Programmable oligomers for minor groove DNA recognition

The four Watson-Crick base pairs of DNA can be distinguished in the minor groove by pairing side-by-side three five-membered aromatic carboxamides, imidazole (Im), pyrrole (Py), and hydroxypyrrole (Hp), four different ways. On the basis of the paradigm of unsymmetrical paired edges of aromatic rings for minor groove recognition, a second generation set of heterocycle pairs, imidazopyridine/pyrrole (Ip/Py) and hydroxybenzimidazole/pyrrole (Hz/Py), revealed that recognition elements not based on analogues of distamycin could be realized. A new set of end-cap heterocycle dimers, oxazole-hydroxybenzimidazole (No-Hz) and chlorothiophene-hydroxybenzimidazole (Ct-Hz), paired with Py-Py are shown to bind contiguous base pairs of DNA in the minor groove, specifically 5'-GT-3' and 5'-TT-3', with high affinity and selectivity. Utilizing this technology, we have developed a new class of oligomers for sequence-specific DNA minor groove recognition no longer based on the N-methyl pyrrole carboxamides of distamycin.     

Photophysical properties of ruthenium(II) tris(2,2'-bipyridine) complexes bearing conjugated thiophene appendages

A small series of ruthenium(II) tris(2,2'-bipyridine) complexes has been synthesized in which ethynylated thiophene residues are attached to one of the 2,2'-bipyridine ligands. The photophysical properties depend on the conjugation length of the thiophene-based ligand, and in each case, dual emission is observed. The two emitting states reside in thermal equilibrium at ambient temperature and can be resolved by emission spectral curve-fitting routines. This allows the properties of the two states to be evaluated in both fluid butyronitrile solution and a transparent KBr disk. It is concluded that both emitting states are of metal-to-ligand charge-transfer (MLCT) character, and despite the presence of conjugated thiophene residues, there is no indication for a low-lying pi,pi*-triplet state that promotes nonradiative decay of the excited-state manifold. A key feature of these systems is that the conjugation length imposed by the thiophene-based ligand helps to control the rate constants for both radiative and nonradiative decay from the two MLCT triplet states.     

Laser-driven shock experiments on precompressed water: Implications for "icy" giant planets

Laser-driven shock compression of samples precompressed to 1 GPa produces high-pressure-temperature conditions inducing two significant changes in the optical properties of water: the onset of opacity followed by enhanced reflectivity in the initially transparent water. The onset of reflectivity at infrared wavelengths can be interpreted as a semiconductor<-->electronic conductor transition in water, and is found at pressures above approximately 130 GPa for single-shocked samples precompressed to 1 GPa. Our results indicate that conductivity in the deep interior of "icy" giant planets is greater than realized previously because of an additional contribution from electrons.     

Characterization of self-assembled supramolecular [Ga4L6] host-guest complexes by electrospray ionization mass spectrometry

Self-assembled supramolecular host-guest complexes have been characterized by electrospray ionization mass spectrometry. The spectra obtained by use of a Q-TOF instrument equipped with a Z-spray ion source show primarily the 3- and 4- charge states of the assemblies. The assemblies have the general formula [guest subset Ga4L6]11- where L represents the chelating bidentate catechol ligand 1,5-bis(2',3'-dihydroxy-benzamido)naphthalene and guests are tetramethyl ammonium (Me4N+), tetraethyl ammonium (Et4N+), tetra-n-propyl ammonium (Pr4N+) and decamethylcobaltocenium (Cp*2Co+) cations. For the first time, the mass spectrum of the empty assembly [Ga4L6]12- is reported. This article also reports that provided the electrospray ion source is capable of preserving noncovalent interactions, it is possible to observe host-guest complexes containing both weak binding guests as well as sterically demanding guests in the mass spectra. The present data suggest that electrospray mass spectrometry is a powerful tool for characterization of supramolecular host-guest complexes.     

A priori resolution of the intermediate spectra in the bacteriorhodopsin photocycle: the time evolution of the L spectrum revealed

Resolution of the spectra of the intermediates in the photocycle of wild-type bacteriorhodopsin (BR) was achieved by singular value decomposition with exponential-fit-assisted self-modeling (SVD-EFASM) treatment of multichannel difference spectra measured at 5 degrees C during the course of the photocycle. New is the finding that two spectrally distinct L intermediates, L(1) and L(2), form sequentially. Our conclusion is that the photocycle is more complex than most published schemes. The dissection of the spectrally different L forms eliminates stoichiometric discrepancies usually appearing as systematically varying total intermediate concentrations before the onset of BR recovery. In addition, our analysis reveals that the red tails in the spectra of K and L(1) are more substantial than those of L(2) and BR. We suggest that these subtle differences in the shapes of the spectra reflect torsional and/or environmental differences in the retinyl chromophore.     

