Watmough, and Pia Ädelroth | Defining the proton entry point in the bacterial respiratory nitric oxide reductase | 2007 | nitric oxide reductase, NOR, NO, heme-copper oxidase, NorB, enzyme catalysis | J BIOL CHEM, 2007, Vol 282 | |
| Abstract: The bacterial respiratory nitric oxide reductase (NOR) is a member of the super-family of O2-reducing, proton-pumping, heme-copper oxidases. Even though NO reduction is a highly exergonic reaction, NOR is not a proton pump and rather than taking up protons from the cytoplasmic (membrane potential negative) side of the membrane, like the heme-copper oxidases, NOR derives its substrate protons from the periplasmic (membrane potential positive) side of the membrane. The molecular details of this non-electrogenic proton transfer are not yet resolved, so in this study we have explored a role in a proposed proton pathway for a conserved surface glutamate (Glu-122) in the catalytic subunit (NorB). The effect of substituting Glu-122 with Ala, Gln or Asp on a single turnover of O2, an alternative and experimentally tractable substrate for NOR, was determined. Electron transfer coupled to proton-uptake to the bound O2 is severely and specifically inhibited in both the E122A and E122Q variants, establishing the importance of a protonatable side-chain at this position. Although in the E122D mutant proton-uptake is retained, it is associated with a significant increase in the observed pKa of the group donating protons to the active site. This suggests that Glu-122 is important in defining this proton donor. A second nearby glutamate (Glu-125) is also required for the electron transfer coupled to proton-uptake, further emphasising the importance of this region of NorB in proton transfer. Since Glu-122 is predicted to lie near the periplasmic surface of NOR, the results provide strong experimental evidence that this residue contributes to defining the aperture of a non-electrogenic ‘E-pathway’ that serves to deliver protons from the periplasm to the buried active site in NOR. | |||||
| Oliver P. Ernst, Pedro A. Sànchez Murcia, Peter Daldrop, Satoshi P. Tsunoda, Suneel Kateriya, and Peter Hegemann | Photoactivation of Channelrhodopsin | 2007 | Channelrhodopsins, ChR, ion channels, photomovement | J BIOL CHEM, 2007, Vol 282 | |
| Abstract: Channelrhodopsins (ChRs) are light-gated ion channels that control photomovement of microalgae. In optogenetics, ChRs are widely applied for light-triggering action potentials in cells, tissues and living animals, yet the spectral properties and photocycle of ChR remain obscure. In this study, we cloned a ChR from the colonial alga Volvox carteri, VChR. After electrophysiological characterization in Xenopus oocytes, VChR was expressed in COS-1 cells and purified. Time-resolved UV/visible spectroscopy revealed a pH-dependent equilibrium of two dark species, D470 / D480. Laser flashes converted both with tau ca. 200 µs into major photointermediates P510 / P530, which reverted back to the dark states with tau ca. 15-100 ms. Both intermediates were assigned to conducting states. Three early intermediates P500 / P515 and P390 were detected on a ns - µs time scale. The spectroscopic and electrical data were unified in a photocycle model. The functional expression of VChR we report here paves the way towards a broader structure/ function analysis of the recently identified class of light-gated ion channels. | |||||
| Derren J. Heyes, Michiyo Sakuma, and Nigel S. Scrutton | Laser Excitation Studies of the Product Release Steps in the Catalytic Cycle of the Light-driven Enzyme, Protochlorophyllide Oxidoreductase | 2007 | Protochlorophyllide Oxidoreductase, Light-driven Enzyme, Laser Excitation, enzyme catalysis | J BIOL CHEM, 2007, Vol 282, Iss 44, pp 32015-32020 | |
| Abstract: The latter stages of the catalytic cycle of the light-driven enzyme, protochlorophyllide oxidoreductase, have been investigated using novel laser photoexcitation methods. The formation of the ternary product complex was initiated with a 6-ns laser pulse, which allowed the product release steps to be kinetically accessed for the first time. Subsequent absorbance changes associated with the release of the NADP+ and chlorophyllide products from the enzyme could be followed on a millisecond timescale. This has facilitated a detailed kinetic and thermodynamic characterization for the interconversion of all the various bound and unbound product species. Initially, NADP+ is released from the enzyme in a biphasic process with rate constants of 1210 and 237 s–1. The rates of both phases show a significant dependence on the viscosity of the solvent and become considerably slower at higher glycerol concentrations. The fast phase of this process exhibits no dependence on NADP+ concentration, suggesting that conformational changes are required prior to NADP+ release. Following NADP+ release, the NADPH rebinds to the enzyme with a maximum rate constant of ~72 s–1. At elevated temperatures (>298 K) chlorophyllide is released from the enzyme to yield the free product with a maximum rate constant of 20 s–1. The temperature dependencies of the rates of each of these steps were measured, and enthalpies and entropies of activation were calculated using the Eyring equation. A comprehensive kinetic and thermodynamic scheme for these final stages of the reaction mechanism is presented. | |||||
