Coherent and incoherent orientation and alignment of ICN photoproducts

We report extended measurements of the rotational polarization and correlated angular distribution of CN photofragments from ICN photodissociation, with a particular emphasis on the creation and detection of molecular orientation with circularly-polarized light. Doppler profiles of the nascent photoproducts are measured by Frequency-Modulated (FM) transient absorption, and the resulting high signal-to-noise data are valuable for verifying the form of the angular correlations between the recoil velocity, the photofragment rotational angular momentum, and the space-fixed frame defined by the dissociation polarization. A space-fixed bipolar moment notation can be used for an unambiguous characterization of the maximal set of polarization properties that can be created with one-photon excitation and detected with one-photon Doppler-resolved absorption spectroscopy. Relating the observed polarization moments to the various coherent and incoherent, adiabatic and non-adiabatic mechanisms, that have been derived and verified extensively in the case of diatomic photodissociation to polarized atomic fragments, is not unambiguous in the case of diatomic fragments from triatomic precursors. Constraints among various polarization moments confirmed in the case of diatomic dissociation are not confirmed in this triatomic case, where the perpendicular transitions to non-degenerate A' and A' components of a linear Omega = 1 state are qualitatively different from excitation to degenerate Omega = +/-1 states in a diatomic molecule.     

Improved synthesis of O-linked, and first synthesis of S- linked, carbohydrate functionalised N-carboxyanhydrides (glycoNCAs)

An improved method for the synthesis of glycosylated N-carboxyanhydrides, which are monomers for glycopeptide synthesis, is presented.     

Self-assembly of chemically linked rod-disc mesogenic liquid crystals

A series of new molecular discs (RDn, here n is the number of carbon atoms between the rod and disc mesogens) was synthesized via the chemical attachment of six cyanobiphenyl calamitic (rod) mesogens (R) linked to the triphenyl discotic (disc) mesogen (D) with a series of six alkyl chain linkages (n = 6-12). In this study, phase structures, transitions, and liquid crystalline (LC) behavior of the RD12 compound with 12 carbon atoms in each alkyl chain linkage between the rod and disc mesogens were investigated. Differential scanning calorimetry, polarized light microscopy, wide-angle X-ray diffraction (WAXD), and selected area electron diffraction (SAED) allowed us to identify three ordered phases below the isotropization temperature: nematic (N) LC and K1 and K2 crystalline phases. On the basis of the structural results obtained via 2D WAXD experiments on oriented samples and SAED experiments on single crystals, the K1 crystalline unit cell was determined to be triclinic with the dimensions of a = 1.36 nm, b = 1.45 nm, c = 2.11 nm, alpha = 85 degrees, beta = 100 degrees, and gamma = 50 degrees. The K2 phase was metastable with respect to the K1 phase. It also possessed a triclinic unit cell with a = 1.40 nm, b = 1.51 nm, c = 1.92 nm, alpha = 87 degrees, beta = 117 degrees, and gamma = 62 degrees. Molecular packing models for the crystalline phases were proposed on the basis of the diffraction results. In the whole range of ordered structures, it was found that RD12 molecular discs are intercalated. Both triphenyl discotic mesogens and cyanobiphenyl calamitic mesogens are completely interdigitated.     

Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA

The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.     

An ultrafast study of phenyl azide: the direct observation of phenylnitrenium ion

Ultrafast photolysis (lambda(ex) = 308 nm) of phenyl azide in 100% formic acid produces a broadly absorbing transient within the instrument time resolution (300 fs), which is assigned to an excited state of the azide. The azide excited state fragments within 300 fs to form singlet phenylnitrene. The decay of the nitrene (tau = 12.0 ps) produces a new species with absorption centered at 500 nm, which is assigned to phenylnitrenium ion. The lifetime of phenylnitrenium ion is 110 ps in 100% formic acid. This is the first spectroscopic observation of phenylnitrenium ion.     

Total synthesis of isoprekinamycin: structural evidence for enhanced diazonium ion character and growth inhibitory activity toward cancer cells

The structurally novel diazobenzo[a]fluorene antibiotic isoprekinamycin (IPK) has been synthesized for the first time employing a Suzuki coupling of a brominated AB ring synthon with a boronate ester representing the D ring, followed by anionic cyclization and appropriate functional group manipulations. The first indication that the diazobenzo[a]fluorene system exhibits in vitro anticancer activity is provided and X-ray crystallographic evidence for enhancement of diazonium ion character as a consequence of intramolecular H-bonding is described.     

A concise synthesis of quinazolinone TGF-β RI inhibitor through one-pot three-component Suzuki-Miyaura/etherification and imidate-amide rearrangement reactions

A simple and efficient synthesis of dihydropyrrolopyrazole boronic acid intermediate (5) has been developed. Utilization of a three-component Suzuki-Miyaura/etherification with microwave heating led to advanced compound 11 in high yield and with easy purification. Reaction of compound 11 with methanesulfonyl chloride at room temperature furnished the 1,3 O-N rearranged product (12), which is postulated to proceed via an intramolecular mechanism. The outlined synthesis provides a highly efficient and high-yielding route that is amenable to rapid analog synthesis.     

Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: evaluation of simulation parameters

We have explored the impact of a number of basic simulation parameters on the results of a recently developed hybrid molecular dynamics-quantum mechanics (MD-QM) method (Mercer et al., J Phys Chem B 1999, 103, 7720). The method utilizes MD simulations to explore the ground-state configuration space of the system and QM evaluation of those structures to yield the time-dependent electronic transition energy, which is transformed into the optical line-broadening function using the second-order cumulant expansion. Both linear and nonlinear optical spectra can then be generated for comparison to experiment. The dependence of the resulting spectra on the length of the MD trajectory, the QM sampling rate, and the QM model chemistry have all been examined. In particular, for the system of oxazine-4 in methanol studied here, at least 20 ps of MD trajectory are needed for qualitative convergence of linear spectral properties, and >100 ps is needed for quantitative convergence. Surprisingly, little difference is found between the 3-21G and 6-31G(d) basis sets, and the CIS and TD-B3LYP methods yield remarkably similar spectra. The semiempirical INDO/s method yields the most accurate results, reproducing the experimental Stokes shift to within 5% and the FWHM to within 20%. Nonlinear 3-pulse photon echo peak shift (3PEPS) decays have also been simulated. Decays are generally poorly reproduced, though the initial peak shift which depends on the overall coupling of motions to the solute transition energy is within 15% of experiment for all model chemistries other than those using the STO-3G basis.