The syntheses of 16a'-homo-leurosidine and 16a'-homo-vinblastine. Generation of atropisomers

The synthesis of 16a'-homo-leurosidine was achieved through enantioselective generation of a ring D'-seco-precursor 33 (without requirement of a chiral auxiliary). Its cyclization provided the N(b')-quaternary salt 35 with a configuration corresponding to the atropisomeric form 8a rather than 8b of the target product. On debenzylation, the amine 8a was obtained and found not to isomerize thermally to the anticipated atropisomer 8b (in contrast to its lower homologue, with its formation of natural leurosidine). However, on protonation, a 1:1 mixture of atropisomers of 16a'-homo-leurosidine was obtained. A synthesis of 16a'-homo-vinblastine provided two atropisomers 5a and 5b for the free base at equilibrium (1:2.3 at room temperature in CDCl(3)), with a shift to the major conformer 5b with increasing solvent acidity or decreasing temperature. The synthesis was achieved through a stereoselective inversion of the tertiary hydroxyl function in the enantioselectively generated C-20' progenitor 39.     

C6-C8 bridged epothilones: consequences of installing a conformational lock at the edge of the macrocycle

A series of conformationally restrained epothilone analogues with a short bridge between the methyl groups at C6 and C8 was designed to mimic the binding pose assigned to our recently reported EpoA-microtubule binding model. A versatile synthetic route to these bridged epothilone analogues has been successfully devised and implemented. Biological evaluation of the compounds against A2780 human ovarian cancer and PC3 prostate cancer cell lines suggested that the introduction of a bridge between C6-C8 reduced potency by 25-1000 fold in comparison with natural epothilone D. Tubulin assembly measurements indicate these bridged epothilone analogues to be mildly active, but without significant microtubule stabilization capacity. Molecular mechanics and DFT energy evaluations suggest the mild activity of the bridged epo-analogues may be due to internal conformational strain.     

Extremely low vertical-emittance beam in the accelerator test facility at KEK

Electron beams with the lowest, normalized transverse emittance recorded so far were produced and confirmed in single-bunch-mode operation of the Accelerator Test Facility at KEK. We established a tuning method of the damping ring which achieves a small vertical dispersion and small x-y orbit coupling. The vertical emittance was less than 1% of the horizontal emittance. At the zero-intensity limit, the vertical normalized emittance was less than 2.8 x 10(-8) rad m at beam energy 1.3 GeV. At high intensity, strong effects of intrabeam scattering were observed, which had been expected in view of the extremely high particle density due to the small transverse emittance.     

Synthesis and Spectroscopic Characterization of Fluorescent Boron Dipyrromethene-Derived Hydrazones

Derivatives of 4,4-difluoro-4-bora-3a,4a,diaza-s-indacene (BODIPY? or BDP) that possess a hydrazine substituent on position 5 are potential "turn-on" fluorophores for labeling aldehydes The unnatural amino acid L-3-formyltyrosine can be incorporated into a protein or peptide; thus, these hydrazines are potentially site specific labels for such polymers. In this work, model compounds were synthesized to assess whether the photochemical properties of the BDP-hydrazone would be suitable for protein labeling. Hydrazones were synthesized from the fluorophore 3-chloro-5-hydrazino-BDP and different aldehydes, and the absorption and emission spectra of the products were compared. The hydrazone of an unsubstituted aromatic aldehyde displays absorption and emission maxima (531 nm and 559 nm, respectively in dioxane) that are red shifted relative to those of a hydrazone from an aliphatic aldehyde (513 nm and 543 nm, respectively, in dioxane) and an increased quantum yield (0.21 vs. 0.11, respectively, in dioxane). The presence of a hydroxyl group ortho- to the aldehyde produces a hydrazone in which the absorption and emission maxima are slightly red shifted (528 nm and 564 nm, respectively in dioxane) from the unsubstituted aromatic hydrazone, but the quantum yields of the two hydrazones are equivalent. Thus, an ortho-hydroxy substituted aromatic aldehyde is a suitable electrophile for "turn on" protein labeling using the hydrazino-BDP. The specificity of this labeling reaction for the unnatural amino acid was demonstrated through fluorescent labeling of just the 3-formyltyrosine-containing α-subunit of α,β-tubulin.     

