Reaction of pyridine N-oxides with Grignard reagents: a stereodefined synthesis of substituted dienal oximes

Rapid addition of Grignard reagents to pyridine N-oxides under mild conditions gave stereodefined dienal oximes in good to excellent yields. This reaction provides an efficient access to substituted olefins with defined stereochemistry that are potentially of interest as bioactives themselves or as versatile synthetic intermediates.     

An adaptive kernel-split quadrature method for parameter-dependent layer potentials

Advances in Computational Mathematics - It is well known in the literature that standard hierarchical matrix ( ${\mathscr{H}}$ -matrix)-based methods, although very efficient for asymptotically...     

Data parallel large-scale molecular dynamics for liquids

An efficient data parallel computational scheme is presented for large-scale molecular dynamics (MD ) simulations of liquids with short-range interactions. The method is based on decomposition of the simulation cell into equally sized subcells, with the shortest side length equal to the cutoff radius. Inter- and intracell interactions are calculated in a coarse-grained manner. A geometric sorting procedure, based on particle distances to subcell boundaries, is used to minimize the overall computations and the nonproductive communications. Using only nearest-neighbor communications, an efficient scheme is developed for periodic updates of the contents of subcells due to the migration of particles. Special “null-particles” are introduced, which act as buffers during the periodic updates and allow for a globally uniform algorithm during the calculations. Communication cost is about 7% of the total CPU time. The method is found to be linearly scalable with the number of particles, performing better as the ratio of virtual to physical processors increases. The MD code is written in Fortran 90 and implemented on a CM-200. The overall speed is approximately 5.9 μs. per MD step and per particle for 1 million particles and 5.5 μs for 5 million particles. The method should be easily transferred to other massively parallel computers of SIMD and MIMD type. © 1993 John Wiley & Sons, Inc.     

Vibrationally resolved rate coefficients and branching fractions in the dissociative recombination of O2+

We have studied the dissociative recombination of the first three vibrational levels of O(2) (+) in its electronic ground X (2)Pi(g) state. Absolute rate coefficients, cross sections, quantum yields and branching fractions have been determined in a merged-beam experiment in the heavy-ion storage ring, CRYRING, employing fragment imaging for the reaction dynamics. We present the absolute total rate coefficients as function of collision energies up to 0.4 eV for five different vibrational populations of the ion beam, as well as the partial (vibrationally resolved) rate coefficients and the branching fractions near 0 eV collision energy for the vibrational levels v=0, 1, and 2. The vibrational populations used were produced in a modified electron impact ion source, which has been calibrated using Cs-O(2)(+) dissociative charge transfer reactions. The measurements indicate that at low collision energies, the total rate coefficient is weakly dependent on the vibrational excitation. The calculated thermal rate coefficient at 300 K decreases upon vibrational excitation. The partial rate coefficients as well as the partial branching fractions are found to be strongly dependent on the vibrational level. The partial rate coefficient is the fastest for v=0 and goes down by a factor of two or more for v=1 and 2. The O((1)S) quantum yield, linked to the green airglow, increases strongly upon increasing vibrational level. The effects of the dissociative recombination reactions and super elastic collisions on the vibrational populations are discussed.     

Polymer-assisted laser desorption/ionization analysis of small molecular weight compounds

The use of non-polar, small polymers as matrices for the analysis of low molecular weight compounds in polymer-assisted laser desorption/ionization mass spectrometry (PALDI-MS) is demonstrated. The matrices evaluated were either based on an oligothiophene or a benzodioxin backbone. Metallocenes, polycyclic hydrocarbons, a fluorosurfactant, and a subset of small organic compounds with various functionalities, served as model analytes. The mechanism of ionization charge transfer is discussed and ionization potentials for the matrices in the study have been estimated using density functional theory (DFT) calculations. Some of the results are possibly contradictory to the generally accepted limiting conditions for gas-phase charge-transfer reactions. These results are interpreted in the light of energy pooling. Also a new mass calibration procedure for the low-mass region in positive ion mode is presented, and some aspects of the ionization/desorption process leading to radical cations are studied.     