| Oleg V. Moskvin, Samuel Kaplan, Marie-Alda Gilles-Gonzalez, and Mark Gomelsky | Novel Heme-based Oxygen Sensor with a Revealing Evolutionary History | 2007 | Signal transduction, Oxygen Sensor, hemeprotein | J BIOL CHEM, 2007, Vol 282, Iss 39, pp 28740-28748 | |
| Abstract: To monitor fluctuations in oxygen concentration, cells use sensory proteins often containing heme cofactors. Here, we identify a new class of heme-binding oxygen sensors, reveal their unusual phylogenetic origin, and propose a sensing mode of a member of this class. We show that heme is bound noncovalently to the central region of AppA, an oxygen and light sensor from Rhodobacter sphaeroides. The addition of oxygen to ferrous AppA discoordinated the heme, and subsequent oxygen removal fully restored the heme coordination. In vitro, the extent of heme discoordination increased gradually with the rise in oxygen levels over a broad concentration range. This response correlated well with the gradual decrease in transcription of photosynthesis genes regulated by AppA and its partner repressor PpsR. We conclude that the AppA-PpsR regulatory system functions as an oxygen-dependent transcriptional rheostat. We identified a new domain embedded in the central region of AppA and designated it SCHIC for sensor containing heme instead of cobalamin. A phylogenetic analysis revealed that SCHIC domain proteins form a distinct cluster within a superfamily that includes vitamin B12-binding proteins and other proteins that may bind other kinds of tetrapyrroles. | |||||
| Adrian J. Dunford, Kirsty J. McLean, Muna Sabri, Harriet E. Seward, Derren J. Heyes, Nigel S. Scrutton, and Andrew W. Munro | Rapid P450 Heme Iron Reduction by Laser Photoexcitation of Mycobacterium tuberculosis CYP121 and CYP51B1: ANALYSIS OF CO COMPLEXATION REACTIONS AND REVERSIBILITY OF THE P450/P420 EQUILIBRIUM | 2007 | p450, laser flash photolysis, heme | J BIOL CHEM, 2007, Vol 282, Iss 34, pp 24816-24824 | |
| Abstract: We demonstrate that photoexcitation of NAD(P)H reduces heme iron of Mycobacterium tuberculosis P450s CYP121 and CYP51B1 on the microsecond time scale. Rates of formation for the ferrous-carbonmonoxy (FeII-CO) complex were determined across a range of coenzyme/CO concentrations. CYP121 reaction transients were biphasic. A hyperbolic dependence on CO concentration was observed, consistent with the presence of a CO binding site in ferric CYP121. CYP51B1 absorption transients for FeII-CO complex formation were monophasic. The reaction rate was second order with respect to [CO], suggesting the absence of a CO-binding site in ferric CYP51B1. In the absence of CO, heme iron reduction by photoexcited NAD(P)H is fast (~10,000–11,000 s–1) with both P450s. For CYP121, transients revealed initial production of the thiolate-coordinated (P450) complex (absorbance maximum at 448 nm), followed by a slower phase reporting partial conversion to the thiol-coordinated P420 species (at 420 nm). The slow phase amplitude increased at lower pH values, consistent with heme cysteinate protonation underlying the transition. Thus, CO binding occurs to the thiolate-coordinated ferrous form prior to cysteinate protonation. For CYP51B1, slow conversions of both the ferrous/FeII-CO forms to species with spectral maxima at 423/421.5 nm occurred following photoexcitation in the absence/presence of CO. This reflected conversion from ferrous thiolate- to thiol-coordinated forms in both cases, indicating instability of the thiolate-coordinated ferrous CYP51B1. CYP121 FeII-CO complex pH titrations revealed reversible spectral transitions between P450 and P420 forms. Our data provide strong evidence for P420 formation linked to reversible heme thiolate protonation, and demonstrate key differences in heme chemistry and CO binding for CYP121 and CYP51B1. | |||||
| Andreas Namslauer, Håkan Lepp, Magnus Brändén, Audrius Jasaitis, Michael I. Verkhovsky, and Peter Brzezinski | Plasticity of Proton Pathway Structure and Water Coordination in Cytochrome c Oxidase | 2007 | Cytochrome c Oxidase, proton pathways, proton pumping, laser flash photolysis | J BIOL CHEM, 2007, Vol 282, Iss 20, pp 15148-15158 | |
