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Xiaobing Zuo

Publications and source records attributed to Xiaobing Zuo.

At least 19 recordsLinked to original sources
PubMed2006

Charge separation and surface reconstruction: a Mn2+ doping study.

Hydrothermal synthesis of Mn doped anatase (TiO2) nanoparticles using scrolled nanotubes of TiO2 and MnCl2 as the starting materials is described. Incorporation of Mn2+ ions on the substitutional sites was confirmed using X-ray absorption fine structure (FT-XAFS) while the oxidation state Mn(II) and coordination environment were determined using both electron paramagnetic resonance (EPR) and X-ray absorption near edge spectroscopy (XANES). Two different hyperfine couplings of 96 and 86 G were found using high-field (130 GHz) EPR reporting that Mn atoms occupy two distinct sites: one undercoordinated (reconstructed surface) and the other octahedral crystalline geometry (nanoparticle core), respectively. It was found that Mn atoms that occupy surface layers are weakly bound to the anatase lattice and can be easily leached using simple dialysis, while those incorporated in the nanoparticle core are bound more strongly and cannot be removed by dialysis. Light excitation EPR reveals that Mn ions incorporated in the surface layers participate in the charge separation, while those trapped deeply in the nanoparticle core do not show any photoactivity. Doping of the core of nanoparticles with Mn2+ ions, on the other hand, enables synthesis of optically transparent films having superparamagnetic behavior at room temperatures with a saturation magnetic moment of 1.23 microB per Mn atom.

Journal Article↗
PubMed2006

Linearly polarized emission of an organic semiconductor nanobelt.

Linearly polarized emission has been observed for the nanobelts fabricated from a perylene diimide molecule through both solution-based and surface-supported self-assembling. The measurement of polarized emission was performed over single nanobelts with use of a near-field scanning optical microscope (NSOM) adapted with emission polarization (by putting a planar polarizer before the detector). Rotating the emission polarizer (from 0 degrees to 180 degrees) changed the emission intensity in a way depending on the relative angle between the long axis of the belt and the polarizer with a minimum of intensity detected at ca. 78 degrees, which is indicative of the tilted stacking of molecules along the belt direction.

Journal Article↗
PubMed2006

Solvent dependent photocyclization and photophysics of some 2-ethynylbiphenyls.

The spectroscopic properties and photochemical behavior of molecules having 2-ethynylbiphenyl or 2-phenyldiphenylacetylene structures are reported. These molecules undergo photocyclization reactions to yield phenanthrene and dihydrophenanthrene products via putative isophenanthrene (cyclic allene) intermediates. Phenanthrene formation from the isophenanthrene intermediates does not occur via a unimolecular sigmatropic hydrogen shift, but rather by protonation or hydrogen abstraction mechanisms involving the solvent. Cyclization efficiencies are much lower than is the case for previously-investigated 2-vinylbiphenyl systems. The 2-phenyldiphenylacetylenes have high fluorescence quantum yields and long singlet lifetimes when compared to diphenylacetylene. The 2-ethynylbiphenyls decay via a combination of fluorescence and intersystem crossing.

Journal Article↗
PubMed2006

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation.

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space "fingerprints" of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experimental solution x-ray diffraction (SXD). SXD experiments and MD simulations were carried out to test the ability of experiment and simulation to resolve sequence-dependent modifications in helix conformation for B-form DNA. SXD experiments demonstrated that solution-state poly(AT) and poly(A)-poly(T) duplex DNA sequences exist in ensembles close to canonical B-form and B'-form structures, respectively. In contrast, MD simulations analyzed in terms of SXD fingerprints are shown to deviate from experiment, most significantly for poly(A)-poly(T) duplex DNA. Compared with experiment, MD simulation shortcomings were found to include both mismatches in simulated conformer structures and number population within the ensembles. This work demonstrates an experimental approach for quantitatively evaluating MD simulations and other coordinate models to simulate biopolymer structure in solution and suggests opportunities to use solution diffraction data as experimental benchmarks for developing supramolecular force fields optimized for a range of in situ applications.

DNA↗
PubMed2005

Competitive 1,2- and 1,5-hydrogen shifts following 2-vinylbiphenyl photocyclization.

