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David M Tiede

Publications and source records attributed to David M Tiede.

13 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

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

Low-temperature interquinone electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides and Blastochloris viridis: characterization of Q(B)- states by high-frequency electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR).

High-frequency electron paramagnetic resonance (HF EPR) techniques have been employed to look for localized light-induced conformational changes in the protein environments around the reduced secondary quinone acceptor (Q(B)(-)) in Rhodobacter sphaeroides and Blastochloris viridis RCs. The Q(A)(-) and Q(B)(-) radical species in Fe-removed/Zn-replaced protonated RCs substituted with deuterated quinones are distinguishable with pulsed D-band (130 GHz) EPR and provide native probes of both the low-temperature Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron-transfer event and the structure of trapped conformational substates. We report here the first spectroscopic evidence that cryogenically trapped, light-induced changes enable low-temperature Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron transfer in the B. viridis RC and the first observation of an inactive, trapped P(+)Q(B)(-) state in both R. sphaeroides and B. viridis RCs that does not recombine at 20 K. The high resolution and orientational selectivity of HF electron-nuclear double resonance (ENDOR) allows us to directly probe protein environments around Q(B)(-) for distinct P(+)Q(B)(-) kinetic RC states by spectrally selecting specific nuclei in isotopically labeled samples. No structural differences in the protein structure near Q(B)(-) or reorientation (within 5 degrees ) of Q(B)(-) was observed with HF ENDOR spectra of two states of P(+)Q(B)(-): "active" and "inactive" states with regards to low-temperature electron transfer. These results reveal a remarkably enforced local protein environment for Q(B) in its reduced semiquinone state and suggest that the conformational change that controls reactivity resides beyond the Q(B) local environment.

Binding Sites↗
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

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

Structural characterization of modular supramolecular architectures in solution.

Structures of modular supramolecular architectures consisting of a hexameric, diphenylethyne-linked porphyrin macrocyclic array and the corresponding host-guest complex formed by inclusion of a tripyridyl guest molecule were characterized in solution using high-angle X-ray scattering. Scattering measurements made to 6 A resolution coupled with pair distance function (PDF) analyses demonstrated that (1) the porphyrin architectures are not rigid but are distributed across a conformational ensemble with a mean diameter that is 1.5 A shorter than the diameter of a symmetric, energy-minimized model structure, (2) the conformational envelope has limits of 3 A positional dispersion and full rotational freedom for all six porphyrin groups, and (3) insertion of the tripyridyl guest molecule expands the diameter of the host conformer by 0.6 A and decreases the configurational dispersion by approximately 2-fold. These results validate the molecular design, provide a new measure of conformational ensembles in solution that cannot be obtained by other techniques, and establish a structural basis for understanding the photophysical and guest-hosting functions of the hexameric porphyrin architectures in liquids.

Journal Article↗
PubMed2004

Self-assembly of supramolecular light-harvesting arrays from covalent multi-chromophore perylene-3,4:9,10-bis(dicarboximide) building blocks.

We report on two multi-chromophore building blocks that self-assemble in solution and on surfaces into supramolecular light-harvesting arrays. Each building block is based on perylene-3,4:9,10-bis(dicarboximide) (PDI) chromophores. In one building block, N-phenyl PDI chromophores are attached at their para positions to both nitrogens and the 3 and 6 carbons of pyromellitimide to form a cross-shaped molecule (PI-PDI(4)). In the second building block, N-phenyl PDI chromophores are attached at their para positions to both nitrogens and the 1 and 7 carbons of a fifth PDI to produce a saddle-shaped molecule (PDI(5)). These molecules self-assemble into partially ordered dimeric structures (PI-PDI(4))(2) and (PDI(5))(2) in toluene and 2-methyltetrahydrofuran solutions with the PDI molecules approximately parallel to one another primarily due to pi-pi interactions between adjacent PDI chromophores. On hydrophobic surfaces, PDI(5) grows into rod-shaped nanostructures of average length 130 nm as revealed by atomic force microscopy. Photoexcitation of these supramolecular dimers in solution gives direct evidence of strong pi-pi interactions between the excited PDI chromophore and other PDI molecules nearby based on the observed formation of an excimer-like state in <130 fs with a lifetime of about 20 ns. Multiple photoexcitations of the supramolecular dimers lead to fast singlet-singlet annihilation of the excimer-like state, which occurs with exciton hopping times of about 5 ps, which are comparable to those observed in photosynthetic light-harvesting proteins from green plants.