| Abstract: Cytochrome c oxidase (CytcO) is a redox-driven, membrane-bound proton pump. One of the proton transfer pathways of the enzyme, the D pathway, used for the transfer of both substrate and pumped protons, accommodates a network of hydrogen-bonded water molecules that span the distance between an aspartate (Asp132), near the protein surface, and glutamate Glu286, which is an internal proton donor to the catalytic site. To investigate how changes in the environment around Glu286 affect the mechanism of proton transfer through the pathway, we introduced a non-hydrogen-bonding (Ala) or an acidic residue (Asp) at position Ser197 (S197A or S197D), located ~7 Å from Glu286. Although Ser197 is hydrogen-bonded to a water molecule that is part of the D pathway `proton wire,` replacement of the Ser by an Ala did not affect the proton transfer rate. In contrast, the S197D mutant CytcO displayed a turnover activity of ~35% of that of the wild-type CytcO, and the O2 reduction reaction was not linked to proton pumping. Instead, a fraction of the substrate protons was taken from the positive (`incorrect`) side of the membrane. Furthermore, the pH dependence of the proton transfer rate was altered in the mutant CytcO. The results indicate that there is plasticity in the water coordination of the proton pathway, but alteration of the electrostatic potential within the pathway results in uncoupling of the proton translocation machinery. | |||||
| Beat Fierz, Helmut Satzger, Christopher Root, Peter Gilch, Wolfgang Zinth, and Thomas Kiefhaber | Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale | 2007 | conformational substates , femtoseconds spectroscopy , peptide dynamics, protein folding, triplet–triplet energy transfer | PROC NAT ACAD SCI USA, 2007, Vol 104, Iss 7, pp 2163-2168 | |
| Abstract: Intrachain loop formation allows unfolded polypeptide chains to search for favorable interactions during protein folding. We applied triplet–triplet energy transfer between a xanthone moiety and naphthylalanine to directly measure loop formation in various unfolded polypeptide chains with loop regions consisting of polyserine, poly(glycine–serine) or polyproline. By combination of femtosecond and nanosecond laserflash experiments loop formation could be studied over many orders of magnitude in time from picoseconds to microseconds. The results reveal processes on different time scales indicating motions on different hierarchical levels of the free energy surface. A minor (<15%) very fast reaction with a time constant of ~3 ps indicates equilibrium conformations with donor and acceptor in contact at the time of the laserflash. Complex kinetics of loop formation were observed on the 50- to 500-ps time scale, which indicate motions within a local well on the energy landscape. Conformations within this well can form loops by undergoing local motions without having to cross major barriers. Exponential kinetics observed on the 10- to 100-ns time scale are caused by diffusional processes involving large-scale motions that allow the polypeptide chain to explore the complete conformational space. These results indicate that the free energy landscape for unfolded polypeptide chains and native proteins have similar properties. The presence of local energy minima reduces the conformational space and accelerates the conformational search for energetically favorable local intrachain contacts. | |||||
| Changyuan Lu, Tsuyoshi Egawa, Laura M. Wainwright, Robert K. Poole, and Syun-Ru Yeh | Structural and Functional Properties of a Truncated Hemoglobin from a Food-borne Pathogen Campylobacter jejuni | 2007 | NO, nitric oxide, hemoglobin, NO detoxification, heme | J BIOL CHEM, 2007, Vol 282, Iss 18, pp 13627-13636 | |
| Abstract: Campylobacter jejuni contains two hemoglobins, Cgb and Ctb. Cgb has been suggested to perform an NO detoxification reaction to protect the bacterium against NO attack. On the other hand, the physiological function of Ctb, a class III truncated hemoglobin, remains unclear. By using CO as a structural probe, resonance Raman data show that the distal heme pocket of Ctb exhibits a positive electrostatic potential. In addition, two ligand-related vibrational modes, vFe-O2 and vO-O, were identified in the oxy derivative, with frequencies at 542 and 1132 cm-1, respectively, suggesting the presence of an intertwined H-bonding network surrounding the heme-bound ligand, which accounts for its unusually high oxygen affinity (222 µM-1). Mutagenesis studies of various distal mutants suggest that the heme-bound dioxygen is stabilized by H-bonds donated from the Tyr(B10) and Trp(G8) residues, which are highly conserved in the class III truncated hemoglobins; furthermore, an additional H-bond donated from the His(E7) to the Tyr(B10) further regulates these H-bonding interactions by restricting the conformational freedom of the phenolic side chain of the Tyr(B10). Taken together, the data suggest that it is the intricate balance of the H-bonding interactions that determines the unique ligand binding properties of Ctb. The extremely high oxygen affinity of Ctb makes it unlikely to function as an oxygen transporter; on the other hand, the distal heme environment of Ctb is surprisingly similar to that of cytochrome c peroxidase, suggesting a role of Ctb in performing a peroxidase or P450-type of oxygen chemistry. | |||||