[reaction: see text] The photocyclization of 2-vinylbiphenyl and its derivatives has been proposed to occur via a two-step mechanism: photocyclization to form an unstable 8a,9-dihydro-phenanthrene intermediate, followed by exothermic unimolecular isomerization to a 9,10-dihydrophenanthrene. The mechanism of the hydrogen shift process has been investigated using deuterated derivatives of 2-isopropenylbiphenyl and 2,6-diphenylstyrene. 1H NMR analysis of the photoproducts indicates that the thermally allowed 1,5-hydrogen or deuterium shift is a minor product-forming pathway and that an unusual double 1,2-hydrogen or deuterium shift is the major product-forming pathway. The potential energy surface for photocyclization and hydrogen shift processes has been explored computationally. The calculated barrier for the 1,5-shift is predicted to be significantly lower than that for the 1,2-shift. Alternative mechanisms for the occurrence of 1,2-hydrogen or deuterium migration are presented.

Journal Article↗
PubMed2005

DNA as helical ruler: exciton-coupled circular dichroism in DNA conjugates.

The structure and properties of oligonucleotide conjugates possessing stilbenedicarboxamide chromophores at both ends of a poly(dA):poly(dT) base-pair domain of variable length have been investigated using a combination of spectroscopic and computational methods. These conjugates form capped hairpin structures in which one stilbene serves as a hairpin linker and the other as a hydrophobic end-cap. The capping stilbene stabilizes the hairpin structures by ca. 2 kcal/mol, making possible the formation of a stable folded structure containing a single A:T base pair. Exciton coupling between the stilbene chromophores has little effect on the absorption bands of capped hairpins. However, exciton-coupled circular dichroism (EC-CD) can be observed for capped hairpins possessing as many as 11 base pairs. Both the sign and intensity of the EC-CD spectrum are sensitive to the number of base pairs separating the stilbene chromophores, as a consequence of the distance and angular dependence of exciton coupling. Calculated spectra obtained using a static vector model based on canonical B-DNA are in good agreement with the experimental spectra. Molecular dynamics simulations show that conformational fluctuations of the capped hairpins result in large deviations of the averaged spectra in both the positive and negative directions. These results demonstrate for the first time the ability of B-DNA to serve as a helical ruler for the study of electronic interactions between aligned chromophores. Furthermore, they provide important tests for atomistic theoretical models of DNA.

Circular Dichroism↗
PubMed2005

Excited state dynamics and structures of functionalized phthalocyanines. 1. Self-regulated assembly of zinc helicenocyanine.

Recently synthesized zinc helicenocyanine (ZnHc), where four helicene groups are fused with a phthalocyanine (Pc) core through all-carbon linkages, exhibits an unusually strong tendency of forming soluble molecular aggregates in organic solvents. The aggregation results in a strong optical absorption across most of the visible region, which is drastically different from that of its monomer. The aggregation is suppressed by dissolving ZnHc in a liquid crystal, octylbiphenylcarbonitrile (OBCN), where the monomer ZnHc dominates and exhibits a typical optical absorption spectrum of monomeric zinc phthalocyanine, except red shift in both Q- and B- bands due to pi-conjugation expansion. This study correlates optical properties and excited state dynamics of ZnHc with intra- and intermolecular electronic interactions, using quantum mechanical calculations and ultrafast transient absorption spectroscopy. Structural details of the aggregates are revealed by small-angle X-ray scattering (SAXS) to be uniformly dimers with alkoxy chains wrapped around the core of a face-to-face dimer. The results suggest that while the peripheral helicene moieties in ZnHc are electronically coupled to the Pc core via expansion of the pi-conjugation of the macrocycle, the coupling is attenuated by the "lock washer" conformation of the nonplanar peripheral helicenes which prevents pi-conjugation throughout the entire macrocycle. The interplay between pi-conjugation expansion in the macrocyle plane and the pi-pi stacking out of the macrocyle plane produces a structure that facilitates the unique optical properties and self-regulated assembly into nanoscale structures in solution. These novel optical properties are explored for potential applications in various areas.

Indoles↗
PubMed2005

Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold.

The efficiency of fluorescence resonance energy transfer (FRET) between two chromophores positioned at opposite ends of DNA base pair domains has been investigated. The base pair domain serves as a helical scaffold which defines both the distance between chromophores and the dihedral angle between their electronic transition dipole moments, each incremental base pair increasing the distance and stepping the dihedral angle. Fluorescence quantum yields and lifetimes have been determined for both the donor and acceptor chromophores. The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipole model conventionally assumed for FRET.

