Predicting polycyclic aromatic hydrocarbon formation with an automatically generated mechanism for acetylene pyrolysis

Using Reaction Mechanism Generator (RMG), we have automatically constructed a detailed mechanism for acetylene pyrolysis, which predicts formation of polycyclic aromatic hydrocarbons (PAHs) up to pyrene. To improve the data available for formation pathways from naphthalene to pyrene, new high‐pressure limit reaction rate coefficients and species thermochemistry were calculated using a combination of electronic structure data from the literature and new quantum calculations. Pressure‐dependent kinetics for the CH potential energy surface calculated by Zádor et al. were incorporated to ensure accurate pathways for acetylene initiation reactions. After adding these new data into the RMG database, a pressure‐dependent mechanism was generated in a single RMG simulation which captures chemistry from C to C. In general, the RMG‐generated model accurately predicts major species profiles in comparison to plug‐flow reactor data from the literature. The primary shortcoming of the model is that formation of anthracene, phenanthrene, and pyrene are underpredicted, and PAHs beyond pyrene are not captured. Reaction path analysis was performed for the RMG model to identify key pathways. Notable conclusions include the importance of accounting for the acetone impurity in acetylene in accurately predicting formation of odd‐carbon species, the remarkably low contribution of acetylene dimerization to vinylacetylene or diacetylene, and the dominance of the hydrogen abstraction CH addition (HACA) mechanism in the formation pathways to all PAH species in the model. This work demonstrates the improved ability of RMG to model PAH formation, while highlighting the need for more kinetics data for elementary reaction pathways to larger PAHs.     

Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens

We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.     

Impact of ligand protonation on virtual screening against beta-secretase (BACE1)

Structure-based virtual screens were carried out against beta-secretase (BACE1) to investigate the impact of ligand protonation on screening efficacy. A comparative evaluation of the performance and its dependence on ligand protonation states docking by Surflex, eHiTS, GOLD, and FlexX-Pharm was performed. Virtual screening performed by FlexX-Pharm (EF(1%)=69) and Surflex (EF(1%)=58) provided the best efficiency. Screening protocols by FlexX-Pharm and GOLD were affected by ligand protonation, while performance of Surflex did not depend on ligand protonation.     

Synthesis and structural characterization of cross-linked histidine-phenol Cu(ii) complexes as cytochrome c oxidase active site models

Tridentate cross-linked histidine-phenol Cu(ii) ether and ester complexes, chemical analogs of the active site of several heme-copper oxidases, have been synthesized and crystallized.     

Lumi I --> Lumi II: the last detergent independent process in rhodopsin photoexcitationt

Time-resolved absorbance difference spectra were collected at delays from 1 to 128 micros after photolysis of membrane and detergent suspensions of rhodopsin at 20 degrees C. Fitting both sets of data with two exponential decays plus a constant showed a similar fast process (lifetime 11 micros in membrane, 12 micros in 5% dodecyl maltoside) with a small but similar spectral change. This demonstrates that the Lumi I - Lumi II process, previously characterized in detergent suspensions, has similar properties in membrane without significant effect of detergent. The slower exponential process detected in the data is quite different in membrane compared to detergent solubilized samples, showing that the pronounced effect of detergent on the later rhodopsin photointermediates begins fairly abruptly near 20 micros. Besides affecting the late processes, the data collected here shows that detergent induces a small blue shift in the 1 micros difference spectrum (the Lumi I minus rhodopsin difference spectrum). The blue shift is similar to one induced by chloride ion in the E181Q rhodopsin mutant and may indicate that the ionization state of Glu181 in rhodopsin is affected by detergent.     

Ellipsometry of silica nanoparticulate Langmuir-Blodgett films for the verification of the validity of effective medium approximations

The validity of various effective medium approximations (EMAs) (Bruggeman, Maxwell-Garnett) was studied for nanostructured systems, where the scale of inhomogeneities is comparable to the wavelength. Langmuir-Blodgett (LB) layers of St?ber silica nanospheres of diameters between 40 and 129 nm are excellent model structures for the experimental verification of the validity of the EMA methods in spectroscopic ellipsometry (SE) evaluation. Nanostructured mono- and multilayered silica films were investigated by SE and reflectance spectroscopy. The effective refractive index and film thickness were determined from the results of multiparameter fitting of SE spectra in the 300-759 nm wavelength region. The distribution of the effective refractive index in the particulate films was calculated assuming an ideal close-packed arrangement of particles. The average deviation from such a structure was deduced from the corrected model by introducing a "fill factor". In the EMA approximation, the spherical shape of the silica particle determines the optical behavior, rather than the "depth distribution" of silica or porosity. Therefore, the shape of particles has a dominant effect on the optical properties of nanoparticulate LB films.     