| Ilona Pyszka and Zdzislaw Kucybala | Quinolineimidazopyridinium derivatives as visible-light photoinitiators of free radical polymerization | 2007 | Dyeing photoinitiator; Effect of structure; Kinetics of photoinitiated polymerization | POLYMER, 2006, Vol 48, Iss 4, pp 959-965 | |
| Abstract: Several dyes containing Quinolineimidazopyridinium moiety (QIPD) have been synthesized and evaluated as photoinitiators for free radical polymerization induced with the visible emission of a commercial dental lamp. The tested dyes were tested as photoinitiators in the presence of selected electron donors. Different substituents introduced into both the pyridine ring and quinoline moieties of the dyes influence photophysical properties of the investigated systems. Several different groups were tested including heavy atoms (–Cl, –Br, –I) and electron accepting (–NO2) group. Analysis of the properties of the tested dyes allows one to conclude that there is a significant heavy atom effect on their photoinitiation efficiency. The type of the applied counter-ion has no effect on the overall performance of the photoinitiating system. QIPDs possess broad structured spectra with long-wavelength part located at the boundary of visible and UV parts of light spectrum. This makes QIPDs good candidates for the use as photoinitiating systems for dental restorative materials. | |||||
| Cheng-zhu Zhu,, Bin Ouyang, Jia-quan Wang, Li Huang, Wen-bo Dong and Hui-qi Hou | Photochemistry in the mixed aqueous solution of nitrobenzene and nitrous acid as initiated by the 355 nm UV light | 2007 | Laser flash photolysis, Nitrobenzene, Nitrous acid, Transient absorption spectra, OH radical | CHEMOSPHERE, 2007, Vol 67, Iss 5, pp 855-861 | |
| Abstract: The 355 nm photon-initiated microscopic reaction mechanisms of the mixed aqueous solution of nitrobenzene and nitrous acid in the presence or absence of O2 were studied by the laser flash photolysis technique. The main transient absorption peaks in the recorded spectra were assigned and the growth/decay trends of several transient species were investigated. It was found that the OH radical formed from the photolysis of nitrous acid triggered most of the subsequent radical reactions. The rate constant of the reaction between OH radical and nitrobenzene was measured to be (3.4 ± 0.1) × 109 l mol-1 s-1. The product from this reaction, namely C6H5NO2–OH adduct, was found to react with O2 to yield C6H5NO2–OHO2 adduct with a rate constant of (1.6 ± 0.2) × 109 l mol-1 s-1. Final steady-state products were identified by GC/MS analysis and were in accordance with the transient spectroscopic results. The possible reaction pathways were proposed. | |||||
| Ayman A. Abdel-Shafi, Jose L. Bourdelande and Sameh S. Ali | Photosensitized generation of singlet oxygen from rhenium(I) and iridium(III) complexes | 2007 | singlet oxygen, rhenium(i), Iridium(III), laser flash photolysis | J CHEM SOC DALTON TRANS, 2007, Iss 24, pp 2510-2516 | |
| Abstract: Photophysical properties in dilute acetonitrile solution are reported for a number of iridium(III) and rhenium(I) complexes. The nature of the lowest excited state of the complexes under investigation is either metal-to-ligand charge transfer (3MLCT) or a ligand centred (3LC) state. Rate constants, kq, for quenching of the lowest excited states by molecular oxygen are in the range 1.5 × 108 to 1.4 × 1010 M–1 s–1. Efficiency of singlet oxygen production, fΔT, following oxygen quenching of the lowest excited states of these complexes, are in the range of 0.27–1.00. The rate constants and the efficiency of singlet oxygen formation are quantitatively reproduced by a model that assumes the competition between a non-charge transfer (nCT) and a CT deactivation channel. The balance between CT and nCT deactivation channels, which is described by the relative contribution pCT of CT induced deactivation, is discussed. The kinetic model is found to be successfully applied in the case of quenching of the excited triplet states of coordination compounds by oxygen in acetonitrile, as was proposed for the quenching of π–π* triplet states by oxygen. | |||||
| Benniston, A. C.; Harriman, A.; Llarena, I.; Sams, C. A. | Intramolecular Delayed Fluorescence as a Tool for Imaging Science: Synthesis and Photophysical Properties of a First-Generation Emitter | 2007 | molecular dyad, triplet-triplet annihilation, fluorescence imaging | CHEM MATER, 2007, Vol 19, Iss 8, pp 1931-1938 | |
