Improving spatiotemporal resolution of USPIO-enhanced dynamic imaging of rat kidneys

This paper addresses the problem of enhancing spatiotemporal resolution of ultra-small superparamagnetic iron oxide (USPIO)-enhanced dynamic MRI of rat kidneys. To alleviate the limited resolution problem of conventional full-scan Fourier imaging methods, we use a generalized series-based imaging scheme to reduce coverage of kappa-space. Experimental results demonstrate that the generalized series imaging method with basis functions constructed using two references (pre- and post-contrast) can reduce the number of phase encodings measured during the dynamic contrast wash-in process by a factor of 4 with a negligible or minimal loss of image quality. The method is expected to make 3D studies possible using USPIO-enhanced dynamic imaging of rat kidneys, and prove valuable for early detection of renal rejection after kidney transplantation.     

Amide-based nonheme cobalt(III) olefin epoxidation catalyst: partition of multiple active oxidants Co(V)=O, Co(IV)=O, and Co(III)-OO(O)CR

A mononuclear nonheme cobalt(III) complex of a tetradentate ligand containing two deprotonated amide moieties, [Co(bpc)Cl(2)][Et(4)N] (1; H(2)bpc = 4,5-dichloro-1,2-bis(2-pyridine-2-carboxamido)benzene), was prepared and then characterized by elemental analysis, IR, UV/Vis, and EPR spectroscopy, and X-ray crystallography. This nonheme Co(III) complex catalyzes olefin epoxidation upon treatment with meta-chloroperbenzoic acid. It is proposed that complex 1 shows partitioning between the heterolytic and homolytic cleavage of an O-O bond to afford Co(V)=O (3) and Co(IV)=O (4) intermediates, proposed to be responsible for the stereospecific olefin epoxidation and radical-type oxidations, respectively. Moreover, under extreme conditions, in which the concentration of an active substrate is very high, the Co-OOC(O)R (2) species is a possible reactive species for epoxidation. Furthermore, partitioning between heterolysis and homolysis of the O-O bond of the intermediate 2 might be very sensitive to the nature of the solvent, and the O-O bond of the Co-OOC(O)R species might proceed predominantly by heterolytic cleavage, even in the presence of small amounts of protic solvent, to produce a discrete Co(V) ?O intermediate as the dominant reactive species. Evidence for these multiple active oxidants was derived from product analysis, the use of peroxyphenylacetic acid as the peracid, and EPR measurements. The results suggest that a less accessible Co(V)=O moiety can form in a system in which the supporting chelate ligand comprises a mixture of neutral and anionic nitrogen donors.     

The role of pendant amines in the breaking and forming of molecular hydrogen catalyzed by nickel complexes

We present the results of a comprehensive theoretical investigation of the role of pendant amine ligands in the oxidation of H(2) and formation of H(2) by [Ni(P(R)(2)N(R')(2))(2)](2+) electrocatalysts (P(R)(2)N(R')(2) is the 1,5-R'-3,7-R derivative of 1,5-diaza-3,7-diphosphacyclooctane, in which R and R' are aryl or alkyl groups). We focus our analysis on the thermal steps of the catalytic cycle, as they are known to be rate-determining for both H(2) oxidation and production. We find that the presence of pendant amine functional groups greatly facilitates the heterolytic H(2) bond cleavage, resulting in a protonated amine and a Ni hydride. Only one single positioned pendant amine is required to serve this function. The pendant amine can also effectively shuttle protons to the active site, making the redistribution of protons and the H(2) evolution a very facile process. An important requirement for the overall catalytic process is the positioning of at least one amine in close proximity to the metal center. Indeed, only protonation of the pendant amines on the metal center side (endo position) leads to catalytically active intermediates, whereas protonation on the opposite side of the metal center (exo position) leads to a variety of isomers, which are detrimental to catalysis.     