Micropatterning of DNA-tagged vesicles

We present a novel concept for the creation of lipid vesicle microarrays based on a patterning approach termed Molecular Assembly Patterning by Lift-off (MAPL). A homogeneous MAPL-based single-stranded DNA microarray was converted into a vesicle array by the use of vesicles tagged with complementary DNAs, permitting sequence-specific coupling of vesicles to predefined surface regions through complementary DNA hybridization. In the multistep process utilized to fulfill this achievement, active spots consisting of PLL-g-PEGbiotin with a resistant PLL-g-PEG background, as provided by the MAPL process, was converted into a DNA array by addition of complexes of biotin-terminated DNA and NeutrAvidin. This was then followed by addition of POPC vesicles tagged with complementary cholesterol-terminated DNA, thus providing specific coupling of vesicles to the surface through complementary DNA hybridization. Quartz crystal microbalance with dissipation (QCM-D) and optical waveguide lightmode spectroscopy monitoring were used to optimize the multistep surface modification process. It was found that the amount of adsorbed biotinDNA-NeutrAvidin complexes decreases with increasing molar ratio of biotinDNA to NeutrAvidin and decreasing ionic strength of the buffer solution. Modeling of the QCM-D data showed that the shape of the immobilized vesicles depends on the amount of available anchoring groups between the vesicles and the surface. Fluorescent microscopy images confirmed the possibility to create well-defined patterns of DNA-tagged, fluorescently labeled vesicles in the micrometer range.     

DNA-binding of semirigid binuclear ruthenium complex delta,delta-[mu-(11,11'-bidppz)(phen)(4)ru(2)](4+): extremely slow intercalation kinetics

We here report a remarkably slow rearrangement of binding modes for a binuclear ruthenium(II) complex upon interaction with DNA. It has been previously shown that Delta,Delta-[mu-(11,11'-bidppz)(phen)4Ru2]4+ binds to DNA in one of the grooves. However, we find that this is only an initial, metastable, binding mode, which is extremely slowly reorganized into an intercalative binding geometry. The slow rearrangement and dissociation, revealed by flow linear dichroism and fluorescence spectroscopy, are concluded to be a result from the complex being threaded through the DNA, with one of the bridging aromatic dppz ligands intercalated between the base pairs of the DNA, placing one metal center in the minor groove and one in the major groove. A negative LD, a high luminescence quantum yield, and long luminescence lifetimes, similar to the intercalating complex Delta-[Ru(phen)2dppz]2+, indicate intercalation of the bidppz moiety. The unique slow dissociation of the complex in its final DNA-binding mode suggests that this class of threading, partially intercalated binuclear complexes may be interesting in the context of cancer therapy. Also, their unique optical and photophysical properties could make such complexes, either alone or scaffolded by DNA structures, of interest for the development of nanometer-sized molecular optoelectronic devices.     

Generalized roof duality

The roof dual bound for quadratic unconstrained binary optimization is the basis for several methods for efficiently computing the solution to many hard combinatorial problems. It works by constructing the tightest possible lower-bounding submodular function, and instead of minimizing the original objective function, the relaxation is minimized. However, for higher-order problems the technique has been less successful. A standard technique is to first reduce the problem into a quadratic one by introducing auxiliary variables and then apply the quadratic roof dual bound, but this may lead to loose bounds.We generalize the roof duality technique to higher-order optimization problems. Similarly to the quadratic case, optimal relaxations are defined to be the ones that give the maximum lower bound. We show how submodular relaxations can efficiently be constructed in order to compute the generalized roof dual bound for general cubic and quartic pseudo-boolean functions. Further, we prove that important properties such as persistency still hold, which allows us to determine optimal values for some of the variables. From a practical point of view, we experimentally demonstrate that the technique outperforms the state of the art for a wide range of applications, both in terms of lower bounds and in the number of assigned variables.     

Health-based pharmaceutical pay-for-performance risk-sharing agreements

Many new drugs, such as biologics and cancer drugs, are very costly. However, their effectiveness outside of clinical trial settings is often uncertain at the time they gain market approval. This uncertainty may reflect a lack of real-world outcomes data, as opposed to clinical trials data, for a typical patient population. A risk-sharing agreement is a contract between a drug manufacturer and a healthcare payer to help manage uncertainties regarding the cost and effectiveness of those drugs. In this paper, we model a risk-sharing agreement in which a proportion of total sales is rebated. We model disease progression using a continuous time Markov chain with uncertain transition rates. We examine the performance of this risk-sharing agreement from the manufacturer’s perspective and investigate the conditions under which the manufacturer will make a profit. We illustrate with a numerical model parameterized using data from a Phase 2 clinical trial of an oncology drug that was subjected to a risk-sharing agreement in the UK.