Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data,MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State‐of‐the‐art search programs show a high tolerance for variability in compound‐specific fragmentation patterns produced by collision‐induced decomposition and enable sensitive and specific ‘identity search’. In this communication, performance characteristics of two search algorithms combined with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30 000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem‐in‐space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS. Copyright © 2013 John Wiley & Sons, Ltd.     

Toward a Raman/FORS discrimination between Art Nouveau and contemporary stained glasses from CdSxSe1 − x nanoparticles signatures

CdS_xSe_{1 − x} quantum dots received considerable attention in academic studies and as cut‐off filters and indirect‐gap semiconductors. These later compounds have also been used for artistic purposes to produce colored glass since the 1920s thanks to their bright colors. Because non‐invasive conditions are now mandatory when considering objects belonging to the cultural heritage, the use of Raman and fiber optics reflectance spectroscopy has been identified as potential ones to obtain information about the nanostructure of six samples of historical glass produced between the late 1920s and modern days. The average elemental composition of the nanocrystals has been deduced processing both optical and vibrational data, and the result arising has been compared taking into account the several factors affecting the experimental results. The diffusion of zinc inside the nanocrystals has also been questioned by the shift caused on the CdS‐ and CdSe‐like phonon band wavenumber and on the absorption edge wavelength. An investigation of the size distribution and crystallinity of CdS_xSe_{1 − x} nanoparticles has been also performed considering those parameters that are mainly influenced by the disorder of the system, such as the extent of the Urbach tail and the Raman bandwidth. Thanks to the results obtained, discrimination between the more recent glass and the older Art Nouveau ones has been verified, leading to the identification of a useful analytical protocol for conservation purposes. Copyright © 2015 John Wiley & Sons, Ltd.     

An Anionic Amido-Substituted Seven-Vertex Siliconoid Cluster

The silanide [Si₄{N(SiMe₃)Dipp}₃]⁻ ( 1 ) transforms into the anionic siliconoid cluster [Si₇{N(SiMe₃)Dipp}₃]⁻ ( 2 ) with four unsubstituted silicon atoms as a contact ion pair with [K([18]crown-6)] in C₆D₆ at room temperature within five weeks. Anion 2 was investigated by natural population analysis and visualization of intrinsic atomic orbitals. Magnetically induced current-density calculations of 2 revealed two distinct strong diatropic vortices that sum up in one direction and create a strongly shielded apical silicon atom in 2 .     

Para-Fluorination of Anilides Using Electrochemically Generated Hypervalent Iodoarenes

The para-selective fluorination reaction of anilides using electrochemically generated hypervalent ArIF₂ is reported, with Et₃N ⋅ 5HF serving as fluoride source and as supporting electrolyte. This electrochemical reaction is characterized by a simple set-up, easy scalability and affords a broad variety of fluorinated anilides from easily accessible anilides in good yields up to 86 %.     

Enantioselective Synthesis of Acyclic Orthogonally Functionalized Compounds Bearing a Quaternary Stereocenter Using Chiral Ammonium Salt Catalysis

We herein report an asymmetric protocol to access a series of orthogonally functionalized acyclic chiral target molecules containing a quaternary stereogenic center by carrying out the enantioselective α-alkylation of novel orthogonally functionalized dioxolane-containing cyanoacetates under chiral ammonium salt catalysis. By using just 1 mol % of Maruoka's spirocyclic ammonium salt catalysts enantioselectivities up to e.r.=97.5 : 2.5 could be achieved and further functional group manipulations of the products were carried out as well.     

A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.     

On-Surface Synthesis of Cumulene-Containing Polymers via Two-Step Dehalogenative Homocoupling of Dibromomethylene-Functionalized Tribenzoazulene

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on-surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well-controlled ultrahigh-vacuum conditions. Here we report the on-surface synthesis of a polymer linked by cumulene-like bonds on a Au(111) surface via sequential thermally activated dehalogenative C−C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene-like pentagon–pentagon and heptagon–heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X-ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on-surface synthesis of cumulene-containing compounds, as well as protocols relevant to the stepwise fabrication of carbon–carbon bonds on surfaces.     

Degradation of Structurally Defined Graphene Nanoribbons by Myeloperoxidase and the Photo-Fenton Reaction

As an emerging member of the graphene family, structurally defined graphene nanoribbons (GNRs) have shown promising applications in various fields. The evaluation of the degradability of GNRs is particularly important for assessing the persistence level and risk of these materials in living organisms and the environment. However, there is a void in the study of the degradation of GNRs. Here, we report the degradation behavior of GNRs in the presence of human myeloperoxidase (hMPO) or treated with the photo-Fenton (PF) reaction. With the assistance of potassium hydroxide or imidazole, which facilitates the dispersion of GNRs in the aqueous solution, GNRs underwent only partial degradation after 25-hour incubation with hMPO, while, the PF reaction degraded GNRs almost completely after 120 hours. These results indicate that structurally precise GNRs can be efficiently degraded under suitable conditions, providing more opportunities for future applications in different fields.     

Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein

The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.