The Partial Molar Volumes and Heat Capacities of the Arginyl Side-chain of Proteins in Aqueous Solution over the Temperature Range 288.15 to 328.15 K

Solution densities over the temperature range 288.15 to 328.15 K have been measured for aqueous solutions of N-acetylarginamide monotrifluoroacetate and sodium trifluoroacetate, from which the partial molar volumes at infinite dilution, V₂^oV_{2}^{\mathrm{o}}, were determined. The partial molar heat capacities at infinite dilution, C_p,2^oC_{p,2}^{\mathrm{o}}, were also determined for these solutes over the same temperature range. These V₂^oV_{2}^{\mathrm{o}} and C_p,2^oC_{p,2}^{\mathrm{o}} results, along with relevant data taken from the literature, have been used to calculate the contributions of the protonated arginyl side-chain to the thermodynamic properties. These new side-chain values were critically compared with those obtained previously using alternative side-chain model compounds.     

Identification of marker proteins for Bacillus anthracis using MALDI-TOF MS and ion trap MS/MS after direct extraction or electrophoretic separation

Direct extraction of bacterial vegetative cells or spores followed by matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI TOF MS) has become popular for bacterial identification, since it is simple to perform and mass spectra are readily interpreted. However, only high-abundance proteins that are of low mass and ionize readily are observed. In the case of B. anthracis spores, small acid-soluble spore proteins (SASPs) have been the most widely studied. Additional information can be obtained using tandem mass spectrometry (MS-MS) to confirm the identity of proteins by sequencing. This is most readily accomplished using ion trap (IT) MS-MS. However, enzymatic digestion of these proteins is needed to generate peptides that are within the mass range of the ion trap. The use of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), or other forms of electrophoresis, allows one to focus on specific proteins of interest (e.g. the high mass exosporium glycoproteins BcIA and BcIB) that provide additional species- and strain-specific discrimination.     

Rapid characterization of Bacillus spores targeting species-unique peptides produced with an atmospheric pressure matrix-assisted laser desorption/ionization source

New and improved strategies are eagerly sought for the rapid identification of microorganisms, particularly in mixtures. Mass spectrometry remains a powerful tool for this purpose. Small acid-soluble proteins (SASPs), which are relatively abundant in Bacillus spores, represent potential biomarkers for species characterization. Despite sharing extensive sequence homology, these proteins differ sufficiently in sequence for discrimination between species. This work focuses on the differences in sequence between SASPs from various Bacillus species. Compilation of SASP sequences from protein database searches, followed by in silico trypsin digestion and analysis of the resulting fragments, identified several species-specific peptides that could be targeted for analysis using mass spectrometry. This strategy was tested and found to be successful in the characterization of Bacillus spores both from individual species and in mixtures. Analysis was performed using an ion trap mass spectrometer with an atmospheric pressure MALDI source. This instrumentation offers the advantage of increased speed of analysis and accurate precursor ion selection for tandem mass spectrometric analysis compared with vacuum matrix-assisted laser desorption/ionization and time-of-flight instruments. The identification and targeting of species-specific peptides using this type of instrumentation offers a rapid, efficient strategy for the identification of Bacillus spores and can potentially be applied to different microorganisms.     

The design and synthesis of porphyrin/oligiothiophene hybrid monomers

In an effort to build effective photovoltaic cells based on porphyrin-functionalised polythiophenes we have focused on synthetic routes to three monomer types. By controlling the geometric structure of the monomer, oxidation of these materials should produce polymers with different architectural structures, and as a result, different opto-electronic properties. Employing Wittig protocols allowed access to monomers in which the porphyrin moiety is connected to the beta-position of the thiophene via an alkene linkage. In addition, monomers were constructed using porphyrin condensation methods to afford alpha-thiophene meso-substituted porphryins. Another set of monomers was also prepared via porphyrin condensation routes, but instead utilising beta-formylthiophenes. By utilising different formyloligothiophenes we were able to generate a series of monomers that can be used to control the loading of the porphyrin in the polythiophene matrix.     

Electrocatalytic Hydrogen Evolution Using A Molecular Antimony Complex under Aqueous Conditions: An Experimental and Computational Study on Main-Group Element Catalysis

Electrocatalytic hydrogen gas production is considered a potential pathway towards carbon-neutral energy sources. However, the development of this technology is hindered by the lack of efficient, cost-effective, and environmentally benign catalysts. In this study, a main-group-element-based electrocatalyst, SbSalen , is reported to catalyze the hydrogen evolution reaction (HER) in an aqueous medium. The heterogenized molecular system achieved a Faradaic efficiency of 100 % at −1.4 V vs. NHE with a maximum current density of −30.7 mA/cm². X-ray photoelectron spectroscopy of the catalyst-bound working electrode before and after electrolysis confirmed the molecular stability during catalysis. The turnover frequency was calculated as 43.4 s⁻¹ using redox-peak integration. The kinetic and mechanistic aspects of the electrocatalytic reaction were further examined by computational methods. This study provides mechanistic insights into main-group-element electrocatalysts for heterogeneous small-molecule conversion.     

