Freedom and trying: Understanding agent-causal exertions

In this paper, I argue that trying is the locus of freedom and moral responsibility. Thus, any plausible view of free and responsible action must accommodate and account for free tryings. I then consider a version of agent causation whereby the agent directly causes her tryings. On this view, the agent is afforded direct control over her efforts and there is no need to posit—as other agent-causal theorists do—an uncaused event. I discuss the potential advantages of this sort of view, and its challenges.     

Charge-mediated recognition of N-terminal tryptophan in aqueous solution by a synthetic host

The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8.MV with (i) the four natural aromatic alpha-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV-visible, fluorescence, and (1)H NMR spectroscopy. We find that Q8.MV binds Trp-Gly-Gly with high affinity (K(a) = 1.3 x 10(5) M(-1)), with 6-fold specificity over Gly-Trp-Gly, and with 40-fold specificity over Gly-Gly-Trp. Analysis of the nine indole-containing compounds suggests that peptide recognition is mediated by the electrostatic charge(s) proximal to the indole, and that the mode of binding is consistent for these compounds. Complex formation is accompanied by the growth of a visible charge-transfer band and the quenching of indole fluorescence. These optical properties, combined with the stability and selectivity of this system, are promising for applications in sensing and separating specific peptides.     

Imaged deconvolution: a method for extracting high-resolution NMR spectra from inhomogeneous fields

We present a novel method for obtaining high resolution NMR spectra in the presence of grossly inhomogeneous magnetic fields, such as those encountered in one-sided access NMR. Our method combines the well-known principle of reference deconvolution with NMR imaging in order to resolve spectral features with frequency resolution orders of magnitude smaller than the prevailing line-broadening due to field inhomogeneity. We demonstrate that, in cases of inhomogeneous field line-broadening more than an order of magnitude larger than the spectral features to be resolved, rather than performing reference deconvolution on the sample as a whole, it is more favourable in terms of SNR to divide the target region of a sample into smaller sub-regions, by means of chemical shift imaging, and then to perform reference deconvolution on the individual sub-region spectra, finally summing the results In this way, significant resolution enhancements can be obtained in the presence of severe magnetic field inhomogeneity without an unacceptable loss in SNR.     

Effect of pharmaceuticals on thermoreversible gelation of PEO-PPO-PEO copolymers

Pluronic F127, a triblock copolymer of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), has generated considerable interest as a drug delivery vehicle due to its ability to gel at physiological temperatures. This work examines the gelation behavior of Pluronic F127 in the presence of a series of hydrophobic pharmaceuticals, to determine whether there is any correlation between gelation and physicochemical parameters of drug solutes. The study includes the local anesthetics dibucaine, lidocaine, and tetracaine; the pharmaceutical additives methyl paraben, ethyl paraben, and propyl paraben; the anti-cancer agents paclitaxel and baccatin III; and the anti-inflammatory agent sulindac. The results indicate that the presence of local anesthetics and pharmaceutical additives allows F127 solutions to form gels at lower copolymer concentrations; local anesthetics and pharmaceutical additives also shift gelation down to a lower gelation temperature. This behavior is strongly dependent on drug solubility; poorly soluble drugs (paclitaxel, baccatin III, sulindac) do not change the lower gelation temperature or minimum F127 concentration for gelation. An equation relating the decrease in gelation temperature to drug solubility is presented, and the equation fits the data well. The results have significant positive implications on the toxicity and economic issues related to use of Pluronic F127 in drug delivery.     

