Molecular modeling study of the differential ligand–receptor interaction at the μ, δ and κ opioid receptors

3D models of the opioid receptors , and were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.     

A Three-Dimensional Two-Phase Model for Thermal Plasma Chemical Vapor Deposition with Liquid Feedstock Injection

In this paper, a comprehensive model for thermal plasma chemical vapor deposition (TPCVD) with liquid feedstock injection is documented. The gas flow is assumed to be steady, of a single temperature. Radiation and charged species contributions are excluded, but extensive homogeneous and heterogeneous chemistry is included. The liquid phase is traced by considering individual droplets. Discussion on the model's application to diamond production from acetone in a hydrogen–argon plasma is included. The major conclusions are: (1) Liquid injection possesses a capability to deliver the hydrocarbon precursor directly onto the deposition target. (2) For the case of complete evaporation of the droplet before reaching the substrate, the deposition rate is similar to that obtained with gaseous precursors. (3) The computational results compare well with experimental data. The modeling results can be used to optimize the injection parameters with regard to the deposition rate.     

Synthese und Geruch von (Z)-Dehydro-homo-β-santalol

Summary Guided by molecular modeling studies, the synthesis of the title compound is described. The organoleptic evaluation proved the predicted real sandal like odour of (Z)-dehydro-homo--santalol.

Aus den Diplomarbeiten von C.P. (1991), I.P. und B.Ö. (1992), Universität Wien     

Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Modeling high-pressure densities at wide temperature range with volume scaling: Cyclohexane + n-hexadecane mixtures

High-pressure density data for cyclohexane + n-hexadecane mixtures at a wide temperature range was modeled with several classical equations of state (EOS) and correlative models. A modification for softening the co-volume and another for a volume scaling of the Peng–Robinson EOS (VS-PR) were proposed. The VS-PR model is able to correlate the pure component experimental data employing only five adjustable parameters, with root-mean-square deviation (RMSD) between calculated and experimental densities essentially within the experimental error. This result is superior to widely used approaches, i.e., a six parameter Tait model and six parameter volume translations (temperature and pressure dependent) for Peng–Robinson and Patel–Teja EOS. The VS-PR model also represents well the isobaric thermal expansion and the isothermal compressibility coefficients of the pure cyclohexane, a small naphthenic substance as well as a long chain n-alkane hydrocarbon, n-hexadecane. When modeling the mixture data, the use of VS-PR model of pure components along with the Redlich–Kister expansion, truncated at the first term, the density was correlated within a RMSD only 60% greater than the experimental error. The proposed model is able to accurately represent all the tested mixture data with a relatively small number of parameters.     

Solubility enhancement of triflumizole by host-guest interaction with β-cyclodextrin

Summary The solubility enhancement of triflumizole, a systemic fungicide, by -cyclodextrin inclusion complexation was investigated by electron absorption spectroscopy. The respective association constant determined by different methods was estimated to 470±20M ^–1 in aqueous solution. A model for the host-guest complexation was deduced by molecular calculations.

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Löslichkeitsverbesserung von Triflumizole durchHost-Guest-Complexierung mit -Cyclodextrin

Zusammenfassung Die Löslichkeitsverbesserung des systemischen Fungizids Triflumizole durch Komplexierung mit -Cyclodextrin wurde mittels Elektronenabsorptionsspektroskopie untersucht. Die entsprechende Stabilitätskonstante wurde durch verschiedene Methoden erfaßt und betrug im wäßrigen Medium 470±20M ^–1. Ein Model für denHost-Guest-Complex wurde durch Molekülrechnungen erstellt.

     

Classification of cultivation area of ginseng by near infrared spectroscopy and ICP-AES

A rapid and nondestructive near infrared (NIR) method using soft independent modeling of class analogy (SIMCA) for the classification of cultivation area (Korea and China) was evaluated and confirmed. Raw, first, and second derivative NIR spectra were compared to develop a robust classification rule. The chemical properties of ginseng samples were also investigated to find out the differences between Korean samples and Chinese samples. These differences make NIR spectroscopic method viable. The average value of each Korean and Chinese ginseng sample for crude fiber, crude protein, starch, and 10 inorganic constituents were measured and compared with F-test and t-test. The inorganic constituents were also measured by induced coupled plasma-atomic emission spectroscopy (ICP-AES). It could be found that the amount of starch and ten inorganic elements for example Na, Mg, P, K, Ca, Mn, Fe, Ni, Cu and Zn in ginseng samples are considerably different based on cultivation area. SIMCA has been applied to the inorganic data to investigate the possibility of ICP-AES as classification tool. However, it was observed that the result was not equal to than NIR spectra data. The overall results showed the availability of NIR method using SIMCA would be adequate for classification of cultivation of ginseng, since NIR spectra includes useful and various information on chemical properties in spite of broad and overlapped bands.     

Parametric study of the flow and temperature fields in an inductively coupled r.f. plasma torch

A theoretical investigation of the effect of different parameters on the flow and the temperature fields in a radiofrequency inductively coupled plasma is carried out. The parameters studied are: central injection gas flow rate, total gas flow rate, input power, and the type of plasma gas. The results obtained for argon and nitrogen plasmas at atmospheric pressure indicate that the flow and the temperature fields in the coil region, as well as the heat flux to the wall of the plasma confinement tube, are considerably altered by the changes in the torch operating conditions.