Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

Separation ofN-carbamoyl aspartate andl-dihydroorotate from serum by high-performance liquid chromatography with fluorimetric detection

Summary A high-performance liquid chromatographic method, with 9-anthryldiazomethane as derivatizing agent, has been developed for the simultaneous determination ofN-carbamoyl aspartate andl-dihydroorotate in serum. Sample preparation for 1 mL serum was by simple liquid-liquid extraction and then derivatization. The compounds were separated on a Luna C18(2) column by use of a gradient prepared from acetonitrile and 10 mM sodium acetate buffer, pH 6.0, and fluorimetric detection was performed at excitation and emission wavelengths of 365 nm and 412 nm, respectively. The response was found to be linearly dependent on concentration between 0.8 and 60 μg mL⁻¹ forl-dihydrooratate and between 0.9 and 90 μg mL⁻¹ forN-carbamoyl aspartate; the mean recovery rates were 50 and 51%, respectively. The limits of detection and quantification were 0.33 μg mL⁻¹ and 0.6 μg mL⁻¹, respectively, forl-dihydroorotate and 0.4 μg mL⁻¹ and 0.7 μg mL⁻¹ forN-carbamoyl aspartate. This method can be used to assess accumulation ofN-carbamoyl aspartate andl-dihydroorotate in body fluids in situations where cellular pyrimidine de novo synthesis is impaired.     

The optimization of silica gel synthesis from chemical bottle waste using response surface methodology

To reduce the amount of hazardous chemical bottle waste in the environment, we report the optimization research of silica extraction in chemical bottle waste into silica gel. Alkali fusion and sol–gel process were utilised to prepare silica gel effectively. The alkali fusion process was carried out by adding sodium hydroxide to produce sodium silicate. Afterwards, silica gel was prepared by the sol–gel method using hydrochloric acid. Box-Behnken Design (BBD) was applied to Optimisation factors the poptimiseactors affecting the silica recovery. The factors that optimised mass ratio, particle size, and temperature. The optimum recovery of silica gel was obtained by SiO₂: NaOH mass ratio of 1:3, the particle size of 63–74 µm, and a temperature of 800 °C. The purity of silica gel optimum is 63.74% characterised using X-ray fluorescence. The structure of silica gel is the appearance of amorphous peaks at 2θ 20-30° characterised using an x-ray diffractogram. The silica gel surface was characterises using scanning electron microscopy-energy dispersive x-ray. It showed an irregular surface and characteristic showed that silica gel had a radius of 15.74 nm and a specific surface area of 297.08 m².     

Advanced oxidation processes for decolorization of aqueous solution containing acid red G azo dye

Some investigations concerning the decolorization of Acid Red G azo dye by photooxidation with hydrogen peroxide were performed. The influences of pH, oxidant concentration, and the presence of Fe²⁺ or other metal ions (Co²⁺, Cu²⁺, Ni²⁺, Mn²⁺) as potential catalysts, were investigated. The best results were obtained in the presence of ferrous ions in acid and neutral media. The other ions are not as effective as Fe²⁺ for dye decolorization. Co²⁺ and Cu²⁺ ions have a catalytic action, at low concentration, within a wide range of pH. Ni²⁺ and Mn²⁺ ions have no catalytic effect in photooxidation with hydrogen peroxide at acid Ni²⁺ and Mn²⁺ ions have no catalytic effect in photooxidation with hydrogen peroxide at acid pH values, but show a weak action in alkaline media.     

Nucleophilic addition of bifunctional sulfimidosulfides to platinum(<Emphasis Type="SmallCaps">IV</Emphasis>)-coordinated nitriles

Reactions of the platinum(IV) nitrile complexes [PtCl₄(RCN)₂] (R = Me, CH₂Ph, Ph) with 1,2- and 1,4-PhS(=NH)C₆H₄SPh in CH₂Cl₂ afforded addition products of sulfimides and coordinated nitriles, viz., the [PtCl₄{NH=C(R)N=S(Ph)(C₆H₄SPh)}₂] complexes. The latter were isolated in 75—90% yields and characterized by elemental analysis, positive-ion FAB mass spectrometry, IR spectroscopy, and ¹H and ¹³C¹H NMR spectroscopy. The temperature dependence of the ¹H NMR spectra of the model [PtCl₄{NH=C(R)N=SPh₂}₂] complexes (R = Me, Et) in CD₂Cl₂ studied in a temperature range from +40 to -70 °C demonstrated that E—Z isomerization of the ligands is a dynamic process in a range from +40 to -10 °C. The activation free energy of this process was calculated.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1618–1622, August, 2004.     

