Graphs to chemical structures. 4: Combinatorial enumeration of planted three-dimensional trees as stereochemical models of monosubstituted alkanes

Planted three-dimensional (3D) trees, which are defined as a 3D version of planted trees, are enumerated by means of Fujita’s proligand method formulated in Parts 1–3 of this series [Fujita in Theor Chem Acc 113:73–79, 80–86, 2005; Fujita in Theor Chem Acc 115:37–53, 2006]. By starting from the concepts of proligand and promolecule introduced previously [Fujita in Tetrahedron 47:31–46, 1991], a planted promolecule is defined as a 3D object in which the substitution positions of a given 3D skeleton are occupied by a root and proligands. Then, such planted promolecules are introduced as models of planted 3D-trees. Because each of the proligands in a given planted promolecule is regarded as another intermediate planted promolecule in a nested fashion, the given planted promolecule is recursively constructed by a set of such intermediates planted promolecules. The recursive nature of such intermediate planted promolecules is used to derive generating functions for enumerating planted promolecules or planted 3D-trees. The generating functions are based on cycle indices with chirality fittingness (CI-CFs), which are composed of three kinds of sphericity indices (SIs), i.e., a _d for homospheric cycles, c _d for enantiospheric cycles, and b _d for hemispheric cycles. For the purpose of evaluating c _d recursively, the concept of diploid is proposed, where the nested nature of c _d is demonstrated clearly. The SIs are applied to derive functional equations for recursive calculations, i.e., a(x), c(x ²), and b(x). Thereby, planted 3D-trees or equivalently monosubstituted alkanes as stereoisomers are enumerated recursively by counting planted promolecules. The resulting values are collected up to 20 carbon content in a tabular form. Now, the enumeration problem initiated by mathematician Cayley [Philos Mag 47(4):444–446, 1874] has been solved in such a systematic and integrated manner as satisfying both mathematical and chemical requirements.     

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase

Reactive flux molecular dynamics simulations have been carried out using a combined QM/MM potential to study the dynamics of the nucleophilic substitution reaction of dichloroethane by a carboxylate group in haloalkane dehalogenase and in water. We found that protein dynamics accelerates the reaction rate by a factor of 2 over the uncatalyzed reaction. Compared to the thermodynamic effect in barrier reduction, protein dynamic contribution is relatively small. However, analyses of the friction kernel reveal that the origins of the reaction dynamics in water and in the enzyme are different. In aqueous solution, there is significant electrostatic solvation effect, which is reflected by the slow reorganization relaxation of the solvent. On the other hand, there is no strong electrostatic coupling in the enzyme and the major effect on reaction coordinate motion is intramolecular energy relaxation.     

Cellulose microfibrils from banana farming residues: isolation and characterization

Cellulose microfibrils have been prepared from banana rachis using a combination of chemical and mechanical treatments. The morphology and structure of the samples were characterized using transmission electron microscopy, atomic force microscopy, and X-ray diffraction. Fourier-transformed infrared spectroscopy (FTIR) was used to characterize the chemical modifications of the samples after each treatment. Suspensions of bundled or individualized 5-nm-wide microfibrils were obtained after homogenization (PH) whereas an organosolv (PO) treatment resulted in shorter aggregates of parallel cellulose microcrystallites. The sharper rings in the X-ray diffraction pattern of the PO-treated sample suggest a higher crystallinity due to a more efficient removal of hemicelluloses and dissolution of amorphous zones by the acid treatment. Both microfibrils and microcrystals prepared by both methods can be used as reinforcing filler in nanocomposite materials.     

A way of establishing quality of measurements in gas analysis—national and international aspects

Standardising quality of measurements at both the national and international level results in a unity in measurement that may be regarded a synonym of traceability. In gas analysis, the key issue in achieving this aim is production of gaseous reference materials. Establishing a network of secondary measurement standards at gaseous CRM producers’ sites in Ukraine might be interesting for those involved in gas analysis activities. Inevitably, problems concerning the recognition of measuring capabilities of both national metrological institutes and local CRM producers are now an international issue. Thus, the problems of national adoption of international standards, as well as harmonisation between different international documents are currently relevant, and Ukrainian experience may be useful to others in this field. Presented at the 3rd International Conference on Metrology, November 2006, Tel Aviv, Israel.     

