Automated chemical resonance generation and structure filtration for kinetic modeling

This work discusses efficient and automated methods for constructing a set of representative resonance structures for arbitrary chemical species, including radicals and biradicals, consisting of the elements H, C, O, N, and S. Determining the representative reactive structures of chemical species is crucial for identification of reactive sites and consequently applying the correct reaction templates to generate the set of important reactions during automated chemical kinetic model generation. We describe a fundamental set of resonance pathway types, accounting for simple resonating structures, as well as global approaches for polycyclic aromatic species. Automatically discovering potential localized structures along with filtration to identify the representative structures was shown to be robust and relatively fast. The algorithms discussed here were recently implemented in the Reaction Mechanism Generator (RMG) software. The final structures proposed by this method were found to be in reasonable agreement with quantum chemical computation results of localized structure contributions to the resonance hybrid.     

Solvable Model of a Generic Driven Mixture of Trapped Bose–Einstein Condensates and Properties of a Many-Boson Floquet State at the Limit of an Infinite Number of Particles

A solvable model of a periodically driven trapped mixture of Bose–Einstein condensates, consisting of N1 interacting bosons of mass m1 driven by a force of amplitude fL,1 and N2 interacting bosons of mass m2 driven by a force of amplitude fL,2, is presented. The model generalizes the harmonic-interaction model for mixtures to the time-dependent domain. The resulting many-particle ground Floquet wavefunction and quasienergy, as well as the time-dependent densities and reduced density matrices, are prescribed explicitly and analyzed at the many-body and mean-field levels of theory for finite systems and at the limit of an infinite number of particles. We prove that the time-dependent densities per particle are given at the limit of an infinite number of particles by their respective mean-field quantities, and that the time-dependent reduced one-particle and two-particle density matrices per particle of the driven mixture are 100% condensed. Interestingly, the quasienergy per particle does not coincide with the mean-field value at this limit, unless the relative center-of-mass coordinate of the two Bose–Einstein condensates is not activated by the driving forces fL,1 and fL,2. As an application, we investigate the imprinting of angular momentum and its fluctuations when steering a Bose–Einstein condensate by an interacting bosonic impurity and the resulting modes of rotations. Whereas the expectation values per particle of the angular-momentum operator for the many-body and mean-field solutions coincide at the limit of an infinite number of particles, the respective fluctuations can differ substantially. The results are analyzed in terms of the transformation properties of the angular-momentum operator under translations and boosts, and as a function of the interactions between the particles. Implications are briefly discussed.     

Influence of Solution Volume on the Dissolution Rate of Silicon Dioxide in Hydrofluoric Acid

Experimental data and modeling of the dissolution of various Si/SiO₂ thermal coatings in different volumes of hydrofluoric acid (HF) are reported. The rates of SiO₂‐film dissolution, measured by means of various electrochemical techniques, and alteration in HF activity depend on the thickness of the film coating. Despite the small volumes (0.6–1.2 mL) of the HF solution, an effect of SiO₂‐coating thickness on the dissolution rate was detected. To explain alterations detected in HF activity after SiO₂ dissolution, spectroscopic analyses (NMR and FTIR) of the chemical composition of the solutions were conducted. This is associated with a modification in the chemical composition of the HF solution, which results in either the formation of an oxidized species in solution or the precipitation of dissolution products. HF₂^? accumulation in the HF solution, owing to SiO₂ dissolution was identified as the source of the chemical alteration.     

A New Pulsed Flow Modulation GC × GC–MS with Cold EI System and Its Application for Jet Fuel Analysis

We designed and operated a new system of pulsed flow modulation (PFM) two dimensional comprehensive gas chromatography (GC × GC) mass spectrometry (MS). This system is based on the combination of PFM–GC × GC with a quadrupole mass spectrometer of GC–MS via a supersonic molecular beams interface and its fly-through Cold EI ion source and applied this system for the analysis of JP8 jet fuel. PFM is a simple GC × GC modulator that does not consume cryogenic gases while providing tunable second GC × GC column injection time for enabling the use of quadrupole based mass spectrometry regardless its limited scanning speed. We analyzed JP8 jet fuel with our new PFM–GC × GC–MS with Cold EI system and found that as the second dimension GC elution time is increased the observed molecular ion mass is reduced. This unique observation that helped in improved sample compounds identification under co-elution conditions was enabled via having abundant molecular ions in Cold EI for all the fuel compounds. We named this type of analysis as PFM–GC × GC × MS. We found and discuss in this paper that PFM–GC × GC–MS with Cold EI combines improved separation of GC × GC with Cold EI benefits of tailing-free ultra-fast ion source response time and enhanced molecular ions and mass spectral isomer and isotope information for the provision of increased sample identification information.

     

Engineered-membranes: A novel concept for clustering of native lipid bilayers

A strategy for clustering of native lipid membranes is presented. It relies on the formation of complexes between hydrophobic chelators embedded within the lipid bilayer and metal cations in the aqueous phase, capable of binding two (or more) chelators simultaneously Fig. 1. We used this approach with purple membranes containing the light driven proton pump protein bacteriorhodopsin (bR) and showed that patches of purple membranes cluster into mm sized aggregates and that these are stable for months when incubated at 19 °C in the dark. The strategy may be general since four different hydrophobic chelators (1,10-phenanthroline, bathophenanthroline, Phen-C10, and 8-hydroxyquinoline) and various divalent cations (Ni²⁺, Zn²⁺, Cd²⁺, Mn²⁺, and Cu²⁺) induced formation of membrane clusters. Moreover, the absolute requirement for a hydrophobic chelator and the appropriate metal cations was demonstrated with light and atomic force microscopy (AFM); the presence of the metal does not appear to affect the functional state of the protein. The potential utility of the approach as an alternative to assembled lipid bilayers is suggested.     

