Synthesis and testing of new end-functionalized oligomers for molecular electronics

Several new classes of oligomers have been synthesized with functionalities designed to aid in the understanding of molecular device behavior, specifically when molecules are interfaced between proximal electronic probes. The compounds synthesized are series of azobenzenes, bipyridines and oligo(phenylene vinylene)s that bear acetyl-protected thiols for ultimate attachment to metallic surfaces. Some initial electrochemical and solid-state test results are also reported.     

Single crystal X-ray structure determinations of the reaction products of cis- and trans-cyclohexanedicarboxylic anhydrides and methylhydrazine

The structures of two of the three isomeric products of the reactions between cis- and trans-cyclohexanedicarboxylic anhydrides and methylhydrazine were determined by single-crystal X-ray methods to ascertain their tautomeric forms and stereochemistries. One product was found to be cis-N-methylamino-1,2-cyclohexanedicarboximide and the other trans-hexahydro-2-methylcyclohexa[d]pyridazine-1,2-dione.     

Photophysical properties of biologically compatible CdSe quantum dot structures

The photophysical properties of CdSe and ZnS(CdSe) semiconductor quantum dots in nonpolar and aqueous solutions were examined with steady-state (absorption and emission) and time-resolved (time-correlated single-photon-counting) spectroscopy. The CdSe structures were prepared from a single CdSe synthesis, a portion of which were ZnS-capped, thus any differences observed in the spectral behavior between the two preparations were due to changes in the molecular shell. Quantum dots in nonpolar solvents were surrounded with a trioctylphosphine oxide (TOPO) coating from the initial synthesis solution. ZnS-capped CdSe were initially brighter than bare uncapped CdSe and had overall faster emission decays. The dynamics did not vary when the solvent was changed from hexane to dichloromethane; however, replacement of the TOPO cap by pyridine affected CdSe but not ZnS(CdSe). CdSe was then solubilized in water with mercapto-acetic acid or dihydrolipoic acid, whereas ZnS(CdSe) could be solubilized only with dihydrolipoic acid. Both solubilization agents quenched the nanocrystal emission, though with CdSe the quenching was nearly complete. Additional quenching of the remaining emission was observed when the redox-active molecule adenine was conjugated to the water-soluble CdSe but was not seen with ZnS(CdSe). The emission of aqueous CdSe could be enhanced under prolonged exposure to room light and resulted in a substantial increase of the emission lifetimes; however, the enhancement occurred concurrently with precipitation of the nanocrystals, which was possibly caused by photocatalytic destruction of the mercaptoacetic acid coating. These results are the first presented on aqueous CdSe quantum dot structures and are presented in the context of designing better, more stable biological probes.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

Field evaluations of the VDmax approach for substantiation of a 25 kGy sterilization dose and its application to other preselected doses

The International and European standards for radiation sterilization require evidence of the effectiveness of a minimum sterilization dose of 25 kGy but do not provide detailed guidance on how this evidence can be generated. An approach, designated VD_max, has recently been described and computer evaluated to provide safe and unambiguous substantiation of a 25 kGy sterilization dose. The approach has been further developed into a practical method, which has been subjected to field evaluations at three manufacturing facilities which produce different types of medical devices. The three facilities each used a different overall evaluation strategy: Facility A used VD_max for quarterly dose audits; Facility B compared VD_max and Method 1 in side-by-side parallel experiments; and Facility C, a new facility at start-up, used VD_max for initial substantiation of 25 kGy and subsequent quarterly dose audits. A common element at all three facilities was the use of 10 product units for irradiation in the verification dose experiment.

The field evaluations of the VD_max method were successful at all three facilities; they included many different types of medical devices/product families with a wide range of average bioburden and sample item portion values used in the verification dose experiments. Overall, around 500 verification dose experiments were performed and no failures were observed. In the side-by-side parallel experiments, the outcomes of the VD_max experiments were consistent with the outcomes observed with Method 1.

The VD_max approach has been extended to sterilization doses >25 and <25 kGy; verification doses have been derived for sterilization doses of 15, 20, 30, and 35 kGy. Widespread application of the VD_max method for doses other than 25 kGy must await controlled field evaluations and the development of appropriate specifications/standards.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Allylic interactions in organometallics: probing Electronic structure in (η5-C5H5)Fe(CO)2R,R = CH3, η1-C3H5, η1-C5H5.

The He(I) photoelectron spectra of (η⁵-C₅H₅)Fe(CO)₂R, where R = CH₃, η¹-C₃H₅ and η¹-C₅H₅, have been recorded. The lowest lying ion states result from ionization of molecular orbitals with large Fe 3d character; these move to lower anergy when R places double bonds in an allylic relationship to the metal atom. The cyclic voltammetric oxidation potential correlates well with the energies of the lowest ion states. A significant interaction between olefin π orbitals and the allylic metal center is proposed.     

Epitaxial electrodeposition of Prussian blue thin films on single-crystal Au(110)

Epitaxial Prussian blue (PB) films are deposited electrochemically onto a Au(110) substrate. High-resolution X-ray diffraction shows that the PB films have a [111] out-of-plane orientation. The very large lattice mismatch of 148% is reduced to about 1% by the formation of (1 x 2)PB(111)[onemacr;10]//(6 x 5)Au(110)[onemacr;10] and (1 x 2)PB(111)[01onemacr;]//(6 x 5)Au(110)[onemacr;10] epitaxial relationships. Peaks in the cyclic voltammogram of PB on Au(110) are sharper than those on polycrystalline Au, consistent with higher structural order and a single out-of-plane orientation. The development of epitaxial films of PB and PB analogues will allow the measurement of the orientation-dependent properties of these molecular magnets. It will also open the door to the development of novel molecular spintronic devices, such as those which exhibit spin-dependent electron transfer.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Theoretical study of the spin trapping of hydroxyl radical by cyclic nitrones: a density functional theory approach

The hydroxyl radical (*OH) is an important mediator of biological oxidative stress, and this has stimulated interest in its detection. 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and its alkoxycarbonyl and alkoxyphosphoryl analogues have been employed as spin traps for electron paramagnetic resonance (EPR) spectroscopic radical detection. Energies of optimized geometries of nitrones and their corresponding *OH adducts were calculated using density functional theory (DFT) at the B3LYP/6-31+G//B3LYP/6-31G level. Calculations predict that the trans adduct formation is favored in alkoxycarbonyl nitrones, while cis adducts with intramolecular H-bonding is favored for alkoxyphosphoryl nitrones. Addition of *OH to a phosphoryl-substituted nitrone is more exoergic than the carbonylated nitrones. Charge and spin densities on the nitrone spin traps were correlated with their rates of addition with *OH, and results show that the charge density on the nitronyl C, the site of *OH addition, is more positive in phosphorylated nitrones compared to DMPO and the alkoxycarbonyl nitrones. The dihedral angle between the beta-H and nitroxyl O bonds is smaller in phosphorylated nitrones, and that aspect appears to account for the longer half-lives of the spin adducts compared to those in DMPO and alkoxycarbonyl nitrones. Structures of nitrones with trifluoromethyl-, trifluoromethylcarbonyl-, methylsulfonyl-, trifluoromethylsulfonyl-, amido-, spiropentyl-, and spiroester substituents were optimized and their energies compared. Amido and spiroester nitrones were predicted to be the most suitable nitrones for spin trapping of *OH due to the similarity of their thermodynamic and electronic properties to those of alkoxyphosphoryl nitrones. Moreover, dimethoxyphosphoryl substitution at C-5 was found to be the most efficient substitution site for spin trapping of *OH, and their spin adducts are predicted to be the most stable of all of the isomeric forms.