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Nicholas J Turro

Publications and source records attributed to Nicholas J Turro.

At least 19 recordsLinked to original sources
PubMed2004

Reversible surface oxidation and efficient luminescence quenching in semiconductor single-wall carbon nanotubes.

We have investigated reversible single-wall carbon nanotube (SWNT) oxidation by quantitative analysis of the oxide-induced absorption bleaching and luminescence quenching at low pH. These data, in combination with DFT structure calculations, suggest that the nanotube oxide is a 1,4-endoperoxide. At low pH, the endoperoxide protonates to create a hydroperoxide carbocation, introducing a hole in the SWNT valence band. Nanotube luminescence is extremely sensitive to quenching by hole-doping, while the absorption is relatively robust.

Journal Article↗
PubMed2004

Interactions of dendrimers with selected amino acids and proteins studied by continuous wave EPR and Fourier transform EPR.

Interactions of polyamidoamine dendrimers, termed Gn, where n indicates the generation (=number of amidoamine layers), at different protonation levels with selected amino acids and proteins have been investigated by means of continuous wave electron paramagnetic resonance (cw-EPR) and pulsed-EPR (electron spin-echo = ESE) analyses. A low-generation dendrimer (G2) and a high-generation one (G6) were labeled with nitroxides for the EPR measurements. Gly, Glu, Arg, and Leu were selected as representative of neutral(zwitterionic)-polar, acidic, basic, and low-polar amino acids, respectively. The water-soluble proteins alpha-chymotrypsin and albumin were selected on the basis of a basic and an acidic isoelectric point, respectively. The cw-EPR spectra were analyzed by computing the line shapes to extract information about the dendrimer-biomolecule interactions. In general, dendrimers at a high protonation level interact stronger with amino acids than those at a low level of protonation. However, even for highly protonated dendrimers, a synergistic effect between hydrophilic and hydrophobic interactions promoted the formation of stable Gn-amino acid adducts, as demonstrated by the enhanced interactions with Leu. As expected from acid-base interactions, stable adducts were formed between Arg and highly protonated dendrimers and between Glu and low level protonated dendrimers. The relatively strong dendrimer interactions with the protein chymotrypsin and the poor interactions of dendrimers with albumin demonstrated that the protonated amino groups of the dendrimers are predominantly involved in the interactions with these proteins and indicated a significant role in the interactions with the dendrimers of the hydrophobic external residues of chymotrypsin. Computer-aided analysis of the ESE experiments was consistent with the cw-EPR results and supported the conclusion of a partial complexation of the nitroxides of the dendrimer with Leu and alpha-chymotrypsin.

Albumins↗
PubMed2004

Stereocontrol within confined spaces: enantioselective photooxidation of enecarbamates inside zeolite supercages.

Dye-exchanged Y zeolite is shown to be an effective medium to control the stereoselectivity in the photooxygenation of chiral oxazolidinone-functionalized Z/E-1 enecarbamates. An enantioselectivity (ee) as high as 80% was observed in the methyldesoxybenzoin (MDB) product, obtained in the methylene-blue-exchanged NaY zeolite at room temperature. The efficacy of the asymmetric induction in the MDB product depends on the Z/E geometry of the alkene, the Z-isomer being more effective than the corresponding E-isomer. The stereoselectivity is rationalized in terms of conformational effects through cationic interactions between the zeolite and the substrate.

Journal Article↗
PubMed2004

Temperature and solvent control of the stereoselectivity in the reactions of singlet oxygen with oxazolidinone-substituted enecarbamates.

Oxazolidinone-functionalized enecarbamates react stereoselectively with singlet oxygen to give methyldesoxybenzoin (MDB) in moderate to high enantiomeric excess. The stereochemical outcome depends on the E/Z substrate geometry, temperature, and solvent variables. The analysis of the differential activation parameters suggests a large contribution from the entropy term in determining the enantioselectivity. We demonstrate the utility of the temperature and solvent variables in determining the degree of the photochemical kinetic resolution of the enecarbamates; for example, in the photooxygenation at -70 degrees C in methanol, MDB may be obtained in methanol.

Benzoin↗
PubMed2004

Porphyrins as photosensitizers to enhance night vision.

Relative bleaching rates of bovine rhodopsin (rod outer segments) in the presence and absence of seven porphyrins and methylene blue were measured under exposure to lambdamax = 675 nm light, using UV-vis spectroscopy. Rate enhancements on the order of up to three times compared to the bleaching of rhodopsin alone where observed. Fluorescence measurements and other data suggests that the porphyrins act as photosensitizers and excite the visual pigment via electron or triplet state energy transfer. These mechanisms suggest that rhodopsin possesses a pocket, proximal to the Schiff base so that porphyrins act as photosensitizers.

