Synthesis and characterization of dinuclear ruthenium complexes covalently linked to Ru(II) tris-bipyridine: an approach to mimics of the donor side of photosystem II

To mimic the electron-donor side of photosystem II (PSII), three trinuclear ruthenium complexes (2, 2a, 2b) were synthesized. In these complexes, a mixed-valent dinuclear Ru2(II,III) moiety with one phenoxy and two acetato bridges is covalently linked to a Ru(II) tris-bipyridine photosensitizer. The properties and photoinduced electron/energy transfer of these complexes were studied. The results show that the Ru2(II,III) moieties in the complexes readily undergo reversible one-electron reduction and one-electron oxidation to give the Ru2(II,III) and Ru2(III,III) states, respectively. This could allow for photooxidation of the sensitizer part with an external acceptor and subsequent electron transfer from the dinuclear ruthenium moiety to regenerate the sensitizer. However, all trinuclear ruthenium complexes have a very short excited-state lifetime, in the range of a few nanoseconds to less than 100 ps. Studies by femtosecond time-resolved techniques suggest that a mixture of intramolecular energy and electron transfer between the dinuclear ruthenium moiety and the excited [Ru(bpy)3]2+ photosensitizer is responsible for the short lifetimes. This problem is overcome by anchoring the complexes with ester- or carboxyl-substituted bipyridine ligands (2a, 2b) to nanocrystalline TiO2, and the desired electron transfer from the excited state of the [Ru(bpy)3]2+ moiety to the conduction band of TiO2 followed by intramolecular electron transfer from the dinuclear Ru2(II,III) moiety to photogenerated Ru(III) was observed. The resulting long-lived Ru2(III,III) state decays on the millisecond timescale.     

Vibrational spectroscopy of 3,4-difluorocyclobutenes: cis-d0, trans-d0 and trans-d4 species

Infrared and Raman spectra were recorded for cis-3,4-difluorocyclobutene (cDFCB) and trans-3,4-difluorocyclobutene-d4. Unscaled density functional theory (DFT) calculations of frequencies and intensities at the B3LYP/6-311++G(d,p) level supported the complete assignment of the vibrational fundamentals. The previous assignment of fundamentals of trans-3,4-difluorocyclobutene was revised. An unusual blue shift occurs for the methylenic CH-stretching frequencies of cis-3,4-difluorocyclobutene in going from the gas phase to the liquid phase. This hydrogen bond effect is related to similar observations recently reported and interpreted. The blue shift does not occur for the vinylic CH bonds of the cis isomer and does not occur for either type of CH bond in the trans isomer.     

Solvothermal syntheses of Cu3P via reactions of amorphous red phosphorus with a variety of copper sources

Polycrystalline Cu₃P was successfully prepared under a wide variety of solvothermal conditions. The reaction of red phosphorus with several copper sources (copper metal, copper (I) iodide, copper (I) chloride and copper (II) chloride) at 150-200 °C for 1-2 days in water produced Cu₃P. Products were examined with powder X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy. Thermal analyses and optical spectroscopy were also performed. A detailed list of reaction conditions, products and impurity phases (where applicable) are reported.     

Automated sample preparation method for suspension arrays using renewable surface separations with multiplexed flow cytometry fluorescence detection

In this paper, we describe a new method of automated sample preparation for multiplexed biological analysis systems that use flow cytometry fluorescence detection. In this approach, color-encoded microspheres derivatized to capture particular biomolecules are temporarily trapped in a renewable surface separation column to enable perfusion with sample and reagents prior to delivery to the detector. This method provides for separation of the biomolecules of interest from other sample matrix components as well as from labeling solutions. After sample preparation, the beads can be released from the renewable surface column and delivered to a flow cytometer for direct on-bead analysis one bead at a time. Using mixtures of color-encoded beads derivatized for various analytes yields suspension arrays for multiplexed analysis. Development of this approach required a new technique for automated capture and release of the color-encoded microspheres within a fluidic system. We developed a method for forming a renewable filter and demonstrate its use for capturing microspheres that are too small to be easily captured in previous flow cells for renewable separation columns. The renewable filter is created by first trapping larger beads in the flow cell, and then smaller beads are captured either within or on top of the bed of larger beads. Both the selective microspheres and filter bed are automatically emplaced and discarded for each sample. A renewable filter created with 19.9 μm beads was used to trap 5.6 μm optically encoded beads with trapping efficiencies of 99%. The larger beads forming the renewable filter did not interfere with the detection of color-encoded 5.6 μm beads by the flow cytometer fluorescence detector. The use of this method was demonstrated with model reactions for a variety of bioanalytical assay types including a one-step capture of a biotinylated label on Lumavidin beads, a two-step sandwich immunoassay, and a one-step DNA binding assay. A preliminary demonstration of multiplexed detection of two analytes using color-encoded beads was also demonstrated. The renewable filter for creating separation columns containing optically encoded beads provides a general platform for coupling renewable surface methods for sample preparation and analyte labeling with flow cytometry detectors for suspension array multiplexed analyses.     

