Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765) structures: their long c axis and composite crystals, chemical twinning, and atomic site preferences

We present single-crystal studies of Pd(0.213)Cd(0.787) and Pd(0.235)Cd(0.765), synchrotron powder studies of Pd(1-x)Cd(x), 0.755> or =x> or =0.800, and LDA-DFT and extended Hückel (eH) calculations on these or related phases. The two single-crystal structures have a, b, and c axis lengths of 9.9013(7), 14.0033(10), 37.063(24) and 9.9251(3), 14.0212(7), 60.181(3) A, respectively and they crystallize in the space groups Ccme and F2mm, respectively (solved as (3+1)-dimensional crystals their most convenient superspace group is Xmmm(00gamma)s00). The structures have two different structural components each with their own separate axis parameters. Powder data shows that the ratio of these separate axes (S/L) varies from 1.615 to 1.64, values near the golden mean (1.618). For Pd(0.213)Cd(0.787), different Pd and Cd site occupancies lead to variation in the R factor from 2.6-3.6 %. The site occupancy pattern with the lowest R factor (among the 26 820 variants studied) is the exact site occupancy pattern predicted by LDA-DFT parameterized eH Mulliken charge populations. The phases can be understood through a chemical twinning principle found in gamma-brass, the parent structure for the above phases (a relation with the MgCu(2) Laves phase is also noted). This twinning principle can be used to account for Cd and Pd site preferences. At the same time there is a clean separation among the Cd and Pd atoms for the two separate chain types at height b=0 and 1/2. These results indicate that Cd:Pd stoichiometry plays a role in phase stability.     

Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces

Enhancements to the properties based on Hirshfeld surfaces enable quantitative comparisons between contributions to crystal packing from various types of intermolecular contacts.     

Photoinduced reduction of catalytically and biologically active Ru(II)bisterpyridine-cytochrome c bioconjugates

Ruthenium(II)bisterpyridine chromophores were covalently linked to iso-1 cytochrome c from yeast to create light-activated donor-acceptor bioconjugates.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 5-amino-o-cresol

The Fourier transform Raman and Fourier transform infrared spectra of 5-amino-o-cresol (5AOC) were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and density functional B3LYP method with the 6-311G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels of theory. A detailed interpretation of the infrared and Raman spectra of 5-amino-o-cresol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

FT-Raman and FT-IR spectra, ab initio and density functional studies of 2-amino-4,5-difluorobenzoic acid

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-4,5-difluorobenzoic acid (2A45DFBA) were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, depolarization ratios were calculated by HF and density functional B3LYP method with the 6-31+G(d, p) and 6-311+G(d, p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31+G(d, p)/6-311+G(d, p) and B3LYP/6-31+G(d, p)/6-311+G(d, p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 2-amino-4,5-difluorobenzoic acid is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Accurate single molecule FRET efficiency determination for surface immobilized DNA using maximum likelihood calculated lifetimes

Single molecule fluorescent lifetime trajectories of surface immobilized double-stranded DNA coupled with a tetramethylrhodmaine and Cy5 FRET pair were directly measured using time-tagged single-photon counting and scanning confocal microscopy. A modified maximum likelihood estimator (MLE) was developed to compensate for localized background fluorescence and instrument response. With this algorithm, we were able to robustly extract fluorescent lifetimes from their respective decays with as few as 20 photons. Fluorescent lifetimes extracted using an MLE were found to be highly dependent on background fluorescence. We show that appropriate factors are required to extract true lifetime trajectories from single fluorophores.     

Cobalt-catalyzed intramolecular C-H amination with arylsulfonyl azides

Cobalt complexes of porphyrins are effective catalysts for intramolecular C-H amination with arylsulfonyl azides. The cobalt-catalyzed process can proceed efficiently under mild and neutral conditions in low catalyst loading without the need of other reagents or additives, generating nitrogen gas as the only byproduct. The catalytic system can be applied to primary, secondary, and tertiary C-H bonds and is suitable for a broad range of arylsulfonyl azides, leading to high-yielding syntheses of various benzosultams.     

De novo formal synthesis of (-)-virginiamycin M2 via the asymmetric hydration of dienoates

A de novo approach to the formal total synthesis of the macrolide natural product (-)-virginiamycin M2 has been achieved via a convergent approach. The absolute and relative stereochemistry of the nonpeptide portion of (-)-virginiamycin M2 was introduced by two Sharpless asymmetric dihydroxylation reactions.     

Characterization of self-assembled monolayers from lithium dialkyldithiocarbamate salts

We report the formation of self-assembled monolayers (SAMs) onto gold substrates by exposure to lithium dialkyldithiocarbamate salts [(Li+(R2DTC-), where R = n-propyl, n-butyl, n-octyl, n-decyl, n-dodecyl, or n-octadecyl] in ethanol or methylene chloride. The crystallinity and composition of the monolayers were assessed by polarized modulation infrared reflection absorption spectroscopy (PM-IRRAS), wettability was characterized by contact angles of water and hexadecane, thickness was measured by spectroscopic ellipsometry, and barrier properties determined by electrochemical impedance spectroscopy. While the shorter R2DTC-s formed monolayers with liquid-like packing, monolayers prepared from the longest R2DTC- (where R = n-octadecyl) exhibit similar thickness, crystallinity, wettability, and capacitance as monolayers prepared from n-octadecanethiol. The hydrocarbon chains within the monolayers prepared from (C18)2DTC- are less canted on average than those prepared from n-octadecanethiol. Nonetheless, the (C18)2DTC- SAM exhibits an order of magnitude lower resistance against the penetration of redox probes, which is attributed to a higher density of pinhole defect sites.     

Structural characterization of 4-bromostyrene self-assembled monolayers on si(111)

Organic functionalization of silicon holds promise for a variety of applications ranging from molecular electronics to biosensing. Because the performance and reliability of organosilicon devices will be intimately tied to the detailed structure of the organic adlayers, it is imperative to develop systematic strategies for forming and characterizing self-assembled monolayers (SAMs) on silicon with submolecular spatial resolution. In this study, we use 4-bromostyrene for the photochemical growth of Br-terminated SAMs on Si(111). A variety of experimental and theoretical techniques including atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), X-ray reflectivity (XRR), X-ray standing waves (XSW), X-ray fluorescence (XRF), and density functional theory (DFT) have been employed to determine the coverage and conformation of the 4-bromostryene molecules within the SAM. In particular, AFM verifies a continuous and atomically flat SAM, and the XRR data indicate a SAM thickness of 8.50 A and a molecular coverage of 46% of the surface silicon atoms. Because the DFT calculations indicate a molecular length of 8.89 A, the measured XRR thickness implies a molecular tilt angle of approximately 17 degrees. The XRR analysis also suggests that the Br atoms are preserved on top of the SAM in agreement with XPS measurements that show bromine bound solely to carbon and not to silicon. XRF reveals a Br atomic coverage of 50%, again in close agreement to that found by XRR. Single-crystal Bragg diffraction XSW is used to generate a three-dimensional map of the Br distribution within the SAM, which in conjunction with the XRR result suggests that the 4-bromostyrene molecules are tilted such that the Br atoms are located over the T4 sites at a height of 8.50 A above the top bulklike Si(111) layer. The direction of molecular tilt toward the T4 sites is consistent with that predicted by the DFT calculation. Overall, through this unique suite of complementary structural characterization techniques, it is concluded that the Br functional handle is preserved at the top of the SAM and is available for further substitutional chemistry.