DNA↗
PubMed2005

Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction.

We report on synchrotron-based high-angle X-ray solution scattering measured to 2 A resolution for two synthetic DNA sequences for which there are conflicting X-ray crystal and solution NMR models. Our results demonstrate that high-angle X-ray scattering discriminates between differing X-ray crystal and NMR models for solution-state DNA and provides a direct, independent method for testing structural models and measuring solution-state configurational dispersions.

Crystallography, X-Ray↗
PubMed2004

DNA-mediated exciton coupling and electron transfer between donor and acceptor stilbenes separated by a variable number of base pairs.

The synthesis, steady-state spectroscopy, and transient absorption spectroscopy of DNA conjugates possessing both stilbene electron donor and electron acceptor chromophores are described. These conjugates are proposed to form nicked DNA dumbbell structures in which a stilbenedicarboxamide acceptor and stilbenediether donor are separated by variable numbers of A-T or G-C base pairs. The nick is located either adjacent to one of the chromophores or between two of the bases. Thermal dissociation profiles indicate that stable structures are formed possessing as few as two A-T base pairs. Circular dichroism (CD) spectra in the base pair region are characteristic of B-DNA duplex structures, whereas CD spectra at longer wavelengths display two bands attributed to exciton coupling between the two stilbenes. The sign and intensity of these bands are dependent upon both the distance between the chromophores and the dihedral angle between their transition dipoles [Deltaepsilon approximately Rda(-2) sin(2theta)]. Pulsed laser excitation of the stilbenediamide results in creation of the acceptor-donor radical ion pair, which decays via charge recombination. The dynamics of charge separation and charge recombination display an exponential distance dependence, similar to that observed previously for systems in which guanine serves as the electron donor. Unlike exciton coupling between the stilbenes, there is no apparent dependence of the charge-transfer rates upon the dihedral angle between donor and acceptor stilbenes. The introduction of a single G-C base pair between the donor and acceptor results in a change in the mechanism for charge separation from single step superexchange to hole hopping.

Chromatography, High Pressure Liquid↗
PubMed2003

Stepwise evolution of the structure and electronic properties of DNA.

The optical properties of a family of duplex DNA conjugates possessing from 1 to 11 A:T base pairs and covalently attached stilbene chromophores at both ends have been investigated. As few as from two to four base bairs are needed to establish base-pair absorption and circular dichroism spectra similar to those of longer oligomers. The stilbene chromophores exhibit exciton-coupled circular dichroism, which can be observed even with 11 intervening base pairs, a distance of ca. 40 A. The dependence of the sign and amplitude of these spectra reveals the ability of B-DNA to serve as a helical ruler.

Circular Dichroism↗
PubMed2003

Activated decay pathways for planar vs twisted singlet phenylalkenes.

The ground state conformation, spectroscopy, and photochemical behavior of styrene and eight of its vinyl- and ring-methylated derivatives have been investigated. Introduction of methyl groups at the alpha-position of the vinyl group or the ortho positions of the phenyl results in increased phenyl-vinyl dihedral angles. Styrenes possessing both alpha-methyl and ortho-methyl groups adopt orthogonal geometries. Decreased planarity results in a progressive blue-shift in the lowest energy allowed pi,pi transition and a decrease in the singlet lifetime. Kinetic modeling of the temperature-dependent singlet lifetimes provides activation parameters for the activated decay pathway, which is assigned to C=C torsion for styrenes with phenyl-vinyl dihedral angles, phi, < 60 degrees. Planar styrenes have large torsional barriers (7 +/- 1 kcal/mol) and decay predominantly via intersystem crossing and fluorescence at room temperature. Styrenes with values of 30 degrees < phi < 60 degrees have smaller torsional barriers and decay predominantly via C=C torsion at room temperature. Highly nonplanar styrenes decay predominantly via relatively rapid, weakly activated intersystem crossing.

Journal Article↗
PubMed2003

Dynamics and energetics of single-step hole transport in DNA hairpins.