Rearrangement of epoxynitriles: a convenient homologation of acyclic and cyclic ketones to carboxylic acids

A convenient two-step homologation of both aliphatic and aromatic ketones to the corresponding carboxylic acid has been developed. First ketones were converted to epoxynitriles with the Darzens reaction. Second, a Lewis acid mediated rearrangement of these epoxynitriles with lithium bromide was achieved to give homologated secondary alkanoic acids (as well as aryl-alkanoic) in good yields. The mechanism and the scope of the rearrangement reaction were investigated. This strategy constitutes a two-step homologation of ketones to secondary carboxylic acids.     

Terpenoic acid glycerides from the dorid nudibranch Archidoris montereyensis

Extracts of the dorid nudibranch $\text{Archidoris montereyensis}$ contain a diterpenoic acid glyceride 1 whose structure has been determined by x-ray diffraction analysis. The structure of a minor metabolite, the sesquiterpenoic acid glyceride 2, was determined by chemical correlation.     

Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.     

Pharmacomodulation of a ligand targeting the HBV capsid hydrophobic pocket

Hepatitis B virus (HBV) is a small enveloped retrotranscribing DNA virus and an important human pathogen. Its capsid-forming core protein (Cp) features a hydrophobic pocket proposed to be central notably in capsid envelopment. Indeed, mutations in and around this pocket can profoundly modulate, and even abolish, secretion of enveloped virions. We have recently shown that Triton X-100, a detergent used during Cp purification, binds to the hydrophobic pocket with micromolar affinity. We here performed pharmacomodulation of pocket binders through systematic modifications of the three distinct chemical moieties composing the Triton X-100 molecule. Using NMR and ITC, we found that the flat aromatic moiety is essential for binding, while the number of atoms of the aliphatic chain modulates binding affinity. The hydrophilic tail, in contrast, is highly tolerant to changes in both length and type. Our data provide essential information for designing a new class of HBV antivirals targeting capsid–envelope interactions.

Small-molecule binding to the Hepatitis B virus core protein hydrophobic pocket, a possible strategy for targeting viral particle assembly.     

Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery

We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usability challenges common to many open-source CADD tools. To address these challenges, we propose a browser-based approach to CADD tool deployment in which CADD calculations run in modern web browsers on users’ local computers. The browser app approach eliminates the need for user-initiated download and installation, ensures broad operating system compatibility, enables easy updates, and provides a user-friendly graphical user interface. Unlike server apps—which run calculations “in the cloud” rather than on users’ local computers—browser apps do not require users to upload proprietary information to a third-party (remote) server. They also eliminate the need for the difficult-to-maintain computer infrastructure required to run user-initiated calculations remotely. We conclude by describing some CADD browser apps developed in our lab, which illustrate the utility of this approach. Aside from introducing readers to these specific tools, we are hopeful that this review highlights the need for additional browser-compatible, user-friendly CADD software.     

Novel Copolymers of Styrene and Some Ring‐Substituted 2‐Cyano‐N,N‐Dimethyl‐3‐Phenyl‐2‐Propenamides

Electrophilic trisubstituted ethylene monomers, ring‐substituted 2‐cyano‐N,N‐dimethyl‐3‐phenyl‐2‐propenamides, RC₆H₄CH?C(CN)CON(CH₃)₂ (where R is 4‐(CH₃)₂N, 4‐CH₃CO₂, 4‐CH₃CONH, 2‐CN, 3‐CN, 4‐CN, 4‐(C₂H₅)₂N) were synthesized by potassium hydroxide catalyzed Knoevenagel condensation of ring‐substituted benzaldehydes and N,N‐dimethyl cyanoacetamide, and characterized by CHN elemental analysis, IR, ¹H‐ and ¹³C‐NMR. Novel copolymers of the ethylenes and styrene were prepared at equimolar monomer feed composition by solution copolymerization in the presence of a radical initiator, ABCN at 70°C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by IR, ¹H and ¹³C NMR, GPC, DSC, and TGA. High T_g of the copolymers in comparison with that of polystyrene indicates a substantial decrease in chain mobility of the copolymer due to the high dipolar character of the trisubstituted ethylene monomer unit. The gravimetric analysis indicated that the copolymers decompose in the 300–450°C range.