Determination of Dopamine in the Presence of Ascorbic Acid Using a Poly(Amidosulfonic Acid) Modified Glassy Carbon Electrode

A glassy carbon electrode (GCE) was modified with electropolymerized films of amidosulfonic acid in pH 7.0 phosphate buffer solution (PBS) by cyclic voltammetry (CV). The modified electrode showed an excellent electrocatalytical effect on the oxidation of dopamine (DA). In pH 7.0 PBS, the anodic peak current increased linearly with the concentration of DA in the range of 5.0×10^–7 1.0×10^–4moldm^–3, with a correlation coefficient of 0.9932, and a detection limit (S/N=3) of 1.0× 10^–7moldm^–3. The relative standard deviation of 10 successive scans was 2.5% for 1.0×10^–6moldm^–3 DA. The interference of ascorbic acid (AA) with the determination of DA could be eliminated because of the very distinct attracting interaction between DA cations and the negatively poly(amidosulfonic acid) film in pH 7.0 PBS. The proposed method exhibited good recovery and reproducibility.     

Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition–elimination mechanism by ab initio calculations in gas phase and water

 Addition–elimination reactions involving a nucleophile and a remote leaving group [S^H _N(AE)^tele] are well-known under basic conditions, especially amongst electron-poor six-membered heterocycles, but are less commonly encountered for five-membered heterocycles and are rare under acidic conditions. Concentrated HCl converts 1-hydroxy-1H-pyrazolo[3,4-c] isoquinoline and 1-hydroxy-1H-pyrazolo[3,4-c]quinoline into 3-chloro-1H-pyrazolo[3,4-c]isoquinoline and 3-chloro-1H-pyrazolo[3,4-c]quinoline, respectively. However, apparently neither the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)-quinolines nor the parent 1-hydroxypyrazole undergo this reaction. Additionally, all these systems are refractory under basic conditions. We present a plausible mechanism for the reaction, involving the 3-addition of Cl^- to the diprotonated heterocycle, followed by the elimination of water. Calculations of the initial transition states and intermediates, using optimisation at B3LYP/6-311+G(d,p), including thermochemistry [HF/6-31+G(d)], and single-point Poisson–Boltzmann self-consistent reaction field determination of the free energy of solvation (Jaguar Poisson–Boltzmann self-consistent reaction field), support this mechanism and reproduce the observed order of reactivity, the addition step being 2–4 kcal less favourable for the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)quinolines and provide a rationalisation for the role of strong acid. Received: 27 June 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

Synthesis of molecular ferromagnetics [R3R′X]MCr(C2O4)3 (X = N,R = Bun,R′ = Prn,Et, Me; X = P,R = Ph,R′ = Bun; M = Mn,Fe, Co,Ni, Cu)

The synthesis, IR spectra, and the temperatures of the transition into a ferromagnetic state (T _c) of layered ferromagnetics [R₃RX[MCr(C₂O₄)₃ (M = Mn, Fe, Co, Cu, and Ni) with the [Ph₃BuP]⁺, [Bu₃RN]⁺ (R = Pr, Et, and Me) cations capable of subsequently changing the distances between metallooxalate layers have been considered. The temperatureT _c has been found to be independent of the size of the organic cation. It is believed that the determining factors in the transition to a ferromagnetic state are exchange interactions inside the metallooxalate layer.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2327–2330, September, 1996.     

Improvement of plant parameters of the ROBO gamma irradiation facility due to design modification

Two industrial scale, “ROBO” type ⁶⁰Co gamma irradiation facilities have recently been put into operation in Syria and Peru, and the dosimetry commissioning of both plants have been carried out to determine dose distribution within products and to calculate plant parameters such as efficiency, dose uniformity ratio and throughput. There are some design modifications between the two plants in connection with the location of the carriers with respect to the source plaque and also to each other. The effect of these construction modifications on the plant parameters is discussed in the analysis of the dose distribution data measured in the carriers with depth and height among the four irradiation rows on both sides of the source plaque. The plant parameters were also calculated for different product densities using the technical data of the facilities, and the calculated and measured results were compared to each other.     

Density functional calculations of NMR chemical shifts and ESR g-tensors

An overview is given on recent advances of density functional theory (DFT) as applied to the calculation of nuclear magnetic resonance (NMR) chemical shifts and electron spin resonance (ESR) g-tensors. This is a new research area that has seen tremendous progress and success recently; we try to present some of these developments. DFT accounts for correlation effects efficiently. Therefore, it is the only first-principle method that can handle NMR calculations on large systems like transition-metal complexes. Relativistic effects become important for heavier element compounds; here we show how they can be accounted for. The ESR g-tensor is related conceptually to the NMR shielding, and results of g-tensor calculations are presented. DFT has been very successful in its application to magnetic properties, for metal complexes in particular. However, there are still certain shortcomings and limitations, e.g., in the exchange-correlation functional, that are discussed as well. Received: 24 October 1997 / Accepted: 19 December 1997