Excited-state characters and dynamics of [W(CO)(5)(4-cyanopyridine)] and [W(CO)(5)(piperidine)] studied by picosecond time-resolved IR and resonance Raman spectroscopy and DFT calculations: roles of W --> L and W --> CO MLCT and LF excited states revised

The characters, dynamics, and relaxation pathways of low-lying excited states of the complexes [W(CO)(5)L] [L = 4-cyanopyridine (pyCN) and piperidine (pip)] were investigated using theoretical and spectroscopic methods. DFT calculations revealed the delocalized character of chemically and spectroscopicaly relevant molecular orbitals and the presence of a low-lying manifold of CO pi-based unoccupied molecular orbitals. Traditional ligand-field arguments are not applicable. The lowest excited states of [W(CO)(5)(pyCN)] are W --> pyCN MLCT in character. They are closely followed in energy by W --> CO MLCT states. Excitation at 400 or 500 nm populates the (3)MLCT(pyCN) excited state, which was characterized by picosecond time-resolved IR and resonance Raman spectroscopy. Excited-state vibrations were assigned using DFT calculations. The (3)MLCT(pyCN) excited state is initially formed highly excited in low-frequency vibrations which cool with time constants between 1 and 20 ps, depending on the excitation wavelength, solvent, and particular high-frequency nu(CO) or nu(CN) mode. The lowest excited states of [W(CO)(5)(pip)] are W --> CO MLCT, as revealed by TD-DFT interpretation of a nanosecond time-resolved IR spectrum that was measured earlier in a low-temperature glass (Johnson, F. P. A.; George, M. W.; Morrison, S. L.; Turner, J. J. J. Chem. Soc., Chem. Commun. 1995, 391-393). MLCT(CO) excitation involves transfer of electron density from the W atom and, to a lesser extent, the trans CO to the pi orbitals of the four cis CO ligands. Optical excitation into MLCT(CO) transition of either complex in fluid solution triggers femtosecond dissociation of a W-N bond, producing [W(CO)(5)(solvent)]. It is initially vibrationally excited both in nu(CO) and anharmonicaly coupled low-frequency modes. Vibrational cooling occurs with time constants of 16-22 ps while the intramolecular vibrational energy redistribution from the v = 1 nu(CO) modes is much slower, 160-220 ps. No LF excited states have been found for the complexes studied in a spectroscopically relevant range up to 6-7 eV. It follows that spectroscopy, photophysics, and photochemistry of [W(CO)(5)L] and related complexes are well described by an interplay of close-lying MLCT(L) and MLCT(CO) excited states. The high-lying LF states play only an indirect photochemical role by modifying potential energy curves of MLCT(CO) states, making them dissociative.     

End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

Bromination of 2,1,3-benzothiadiazoles

The bromination of 2,1,3-benzothiadiazoles in 47% hydrobromic acid at elevated temperature has led to a general preparative method for the synthesis in high yield of otherwise difficulty accessible brominated 2,1,3-benzothiadiazoles. The typical addition reaction is apparently eliminated under these reaction conditions and substitution takes place exclusively. Bromination of 2,1,3-benzothiadiazole occurs successively at positions 4 and 7. 4-Substituted 2,1,3-benzothia-diazoles are selectively brominated at position 7. 5-Bromo- and 5-methyl-2,1,3-benzothiadiazole are brominated consecutively at positions 4 and 7.     

DNA sequencing and genotyping in miniaturized electrophoresis systems

Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.     