Computational studies of the cone and 1,2,3 alternate calix[6]arene bis‐crown‐4 isomers: structures,NMR shifts,atomic charges,and steric compression

The cone and 1,2,3 alternate isomers of calix[6]arene bis‐crown‐4 were investigated computationally. Structural optimizations, energies, bond distances, and Mulliken charges were calculated by the application of the B3LYP/6‐31g(d) method/basis, followed by NMR calculations via both B3LYP/6‐31g(d) and HF/6‐31g(d). Calculations were completed at three different levels of imposed symmetry, and two calculations investigated the chloroform solvent effects. Better NMR results were obtained from HF/6‐31g(d) calculations that did not impose molecular symmetry constraints. Consideration of solvent effects improved ground state energies, but other improvements were minimal and not significant enough to justify the added computational expense of solvent calculations. Overall results are consistent with known experimental assignments and were valuable for assigning previously unknown NMR peaks. Net charges, electrostatic forces, and local dipoles – but not bond lengths – are strongly correlated to spectroscopic manifestations of steric compression. Copyright © 2009 John Wiley & Sons, Ltd.     

Substrate electric dipole moment exerts a pH-dependent effect on electron transfer in Escherichia coli photolyase

Transient absorption spectroscopy is used to demonstrate that the electric dipole moment of the substrate cyclobutane thymine dimer affects the charge recombination reaction between fully reduced flavin adenine dinucleotide (FADH-) and the neutral radical tryptophan 306 (Trp306*) in Escherichia coli DNA photolyase. At pH 7.4, the charge recombination is slowed by a factor of 1.75 in the presence of substrate, but not at pH 5.4. Photolyase does bind substrate at pH 5.4, and it seems that this pH effect originates from the conversion of FADH- to FADH2 at lower pH. The free-energy changes calculated from the electric field parameters and from the change in electron transfer rate are in good agreement and support the idea that the substrate electric dipole is responsible for the observed change in electron transfer rate. It is expected that the substrate electric field will also modify the physiologically important from excited 1FADH- to the substrate in the DNA repair reaction.     

Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals

Oligonucleotide chemistry has been developed greatly over the past three decades, with many advances in increasing nuclease resistance, enhancing duplex stability and assisting with cellular uptake. Locked nucleic acid (LNA) is a structurally rigid modification that increases the binding affinity of a modified-oligonucleotide. In contrast, unlocked nucleic acid (UNA) is a highly flexible modification, which can be used to modulate duplex characteristics. In this tutorial review, we will compare the synthetic routes to both of these modifications, contrast the structural features, examine the hybridization properties of LNA and UNA modified duplexes, and discuss how they have been applied within biotechnology and drug research. LNA has found widespread use in antisense oligonucleotide technology, where it can stabilize interactions with target RNA and protect from cellular nucleases. The newly emerging field of siRNAs has made use of LNA and, recently, also UNA. These modifications are able to increase double-stranded RNA stability in serum and decrease off-target effects seen with conventional siRNAs. LNA and UNA are also emerging as versatile modifications for aptamers. Their application to known aptamer structures has opened up the possibility of future selection of LNA-modified aptamers. Each of these oligonucleotide technologies has the potential to become a new type of therapy to treat a wide variety of diseases, and LNA and UNA will no doubt play a part in future developments of therapeutic and diagnostic oligonucleotides.     

Chemical behavior of electrochemically generated nanostructured silver surfaces

A simple electrochemical method has been proposed for the preparation of silver nanoparticles that can be used for the detection of cyanide. Both the electrochemical behavior and morphology of the Ag nanoparticles have been characterized in the presence of KCN or diethyl cyanophosphonate (DECP) as well as in alkaline media. These were investigated by cyclic voltammetry and scanning electron microscopy (SEM). DECP is a simulant of the chemical warfare agent tabun.     

Do hydroxyl radical-water clusters, OH(H2O)n, n = 1-5, exist in the atmosphere?

It has been speculated that the presence of OH(H2O)n clusters in the troposphere could have significant effects on the solar absorption balance and the reactivity of the hydroxyl radical. We have used the G3 and G3B3 model chemistries to model the structures and predict the frequencies of hydroxyl radical/water clusters containing one to five water molecules. The reaction between hydroxyl radical clusters and methane was examined as a function of water cluster size to gain an understanding of how cluster size affects the hydroxyl radical reactivity.