Retention Mechanism Studies of Selected Amino Acids and Vitamin B6 on HILIC Columns with Evaporative Light Scattering Detection

The goal of the study was to investigate separation mechanism of selected “essential” amino acids (leucine, isoleucine, threonine, tryptophan, proline, and glycine) and vitamin B6 in hydrophilic interaction liquid chromatography (HILIC) with the evaporative light scattering detection. Chromatographic measurements were made on three different HILIC columns: amide-silica (TSK-gel Amide-80), amino-silica (TSK-gel NH₂-100), and cross-linked diol (Luna HILIC). The retention behaviour of the analytes was investigated as a function of different binary hydro-organic mobile phases containing 10–90 % (v/v) acetonitrile. The compounds studied were separated under isocratic and gradient conditions. The best results of tested biologically active compounds separation were obtained on the TSK-gel NH₂-100 column. TSK-gel NH₂ column showed mixed HILIC–ion-exchange mechanism, the highest separation efficiency and better selectivity and resolution for tested analytes than the other studied column, especially at concentration of water in mobile phase lower than 30 % (v/v). Special attention was dedicated to the study of interactions among the stationary phase, mobile phase and the analytes.

     

An Autonomous Chemical Robot Discovers the Rules of Inorganic Coordination Chemistry without Prior Knowledge

We present a chemical discovery robot for the efficient and reliable discovery of supramolecular architectures through the exploration of a huge reaction space exceeding ten billion combinations. The system was designed to search for areas of reactivity found through autonomous selection of the reagent types, amounts, and reaction conditions aiming for combinations that are reactive. The process consists of two parts where reagents are mixed together, choosing from one type of aldehyde, one amine and one azide (from a possible family of two amines, two aldehydes and four azides) with different volumes, ratios, reaction times, and temperatures, whereby the reagents are passed through a copper coil reactor. Next, either cobalt or iron is added, again from a large number of possible quantities. The reactivity was determined by evaluating differences in pH, UV‐Vis, and mass spectra before and after the search was started. The algorithm was focused on the exploration of interesting regions, as defined by the outputs from the sensors, and this led to the discovery of a range of 1‐benzyl‐(1,2,3‐triazol‐4‐yl)‐N‐alkyl‐(2‐pyridinemethanimine) ligands and new complexes: [Fe(L¹)₂](ClO₄)₂ ( 1 ); [Fe(L²)₂](ClO₄)₂ ( 2 ); [Co₂(L³)₂](ClO₄)₄ ( 3 ); [Fe₂(L³)₂](ClO₄)₄ ( 4 ), which were crystallised and their structure confirmed by single‐crystal X‐ray diffraction determination, as well as a range of new supramolecular clusters discovered in solution using high‐resolution mass spectrometry.     

Preparation and evaluation of carbon coated alumina as a high surface area packing material for high performance liquid chromatography

The retention of polar compounds, the separation of structural isomers and thermal stability make carbonaceous materials very attractive stationary phases for liquid chromatography (LC). Carbon clad zirconia (C/ZrO₂), one of the most interesting, exhibits unparalleled chemical and thermal stability, but its characteristically low surface area (20–30 m²/g) limits broader application as a second dimension separation in two-dimensional liquid chromatography (2DLC) where high retentivity and therefore high stationary phase surface area are required. In this work, we used a high surface area commercial HPLC alumina (153 m²/g) as a support material to develop a carbon phase by chemical vapor deposition (CVD) at elevated temperature using hexane vapor as the carbon source. The loading of carbon was varied by changing the CVD time and temperature, and the carbon coated alumina (C/Al₂O₃) was characterized both physically and chromatographically. The resulting carbon phases behaved as a reversed phase similar to C/ZrO₂. At all carbon loadings, C/Al₂O₃ closely matched the unique chromatographic selectivity of carbon phases, and as expected the retentivity was increased over C/ZrO₂. Excess carbon – the amount equivalent to 5 monolayers – was required to fully cover the oxide support in C/Al₂O₃, but this was less excess than needed with C/ZrO₂. Plate counts were 60,000–76,000/m for 5 μm particles. Spectroscopic studies (XPS and FT-IR) were also conducted; they showed that the two materials were chemically very similar.     

Cellular Fucosylation Inhibitors Based on Fluorinated Fucose-1-phosphates**

Fucosylation of glycans impacts a myriad of physiological and pathological processes. Inhibition of fucose expression emerges as a potential therapeutic avenue for example in cancer, inflammation, and infection. In this study, we found that protected 2-fluorofucose 1-phosphate efficiently inhibits cellular fucosylation with a four to seven times higher potency than known inhibitor 2FF, independently of the anomeric stereochemistry. Nucleotide sugar analysis revealed that both the α- and β-GDP-2FF anomers are formed inside the cell. In conclusion, we developed A2FF1P and B2FF1P as potent new tools for studying the role of fucosylation in health and disease and they are potential therapeutic candidates.