Thermoresponsive N,N-dialkylacrylamide copolymer blends as DNA sieving matrices with a thermally tunable mesh size

In an earlier study we showed that a blend of thermoresponsive and nonthermoresponsive hydroxyalkylcelluloses could be used to create a thermally tunable polymer network for double-stranded (ds) DNA separation. Here, we show the generality of this approach using a family of polymers suited to a wider range of DNA separations: a blended mixture of N,N-dialkylacrylamide copolymers with different thermoresponsive behaviors. A mixture of 47% w/w N,N-diethylacrylamide (DEA)/53% w/w N,N-dimethylacrylamide (DMA) (DEA47; thermoresponsive, transition temperature = 55 degrees C in water) and 30% w/w DEA/70% w/w DMA (DEA30; nonthermoresponsive, transition temperature > 85 degrees C in water) copolymers in the ratio of 1:5 w/w DEA47:DEA30 was used to separate a dsDNA restriction digest (PhiX174-HaeIII). We investigated the effects of changing mesh size on dsDNA separation, as controlled by temperature. We observed good DNA separation performance with the copolymer blend at temperatures ranging from 25 degrees C to 48 degrees C. The separation selectivity was evaluated quantitatively for certain DNA fragment pairs as a function of temperature. The results were compared with those obtained with a control matrix consisting only of the nonthermoresponsive DEA30. Different DNA fragment pairs of various sizes show distinct temperature-dependent selectivities. Over the same temperature range, no significant temperature dependence of selectivity is observed for these DNA fragment pairs in the nonthermoresponsive control matrix. Overall, the results show similar trends in the temperature dependency of separation selectivity to what was previously observed in hydroxyalkylcellulose blends, for the same DNA fragment pairs. Finally, we showed that a ramped temperature scheme enables improved separation in the blended copolymer matrix for both small and large DNA fragments, simultaneously in a single capillary electrophoresis (CE) run.     

Universal quenching of common fluorescent probes by water and alcohols

Although biological imaging is mostly performed in aqueous media, it is hardly ever considered that water acts as a classic fluorescence quencher for organic fluorophores. By investigating the fluorescence properties of 42 common organic fluorophores recommended for biological labelling, we demonstrate that H₂O reduces their fluorescence quantum yield and lifetime by up to threefold and uncover the underlying fluorescence quenching mechanism. We show that the quenching efficiency is significantly larger for red-emitting probes and follows an energy gap law. The fluorescence quenching finds its origin in high-energy vibrations of the solvent (OH groups), as methanol and other linear alcohols are also found to quench the emission, whereas it is restored in deuterated solvents. Our observations are consistent with a mechanism by which the electronic excitation of the fluorophore is resonantly transferred to overtones and combination transitions of high-frequency vibrational stretching modes of the solvent through space and not through hydrogen bonds. Insight into this solvent-assisted quenching mechanism opens the door to the rational design of brighter fluorescent probes by offering a justification for protecting organic fluorophores from the solvent via encapsulation.

Overtones and combinations of O–H vibrations in the solvent efficiently quench red-emitting fluorophores by resonant energy transfer.     

Evaluation of molecule-microbe interactions with capillary electrophoresis: procedures, utility and restrictions

Understanding the interactions between molecules and living organisms is of paramount importance for the evaluation of pharmaceutical activity, chemical toxicity and all manner of microbiological studies. The capability of capillary electrophoresis (CE) in the evaluation of molecule-microbe interactions is examined in the present paper. The fundamental chemical concept of the binding or association constant for molecular systems measured in free solution is discussed for biological systems where microorganisms uptake or associate with molecules from their environment. The heterogeneity of the living organisms must be understood and accounted for including differences related to semantics such as concentration units and the nature of the associations between two entities and large differences in the size and number of microorganisms as compared to molecules. Finally, the added complexity and even inhomogeneity of a cell compared to most molecular systems must be considered and possibly controlled. The binding of specific molecules to viruses is discussed. CE can be utilized to quickly determine if a molecule binds very strongly or not at all to a cell (i.e., a binary yes/no answer). This could be useful for initial high-throughput screening purposes when using capillary arrays, for example. CE can be useful for determining unusual (large) molecule/microbe stoichiometries. Finally, CE can sometimes be used to determine the size of binding constants (K(RL)) within certain limits provided experimental conditions can be formulated that minimize problems of biological heterogeneity.