The series of complexes [XRu(CO)(L–L)(L′)2][PF6] (X = H, TFA, Cl; L–L = 2,2′-bipyridyl, 1,10-phenanthroline, 5-amino-1,10-phenanthroline and 4,4′-dicarboxylic-2,2′-bipyridyl; L′2 = 2PPh3, Ph2 PC2H4PPh2, Ph2PCH═CHPPh2) have been synthesized from the starting complex K[Ru(CO)3(TFA)3] (TFA = CF3CO2) by first reacting with the phosphine ligand, followed by reaction with the L–L and anion exchange with NaPF6. In the case of L–L = phenanthroline and L′2 = 2PPh3, the neutral complex Ru(Ph3P)(CO)(1,10-phenanthroline)( TFA)2 is also obtained and its solid state structure is reported. Solid state structures are also reported for the cationic complexes where L–L = phenanthroline, L2 = 2PPh3 and X = Cl and for L–L = 2,2′-bipyridyl, L2 = 2PPh3 and X = H. All the complexes were characterized in solution by a combination of 1H and 31P NMR, IR, mass spectrometry and elemental analyses. The purpose of the project was to synthesize a series of complexes that exhibit a range of excited-state lifetimes and that have large Stokes shifts, high quantum yields and high intrinsic polarizations associated with their metal-to-ligand charge-transfer (MLCT) emissions. To a large degree these goals have been realized in that excited-state lifetimes in the range of 100 ns to over 1 μs are observed. The lifetimes are sensitive to both solvent and the presence of oxygen. The measured quantum yields and intrinsic anisotropies are higher than for previously reported Ru(II) complexes. Interestingly, the neutral complex with one phosphine ligand shows no MLCT emission. Under the conditions of synthesis some of the initially formed complexes with X = TFA are converted to the corresponding hydrides or in the presence of chlorinated solvents to the corresponding chlorides, testifying to the lability of the TFA Ligand. The compounds show multiple reduction potentials which are chemically and electrochemically reversible in a few cases as examined by cyclic voltammetry. The relationships between the observed photophysical properties of the complexes and the nature of the ligands on the Ru(II) is discussed.

The commercial availability of inexpensive fiber optics and small volume pumps in the early 1990's provided the components necessary for the successful development of low power, low reagent consumption, autonomous optofluidic analyzers for marine applications. It was evident that to achieve calibration-free performance, reagent-based sensors would require frequent renewal of the reagent by pumping the reagent from an impermeable, inert reservoir to the sensing interface. Pumping also enabled measurement of a spectral blank further enhancing accuracy and stability. The first instrument that was developed based on this strategy, the Submersible Autonomous Moored Instrument for CO 2 (SAMI-CO 2 ), uses a pH indicator for measurement of the partial pressure of CO 2 (pCO 2 ). Because the pH indicator gives an optical response, the instrument requires an optofluidic design where the indicator is pumped into a gas permeable membrane and then to an optical cell for analysis. The pH indicator is periodically flushed from the optical cell by using a valve to switch from the pH indicator to a blank solution. Because of the small volume and low power light source, over 8,500 measurements can be obtained with a ∼500 mL reagent bag and 8 alkaline D-cell battery pack. The primary drawback is that the design is more complex compared to the single-ended electrode or optode that is envisioned as the ideal sensor. The SAMI technology has subsequently been used for the successful development of autonomous pH and total alkalinity analyzers. In this manuscript, we will discuss the pros and cons of the SAMI pCO 2 and pH optofluidic technology and highlight some past data sets and applications for studying the carbon cycle in aquatic ecosystems.

In the crystal structure of the complex between the soluble extracellular domain of tissue factor (sTF) and active-site-inhibited VIIa, residues 91 and 92 in the Pro(79)-Pro(92) loop of sTF interact with the catalytic domain of VIIa. It is not known, however, whether this loop has a role in allosteric activation of VIIa. Time-resolved fluorescence anisotropy measurements of probes covalently bound to sTF mutants E84C and T121C show that binding uninhibited Factor VIIa affects segmental motions in sTF. Glu(84) resides in the Pro(79)-Pro(92) loop, and Thr(121) resides in the turn between the first and second antiparallel beta-strands of the sTF subdomain that interacts with the Gla and EGF1 domains of VIIa; neither Glu(84) nor Thr(121) makes direct contact with VIIa. Probes bound to T121C report limited segmental flexibility in free sTF, which is lost after VIIa binding. Probes bound to E84C report substantial segmental flexibility in the Pro(79)-Pro(92) loop in free sTF, which is greatly reduced after VIIa binding. Thus, VIIa binding reduces dynamic motions in sTF. In particular, the decrease in the Pro(79)-Pro(92) loop motions indicates that loop entropy has a role in the thermodynamics of the protein-protein interactions involved in allosteric control of VIIa activation.

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236–39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences with differing flexibility have interactions with IHF that compensate for unfavorable deformation energy. Time-resolved Förster resonance energy transfer (FRET) shows that global topologies are indistinguishable for three complexes with oligonucleotides of different flexibility. However, pressure perturbation shows that the volume change upon binding is smaller with increasing flexibility. We interpret these results in the context of Record and coworker's model for IHF binding (J. Mol. Biol. 310, 379–401, 2001). We propose that the volume changes reflect differences in hydration that arise from structural variation at IHF–DNA interfaces while the resulting energetic compensation maintains the same net binding energy.