| Abstract: The synthesis of a molecular dyad comprising two pyrene-based terminals covalently linked via a Hantzsch 1,4-dihydropyridine is described. The dyad is sufficiently flexible to allow the end groups to approach each other in fluid solution, as is evident from the appearance of excimer fluorescence. Transient absorption spectroscopy indicates that both intra- and intermolecular triplet-triplet annihilation (TTA) takes place at modest laser intensities and leads to delayed fluorescence. The spectral distribution of the delayed fluorescence signal matches that of the excimer. The kinetics of TTA and the overall yield of delayed fluorescence are considered in terms of the molecule adopting disparate conformations that interconvert slowly. Consideration is also given to the possible application of such delayed fluorescence in imaging technology. | |||||
| Girvan, H. M.; Heyes, D. J.; Scrutton, N. S.; Munro, A. W. | Laser Photoexcitation of NAD(P)H Induces Reduction of P450 BM3 Heme Domain on the Microsecond Time Scale | 2007 | Laser Photoexcitation, P450 BM3, NAD(P)H | J AM CHEM SOC, 2007, Vol 129, Iss 20, pp 6647-6653 | |
| Abstract: We demonstrate that photoexcitation of NAD(P)H at 355 nm using a Nd:YAG laser leads to rapid reduction of the heme domain of the Bacillus megaterium fatty acid hydroxylase flavocytochrome P450 BM3. An aqueous electron derived from photoexcited NAD(P)H is rapidly transferred to the heme domain, enabling the formation of a carbon monoxy complex of the ferrous P450 (FeII-CO) on the microsecond time scale. Using this approach we have determined the limiting rate constant (1770 s-1 for substrate-free heme domain) for formation of the FeII-CO complex. We find no dependence of the observed rate of FeII-CO complex formation on NAD(P)H concentration but demonstrate a hyperbolic dependence on carbon monoxide concentration. The apparent dissociation constant for the complex of carbon monoxide bound noncovalently to the ferric form of the BM3 heme domain (and with NADH as reductant) is 0.323 mM. Binding of a P450 substrate (N-palmitoylglycine) weakened the complex between carbon monoxide and the ferric BM3 heme domain (Kd increased to 1.404 mM) but enhanced the rate of formation of the FeII-CO complex (3036 s-1 for substrate-free heme domain). This study demonstrates the applicability of NAD(P)H photoexcitation as a method for rapid electron delivery to P450 enzymes and provides a new route to probing the P450 catalytic cycle and its transient intermediates. | |||||
| Fierz, B.; Kiefhaber, T. | End-to-End vs Interior Loop Formation Kinetics in Unfolded Polypeptide Chains | 2007 | peptide dynamics, protein folding kinetics, protein folding | J AM CHEM SOC, 2007, Vol 129, Iss 3, pp 672-679 | |
| Abstract: The conformational search for favorable intramolecular interactions during protein folding is limited by intrachain diffusion processes. Recent studies on the dynamics of loop formation in unfolded polypeptide chains have focused on loops involving residues near the chain ends. During protein folding, however, most contacts are formed between residues in the interior of the chain. We compared the kinetics of end-to-end loop formation (type I loops) to the formation of end-to-interior (type II loops) and interior-to-interior loops (type III loops) using triplet-triplet energy transfer from xanthone to naphthylalanine. The results show that formation of type II and type III loops is slower compared to type I loops of the same size and amino acid sequence. The rate constant for type II loop formation decreases with increasing overall chain dimensions up to a limiting value, at which loop formation is about 2.5-fold slower for type II loops compared to type I loops. Comparing type II loops of different loop size and amino acid sequence shows that the ratio of loop dimension over total chain dimension determines the rate constant for loop formation. Formation of type III loops is 1.7-fold slower than formation of type II loops, indicating that local chain motions are strongly coupled to motions of other chain segments which leads to faster dynamics toward the chain ends. Our results show that differences in the kinetics of formation of type I, type II, and type III loops are mainly caused by differences in internal flexibility at the different positions in the polypeptide chain. Interactions of the polypeptide chain with the solvent contribute to the kinetics of loop formation, which are strongly viscosity-dependent. However, the observed differences in the kinetics of formation of type I, type II, and type III loops are not due to the increased number of peptide-solvent interactions in type II and type III loops compared to type I loops as indicated by identical viscosity dependencies for the kinetics of formation of the different types of loops. | |||||
