A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Synthesis and polymerization of a new nitrogen‐containing bis‐ortho‐diynylarene monomer

This study focuses on the preparation, characterization, and optical properties of new bis(3,4‐diphenylethynylphenyl)phenylamine. This is the first nitrogen‐containing bis‐ortho‐diynylarene (BODA) monomer having a nitrogen atom as the spacer group. BODA monomers are usually prepared from common bisphenols, thereby providing great synthetic versatility and the opportunity to develop a wide array of novel polyarylene thermosets by varying the aromatic spacer group. The new bis(3,4‐bisphenylethynylphenyl)phenylamine was synthesized in five steps. This compound emits an intense blue color (λ = 438 nm) upon irradiation by UV light and may be suitable for use as an emitting layer in electroluminescent devices. Bis‐(3,4‐bisphenylethynylphenyl)phenylamine and its polymer have photoluminescence quantum yields 34 and 38%, respectively, and long excited‐state lifetimes of 3.2 and 3.6 ns, respectively. The structure of the monomer and its polymer were characterized using spectroscopic techniques including Ultraviolet–visible Spectrophotometer, Photoluminescence Spectrophotometer, Fourier Transform infrared spectroscopy, and Gel Permeation Chromatography. The polymerizations were studied by Differential Scanning Calorimeter. The amount of weight loss and the thermostability of the nitrogen‐containing polymer were determined from thermogravimetric analysis. The electrical conductivity of neat HCl‐doped BODA‐derived polymer film was measured according to the standard four‐point probe technique. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6988–6996, 2006     

Koexistenzbeziehungen,Darstellung und Eigenschaften ternärer Phasen im System Cu/Mo/O

Coexistence Relations, Preparation and Properties of Ternary Compounds in the System Cu/Mo/O The phase diagram of the ternary system Cu/Mo/O is presented at 773 K. The compounds CuMoO₄, Cu₃Mo₂O₉, Cu₄Mo₅O₁₇, Cu₆Mo₅O₁₈, Cu_4–xMo₃O₁₂, and Cu_xMoO₃ are found to be thermodynamical stable. The homogeneity range of Cu_4–xMo₃O₁₂ runs to x = 0.1–0.2. Single crystals of CuMoO₄ and Cu₃Mo₂O₉ were grown by chemical transport reactions with TeCl₄, Cl₂, HCl, and Br₂ as transport agent. The results were compared with thermochemical calculations. The decomposition of CuMoO₄ and Cu₃Mo₂O₉ was investigated with thermal analysis and decompositon pressure measurements.     

An electrothermal vaporization unit with axially focusing convection upstream. Part II: Modeling of the condensation process

A model is presented that describes quantitatively the condensation of analytes in pico- and nanogram masses sampled with electrothermal vaporization (ETV). It presumes that the analyte vapor condensation of such low amounts occurs mainly heterogeneously, predominantly on growing carbon particulates originating from the graphite furnace before the analyte vapor achieves saturation via cooling. The model regards the coagulation of carbon particles and the diffusion of analyte atoms. The criterion whether or not an analyte atom sticks to a colliding particle is chosen as a function depending on its temperature and on the common GFAAS pretreatment temperatures. Heterogeneous condensation of six analytes with different volatilities, Ag, Cu, Fe, Ni, Mn, and Pb, is calculated for the ETV unit with an axially focusing convection upstream described in Part I. Modifier effects are taken into account. The results are compared to measured data.     

Pure Organic Phase Phenol Biosensor Based on Tyrosinase Entrapped in a Vapor Deposited Titania Sol‐Gel Membrane

A novel amperometric biosensor was constructed for the determination of phenols in pure organic phase. This biosensor was fabricated by immobilizing tyrosinase in a titania sol‐gel membrane which was obtained with a vapor deposition method. This method was facile and avoided the calcination step needed in conventional titania sol‐gel process. The titania sol‐gel membrane could effectively retain the essential water layer around the enzyme molecule needed for maintaining its activity in organic phase. The experimental parameters such as solvent and operating potential were optimized. At ?100 mV this biosensor showed a good amperometric response to phenols in pure chloroform without any mediator and rehydration of the enzyme. For catechol determination the sensor exhibited a fast response of less than 5 seconds. The sensitivity of different phenols was as follows: catechol > phenol > p‐cresol. Additionally, the apparent Michaelis‐Menten constants of the encapsulated tyrosinase to catechol, phenol and p‐cresol were found to be 0.15±0.003, 0.17±0.008 and 0.21±0.004 mM, respectively. The biosensor had also good reproducibility and stability. This work provided a promising platform for the construction of pure organic phase biosensors and the determination of substrates with poor water solubility.     

