vdW-TSSCDS—An automated and global procedure for the computation of stationary points on intermolecular potential energy surfaces

We present a generalization of the transition state search using chemical dynamics simulations (TSSCDS) methodology (discussed in a previous study) which allows the topographical characterization of intermolecular potential energy surfaces (IPES) for non-covalently bound complexes (vdW-TSSCDS). Starting from a single random input geometry, we show that vdW-TSSCDS is able to globally and automatically locate stationary points of an IPES, even in limiting cases such as extremely flat regions or nontrivial topologies (eg, bifurcation points). The basic idea is the expression of the connectivity matrix in block structure, where diagonal blocks correspond to the isolated fragments and off-diagonal blocks provide the intermolecular connectivity. To this end, we introduce a new definition of bound or not, in a non-covalent sense, utilizing an extra set of van der Waals distances, which encompasses all kinds of non-covalent distances. To discuss the use of the vdW-TSSCDS method, we present a series of 2-body van der Waals systems, namely, Ar-Benzene (3D), N₂-Benzene (6D) and H₂O-Benzene (9D). Finally, we further illustrate its capabilities by presenting some applications for n-body problems (n > 2), (H₂O)₂-Benzene (12D) and (H₂O)₃-Benzene (21D), as well as to a reactive, fully-flexible, system (Benzene-NO₂)⁺ (39D) in which the simultaneous breaking/formation of both covalent and non-covalent interactions takes place.     

THE PECULIAR α-AMIDOALKYLATION OF VINYLTRIMETHYLSILANE

Abstract

α-Amidoalkylation of allyttrimethylsilane with methyl-2-chloro-2-(p-chlorobenzoylamino)-ethanoate 1 gave in the presence of Lewis acid racemic methyl-2- (p-chlorobenzoylamino)-4-penteno ate 2. Under the same conditions, vinlytrimethylsilane afforded (±)-trans-2-(p-chlorophenyl)-5,6-dihydro-4-methoxycarbonyl-6-trimethylsilyl-4H-1, 3-oxazine 4 as the major, by n.m.r. data and x-ray crystallography established product.     

Decarboxylation of α-Amino Acids Containing Two and Three Stereogenic Centers: A Simple One-Step Procedure to Prepare two Optically Active β-Amino Alcohols and a Bicyclic Pyrrolidine Derivative

The decarboxylation of L-threonine (2S,3R)-1, L-hydroxyproline (2S,4R)-2 and D-2-azabicyclo[3.3.0]octan-3-carboxylic acid (1R,3R,5R)-5 yield in a simple one-step procedure the corresponding optically active β-amino alcohols (R)-3 and (R)-4 and the bicyclic pyrrolidine derivative (1R,5R)-6 in 72–82% yield and >99% ee.     

Determination of 13C/12C-ratios of anthropogenic organic contaminants in river water samples by GC-irmMS

This study describes the application of a common analytical procedure adapted for compound-specific stable carbon isotope analyses of riverine contaminants. To evaluate the sensitivity of the analytical method and the precision of the isotopic data obtained, a set of numerous substances at different concentration levels were measured. For most of the anthropogenic contaminants investigated (including chlorinated aliphatics and aromatics, musk fragrances, phthalate-based plasticizers and tetrabutyl tin) acceptable carbon isotope analyses could be obtained down to amounts of approximately 5?ng absolutely applied to the gas chromatograph. These amounts correspond to concentrations in water samples at a natural abundance level of approximately 50–200?ng?L^?1 (low to medium contaminated river systems). However, it has to be considered that the precision and the sensitivity of the analytical method depend partially on the chemical properties of the substances measured. Five recovery experiments were conducted to assess changes in carbon isotope ratios during sample preparation and measurement. The compounds selected for these experiments are known riverine contaminants. Isotopic shifts or higher variations of the isotope ratios as a result of the analytical procedures applied were observed only for a couple of contaminants. Furthermore, compound-specific carbon isotope analyses were performed on eight water extracts of the Rhine river. By comparing the variation of the data of several individual compounds with the deviations obtained from the recovery experiments, it was possible to differentiate contaminants with unaffected isotope ratios and substances with significant alterations of the δ¹³C-values.     

Clickable report tags for identification of modified peptides by mass spectrometry

The identification and quantification of modified peptides are critical for the functional characterization of post-translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom-up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click-chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide-PTM quantification from various experimental conditions.     

Acrylation of biomass: A review of synthesis process: Know-how and future application directions

Over the years, eco-friendly raw biomass is being investigated to develop novel green monomer and oligomer components for sustainable polymer materials synthesis. The use of naturally obtained biomass can reduce the dependence on petrochemical suppliers and the impact of petroleum prices. Polymer materials obtained from biomass are a competitive alternative comparing with those made from petrochemicals. Domestically and industrially used vegetable oil derivatives are considered widely available, while cellulose derivatives are the most abundant natural polymers. Biobased acrylic polymers developed from vegetable oils and cellulose are very popular nowadays. Using acrylic derivatives of vegetable oils and cellulose as naturally obtained materials leads to long-lasting biopolymers with a wide range of high exploitation properties and applications. The characteristics of vegetable oil- and cellulose-based acrylate resins of high-biorenewable carbon content are suitable for industrial application, while their role is still underestimated. A brief analysis of biomass-derived biopolymer resin compositions, properties, and applications is critically outlined herein.     

Frequency-selective quantitation of short-echo time 1H magnetic resonance spectra

Accurate and efficient filtering techniques are required to suppress large nuisance components present in short-echo time magnetic resonance (MR) spectra. This paper discusses two powerful filtering techniques used in long-echo time MR spectral quantitation, the maximum-phase FIR filter (MP-FIR) and the Hankel-Lanczos Singular Value Decomposition with Partial ReOrthogonalization (HLSVD-PRO), and shows that they can be applied to their more complex short-echo time spectral counterparts. Both filters are validated and compared through extensive simulations. Their properties are discussed. In particular, the capability of MP-FIR for dealing with macromolecular components is emphasized. Although this property does not make a large difference for long-echo time MR spectra, it can be important when quantifying short-echo time spectra.     

2- and 2,7-Substituted para-N-Methylpyridinium Pyrenes: Syntheses,Molecular and Electronic Structures,Photophysical, Electrochemical,and Spectroelectrochemical Properties and Binding to Double-Stranded (ds) DNA

Two N-methylpyridinium compounds and analogous N-protonated salts of 2- and 2,7-substituted 4-pyridyl-pyrene compounds were synthesised and their crystal structures, photophysical properties both in solution and in the solid state, electrochemical and spectroelectrochemical properties were studied. Upon methylation or protonation, the emission maxima are significantly bathochromically shifted compared to the neutral compounds, although the absorption maxima remain almost unchanged. As a result, the cationic compounds show very large apparent Stokes shifts of up to 7200 cm⁻¹. The N-methylpyridinium compounds have a single reduction at ca. −1.5 V vs. Fc/Fc⁺ in MeCN. While the reduction process was reversible for the 2,7-disubstituted compound, it was irreversible for the mono-substituted one. Experimental findings are complemented by DFT and TD-DFT calculations. Furthermore, the N-methylpyridinium compounds show strong interactions with calf thymus (ct)-DNA, presumably by intercalation, which paves the way for further applications of these multi-functional compounds as potential DNA-bioactive agents.