Gold-catalyzed hydrosilyloxylation driving tandem aldol and mannich reactions

The chemoselective formation of an enolate from alkyne in the presence of a carbonyl and imine group was realized, which constructed a variety of structural motifs under exceedingly mild reaction conditions in a tandem process. Reaction driving tandem hydrosilyloxylation/aldol reactions was achieved through the formation of enol silyl ethers catalytically generated in situ from readily available alkynes. These reactions were expanded to obtain β-amino enol silyl ethers in good yields via the tandem hydrosilyloxylation/isomerization/Mannich reaction.     

The regioselective switch for amino-NHC mediated C-H activation of benzimidazole via Ni-Al synergistic catalysis

We have disclosed a new mode of a chemically regioselective switch for C-H bond functionalization of benzimidazole derivatives via a cooperative effect invoked by Ni-Al bimetallic catalysis to create a steric requirement for obtaining the linear product of styrene insertion. Yet, excluding the AlMe(3) cocatalyst switches the reaction toward branch selectivity.     

Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery

Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.     

Enhanced refolding of lysozyme with imidazolium-based room temperature ionic liquids: Effect of hydrophobicity and sulfur residue

The expression of recombinant proteins in microorganism frequently leads to the formation of insoluble aggregates, inclusion bodies (IBs). Thus, the additional in vitro protein refolding process is required to convert inactive IBs into water-soluble active proteins. This study investigated the effect of sulfur residue and hydrophobicity of imidazolium-based room temperature ionic liquids (RTILs) on the refolding of lysozyme as a model protein in the batch dilution method which is the most commonly used refolding method. When lysozyme was refolded in the refolding buffer containing [BF4]-based RTILs with a systematic variety of alkyl chain on cations varying from two to eight, less hydrophobic imidazolium cations having shorter alkyl chains were effective to facilitate lysozyme refolding. Compared to the conventional refolding buffer, 2 times higher lysozyme refolding yield was obtained in 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIM][BF4]) containing refolding buffer. The refolding yield of lysozyme was even more increased by 2.5 times when 1-butyl-3-methylimidazolium methylsulfate ([BMIM][MS]) containing sulfur residue on anion was used. The sulfur residue in [BMIM][MS] is supposed to improve the refolding yield of lysozyme which has 4 intramolecular disulfide bonds. For dilution-based refolding of lysozyme, the optimum concentrations of RTILs in refolding buffer were found to be 1.0 M [EMIM][BF4] and 0.5 M [BMIM][MS], respectively. The optimum temperate for dilution-based refolding of lysozyme with RTILs was 4 °C.     

Reversible interpenetration in a metal-organic framework triggered by ligand removal and addition

Caging cages: Crystals of a metal-organic framework, MOF-123 [Zn(7) O(2) (NBD)(5) (DMF)(2) ] have a three-dimensional porous structure in which DMF ligands (see picture, pink) protrude into small channels. Removal of these ligands triggers the transformation of this MOF to the doubly interpenetrating form, MOF-246 [Zn(7) O(2) (NBD)(5) ]. Moreover, addition of DMF into MOF-246 triggers reverse transformation to give MOF-123. NBD=2-nitrobenzene-1,4-dicarboxylate.     

Folding and thermodynamic studies of Trp-cage based on polarized force field

Two replica exchange molecular dynamics (REMD) simulations were carried out to study the thermodynamics of a 20-residue Trp-cage folding based on a newly developed polarized protein-specific charge (PPC). Starting from a fully extended conformation, Trp-cage native conformation was successfully sampled using REMD based on a 3-step PPC update. Next, the obtained Trp-cage folded conformation was then used to calculate the PPC in which another REMD was performed to explore the thermodynamic stability of Trp-cage. The theoretical melting temperature T _m of ≈325 K was found to be in close agreement with experimental melting temperature, T _m of 315 K. This indicates that the PPC was correctly predicting the temperature dependence. The current study provides a direct proof of how electrostatic polarization affects protein folding.