Intermolecular interactions in pi-stacked conjugated molecules. Synthesis,structure, and spectral characterization of alkyl bithiazole oligomers

Syntheses are reported of new 4,4'-dialkyl-2,2'-bithiazole oligomers that have alkenoxy side chains that are capable of easy conversion to oligomers with functionalized side chains, e.g., terminally substituted hydroxy chains. The crystal structures of two representative oligomers (4,4',4' ',4' "-tetra-(2-propenoxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3P2) and 4,4',4' ',4' "-tetra-(3-hydroxypropyloxymethyl)-2,2',5',5' ',2' ',2' "-quaterthiazole (3H2)) were determined; 3P2 crystallizes in a pi-stacked motif with two molecules per unit cell, whereas 3H2 forms pi-stacks that are linked with hydrogen bonds to form infinite two-dimensional sheets with one molecule per unit cell. A comparison of the UV-vis spectra of the compounds in solution and in the solid state provides unequivocal evidence for the presence of a Davydov splitting, W(D) approximately 0.2 eV, in solid 3P2. The spectra are interpreted in the framework of molecular exciton theory to extract a value of the intermolecular transfer integral, J approximately 0.2 eV, for a total exciton bandwidth of ca. 0.8 eV. Monte Carlo calculations were used to determine the density of states of the exciton band and the absorption and emission line shapes of the 0 <-- 0 transition. It is suggested that the "three-humped" absorption profile typical of partially crystalline, regioregular polymers is the "optical signature" of pi-stacking.     

Characterization of low-molecular weight peptides in champagne wine by liquid chromatography/tandem mass spectrometry

This paper reports the use of an on-line LC–ESI–MS/MS method for the identification and quantification of di- and tripeptides in champagne wine without laborious sample pretreatment. The identification of these compounds, in their underivatised form, is based on identical retention times and ESI–MS spectra to those of reference standards. The presence of nine dipeptides (Arg–Ile, Ile–Arg, Ile–Val, Lys–Phe, Lys–Tyr, Phe–Lys, Tyr–Gln, Tyr–Lys, Val–Ile) and the absence of two tripeptides (Phe–Arg–Arg and Lys–Met–Asn) have been evidenced in the matrix. Calibration curves for each analyte were established using Phe–Arg as internal standard. The calibration curves were linear in the concentration range 0.1–10 mg L⁻¹ with a determination coefficient, r², better than 0.992. The accuracy for the calibration standard was estimated at between 92 and 102%. This method allows high recovery and satisfies the necessary requirements with respect to accuracy, repeatability and sensitivity. The first application of this analytical method to the measurement of di- and tri-peptides in different vintages of champagne wine is reported. Compositional changes in the peptides occurred depending on the vintage.     

Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

Peptides are a rapidly growing class of therapeutics with various advantages over traditional small molecules, especially for targeting difficult protein–protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing bioactive cyclic topologies that go beyond natural l-amino acids. Here, we report a generalizable framework that exploits the computational power of Rosetta, in terms of large-scale backbone sampling, side-chain composition and energy scoring, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we developed two new inhibitors (PD-i3 and PD-i6) of programmed cell death 1 (PD-1), a key immune checkpoint in oncology. A comprehensive biophysical evaluation was performed to assess their binding to PD-1 as well as their blocking effect on the endogenous PD-1/PD-L1 interaction. Finally, NMR elucidation of their in-solution structures confirmed our de novo design approach.

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Organoruthenaborane Chemistry. X. The SM2-catalysed formation of [ l-(η6-C6Me6)-isocloso-RuB9H9], and some B-phenylamino derivatives. NMR and X-ray diffraction studies

The action of SMe₂ on the ten-vertex nido-ruthenaborane [6-(η⁶-C₆Me₆)RuB₉H_l3] ( 1 ) provides a high-yield route to the unsubstituted isocloso-ruthenaborane [1-(η⁶-C₆Me₆)RuB₉H₉] (2). The benzene analogue [1-(η⁶-C₆Me₆)RuB₉H₉] is prepared similarly. By contrast, reaction of (1) with PhNH₂ gives a variety of B-phenylamino isocloso derivatives, including orange crystals of [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB 9 H₈] ( 3 ), red-orange [1-(η⁶-C₆Me₆)-2,3-(PhNH)₂-isocloso-1-RuB₉H₇] ( 4 ) and dark-red [1-(η⁶-C₆Me₆)-5,6,7-(PhNH)₃-isocloso-1-RuB₉H₆] ( 5 ). Detailed ¹H and ¹¹B nmr properties of these various compounds are described. The structure of ( 3 ) has been established by a single-crystal X-ray diffraction study of the solvate [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB₉H₈] · 1/2 CH₂Cl₂; the crystals were monoclinic, space group C2/c, with a = 1895.1(3), b = 1556.6(3), c = 1716.4(3) pm, β = 104.37(1)° and z = 8.     

The synthesis of some 4,4′-disubstituted-2,2′-biquinolines

2,2′-Biquinoline dioxide and 4,4′-dichloro-2,2′-biquinoline have been used for the preparation of the following 4,4′-disubstituted-2,2′-biquinolines: dimethoxy, diethoxy, dihydroxy, dipiperidino, dipyrrolidino, dibromo, diphenoxy, dithiophenoxy, di(p-chloro-phenoxy), di(p-bromophenoxy), di(p-fluorophenoxy), di(β-naphthoxy) and the dinitro dioxide. Molar extinction coefficients have been determined for several of the copper (I) complexes of these compounds.     