High-resolution Fourier-transform infrared spectroscopy of the ν6 and Coriolis perturbation allowed ν10 modes of ketenimine

High-resolution FTIR spectra of the short lived species ketenimine have been recorded in the region 700-1300 cm(-1) and over 1500 transitions of the ν(10) and ν(6) modes have been assigned. Effective rotational and centrifugal distortion parameters for the v(10) = 1 and v(6) = 1 (excluding K(a) = 5) states were determined by co-fitting transitions, and treating strong a- and c-axis Coriolis interactions between them. Other perturbations attributed to interactions with the v(8) = 2 and v(12) = 1 + v(8) = 1 dark-states were also observed and treated. The ν(10) transitions are predicted to be inherently very weak, but are enhanced by an intensity stealing effect with the highly IR active ν(6) mode. A mechanism for this intensity stealing in ketenimine is also detailed.     

High-resolution Fourier-transform infrared spectroscopy of the Coriolis coupled ground state and ν7 mode of ketenimine

High resolution FTIR spectra of the short lived species ketenimine have been recorded in the regions 390-1300 cm(-1) and 20-110 cm(-1) using synchrotron radiation. Two thousand six hundred sixty transitions of the ν(7) band centered at 693 cm(-1) and 126 far-IR rotational transitions have been assigned. Rotational and centrifugal distortion parameters for the ν(7) mode were determined and local Fermi and b-axis Coriolis interactions with 2ν(12) are treated. A further refinement of the ground state, ν(12) and ν(8) parameters was also achieved, including the treatment of previously unrecognized ac-axis and ab-axis second order perturbations to the ground state.     

Leakage and water exchange characterization of gadofosveset in the myocardium

Purpose

To determine the compartmentalization of the blood pool agent gadofosveset and the effect of its transient binding to albumin on the quantification of steady-state fractional myocardial blood volume (fMBV).

Methods

Myocardial vascular fraction measurements were simulated assuming the limiting cases (slow or fast) of two-compartment water exchange for different contrast agent injection concentrations, binding fractions, bound and free relaxivities, and true cardiac vascular fractions.fMBV was measured in five healthy volunteers (4 males, 1 female, average age 33) at 1.5 T after administration of five injections of gadofosveset. The measurements in the volunteers were retrospectively compared to measurements of fMBV after three serial injections of the ultra-small, paramagnetic iron oxide (USPIO) blood pool agent ferumoxytol in an experimental animal. The true fMBV and exchange rate of water protons in both human and animal data sets was determined by chi square minimization.

Results

Simulations showed an error in the measurement of fMBV due to partial binding of gadofosveset of less than 30%. Measured fMBV values over-estimate simulation predictions, and approach cardiac extracellular volume (22%), which suggests that the intravascular assumption may not be appropriate for the myocardium, although it may apply to more distal perfusion beds. In comparison, fMBV measured with ferumoxytol (5%, with slow water proton exchange across vascular wall) agree with published values of myocardial vascular fraction. Further comparison between myocardium relaxation rates induced by gadofosveset and by other extracellular and intravascular contrast agents showed that gadofosveset behaves like an extracellular contrast agent.

Conclusions

The distribution of the volunteer data indicates that a three-compartment model, with slow water exchange of gadofosveset and water protons between the vascular and interstitial compartments, and fast water exchange between the interstitium and the myocytes, is appropriate. The ferumoxytol measurements indicate that this USPIO is an intravascular contrast agent that can be used to quantify myocardial blood volume, with the appropriate correction for water exchange using a two-compartment water exchange model.     

FEREBUS: Highly parallelized engine for kriging training

FFLUX is a novel force field based on quantum topological atoms, combining multipolar electrostatics with IQA intraatomic and interatomic energy terms. The program FEREBUS calculates the hyperparameters of models produced by the machine learning method kriging. Calculation of kriging hyperparameters ( θ and p ) requires the optimization of the concentrated log‐likelihood . FEREBUS uses Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms to find the maximum of . PSO and DE are two heuristic algorithms that each use a set of particles or vectors to explore the space in which is defined, searching for the maximum. The log‐likelihood is a computationally expensive function, which needs to be calculated several times during each optimization iteration. The cost scales quickly with the problem dimension and speed becomes critical in model generation. We present the strategy used to parallelize FEREBUS, and the optimization of through PSO and DE. The code is parallelized in two ways. MPI parallelization distributes the particles or vectors among the different processes, whereas the OpenMP implementation takes care of the calculation of , which involves the calculation and inversion of a particular matrix, whose size increases quickly with the dimension of the problem. The run time shows a speed‐up of 61 times going from single core to 90 cores with a saving, in one case, of ～98% of the single core time. In fact, the parallelization scheme presented reduces computational time from 2871 s for a single core calculation, to 41 s for 90 cores calculation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.