Development of a capillary electrophoretic method for the analysis of low-molecular-weight amines from metal working fluid aerosols and ambient air

A method for the determination of low-molecular-weight amines from indoor and ambient air was developed using a concentration device followed by CE coupled with indirect spectrophotometric and mass spectrometric detection that enables a reliable, rapid-response and easy-to-operate method. In indirect detection method, the selected amines were separated from interfering metal ions and amino alcohols present in the samples with an imidazole-based buffer with ethanol and EDTA as modifier. By replacing imidazole with ammonium, the final buffer was applicable for MS detection for the analytes with m/z higher than 50. A novel monolithic polymer material based on poly(methacrylate-acrylate) copolymer was developed for sampling short-chain amines from the gaseous phase. The selected analysis conditions were applied to quantify the selected short-chain amines with detection limits for the whole procedure determined between 1 and 2 microg/filter when 40 L air was sampled with 1 L/min velocity. Improved linearity and precision were obtained when the raw, time-scaled electropherogram data were transformed into mobility-scale applied for the determination of the performance characteristics of the methods. The applicability of the process of data transformation into the mobility scale was demonstrated by studying the matrix effect of water-miscible metal working fluid (stable water-oil emulsion) and of ambient air as real samples. CE-indirect UV and CE-MS, combined with the possibility of rapid air sampling, can be useful for the estimation of short-term exposure of the selected biogenic amines.     

Mössbauer study of novel iron(II)-dioxime complexes with branched alkyl chains

Novel iron(II) oxime complexes with dimethyl-glyoxime, methyl-ethyl-glyoxime, methyl-isopropyl-glyoxime, [Fe(DioxH)₂L₂] with and without axial ligands have been synthesized. ⁵⁷Fe Mössbauer spectroscopy showed different spin states in complexes with short alkyl chain and with branched alkyl chain, respectively. It was shown that the asymmetry observed in the doublet line intensity of iron-bis-glyoximes is due to the texture effect. The effect of back-coordination was also studied in the case of iron-bis-dioxime complexes with branched alkyl chains, having different axial ligands.     

Structural effects of lipophilic methotrexate conjugates on model phospholipid biomembranes

Lipophilic conjugates of the antitumor drug methotrexate (MTX) with lipoamino acids (LAAs) have been previously described as a tool to enhance MTX passive entrance into cells, overcoming a form of transport resistance which makes tumour cells insensitive to the antimetabolite. A knowledge of the mechanisms of interaction of such lipophilic derivatives with cell membranes could be useful for planning further lipophilic MTX derivatives with an optimal antitumour activity. To this aim, a calorimetric study was undertaken using a biomembrane model made from synthetic 1,2-dipalmitoyl-glycero-3-phosphocholine (DPPC) multilamellar liposomes. The effects of MTX and conjugates on the phase transition of liposomes were investigated using differential scanning calorimetry.

The interaction of pure MTX with the liposomes was limited to the outer part of the phospholipid bilayers, due to the polar nature of the drug. Conversely, its lipophilic conjugates showed a hydrophobic kind of interaction, perturbing the packing order of DPPC bilayers. In particular, a reduction of the enthalpy of transition from the gel to the liquid crystal phase of DPPC membranes was observed. Such an effect was related to the structure and mole fraction of the conjugates in the liposomes.

The antitumour activity of MTX conjugates was evaluated against cultures of a CCRF–CEM human leukemic T-cell line and a related MTX resistant sub-line. The in vitro cell growth inhibitory activity was higher for bis(tetradecyl) conjugates than for both the other shorter- and longer-chain derivatives. The biological effectiveness of the various MTX derivatives correlated very well with the thermotropic effects observed on the phase transition of DPPC biomembranes.