Characterization of the new Bi∼6.2Cu∼6.2O8(PO4)5 oxyphosphate; a disordered compound containing 2- and 3-O(Bi, Cu)4 tetrahedra—wide polycationic ribbons

The present work is dedicated to the XRD, ED and HREM characterization of a new bismuth copper oxyphosphate Bi_∼6.2Cu_∼6.2O₈(PO₄)₅ (a=11.599(2)Å, , c=37.541(5)Å, R₁=0.0755, Rw₂₌0.174, G.S Pn2₁a). The relatively long size of its c parameter is due to the arrangement along this direction of two kinds of ribbon-like polycations formed by edge sharing O(Bi, Cu)₄ tetrahedra. The existence of such cations is characterized by the b∼5.2 Å value intrinsic to the ribbons structure and commonly found in bismuth oxyphosphate materials. In the title compound, 2-tetrahedra wide [Bi_∼2.4Cu_∼3.6O₄]^6.4+ and 3-tetrahedra wide [Bi_∼5Cu_∼3O₆]⁹⁺ ribbons are isolated by phosphate groups and alternate along c. The interstitial site created between two different sizes ribbons is occupied by Cu²⁺ cations disordered over several close crystallographic sites. The mixed Bi³⁺/Cu²⁺ nature of certain edge-of-ribbons positions induces a disorder over several configurations of the phosphate groups. The concerned oxygen atoms form the environment of the disordered interstitial Cu²⁺ cations which occupy tunnels formed by the phosphate anions. The high-resolution electron microscope study enables a precise correlation between the observed images and the refined crystal structure, evidencing the polycations visualization. Furthermore, this material being the second example of partially disordered compound similar chemical system, some topological rules can be deduced. The b-axis doubling was observed by ED and HREM and is assigned to the ordering of interstitial Cu²⁺ within tunnels cations. A partial intra-tunnel ordering was also observed.     

Radiation synthesis of superabsorbent poly(acrylic acid)–carrageenan hydrogels

A series of superabsorbent hydrogels were prepared from carrageenan and partially neutralized acrylic acid by gamma irradiation at room temperature. The gel fraction, swelling kinetics and the equilibrium degree of swelling (EDS) of the hydrogels were studied. It was found that the incorporation of even 1% carrageenan (sodium salt) increases the EDS of the hydrogels from 320 to 800 g/g. Thermal analysis were carried out to determine the amount of free water and bound water in the hydrogels. Under optimum conditions, poly(acrylic acid)–carrageenan hydrogels with high gel fraction (80%) and very high EDS (800 g/g) were prepared gamma radiolytically from aqueous solution containing 15% partially neutralized acrylic acid and 1–5% carrageenan. The hydrogels were also found to be sensitive to the pH and the ionic strength of the medium.     

Effect of axial ligation or pi-pi-type interactions on photochemical charge stabilization in "two-point" bound supramolecular porphyrin-fullerene conjugates

Two types of structurally well-defined, self-assembled zinc porphyrin-fullerene conjugates were formed by "two-point" binding strategies to probe the effect of axial ligation or pi-pi-type interactions on the photochemical charge stabilization in the supramolecular dyads. To achieve this, meso-tetraphenylporphyrin was functionalized to possess one or four [18]crown-6 moieties at different locations on the porphyrin macrocycle while fullerene was functionalized to possess an alkyl ammonium cation, and a pyridine or phenyl entities. As a result of the crown ether-ammonium cation complexation, and zinc-pyridine coordination or pi-pi-type interactions, stable zinc porphyrin-fullerene conjugates with defined distance and orientation were formed. Evidence for the zinc-pyridine complexation or pi-pi-type interactions was obtained from the spectral and computational studies. Steady-state and time-resolved emission studies revealed efficient quenching of the zinc-porphyrin singlet excited state in these dyads, and the measured rates of charge separation, k(CS) were found to be slightly better in the case of the dyads held by axial coordination and crown ether-cation complexation. Nanosecond transient absorption studies provided evidence for the electron transfer reactions, and these studies also revealed charge stabilization in these dyads. The lifetimes of the radical ion pairs were found to depend upon the type of porphyrins utilized to form the dyads, that is, porphyrin possessing the crown ether moiety at the ortho position of one of the phenyl rings yielded prolonged charge stabilized states. Addition of pyridine to the supramolecular dyads eliminated the zinc-pyridine coordination or pi-pi-type interactions of the "two-point" bound systems due to the formation of a new zinc-pyridine axial bond thus giving a unique opportunity to probe the effect of axial coordination or pi-pi interactions on k(CS) and k(CR). Under these conditions, the measured electron transfer rates revealed faster k(CS) and slower k(CR) as compared to those obtained in the absence of added pyridine. The evaluated lifetimes of the radical ion-pairs were found to be hundreds of nanoseconds and were longer in the presence of pyridine.     

Determination of selected neurotransmitter metabolites using monolithic column chromatography coupled with chemiluminescence detection

The oxidation of selected clinically important neurotransmitter metabolites with acidic potassium permanganate in the presence of polyphosphates evokes chemiluminescence of sufficient intensity to enable the sensitive determination of these species. Limits of detection for 5-hydroxyindole-3-acetic acid (5-HIAA), vanilmandelic acid (VMA; α,4-dihydroxy-3-methoxybenzeneacetic acid), 4-hydroxy-3-methoxyphenylglycol (MHPG), homovanillic acid (HVA, 4-hydroxy-3-methoxyphenylacetic acid) and 3,4-dihydroxyphenylacetic acid (DOPAC) were between 5 × 10⁻⁹ and 4 × 10⁻⁸ M, using flow-injection analysis methodology. In addition, we demonstrate the rapid determination of homovanillic acid and 5-hydroxyindole-3-acetic acid in human urine - without the need for extraction procedures - using monolithic column chromatography with chemiluminescence detection.