| Benniston, A. C.; Harriman, A.; Pariani, C.; Sams, C. A. | Competition between Energy Transfer and Interligand Electron Transfer in Porphyrin-Osmium(II) Bis(2,2':6',2' '-terpyridine) Dyads | 2007 | electron transfer, charge transfer, Förster dipole-dipole mechanism | J PHYS CHEM A, 2007, Vol 111, Iss 37, pp 8918-8924 | |
| Abstract: Rapid intramolecular energy transfer occurs from a free-base porphyrin to an attached osmium(II) bis(2,2':6',2' '-terpyridine) complex, most likely by way of the Förster dipole-dipole mechanism. The initially formed metal-to-ligand, charge-transfer (MLCT) excited-singlet state localized on the metal complex undergoes very fast intersystem crossing to form the corresponding triplet excited state (3MLCT). This latter species transfers excitation energy to the 3,* triplet state associated with the porphyrin moiety, such that the overall effect is to catalyze intersystem crossing for the porphyrin. Interligand electron transfer (ILET) to the distal terpyridine ligand, for which there is no driving force, competes poorly with triplet energy transfer from the proximal 3MLCT to the porphyrin. Equipping the distal ligand with an ethynylene residue provides the necessary driving force for ILET and this process now competes effectively with triplet energy transfer to the porphyrin. The rate constants for all the relevant processes have been derived from laser flash photolysis studies. | |||||
| Allen, B. D.; Benniston, A. C.; Harriman, A.; Llarena, I.; Sams, C. A. | How the Central Torsion Angle Affects the Rates of Nonradiative Decay in Some Geometrically Restricted p-Quaterphenyls | 2007 | torsional angle, nonradiative decay, geometric restriction | J PHYS CHEM A, 2007, Vol 111, Iss 14, pp 2641-2649 | |
| Abstract: A small series of p-quaterphenyl derivatives has been prepared in which the dihedral angle (phi) for the two central rings is constrained by dialkoxy spacers of varying length. The photophysical properties of these compounds remain comparable, but there is a clear correlation between the rate constants for nonradiative decay of both singlet and triplet excited states and in fluid solution. The rates tend toward a minimum as phi approaches 90 degrees. These effects are attributed to the general phenomenon of extended delocalization and can be traced to a combination of changes in the Huang-Rhys factor and the electron-vibrational coupling matrix element, both relating to displacement of the relevant potential energy surfaces and to the medium-frequency vibronic mode coupled to decay. The latter effect arises because of different levels of conjugation in the ground-state molecule. Such findings might have important implications for the design of improved light-emitting diodes. A similar angle dependence is noted for the yield of the pi-radical cation formed on photoionization in a polar solvent, but here, the effect is due to variations in the respective energy gaps between the relevant excited states. | |||||
| Paul, A.; Samanta, A. | Photoinduced Electron Transfer Reaction in Room Temperature Ionic Liquids: A Combined Laser Flash Photolysis and Fluorescence Study | 2007 | ionic liquids, photoinduced electron transfer, laser flash photolysis | J PHYS CHEM B, 2007, Vol 111, Iss 8, pp 1957-1962 | |
| Abstract: A detailed study of the photoinduced electron transfer (PET) reaction between pyrene and N,N-dimethylaniline has been made in four different room temperature ionic liquids (ILs) using steady state and time-resolved fluorescence and laser flash photolysis techniques. Unlike that in the conventional media, no exciplex emission for this well-known system could be observed in ILs. The rate constants for the PET induced quenching of the fluorescent state of pyrene, which lie between 6.9 and 37 × 107 M-1 s-1 depending on the viscosity, are found to be 2-4 times higher than the diffusion-controlled rates in ILs. The primary photoproducts of the PET process have been characterized by transient absorption spectroscopy, and the yields of the solvent-separated PET products have been determined. Even in the least viscous IL, [emim][Tf2N], the yield of the solvent-separated radical ion is estimated to be only 0.015 ± 0.005. In more viscous ILs such as [bmim][PF6], the yield is found to be so low that absorption due to these species could not be observed. The rate constant for the escape of the ionic products from the geminate ion pair in ILs has been estimated to be nearly 2-3 orders of magnitude lower than the back electron transfer rate. However, the small fraction of the PET products, which manage to escape geminate recombination, have been found to survive much longer compared to those in less viscous conventional solvents. | |||||
