Generalised expressions for the association and dissociation rate constants of molecules with multiple binding sites

ABSTRACT

Many proteins exhibit multiple binding patches. A patch may harbour a key chemical modification site, but may also simply act as a trap for the binding to another site. Here we consider the scenario in which one molecule (enzyme) binds another molecule (substrate) which contains two sites. We present microscopic expressions for the rate at which the enzyme binds to a particular site on the substrate, both for the scenario in which the enzyme directly binds the site without first visiting the other site, and for the case in which it may visit the other site an arbitrary number of times before binding to the site of interest. We also present the expressions for the corresponding dissociation reactions. These expressions can be used to compute in a single rare-event simulation of the dissociation pathway not only both the intrinsic and effective dissociation rate constants but also both association rate constants.     

BOLD MRI response to hypercapnic hyperoxia in patients with meningiomas: correlation with Gadolinium-DTPA uptake rate

Because meningiomas tend to recur after (partial) surgical resection, radiotherapy is increasingly being applied for the treatment of these tumors. Radiation dose levels are limited, however, to avoid radiation damage to the surrounding normal tissue. The radiosensitivity of tumors can be improved by increasing tumor oxygen levels. The aim of this study was to investigate if breathing a hyperoxic hypercapnic gas mixture could improve the oxygenation of meningiomas. Blood oxygen level-dependent magnetic resonance imaging and dynamic Gadolinium (Gd)-DTPA contrast-enhanced MRI were used to assess changes in tumor blood oxygenation and vascularity, respectively. Ten meningioma patients were each studied twice; without and with breathing a gas mixture consisting of 2% CO(2) and 98% O(2). Values of T(2)* and the Gd-DTPA uptake rate k(ep) were calculated under both conditions. In six tumors a significant increase in the value of T(2)* in the tumor was found, suggesting an improved tumor blood oxygenation, which exceeded the effect in normal brain tissue. Contrarily, two tumors showed a significant T(2)* decrease. The change in T(2)* was found to correlate with both k(ep) and with the change in k(ep). The presence of both vascular effects and oxygenation effects and the heterogeneous response to hypercapnic hyperoxia necessitates individual assessment of the effects of breathing a hyperoxic hypercapnic gas mixture on meningiomas. Thus, the current MRI protocol may assist in radiation treatment selection for patients with meningiomas.     

A comparison study of multishot vs. single-shot DWI-EPI in the neonatal brain: reduced effects of ghosting compared to adults

In the neonatal brain, it is important to use a fast imaging technique to acquire all diffusion weighted images (DWI) for apparent diffusion coefficient (ADC) calculation. Taking into account the occurrence of typical echo planar imaging (EPI) artifacts, we have investigated whether single-shot (SSh) or multishot (MSh) DWI-EPI should be preferred. In 14 neonates, 17 adult patients and 5 adult volunteers, DWIs are obtained both with SSh and MSh EPI. The occurrence of artifacts and their influence on the ADC are explored and further quantified using simulations and phantom studies. Two radiologists scored overall image quality and diagnosability of all images. Single-shot and MSh DWI-EPI scored equally well in neonates with respect to overall image quality and diagnosability. In newborns, more motion artifacts in MSh can be noticed while N/2-ghost artifacts in SSh occur less frequently than in adults. Both N/2-ghost and motion artifacts result in significant ADC abnormalities. There is a serious risk that these artifacts will be mistaken for genuine diffusion abnormalities. N/2-ghost artifacts are hardly noticed in the neonatal brain, which might be due to smaller cerebrospinal fluid (CSF) velocity than in adults. Apparent diffusion coefficient values in MSh are unreliable if motion occurs. We conclude that for ADC calculations in neonates SSh DWI-EPI is more reliable than MSh.     

Asymmetric allylic alkylation of acyclic allylic ethers with organolithium reagents

A highly efficient, regio- and enantioselective Cu(I) /phosphoramidite-catalyzed asymmetric allylic alkylation of allyl ethers with organolithium reagents is reported. The use of organolithium reagents is essential for this catalytic C?C bond formation due to their compatibility with different Lewis acids. The versatility of allylic ethers under the copper-catalyzed reaction conditions with organolithium reagents is demonstrated in the shortest synthesis of (S)-Arundic acid.     