Animals↗
PubMed2004

Photochemistry of A1E, a retinoid with a conjugated pyridinium moiety: competition between pericyclic photooxygenation and pericyclization.

The photochemistry of the retinoid analogue A1E shows an oxygen and solvent dependence. Irradiation of A1E with visible light (lambda(irr) = 425 nm) in methanol solutions resulted in pericyclization to form pyridinium terpenoids. Although the quantum yield for this cyclization is low (approximately 10(-4)), nevertheless the photochemical transformation occurs with quantitative chemical yield with remarkable chemoselectivity and diastereoselectivity. Conversely, irradiation of A1E under the same irradiation conditions in air-saturated carbon tetrachloride or deuterated chloroform produced a cyclic 5,8-peroxide as the major product. Deuterium solvent effects, experiments utilizing endoperoxide, phosphorescence, and chemiluminescence quenching studies strongly support the involvement of singlet oxygen in the endoperoxide formation. It is proposed that, upon irradiation, in the presence of oxygen, A1E acts as a sensitizer for generation of singlet oxygen from triplet oxygen present in the solution; the singlet oxygen produced reacts with A1E to produce cyclic peroxide. Thus, the photochemistry of A1E is characterized by two competing reactions, cyclization and peroxide formation. The dominant reaction is determined by the concentration of oxygen, the concentration of A1E, and the lifetime of singlet oxygen in the solvent employed. If the lifetime of singlet oxygen in a given solvent is long enough, then oxidation (peroxide formation) is the major reaction. If the singlet oxygen produced is quenched by the protonated solvent molecules faster than singlet oxygen reacts with A1E, then cyclization dominates.

Cyclization↗
PubMed2004

Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific coupling chemistry.

DNA sequencing by synthesis on a solid surface offers new paradigms to overcome limitations of electrophoresis-based sequencing methods. Here we report DNA sequencing by synthesis using photocleavable (PC) fluorescent nucleotides [dUTP-PC-4,4-difluoro-4-bora-3 alpha,4 alpha-diaza-s-indacene (Bodipy)-FL-510, dCTP-PC-Bodipy-650, and dUTP-PC-6-carboxy-X-rhodamine (ROX)] on a glass chip constructed by 1,3-dipolar azide-alkyne cycloaddition coupling chemistry. Each nucleotide analogue consists of a different fluorophore attached to the base through a PC 2-nitrobenzyl linker. We constructed a DNA microarray by using the 1,3-dipolar cycloaddition chemistry to site-specifically attach azido-modified DNA onto an alkyne-functionalized glass chip at room temperature under aqueous conditions. After verifying that the polymerase reaction could be carried out successfully on the above-described DNA array, we then performed a sequencing reaction on the chip by using a self-primed DNA template. In the first step, we extended the primer using DNA polymerase and dUTP-PC-Bodipy-FL-510, detected the fluorescent signal from the fluorophore Bodipy-FL-510, and then cleaved the fluorophore using 340 nm UV irradiation. This process was followed by extension of the primer with dCTP-PC-Bodipy-650 and the subsequent detection of the fluorescent signal from Bodipy-650 and its photocleavage. The same procedure was also performed by using dUTP-PC-ROX. The entire process was repeated five times by using the three fluorescent nucleotides to identify 7 bases in the DNA template. These results demonstrate that the PC nucleotide analogues can be incorporated accurately into a growing DNA strand during polymerase reaction on a chip, and the fluorophore can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing the continuous identification of the template sequence.

Alkynes↗
PubMed2004

Enecarbamates as selective substrates in oxidations: chiral-auxiliary-controlled mode selectivity and diastereoselectivity in the [2+2] cycloaddition and ene reaction of singlet oxygen and in the epoxidation by DMD and mCPBA.

The stereochemical course of the oxidation of chiral oxazolidinone-substituted enecarbamates has been studied for singlet oxygen ((1)O(2)), dimethyldioxirane (DMD), and m-chloroperbenzoic acid (mCPBA) by examining of the special structural and stereoelectronic features of the enecarbamates. Valuable mechanistic insight into these selective oxidations is gained. Whereas the R(1) substituent on the chiral auxiliary is responsible for the steric shielding of the double bond and determines the sense of the pi-facial diastereoselectivity, structural characteristic such as the Z/E configuration and the nature of the R(2) group on the double bond are responsible for the extent of the diastereoselectivity. Stereoelectronic steering by the vinylic nitrogen functionality controls the mode selectivity (ene reaction vs [2+2] cycloaddition) in the case of (1)O(2).