| Humeres, E.; Mendes de Castro, K.; Moreira, R. de F. P. M.; Peruch, M. da G. B.; Schreiner, W. H.; Aliev, A. E.; Canle, M.; Santaballa, J. A.; Fernandez, I. | Reactivity of the Thermally Stable Intermediates of the Reduction of SO2 on Carbons and Mechanisms of Insertion of Organic Moieties in the Carbon Matrix | 2007 | SO2, laser photolysis, carbon matrix | J PHYS CHEM C, 2007 | |
| Abstract: The reduction of SO2 on carbons proceeds through reactive intermediates bound to the carbon matrix, which were postulated to be 1,2-oxathiene 2-oxide (or sultine), and 1,3,2-dioxathiolane that decomposes to produce an episulfide and CO2. The reactivity of these intermediates was studied in this work through several reactions, using XPS and NMR spectra to postulate their mechanisms. When modified activated carbon obtained after reaction with SO2 at 630 C was heated at 900 C, it was observed that the changes of the XPS spectrum resulted from the forward reaction of decomposition of the oxidized intermediate with S-transfer to produce the episulfide and CO2 and the reverse reaction with expulsion of SO2. Strong bases hydrolyzed the dioxathiolane intermediate and the episulfide. The thiolysis, aminolysis, and reaction of alkyl halides with modified activated carbon occurred with the insertion of the organic moiety in the carbon matrix. Laser photolysis at 266 nm in t-butanol showed insertion of t-butoxide on the matrix. Consistent mechanisms for these reactions were postulated. These results provide additional evidence on the mechanism of reduction of SO2 on carbons and the chemical nature of the intermediates, offering a new method to modify the physical and chemical properties of a carbon matrix by functionalization with an organic moiety. | |||||
| Akatsuka, K.; Ebina, Y.; Muramatsu, M.; Sato, T.; Hester, H.; Kumaresan, D.; Schmehl, R. H.; Sasaki, T.; Haga, M. | Photoelectrochemical Properties of Alternating Multilayer Films Composed of Titania Nanosheets and Zn Porphyrin | 2007 | photoelectrochemical devices, nanosheets, multilayer film | LANGMUIR, 2007, Vol 23, Iss 12, pp 6730-6736 | |
| Abstract: Alternating multilayer films composed of titania nanosheets and Zn porphyrins were prepared by use of a previously reported Langmuir-Blodgett film-transfer method in order to fabricate photoelectrochemical devices. Closely packed titania nanosheet monolayers on indium tin oxide (ITO), mica, and quartz surfaces strongly adsorbed cationic [5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrinatozinc]4+ (ZnTMPyP4+) by electrostatic interactions. The alternating deposition process afforded nanometer-scale multilayer films with the following structure: solid surface/(titania nanosheet/ZnTMPyP4+)n (n is the number of layers). The multilayer films were characterized by various physical measurements, including AFM, XRD, and UV-visible spectra. The visible-light irradiation of this multilayer film on an ITO electrode in the presence of triethanolamine as an electron donor yielded an anodic photocurrent. The action spectrum was consistent with the absorption spectrum of ZnTMPyP4+, which indicates that the photoexcitation of ZnTMPyP4+ is responsible for the photocurrent generation. However, the photocurrent density decreased with an increasing number of layers, which indicates that the harvesting of photoexcited electrons vertically through the titania nanosheets in the ITO/(titania nanosheet/ZnTMPyP4+)n structure was not efficient. To overcome this problem, the use of a lateral interlayer connection to all of the titania nanosheets with Ag paste was examined. As a result, a dramatic improvement in the photocurrent density was obtained. Thus, for efficient photocurrent generation with the titania nanosheet-ZnTMPyP4+ composite material, the lateral connection to all of the titania nanosheet layers is effective. | |||||
| Bartoszewicz, J.; Hug, G. L.; Pietrzak, M.; Kozubek, H.; Paczkowski, J.; Marciniak, B. | Benzophenone-Phenylthioacetic Acid Tetraalkylammonium Salts as Effective Initiators of Free-Radical Photopolymerization of Vinyl Monomers, Mechanistic Studies | 2007 | photooxidation, polymerization initiators, free radical polymerization | MACROMOLECULES, 2007, Vol 40, Iss 24, pp 8642-8648 | |
| Abstract: The mechanism of the photooxidation of tetraalkylammonium salts of phenylthioacetic acid, C6H5-S-CH2-COO-N+R4, was investigated in detail in order to understand why they turned out to be efficient co-initiators of free-radical polymerizations. The photosensitizer was benzophenone (BP), and the alkyl substituents (R) were n-butyl, n-propyl, or ethyl. The techniques used were steady-state and nanosecond flash photolysis. It was shown that electron transfer from the sulfur atom to the benzophenone triplet state was the primary photochemical step followed by a decarboxylation reaction leading to CO2, the C6H5-S-CH2 radical, and a [BP-···N+R4] ion pair. The latter underwent a Hofmann elimination (unexpected in these mild experimental conditions) leading