A bidentate terephthalamide ligand, TAMmeg, as an entry into terephthalamide-containing therapeutic iron chelating agents

A new bidentate 2,3-dihydroxyterephthalamide ligand, 2,3-dihydroxy-N,N'-bis(2-methoxyethyl)terephthalamide (TAMmeg), has been prepared. The ligand, its synthetic precursor 2,3-bis(benzyloxy)-N,N'-bis(2-methoxy-ethyl)-terephthalamide (BnTAMmeg), and its iron complex have been structurally characterized by X-ray diffraction. BnTAMmeg crystallizes in the monoclinic space group P2(1)/n with cell parameters a = 14.4976(14) A, b = 11.5569(11) A, c = 16.3905(16) A, beta = 113.621(1) degrees , and Z = 4. TAMmeg crystallizes in the monoclinic space group P2(1)/c with cell parameters a = 13.8060(36) A, b = 8.0049(21) A, c = 19.4346(50) A, beta = 106.855(4) degrees , and Z = 4. Fe[TAMmeg] crystallizes in the triclinic space group P with cell parameters a = 12.9565(14) A, b = 13.4514(14) A, c = 20.2092(21) A, alpha = 102.093(2) degrees , beta = 95.433(2) degrees , gamma = 101.532(2) degrees , and Z = 2. The aqueous protonation and ferric ion coordination chemistry of TAMmeg were examined using potentiometric and spectrophotometric methods. Proton association constants and iron complex formation constants for the ligand are as follows: log beta(011) = 10.32, log beta(012) = 16.49, log beta(110) = 17.9, log beta(120) = 32.1, and log beta(130) = 43.0. The ferric complex of TAMmeg is surprisingly stable for a bidentate terephthalamide iron complex. The only more-stable bidentate terephthalamide iron complex that has been reported contains a ligand with positively charged pendant arms.     

Synthesis of a naphthyridone p38 MAP kinase inhibitor

Compound 1 is a p38 MAP kinase inhibitor potentially useful for the treatment of rheumatoid arthritis and psoriasis. A novel six-step synthesis suitable for large-scale preparation was developed in support of a drug development program at Merck Research Laboratories. The key steps include a tandem Heck-lactamization, N-oxidation, and a highly chemoselective Grignard addition of 4-(N-tert-butylpiperidinyl)magnesium chloride to a naphthyridone N-oxide. The N-oxide exerted complete chemoselectivity via chelation in directing the Grignard addition to the alpha position as opposed to 1,4-addition on the ene-lactam. The dihydropyridyl adduct was in situ aromatized with isobutylchloroformate followed by heating in pyridine. Syntheses of Grignard precursor, N-tert-butyl-4-chloro-piperidine, were accomplished via transamination with a quaternary ammonium piperidone or via addition of methylmagnesium chloride to an iminium ion. Utilizing this chemistry, multi-kilogram preparation of compound 1 was successfully demonstrated.     

NMR method for the determination of solute hydrogen bond acidity

It is shown that the difference in the 1H NMR chemical shift of a protic hydrogen in DMSO and CDCl3 solvents is directly related to the overall, or summation, hydrogen bond acidity for a wide range of solutes. This provides a new and direct method of measuring the hydrogen bond acidity. For 54 compounds, the observed shifts for 72 protic hydrogens could be correlated to the Abraham solute hydrogen bond acidity parameter, A, with a correlation coefficient squared, R2, of 0.938 and a standard deviation, SD, of 0.054 units in A. A training equation that used half the data could predict A values for the remaining data with an average error of 0.001 and a standard deviation, SD, of 0.053 units, thus demonstrating the predictive power of the method. Unlike any previous method for the determination of solute hydrogen bond acidities, the NMR method allows the determination of A values for individual protic hydrogens in multifunctional solutes.     

Band-edge-induced Bragg diffraction in two-dimensional photonic crystals

Two-dimensional photonic crystals composed of two orthogonal volume diffraction gratings have been photogenerated in photopolymers. When the read beam is set at the Bragg angle, the diffraction efficiency of the transmission grating is strongly enhanced at the band edge of the reflection grating recorded in the material. Such a device provides Bragg operation and enhancement of the diffraction efficiency of the thin diffraction grating together with good wavelength selectivity. Such advantages could be interesting for optical signal processing.     

Parameter estimation of an asymmetric vocal-fold system from glottal area time series using chaos synchronization

In this paper, we apply an iterative parameter adaption scheme based on chaos synchronization to estimate system parameters of the asymmetric vocal folds from glottal area time series. The original asymmetric vocal-fold system associated with recurrent laryngeal paralysis shows chaotic vibrations with positive Lyapunov exponents. Aperiodic glottal area time series from the original system will be applied as the feedback variable coupling the simulative and the original vocal-fold systems. The parameter adaption technique based on chaos synchronization is employed to manipulate the simulative system parameters. The chaotic vibrations, system parameters, and the bifurcation diagram of the original vocal-fold system can be exactly reproduced in the simulative system, and the two chaotic systems can be synchronized. Furthermore, the effects of noise, sampling rate, and equation difference due to nonlinear spring terms on vocal-fold parameter estimations are investigated. Despite large noise perturbations, large equation differences, and low sampling rate, the parameter adaption scheme can effectively estimate the original vocal-fold system parameters. This study provides a theoretical base to apply chaos synchronization to estimate the vocal-fold system parameters from the glottal area data and show its potential application in laryngeal physiology.