Journal Article↗
PubMed2004

Design and synthesis of a photocleavable biotinylated nucleotide for DNA analysis by mass spectrometry.

We report here the design, synthesis and evaluation of a novel photocleavable (PC) biotinylated nucleotide analog, dUTP-PC-Biotin, for DNA polymerase extension reaction to isolate DNA products for mass spectrometry (MS) analysis. This nucleotide analog has a biotin moiety attached to the 5-position of 2'-deoxyribouridine 5'-triphosphate via a photocleavable 2-nitrobenzyl linker. We have demonstrated that dUTP-PC-Biotin can be faithfully incorporated by the DNA polymerase Thermo Sequenase into the growing DNA strand in a DNA polymerase extension reaction and that its incorporation does not hinder the addition of the subsequent nucleotide. Therefore, the DNA extension fragments generated by using the dUTP-PC-Biotin can be efficiently isolated by a streptavidin-coated surface and recovered by near-UV light irradiation at room temperature in mild condition for further analysis without using any chemicals or heat. Single and multiple primer extension reactions were performed using the dUTP-PC-Biotin to generate DNA products for MALDI-TOF MS analysis. Such nucleotide analogs that carry a biotin and a photocleavable linker will allow the isolation and purification of DNA products under mild conditions for MS-based genetic analysis by DNA sequencing or multiplex single nucleotide polymorphism (SNP) detection. Furthermore, these nucleotide analogs should also be useful in isolating DNA-protein complexes under non-denaturing conditions.

Biotin↗
PubMed2003

Stereochemical features of the physical and chemical interactions of singlet oxygen with enecarbamates.

Oxazolidinone-substituted enecarbamates represent a mechanistically rich system for the study of stereoelectronic, steric, and conformational effects on stereoselectivity and mode selectivity in (1)O(2) [2 + 2] and ene reactions. Photooxygenation of these enecarbamates with (1)O(2) leads to diastereomerically pure dioxetanes that decompose to yield an oxazolidinone carbaldehyde and one of the two enantiomers of methyldesoxybenzoin in enantiomeric excess. Stereoselectivity originates at the allylic stereocenter, a result supported by quenching studies, computational analysis, and deuterium solvent isotope effects. [reaction: see text]

Journal Article↗
PubMed2003

Selective solid state photooxidant.

Irradiation of biphenyl encapsulated in the cavities of a NaZSM-5 zeolite framework has been reported to result in the formation of an extremely long-lived radical cation. Here, we show that such zeolite encapsulated radical cations can act as irreversible one-electron oxidants for simple alkenes and dienes, in a solid-state analogue to solution-phase cosensitization. Compared to the well-known semiconductor photooxidizers, such as titanium dioxide, the NaZSM-5 zeolite-based solid photooxidants exhibit enhanced selectivity based on oxidation potential, molecular size and shape, and Lewis base character.

Journal Article↗
PubMed2003

A supramolecular "ship in bottle" strategy for enantiomeric selectivity in geminate radical pair recombination.

[reaction: see text] Reactions in which zeolites are modified with chiral inductors to serve as media for chiral induction are often limited by the propensity of both substrate and inductor to occupy the same supercage. Herein, we report a "ship in bottle" strategy utilizing the thermal decomposition of dioxetanes obtained from oxazolidinone-substituted enecarbamates for the enantioselective generation of methyl desoxybenzoin (MDB). Photoexcitation of the supramolecular geminate molecular pair results in enrichment of the opposite enantiomer of MDB.

Journal Article↗
PubMed2003

Photocleavage of a 2-nitrobenzyl linker bridging a fluorophore to the 5' end of DNA.

Three single-stranded DNA molecules of different lengths were synthesized and characterized, each containing a fluorescent dye (6-carboxyfluorescein) connected to the 5' end via a photocleavable 2-nitrobenzyl linker and a biotin moiety at the 3' end. UV irradiation (lambda approximately 340 nm) of solutions containing these fluorescent DNA molecules caused the complete cleavage of the nitrobenzyl linker, separating the fluorophore from the DNA. The photocleavage products were characterized by HPLC and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. Our experimental results indicated that the proximity of the chromophore 6-carboxyfluorescein to the 2-nitrobenzyl linker did not hinder the quantitative photocleavage of the linker in the DNA molecules. The biotin moiety allowed immobilization of the fluorescent DNA on streptavidin-coated glass chips. The photocleavage of the immobilized DNA was investigated directly by fluorescence spectroscopy. The results demonstrated that close to 80% of the fluorophore was removed from the immobilized DNA after UV irradiation at 340 nm. These results strongly support the application of the 2-nitrobenzyl moiety as an efficient photocleavable linker, connecting fluorescent probes to DNA molecules for a variety of biological analyses such as DNA sequencing by synthesis.