Trigocherrin A, the first natural chlorinated daphnane diterpene orthoester from Trigonostemon cherrieri

Trigocherrin A, a chlorinated and highly oxygenated daphnane diterpenoid orthoester (DDO), was isolated from the bark of Trigonostemon cherrieri. Trigocherrin A is the first example of a naturally occurring halogenated DDO. Its structure was elucidated by comprehensive analysis of NMR spectroscopic data, and its absolute configuration was determined by comparison of experimental and theoretically calculated ECD spectra. Trigocherrin A exhibited a potent and selective effect against Chikungunya virus in Vero cells.     

HERFD XAS/ATR-FTIR batch reactor cell

An autoclave reactor was modified to perform simultaneously high energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy measurements without altering the reactor design. This operando cell allows one to follow changes in the electronic and geometric structure of the catalyst with HERFD XAS and relate them to the simultaneously detected activity and reaction species with ATR-FTIR formed during the reaction in the liquid phase. The capability of the cell is demonstrated by two studies. The first shows the reduction of Au/CeO(2) precursors in different solvents. The second shows that mainly Au(0) is present in the hydrogenation of nitrobenzene over Au/CeO(2).     

Multiple dot-in-rod PbS/CdS heterostructures with high photoluminescence quantum yield in the near-infrared

Pb cations in PbS quantum rods made from CdS quantum rods by successive complete cationic exchange reactions are partially re-exchanged for Cd cations. Using STEM-HAADF, we show that this leads to the formation of unique multiple dot-in-rod PbS/CdS heteronanostructures, with a photoluminescence quantum yield of 45-55%. We argue that the formation of multiple dot-in-rods is related to the initial polycrystallinity of the PbS quantum rods, where each PbS crystallite transforms in a separate PbS/CdS dot-in-dot. Effective mass modeling indicates that electronic coupling between the different PbS conduction band states is feasible for the multiple dot-in-rod geometries obtained, while the hole states remain largely uncoupled.     

Comments on the wetting behavior of non-porous substrates for ceramic coated-conductor applications

This work gives an overview of the possibilities to improve the wetting behavior of precursors for coated conductors on non-porous substrates. Within this work, all coatings were performed on a metallic Ni–W/La₂Zr₂O₇/CeO₂ substrate using water-based Y, Ba, Cu containing precursors. The results described in this paper can be used for different technologies of chemical solution deposition, as there are ink jet printing, dip coating, spin coating etc. Starting from the forces involved during wetting, a separation between solid and liquid modifications was made. This study revealed that if a good cleaning procedure of the substrate, whether or not combined with a targeted modification of the precursor is applied, water-based solutions can be used without restriction towards their wetting behaviour leading to a sustainable technology within the coating industry. Within this work, special attention is given to (1) fast determination of the substrate cleaning procedure quality by the creation of wetting envelopes and (2) the use of a screening design of experiment to study the effects of intrinsic solution factors, such as precursor formulation, influencing the coating behavior. All modification discussed are expandable to all kinds of precursors and substrates.     

New Cu-based catalysts supported on TiO2 films for Ullmann S(N)Ar-type C-O coupling reactions

New routes for the preparation of highly active TiO(2)-supported Cu and CuZn catalysts have been developed for C-O coupling reactions. Slurries of a titania precursor were dip-coated onto glass beads to obtain either structured mesoporous or non-porous titania thin films. The Cu and CuZn nanoparticles, synthesized using a reduction by solvent method, were deposited onto calcined films to obtain a Cu loading of 2 wt%. The catalysts were characterized by inductively coupled plasma (ICP) spectroscopy, temperature-programmed oxidation/reduction (TPO/TPR) techniques, (63)Cu nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction (XRD), scanning and transmission electron microscopy (S/TEM-EDX) and X-ray photo-electron spectroscopy (XPS). The activity and stability of the catalysts obtained have been studied in the C-O Ullmann coupling of 4-chloropyridine and potassium phenolate. The titania-supported nanoparticles retained catalyst activity for up to 12 h. However, catalyst deactivation was observed for longer operation times due to oxidation of the Cu nanoparticles. The oxidation rate could be significantly reduced over the CuZn/TiO(2) catalytic films due to the presence of Zn. The 4-phenoxypyridine yield was 64% on the Cu/nonporous TiO(2) at 120 °C. The highest product yield of 84% was obtained on the Cu/mesoporous TiO(2) at 140 °C, corresponding to an initial reaction rate of 104 mmol g(cat) (-1) s(-1). The activation energy on the Cu/mesoporous TiO(2) catalyst was found to be (144±5) kJ mol(-1), which is close to the value obtained for the reaction over unsupported CuZn nanoparticles (123±3 kJ mol(-1)) and almost twice the value observed over the catalysts deposited onto the non-porous TiO(2) support (75±2 kJ mol(-1)).