to alkene-1 and trialkyl amine. The quantum yields of all the observed transients and the stable products were determined. The mechanism of primary and secondary photochemical reactions was quantitatively described, and it was shown to be similar for all of the alkyl derivatives used. The results of photochemical studies were compared with respect to the polymerization studies where the systems consisting of benzophenone and tetraalkylammonium salts of phenylthioacetic acid (and phenylthioacetic acid for comparison) were used as photoinitiating couples for free-radical polymerizations using 2-ethyl-2-(hydroxymethyl)-1,3-propanediol triacrylate as the monomer. A linear correlation was found for the polymerization rates with respect to the square root of the CO2 quantum yields. This justified the hypothesis that the C6H5SCH2 radical is the initiator of the free-radical polymerizations for the BP/C6H5-S-CH2-COO-N+R4 photoredox pairs studied in this work. | |||||
| Wheeler, K. E.; Nocek, J. M.; Cull, D. A.; Yatsunyk, L. A.; Rosenzweig, A. C.; Hoffman, B. M. | Dynamic Docking of Cytochrome b5 with Myoglobin and a-Hemoglobin: Heme-Neutralization `Squares` and the Binding of Electron-Transfer-Reactive Configurations | 2007 | Cytochrome b5, myoglobin, hemoglobin, electron transfer | J AM CHEM SOC, 2007, Vol 129, Iss 13, pp 3906-3917 | |
| Abstract: Intracomplex electron transfer (ET) occurs most often in intrinsically transient, low affinity complexes. As a result, the means by which adequate specificity and reactivity are obtained to support effective ET is still poorly understood. We report here on two such ET complexes: cytochrome b5 (cyt b5) in reaction with its physiological partners, myoglobin (Mb) and hemoglobin (Hb). These complexes obey the Dynamic Docking (DD) paradigm: a large ensemble of weakly bound protein-protein configurations contribute to binding in the rapid-exchange limit, but only a few are ET-active. We report the ionic-strength dependence of the second-order rate constant, k2, for photoinitiated ET from within all four combinations of heme-neutralized Zn deuteroporphyrin-substituted Mb/Hb undergoing ET with cyt b5, the four `corners` of a `heme-neutralization square`. These experiments provide insights into the relative importance of both global and local electrostatic contributions to the binding of reactive configurations, which are too few to be observed directly. To interpret the variations of k2 arising from heme neutralization, we have developed a procedure by which comparisons of the ET rate constants for a heme-neutralization square permit us to decompose the free energy of reactive binding into individual local electrostatic contributions associated with interactions between (i) the propionates of the two hemes and (ii) the heme of each protein with the polypeptide of its partner. Most notably, we find the contribution from the repulsion between propionates of partner hemes to the reactive binding free energy to be surprisingly small, G(Hb) ~ +1 kcal/mol at ambient temperature, 18 mM ionic strength, and we speculate about possible causes of this observation. To confirm the fundamental assumption of these studies, that the structure of a heme-neutralized protein is unaltered either by substitution of Zn or by heme neutralization, we have obtained the X-ray structure of ZnMb prepared with the porphyrin dimethyl ester and find it to be nearly isostructural with the native protein. | |||||
| Bourdelande, J. L.; Gallardo, I.; Guirado, G. | Inductive vs Solvation Effects in Primary Alkyl Amines: Determination of the Standard Potentials | 2007 | standard potential, primary alkyl amines, | J AM CHEM SOC, 2007, Vol 129, Iss 10, pp 2817-2821 | |
| Abstract: The determination of the standard potential of alkyl primary amines is reported for the first time using the nanosecond equilibrium method. The versatility and accuracy of the method demonstrates that it is not only an alternative to the classical and modern electrochemical methods, but also a powerful tool for quantifying inductive and/or solvation effects in a related family of compounds. Two different trends were observed depending on alkyl chain length. For `short-chain` alkyl primary amines, where the solvation around the amino group is expected to be the same, the standard potential value appears to follow a linear relationship with the number of carbon atoms, which indicates that the methylene group (-CH2-) causes an inductive effect that is responsible for the stabilization of the amine cation radical. Meanwhile, the E rises slightly to a constant potential value 1.500 V for `long-chain` unbranched alkyl primary amines. This interesting result can be explained by a steric inhibition of solvation around the amino group due to a fold of the long alkyl chain following a solvent exclusion mechanism. | |||||