The dynamics of single-step hole transport processes have been investigated in a number of DNA conjugates possessing a stilbenedicarboxamide electron acceptor, a guanine primary donor, and several secondary donors. Rate constants for both forward and return hole transport between the primary and secondary donor are obtained from kinetic modeling of the nanosecond transient absorption decay profiles of the stilbene anion radical. The kinetic model requires that the hole be localized on either the primary or the secondary donor and not delocalized over both the primary and the secondary donor. Rate constants for hole transport are found to be dependent upon the identity of the secondary donor, the intervening bases, and the location of the secondary donor in the same strand as the primary donor or in the complementary strand. Rate constants for hole transport are much slower than those for the superexchange process used to inject the hole on the primary donor. This difference is attributed to the larger solvent reorganization energy for charge transport versus charge separation. The hole transport rate constants obtained in these experiments are consistent with experimental data for single-step hole transport from other transient absorption studies. Their relevance to long-distance hole migration over tens of base pairs remains to be determined. The forward and return hole transport rate constants provide equilibrium constants and free energies for hole transport equilibria. Secondary GG and GGG donors are found to form very shallow hole traps, whereas the nucleobase deazaguanine forms a relatively deep hole trap. This conclusion is in accord with selected strand cleavage data and thus appears to be representative of the behavior of holes in duplex DNA. Our results are discussed in the context of current theoretical models of hole transport in DNA.

Base Pairing↗
PubMed2003

Torsional barriers for planar versus twisted singlet styrenes.

Kinetic modeling of the temperature-dependent lifetimes of styrene and several methyl-substituted styrenes has been used to obtain the torsional barriers for singlet-state C=C rotation. The barrier for C=C torsion is found to be correlated with the ground-state phenyl-vinyl dihedral angle, varphi, planar styrenes having barriers of approximately 6.5 kcal/mol and moderately twisted styrenes having smaller barriers. Highly twisted styrenes undergo exceptionally rapid intersystem crossing. This unexpected dependence of excited-state behavior on varphi is attributed to a change in the character of the excited states from delocalized for planar styrenes to localized for highly twisted styrenes.

Journal Article↗
PubMed2003

Conformer-specific photoisomerizaton of some 2-vinylbiphenyls.

The ground-state conformations, spectroscopy, and photochemistry of 2-vinylbiphenyl and three of its vinylsubstituted derivatives have been investigated. The ground state exists as a mixture of syn and anti conformers in which the vinyl group is directed either toward or away from the unsubstituted phenyl ring. Both conformers are highly non-planarn having large phenyl phenyl and phenyl vinyl dihedral angles. The vinylbiphenyls are found to undergo conformer-specific photochemistry. The syn rotamers are non-fluorescent and undergo rapid and efficient cyclization to 8a,9-dihydrophenanthrene intermediates, which undergo rapid thermal sigmatropic rearrangements to yield 9,10-dihydrophenanthrenes. The intermediates have been generated at 77 K and detected by absorption spectroscopy. The singlet states of the anti rotamers are fluorescent, and undergo competing intersystem crossing and activated C=C torsion. The torsional barriers are of the order of those for styrenes with similar vinyl substituents.

Journal Article↗
PubMed2002

Symmetry-enforced conformational control of photochemical reactivity in 2-vinyl-1,3-terphenyl.

The photocyclization of o-vinylbiphenyl to 9,10-dihydrophenanthrene occurs with very low quantum yield because of the low ground-state population of the reactive syn rotamer. 2-Vinyl-1,3-terphenyl exists as a single rotamer which undergoes highly efficient photocyclization. Irradiation at 77 K in a rigid glass permits observation of the 8a,9-dihydrophenanthrene which rearranges to the 9,10-dihydrophenanthrene upon warming of the glass. The barriers for photocyclization and the thermal sigmatropic hydrogen shift are both remarkably small.

Journal Article↗
PubMed2002

Dynamics of inter- and intrastrand hole transport in DNA hairpins.

The dynamics of photoinduced electron transfer has been investigated in DNA hairpins possessing a stilbenedicarboxamide (Sa) electron acceptor, a guanine (G) primary donor, and two adjacent guanines (GG) as secondary donors. Hole transport from G to GG across a single A is more rapid than across AA or T by factors of 20 +/- 7 and 40 +/- 15, respectively. Intrastrand hole transport across a single A is more rapid than interstrand transport by a factor of 7 +/- 3.

Base Sequence↗