Formation of Ad-Layers and Clusters on Condensation of Metal Vapors on Solid Surfaces

Synthesis of organometallic materials can be accomplished in many cases by cocondensation of metal atoms and organic molecules at low temperatures. The reaction kinetics is determined by the competition between metal cluster growth and formation of the organometallic compound. Interesting compounds may contain one or more metal atoms; the latter type could be obtained by reaction between a cluster containing the desired number of metal atoms and an organic molecule. A precise knowledge of the events occurring on condensation of metal atoms and cluster formation can therefore be of value in the control of chemical synthesis. These phenomena have been investigated in connection with the study of the growth of thin metallic films, both experimentally and theoretically. Direct observation of the formation of very small clusters is difficult. The good agreement between experimental results and recent calculations for the development of large clusters, however, allows reliable theoretical conclusions for the first stages of adsorption and cluster formation. The present contribution describes experimental work on film growth and relevant theoretical concepts, and an attempt is made to develop applications to organometallic synthesis.     

Calculation of the proton affinities of polyfluorobenzenes and the activation energies for 1,2-hydrogen shifts in their carbocations

Isolated polyfluorobenzene (PFB) molecules and their protonated forms are investigated by the AM1 method with full geometry optimization. The proton affinities of PFB are estimated for different protonated positions. The proton affinity of PFB averaged over all isomers is shown to decrease monotonically as the number of fluorine atoms in the molecule increases. The relative populations of different isomers of arenonium ions (AI) formed by PFB protonation are determined. From the calculated data, the value of ⁺ for the F atom in theipso-position is estimated as 1.00. The activation energies of the 1,2-hydrogen shifts in AI are calculated. The dependences of the proton affinity and the activation energies of 1,2-hydrogen shifts on the number of halogen atoms are found to have distinct characters for PFB and polychlorobenzenes. The physical reasons for these difference are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1878–1882, November, 1993.     

Electronic Structure, Aromaticity, and Physicochemical Characteristics of Carbene, Radical, and Ionic Forms of Compounds of the Imidazole Series, and their Oxo and Thio Analogs

The effects of benzannellation, phenyl substitution at the nitrogen atom, protonation at the carbene carbon, ionization, and the state of the carbene center (² or ²) on the electronic structure, diamagnetic susceptibility, induced -electron ring currents, the ¹H, ¹³C, and ¹⁴N chemical shifts, and the energies of the lowest electronic transitions of imidazol-2-ylidenes and their oxo and thio analogs were examined in the bound version of -electron perturbation theory. The calculated and experimental data are compared.     

Mechanism of silicon film deposition in the RF plasma reduction of silicon tetrachloride

Plasma-chemical reduction of SiCl₄ in mixtures with H₂ and Ar has been studied by optical emission spectroscopy (OES) and laser interferometry techniques. It has been found that the Ar:H₂ ratio strongly affects the plasma composition as well as the deposition (r _D) and etch (r _E) rates of Si: H, Cl films and that the electron impact dissociation is the most important channel for the production of SiCl_x species, which are the precursors of the film growth. Chemisorption of SiCl_x and the reactive surface reaction SiCl_x+H–SiCl_(x–1)0+HCl are important steps in the deposition process. The suggested deposition model givesr _D [SiCl_x][H], in agreement with the experimental data. Etching of Si: H, Cl films occurs at high Ar: H₂ ratio when Cl atoms in the gas phase become appreciable and increases with increasing Cl concentration. The etch rate is controlled by the Cl atom chemisorption step.     

Cadmium colloids from non-aqueous solvents

Cadmium colloids have been prepared by Chemical Liquid Deposition (CLD). The metal is evaporated to yield atoms which are solvated at liquid nitrogen temperature, and upon warming, stable liquid colloids are formed with particle size ranging between 25–100 Å. Zeta potentials were calculated according to the conversion of Hunter and the Hückel equation, for ethanol and dimethyl sulphoxide. UV/VIS measurement of most of the black colloids showed absorption band around 280 nm. For comparison, we prepared CdS colloid with size 400–625 Å. The colloids are stable to oxidation in air and/or oxygen bubbling. The synthesis of colloids and films from Cd with acetone, 2-butanone, ethanol, 2-propanol, 2-methoxyethanol, DMF and DMSO is reported. Transmission Electron Microscopy (TEM) allows us to determine particle size.