Synthesis of C-9 oxidised N-acetylneuraminic acid derivatives as biological probes

Sialic acids are 9-carbon acidic sugars involved in a number of important biological processes and human diseases. As part of our ongoing interest in the development of novel sialic acids as biological probes, we have developed an efficient and simple synthesis of C-9 oxidised sialic acid derivatives. The key oxidative step involves the use of TEMPO under carefully controlled aqueous pH conditions.     

Hydrothermal synthesis and extended structure of poly[aqua(μ5‐ethylenediaminetetraacetato)dizinc(II)]

In the extended structure of the title compound, [Zn₂(C₁₀H₁₂N₂O₈)(H₂O)], prepared under hydrothermal conditions, there are two distinct Zn^II sites. The first, with octahedral geometry, bonds to two N and three O atoms from one ethylenediaminetetraacetate tetraanion (EDTA) and one water molecule. The second, with tetrahedral geometry, coordinates to O atoms from four different EDTA ligands. The EDTA ligand almost encapsulates the octahedral Zn^II ion and binds to four symmetry‐related tetrahedral Zn^II ions, hence generating the extended structure. One noncoordinated O‐atom site on the EDTA ligand connects to the water molecule by hydrogen bonding. Structural comparisons are made with other compounds containing zinc, EDTA and water.     

Synthesis and structural characterization of new polynuclear complexes of 1-hydroxymethyl-3,5-dimethylpyrazole with Ni(II) and Fe(II)

The complexation of the simple 1-hydroxymethyl-3,5-dimethylpyrazole (HL) ligand with Fe and Ni salts leads to interesting polynuclear complexes in good yield. X-ray diffraction reveals that the resulting complexes (μ₄-L)₄Ni₄Cl₄(H₂O)₄ and (μ₂-L)₄(μ₃-L)₂Fe₈Cl₁₆(μ₄-O)₆ adopt cubane-type and open-cubane-type structures in the solid state.     

Wide dynamic range detection of bidirectional flow in Doppler optical coherence tomography using a two-dimensional Kasai estimator

We demonstrate extended axial flow velocity detection range in a time-domain Doppler optical coherence tomography (DOCT) system using a modified Kasai velocity estimator with computations in both the axial and transverse directions. For a DOCT system with an 8 kHz rapid-scanning optical delay line, bidirectional flow experiments showed a maximum detectable speed of >56 cm/s using the axial Kasai estimator without the occurrence of aliasing, while the transverse Kasai estimator preserved the approximately 7 microm/s minimum detectable velocity to slow flow. By using a combination of transverse Kasai and axial Kasai estimators, the velocity detection dynamic range was over 100 dB. Through a fiber-optic endoscopic catheter, in vivoM-mode transesophageal imaging of the pulsatile blood flow in rat aorta was demonstrated, for what is for the first time to our knowledge, with measured peak systolic blood flow velocity of >1 m/s, while maintaining good sensitivity to detect aortic wall motion at <2 mm/s, using this 2D Kasai technique.     

Direct Catalytic Enantio‐ and Diastereoselective Ketone Aldol Reactions of Isocyanoacetates

A catalytic asymmetric aldol addition/cyclization reaction of unactivated ketones with isocyanoacetate pronucleophiles has been developed. A quinine‐derived aminophosphine precatalyst and silver oxide were found to be an effective binary catalyst system and promoted the reaction to afford chiral oxazolines possessing a fully substituted stereocenter with good diastereoselectivities and excellent enantioselectivities.     

New microporous metal-organic framework demonstrating unique selectivity for detection of high explosives and aromatic compounds

A highly luminescent three-dimensional microporous metal-organic framework, [Zn(2)(oba)(2)(bpy)]·DMA, demonstrates unique selectivity for the detection of high explosives and other aromatics via a fluorescence quenching and enhancement mechanism.     

Lanthanide Clusters with Chalcogen Encapsulated Ln: NIR Emission from Nanoscale NdSe(x)

Ln(SePh)(3) (Ln = Ce, Pr, Nd) reacts with elemental Se in the presence of Na ions to give (py)(16)Ln(17)NaSe(18)(SePh)(16), a spherical cluster with a 1 nm diameter. All three rare-earth metals form isostructural products. The molecular structure contains a central Ln ion surrounded by eight five-coordinate Se(2-) that are then surrounded by a group of 16 Ln that define the cluster surface, with additional μ(3) and μ(5) Se(2-), μ(3) and μ(4) SePh(-), and pyridine donors saturating the vacant coordination sites of the surface Ln, and a Na ion coordinating to selenolates, a selenido, and pyridine ligands. NIR emission studies of the Nd compound reveal that this material has a 35% quantum efficiency, with four transitions from the excited state (4)F(3/2) ion to (4)I(9/2), (4)I(11/2), (4)I(13/2), and (4)I(15/2) states clearly evident. The presence of Na(+) is key to the formation of these larger clusters, where reactions using identical concentrations of Nd(SePh)(3) and Se with either Li or K led only to the isolation of (py)(8)Nd(8)Se(6)(SePh)(12).     

Using molecular dynamics and quantum mechanics calculations to model fluorescence observables

We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the independent snapshot method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments.