Structural Modifications of cis‐Glycofused Benzopyran Compounds and Their Influence on the Binding to Amyloid‐β Peptide

A small library of glycofused tricyclic compounds with a central pyran ring chemically modified in the position para to the ring oxygen has been synthesised. The influence of the chemical modification on the structural conformation of the compounds and on their ability to bind Aβ peptide has been evaluated respectively using molecular mechanics (MM) and molecular dynamics (MD) simulations, and STD NMR spectroscopy. The introduction of particularly polar/charged groups leads to the loss of binding ability, without a significant change in the conformation, whilst other substitutions does not significantly affect either the structural conformation or the binding.     

Supramolecular Adducts of Cucurbit[7]uril and Amino Acids in the Gas Phase

The complexation of the macrocyclic cavitand cucurbit[7]uril (Q7) with a series of amino acids (AA) with different side chains (Asp, Asn, Gln, Ser, Ala, Val, and Ile) is investigated by ESI-MS techniques. The 1:1 [Q7 + AA + 2H]²⁺ adducts are observed as the base peak when equimolar Q7:AA solutions are electrosprayed, whereas the 1:2 [Q7 + 2AA + 2H]²⁺ dications are dominant when an excess of the amino acid is used. A combination of ion mobility mass spectrometry (IM-MS) and DFT calculations of the 1:1 [Q7 + AA + 2H]²⁺ (AA = Tyr, Val, and Ser) adducts is also reported and proven to be unsuccessful at discriminating between exclusion or inclusion-type conformations in the gas phase. Collision induced dissociation (CID) revealed that the preferred dissociation pathways of the 1:1 [Q7 + AA + 2H]²⁺ dications are strongly influenced by the identity of the amino acid side chain, whereas ion molecule reactions towards N-butylmethylamine displayed a common reactivity pattern comprising AA displacement. Special emphasis is given on the differences between the gas-phase behavior of the supramolecular adducts with amino acids (AA = Asp, Asn, Gln, Ser, Ala, Val, and Ile) and those featuring basic (Lys and Arg) and aromatic (Tyr and Phe) side chains.

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3D Raman imaging of systemic endothelial dysfunction in the murine model of metastatic breast cancer

It was recently reported in the murine model of metastatic breast cancer (4T1) that tumor progression and development of metastasis is associated with systemic endothelial dysfunction characterized by impaired nitric oxide (NO) production. Using Raman 3D confocal imaging with the analysis of the individual layers of the vascular wall combined with AFM endothelial surface imaging, we demonstrated that metastasis-induced systemic endothelial dysfunction resulted in distinct chemical changes in the endothelium of the aorta. These changes, manifested as a significant increase in the protein content (18 %) and a slight decrease in the lipid content (4 %), were limited to the endothelium and did not occur in the deeper layers of the vascular wall. The altered lipid to protein ratio in the endothelium, although more pronounced in the fixed vascular wall, was also observed in the freshly isolated unfixed vascular wall samples in the aqueous environment (12 and 7 % change of protein and lipid content, respectively). Our results support the finding that the metastasis induces systemic endothelial dysfunction that may contribute to cancer progression.

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Graphical Abstract Schematic illustration of methodology of sample preparation and measurement

     

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes

A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the F?rster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 A and rotation angle of 20.5 degrees . The inter-phycocyanin FRET constant between chromophores at positions beta(155) is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system.     

Biodiesel fuel production by the transesterification reaction of soybean oil using immobilized lipase

The enzymatic alcoholysis of soybean oil with methanol and ethanol was investigated using a commercial, immobilized lipase (Lipozyme RMIM). The effect of alcohol (methanol or ethanol), enzyme concentration, molar ratio of alcohol to soybean oil, solvent, and temperature on biodiesel production was determined. The best conditions were obtained in a solvent-free system with ethanol/oil molar ratio of 3.0, temperature of 50 degrees C, and enzyme concentration of 7.0% (w/w). Three-step batch ethanolysis was most effective for the production of biodiesel. Ethyl esters yield was about 60% after 4 h of reaction.     

Modeling and computational simulation of dilution and biochemical materials balance equations for partially emptied batch reactors

Sequencing batch reactors (SBRs) including aerobic SBRs and anaerobic SBRs (ASBRs) are partially emptied batch reactors that are widely used as bioprocesses in pollution control. We present dilution and biochemical materials balance modeling equations and simulation results for the partially emptied batch reactors, especially for ASBR treatment of low-strength wastewater. The simulated substrate and microbial concentrations for both dilution and materials balance equations follow the same pattern during both feeding and reaction times. However, the results of the materials balance equations show microbial activities during feeding as well as during reaction times and were found to be more appropriate for the biologic system in which substrate removal is associated with microbial growth. Further-more, the simulation results point to the need to foster high microbial accumulation in the system during startup to optimize the process performance and the need to operate the system at a short reaction time, especially for low substrate concentrations. The results were found to be in agreement with the results of prior laboratory studies.     