Biotin↗
PubMed2003

A photocleavable fluorescent nucleotide for DNA sequencing and analysis.

DNA sequencing by synthesis during a polymerase reaction using laser-induced fluorescence detection is an approach that has a great potential to increase the throughput and data quality of DNA sequencing. We report the design and synthesis of a photocleavable fluorescent nucleoside triphosphate, one of the essential molecules required for the sequencing-by-synthesis approach. We synthesized this nucleoside triphosphate by attaching a fluorophore, 4,4-difluoro-5,7-dimethyl-4-bora-3alpha,4alpha-diaza-s-indacene propionic acid (BODIPY), to the 5 position of 2'-deoxyuridine triphosphate via a photocleavable 2-nitrobenzyl linker. We demonstrate that the nucleotide analogue can be faithfully incorporated by a DNA polymerase Thermo Sequenase into the growing DNA strand in a DNA-sequencing reaction and that its incorporation does not hinder the addition of the subsequent nucleotide. These results indicate that the nucleotide analogue is an excellent substrate for Thermo Sequenase. We also systematically studied the photocleavage of the fluorescent dye from a DNA molecule that contained the nucleotide analogue. UV irradiation at 340 nm of the DNA molecule led to the efficient release of the fluorescent dye, ensuring that a previous fluorescence signal did not leave any residue that could interfere with the detection of the next nucleotide. Thus, our results indicate that it should be feasible to use four different fluorescent dyes with distinct fluorescence emissions as unique tags to label the four nucleotides (A, C, G, and T) through the photocleavable 2-nitrobenzyl linker. These fluorescent tags can be removed easily by photocleavage after the identification of each nucleotide in the DNA sequencing-by-synthesis approach.

Biotin↗
PubMed2003

Ruthenium(II)-tris-bipyridine/titanium dioxide codoped zeolite Y photocatalysts: II. Photocatalyzed degradation of the model pollutant 2,4-xylidine, evidence for percolation behavior.

A considerably arduous test of a novel class of composite materials consisting of [Ru(bpy)3]2+ and TiO2 codoped zeolites Y is presented here. The [Ru(bpy)3]2+ and TiO2 codoped zeolites Y served as photocatalysts in the oxidation of the model compounds 2,4-dimethylaniline (2,4-xylidine) by H2O2 in an acidic aqueous medium. Zeolite-embedded TiO2 (nano)particles play an important role in the degradation mechanism. The first step in this complex mechanism is the photoelectron transfer from photoexcited [Ru(bpy)3]2+*, located inside the supercage of zeolite Y, to a neighboring TiO2 nanoparticle. During this electron transfer process, electron injection into the conduction band of TiO2 is achieved. The second decisive step is the reaction of this electron with H2O2, which was previously chemisorbed at the surface-region of the TiO2 nanoparticles. In this reaction, a TiO2 bound hydroxyl radical (TiO2-HO.) is created. This highly reactive intermediate initiates then the oxidation of 2,4-xylidine, which enters the zeolites framework in its protonated form (Hxyl+). The formation of 2,4-dimethylphenol as first detectable reaction product indicated that this oxidation proceeds via an electron transfer mechanism. Furthermore, [Ru(bpy)3]3+, which was created in the initiating photoelectron transfer reaction between [Ru(bpy)3]2+* and TiO2, also takes place in the oxidation of Hxyl+. [Ru(bpy)3]2+ is recycled in that reaction, which also belongs to the group of electron transfer reactions. In addition to the primary steps of this particular Advanced Oxidation Process (AOP), the dependence of the efficiency of the 2,4-xylidine degradation as a function of the [Ru(bpy)3]2+ and TiO2 loadings of the zeolite Y framework is also reported here. The quenching of [Ru(bpy)3]2+* by H2O2 as well as the photocatalytic activity of the [Ru(bpy)3]2+ and TiO2 codoped zeolite Y catalysts both follow a distinct percolation behavior in dependence of their TiO2 content.

Journal Article↗
PubMed2003

Photoisomerization of 2,3-diphenylcyclopropane-1-carboxylic acid derivatives.

Contrary to what is known about cis-1,2-diphenylcyclopropane and its derivatives, we find that they have triplet energies of ca. 311 kJ mol(-1), do not undergo intersystem crossing upon direct excitation, undergo the less common adiabatic photoisomerization to the corresponding trans isomers, and show emission from excited 1,3-diradical intermediates.

Journal Article↗