New In-situ Sampling and Analysis of the Production of CeO<Subscript>2</Subscript> Powders from Liquid Precursors using a Novel Wet Collection System in a rf Inductively Coupled Thermal Plasma Reactor. Part 1: Reactor System and Sampling Probe

A new reactor and a novel in-situ sampling technique were developed for the study of the synthesis of CeO₂ powders produced from dissolved cerium nitrate salts. The conical reactor minimized particle recirculation and provided a highly symmetrical and undisturbed plasma flow suitable for the analysis of the phenomena affecting the formation of CeO₂ powders. Both a calorimetric study of the reactor and a thermodynamic analysis of CeO₂ formation were conducted. The sampling probe is described and near-isokinetic sampling was achieved. The sampled particles were collected using a miniature wet collection system, i.e. a mist atomizer and a custom-made spray chamber. A numerical simulation of the velocity and temperature fields of the plasma gas in the reactor was done using Fluent. A comprehensive droplet-to-particle formation mechanism presented elsewhere is revisited and expanded based on calorimetry, thermodynamics of CeO₂ formation, numerical simulations and collected particles. No traces of other oxidation states other than CeO₂ were found.     

Direct, two-step synthetic pathway to novel dibenzo[a,c]phenanthridines

Novel dibenzo[a,c]phenanthridines are prepared regioselectively by the application of a straightforward synthetic pathway, starting from new 3,4-diaryl- and 3,4-dihydro-3,4-diarylisoquinolines prepared via Ritter-type heterocyclization and the more classical two-step reductive amination/Bischler-Napieralski cyclization of triarylethanones, respectively. A comparative study of nonphenolic oxidative coupling methodologies provides a highly efficient procedure, based on the hypervalent iodine reagent phenyliodine(III) bis(trifluoroacetate) (PIFA), to accomplish the final coupling step.     

Preconcentration of Cadmium and Zinc on a Chelating Sorbent and Their Determination by Flame Atomic Absorption Spectrometry

A method is developed for cadmium and zinc preconcentration on a minicolumn packed with a new chelating polymer sorbent. The effects of the test solution pH and volume, the sample matrix composition, the eluent volume, and the sample and eluent flow rates are studied. Zinc and cadmium in the eluate are determined by flame atomic absorption spectrometry. Under optimal conditions, the determined ion recovery is more than 95%. The detection limits (3σ, n = 20) are found to be 15.0 (Cd) and 17.2 (Zn) ng/mL. The developed method is employed for cadmium and zinc determination in samples of seawater and water obtained after oil pumping.     

Flow-injection analysis with a small cylindrical wire type electrode

An amperometric detector with a small thin mercury film electrode is described. The device demonstrates advantageous operational characteristics such as small dispersion (D<2) and “memory effect” (me<0.6%), extensive maximum sample frequency (msf −200 samples/h), and high sensitivity. It has been proven useful in flow-injection analysis at a constant potential under hydrodynamic conditions.     

Case Study: Doping Substances in Equestrian Food Supplements

In the course of investigations on equestrian supplemental products for the presence of doping substances, two products were found to contain forbidden substances. As reported earlier a plant extract (Mexican cactus extract) named “Energy 5” contained the anabolic androgenic steroids (AAS) stanozolol, 17β-hydroxy-17α-methyl-5α-androstane-3β-ol (3β,5α-THMT) as well as mestanolone not declared on the label. In the present study, a product called “Super Kalm Paste” was tested. Analysis by gas chromatography - mass spectrometry (GC-MS) revealed that the preparation contained the class I anti-arrhythmics quinine (trade names Kinidin^TM, Durules) and cinchonine. The samples were prepared according to a sample preparation procedure established for anabolic steroids in nutritional supplements for humans. The sample treatment comprised the extraction and purification of the analytes as well as the chemical conversion with N-methyl-N-trimethylsilyl-trifluoracetamide (MSTFA) to yield the trimethylsilyl (TMS)-derivatives. To verify whether the administration of such products could lead to positive doping tests, a pilot excretion study on “Energy 5” was conducted with two geldings, and urine samples were collected. Gas chromatography - high resolution mass spectrometry (GC-HRMS) after solid phase extraction and mixed derivatisation has demonstrated the presence of the stanozolol metabolite 16β-hydroxy-stanozolol in urine samples after “Energy 5” application.     

Model-free kinetics applied to regeneration of coked alumina

Thermogravimetry is proposed to study the alumina catalyst regeneration deactivated by coke, after being used in the transformation of styrene in a fixed bed continuous flow reactor. The model-free kinetic approach has been applied to data for the thermal oxidation of carbonaceous deposits on the catalyst. The activation energy (E) was calculated as a function of a (conversion) and T (temperature), by using Vyazovkin model-free kinetic method, allowing to estimate time required to remove coke at a given temperature. This revised version was published online in August 2006 with corrections to the Cover Date.