Spectroscopic characterization and Langmuir-Blodgett films of a novel azopolymer material

Spectroscopic characterization and fabrication of Langmuir and Langmuir-Blodgett (LB) films of an azopolymer-pyridine (PAzPy) are reported. UV-visible absorption and fluorescence spectra, Fourier transform infrared (FTIR) spectra, and Raman spectra were recorded. The vibrational assignment of the observed spectra is supported by a complete geometry optimization, followed by vibrational frequency and intensity computations of both the trans and cis forms of the monomer (AzPy) using density functional theory at the B3LYP 6-31G(d,p) level of theory. Langmuir monolayers of the polymer (PAzPy) were formed at the water-air interface, and LB films of high quality were formed onto solid substrates. The polymer LB films were investigated by surface-enhanced Raman scattering.     

Reactions of Sn(NMe2)2 with MPHCy: the effects of alkali metal phosphide coupling (Cy=cyclohexyl; M=Li, Na, K, Rb)

The reactions of the SnII base Sn(NMe2)2 with CyPHM (Cy=cyclohexyl) produce a range of products, depending primarily on the alkali metal (M) involved. The 1:3 stoichiometric reaction of Sn(NMe2)2 with CyPHNa in the presence of the Lewis base donor PMDETA (PMDETA=(Me2NCH2CH2)2NMe) gives [(NaPMDETA)2{Sn(mu-PCy)}3] (3), containing the electron-deficient [{Sn(mu-PCy)}3]2- dianion. Natural bond order (NBO) and electron localisation function (ELF) calculations show that this species is described most appropriately by a two-electron, three-centre Sn3 bonding model. Evidence that 3 results from phosphide coupling is provided by the 1:1 reaction of Sn(NMe2)2 with CyPHNa in the presence of PMDETA, which gives 3 and trace amounts of (NaPMDETA)2[{Sn(mu-PCy)}2(mu-PCyPCy)] (4) (containing one PCyPCy2- dianion). Greater extents of phosphide coupling are observed as the size of the Group 1 metal is increased. Thus, the 1:3 reaction of Sn(NMe2)2 with CyPHK in THF gives the co-crystalline product {(K2 THF)2[{Sn(mu-PCyPCy)}2(mu-PCy)]}0.9{(K2 THF)2[{Sn(mu-PCy)}2(mu-PCyPCy)]}0.1 (5) (containing [{Sn(mu-PCyPCy)}2(mu-PCy)]2- and [{Sn(mu-PCy)}2(mu-PCyPCy)]2- dianions), whereas the analogous reaction of Sn(NMe2)2 with RbPHCy gives [RbPMDETA{(CyP)3SnP(H)Cy}] (6) (containing a cyclic {(CyP)3Sn} unit).     

Total synthesis of peridinin and related C37-norcarotenoid butenolides

As an extension of our synthesis of symmetrical carotenoids, the preparation of the highly functionalized C37-norcarotenoid butenolide peridinin (1), its 6'-epi- and 11'Z stereoisomers has been completed. Featuring a central dihalogenated C8 linchpin unit 6, two synthetic routes, differing in the ordering of the last three steps were explored by using the C3,C3'-bisdehydroxylated target as the model system. The first route uses the combination of a modified Z-selective Julia reaction and two sequential Stille couplings, the last one producing the isomerisation of the polyene Z double bond. The second route inverts these steps and makes the isolation of the 11'Z stereoisomers as major products possible. An efficient Z to E isomerisation of the final carotenoid skeleton simply uses the Stille reaction conditions at ambient temperature. As the reaction of bromoallene 12 with alkenylstannane 11 occurs with inversion of configuration, 6'-epi-peridinin could also be prepared by route A. The advantages and limitations of the sequential Stille cross-coupling approach to carotenoids are highlighted.     

Imidazolium carboxylates as versatile and selective N-heterocyclic carbene transfer agents: synthesis, mechanism, and applications

N,N'-Disubstituted imidazolium carboxylates, readily synthetically available, isolable, air- and water-stable reagents, efficiently transfer N-heterocyclic carbene (NHC) groups to Rh, Ir, Ru, Pt, and Pd, to give novel NHC complexes, e.g., [Pd(NHC)3OAc]OAc and [Pt(NHC)3Cl]Cl (NHC = 1,3-dimethyl imidazol-2-ylidene). The NHC esters are also effective. Tuning the reaction conditions for NHC transfer can give either mono- or bis-NHCs, or bis- and tris-NHCs. A net N to C rearrangement of the N-alkyl imidazole complex to the corresponding NHC complex was seen with (MeO)2CO (DMC). DFT calculations identify the steps needed to form the carboxylate from imidazole and DMC: SN2 methyl transfer from DMC to imidazole, followed by proton transfer from the imidazolium CH to the carboxylate counterion, produces the free NHC H-bonded to MeOH with a weakly associated CO2. The nucleophilic NHC attacks CO2 to form NHC-CO2. NHC transfer to the metal with loss of CO2 has been calculated for Rh(cod)Cl. A proposed two-cis-site reactivity model rationalizes the experimental data: two such vacant sites at the metal are needed to allow coordination of the NHC-CO2 carboxylate and subsequent CC cleavage with NHC transfer. Partial cod decoordination or chloride loss is thus required for Rh(cod)Cl. Chloride dissociation, calculated to be easier in polar solvent, is confirmed experimentally from the retarding effect of excess chloride.