Journal Article↗
PubMed2004

Structural studies of the manganese stabilizing subunit in photosystem II.

Photosystem II (PSII) is the plant photosynthetic reaction center that carries out the light driven oxidation of water. The water splitting reactions are catalyzed at a tetranuclear manganese cluster. The manganese stabilizing protein (MSP) of PSII stabilizes the manganese cluster and accelerates the rate of oxygen evolution. MSP can be removed from PSII, with an accompanying decrease in activity. Either an Escherichia coli expressed version of MSP or native, plant MSP can be rebound to the PSII reaction center; MSP reconstitution reverses the deleterious effects associated with MSP removal. We have employed Fourier transform infrared (FTIR) spectroscopy and solution small angle x-ray scattering (SAXS) techniques to investigate the structure of MSP in solution and to define the structural changes that occur before and after reconstitution to PSII. FTIR and SAXS are complementary, because FTIR spectroscopy detects changes in MSP secondary structure and SAXS detects changes in MSP size/shape. From the SAXS data, we conclude that the size/shape and domain structure of MSP do not change when MSP binds to PSII. From FTIR data acquired before and after reconstitution, we conclude that the reconstitution-induced increase in beta-sheet content, which was previously reported, persists after MSP is removed from the PSII reaction center. However, the secondary structural change in MSP is metastable after removal from PSII, which indicates that this form of MSP is not the lowest energy conformation in solution.

Energy Transfer↗
PubMed2002

Production and preliminary characterization of a recombinant triheme cytochrome c(7) from Geobacter sulfurreducens in Escherichia coli.

Multiheme cytochromes c have been found in a number of sulfate- and metal ion-reducing bacteria. Geobacter sulfurreducens is one of a family of microorganisms that oxidize organic compounds, with Fe(III) oxide as the terminal electron acceptor. A triheme 9.6 kDa cytochrome c(7) from G. sulfurreducens is a part of the metal ion reduction pathway. We cloned the gene for cytochrome c(7) and expressed it in Escherichia coli together with the cytochrome c maturation gene cluster, ccmABCDEFGH, on a separate plasmid. We designed two constructs, with and without an N-terminal His-tag. The untagged version provided a good yield (up to 6 mg/l of aerobic culture) of the fully matured protein, with all three hemes attached, while the N-terminal His-tag appeared to be detrimental for proper heme incorporation. The recombinant protein (untagged) is properly folded, it has the same molecular weight and displays the same absorption spectra, both in reduced and in oxidized forms, as the protein isolated from G. sulfurreducens and it is capable of reducing metal ions in vitro. The shape parameters for the recombinant cytochrome c(7) determined by small angle X-ray scattering are in good agreement with the ones calculated from a homologous cytochrome c(7) of known structure.

Cytochrome c Group↗
PubMed2002

Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C.

We demonstrate the use of high-angle X-ray scattering to explore protein conformational states in solution by resolving oxidation state- and temperature-dependent changes in the conformation of horse heart cytochrome c. Several detailed models exist for oxidation-dependent changes in mitochondrial class I c cytochromes determined by X-ray crystallography and solution NMR techniques. These models differ in the magnitude and locations of structural change. Our scattering measurements show that high-angle X-ray scattering can discriminate between these models, and that the experimental scattering data for horse cytochrome c can be best reconciled with selected NMR models for the same protein. These results demonstrate the ability to use high-angle X-ray scattering to resolve conformational states of proteins in solution, and to relate these measurements to detailed structural models. Furthermore, temperature-dependent changes are found in the high angle scattering patterns for horse cytochrome c, illustrating the sensitivity of these measurements to dynamic aspects of protein structure. These results demonstrate the ability to use difference high angle scattering as a quantitative monitor of reaction-linked changes in protein conformation and structural dynamics. Synchrotron-based high-angle scattering holds promise as a widely applicable, high throughput technique for exploring conformational states linked to physiological protein function, for resolving configurational differences between protein structures in solution and crystalline states, and for bridging the gap between solution NMR and crystallographic structure techniques.

Animals↗