Synthesis of diblock copolymers by combination of organocatalyzed ring‐opening polymerization and atom transfer radical polymerization using trichloroethanol as a bifunctional initiator

This study reports an application of trichloroethanol (TCE) as a bifunctional initiator for the synthesis of block copolymers (BCPs) by organocatalyzed ring‐opening polymerization (OROP) and atom transfer radical polymerization (ATRP). TCE was employed to synthesize a low dispersity poly (valerolactone) macroinitiator, which was subsequently used for the ATRP of tert‐butyl methacrylate. While it is known that TCE can serve as an initiator in ATRP, the ability to induce polymerization under OROP is reported for the first time. The formation of well‐defined BCPs was confirmed by gel permeation chromatography and ¹H NMR. Computational studies were performed to obtain a molecular‐level understanding of the ring‐opening polymerization mechanism involving TCE as initiator. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 563–569     

Structural variation, dynamics, and catalytic application of palladium(II) complexes of di-N-heterocyclic carbene-amine ligands

A series of palladium(II) complexes incorporating di-NHC-amine ligands has been prepared and their structural, dynamic and catalytic behaviour investigated. The complexes [trans-(kappa(2)-(tBu)CN(Bn)C(tBu))PdCl(2)] (12) and [trans-(kappa(2)-(Mes)CN(H)C(Mes))PdCl(2)] (13) do not exhibit interaction between the amine nitrogen and palladium atom respectively. NMR spectroscopy between -40 and 25 degrees C shows that the di-NHC-amine ligand is flexible expressing C(s) symmetry and for 13 rotation of the mesityl groups is prevented. In the related C(1) complex [(kappa(3)-(tBu)CN(H)C(tBu))PdCl][Cl] (14) coordination of NHC moieties and amine nitrogen atom is observed between -40 and 25 degrees C. Reaction between 12-14 and two equivalents of AgBF(4) in acetonitrile gives the analogous complexes [trans-(kappa(2)-(tBu)CN(Bn)C(tBu))Pd(MeCN)(2)][BF(4)](2) (15), [trans-(kappa(2)-(Mes)CN(H)C(Mes))Pd(MeCN)(2)][BF(4)](2) (16) and [(kappa(3)-(tBu)CN(H)C(tBu))Pd(MeCN)][BF(4)](2) (17) indicating that ligand structure determines amine coordination. The single crystal X-ray structures of 12, 17 and two ligand imidazolium salt precursors (tBu)C(H)N(Bn)C(H)(tBu)][Cl](2) (2) and [(tBu)C(H)N(H)C(H)(tBu)][BPh(4)](2) (4) have been determined. Complexes 12-14 and 15-17 have been shown to be active precatalysts for Heck and hydroamination reactions respectively.     

Thermodynamic properties of peptide solutions: 7. Partial molar isentropic pressure coefficients of some dipeptides in aqueous solution

The partial molar isentropic pressure coefficients at infinite dilution, K _S,2 ^o , have been determined for a number of dipeptides in aqueous solution at 25°C. For a series of dipeptides of sequence gly-X, where X is an amino acid with a neutral side chain, the K _S,2 ^o values are all more negative than that for diglycine. The results are discussed in terms of the hydration of the side chains. There are significant differences in the K _S,2 ^o values for sequence isomeric dipeptides. These differences can be rationalized in terms of the mutual interactions between the side chain and the ionic end groups in the dipeptides. Possible relationships between K _S,2 ^o and V ₂ ^o , the partial molar volume at infinite dilution, were investigated. For the dipeptides of sequence gly-X there is an interesting linear relationship between K _S,2 ^o /V ₂ ^o and V ₂ ^o .     

Detailed Structural Characterization of Sphingolipids via 193 nm Ultraviolet Photodissociation and Ultra High Resolution Tandem Mass Spectrometry

Sphingolipids serve not only as components of cellular membranes but also as bioactive mediators of numerous cellular functions. As the biological activities of these lipids are dependent on their structures, and due to the limitations of conventional ion activation methods employed during tandem mass spectrometry (MS/MS), there is a recognized need for the development of improved structure-specific methods for their comprehensive identification and characterization. Here, positive-ionization mode 193 nm ultraviolet photodissociation (UVPD)-MS/MS has been implemented for the detailed structural characterization of lipid species from a range of sphingolipid classes introduced to the mass spectrometer via electrospray ionization as their lithiated or protonated adducts. These include sphingosine d18:1(4E), dihydrosphingosine (sphinganine) d18:0, sphingadiene d18:2(4E,11Z), the isomeric sphingolipids ceramide d18:1(4E)/18:0 and dihydroceramide d18:0/18:1(9Z), ceramide-1-phosphate d18:1(4Z)/16:0, sphingomyelin d18:1(4E)/18:1(9Z) the glycosphingolipids galactosyl ceramide d18:1(4E)/24:1(15Z) and lactosyl ceramide d18:1(4E)/24:0, and several endogenous lipids present within a porcine brain total lipid extract. In addition to the product ions formed by higher energy collision dissociation (HCD), UVPD is shown to yield a series of novel structurally diagnostic product ions resulting from cleavage of both sphingosine carbon–carbon and acyl chain carbon–carbon double bonds for direct localization of site(s) of unsaturation, as well as via diagnostic cleavages of the sphingosine backbone and N–C amide bond linkages. With activation timescales and dissociation efficiencies similar to those found in conventional MS/MS strategies, this approach is therefore a promising new tool in the arsenal of ion activation techniques toward providing complete structural elucidation in automated, high-throughput lipid analysis workflows.

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