Novel alignment method of small molecules using the Hopfield Neural Network

Molecular alignment is an important step in three-dimensional quantitative structure-activity relationship (3D-QSAR) such as comparative molecular field analysis (CoMFA). A reasonable molecular alignment is necessary for building a 3D-QSAR model. In this paper, a novel method for molecular alignment using the Hopfield Neural Network (HNN) is introduced. Four kinds of chemical properties are assigned to each atom of a molecule. Then, those properties between two molecules correspond to each other using HNN. To validate our method, HNN was applied to 12 pairs of enzyme inhibitors cited from the Protein Data Bank (PDB). As a result, our method could successfully reproduce the real molecular alignments obtained from X-ray crystallography.     

Adsorption properties of activated carbon from waste newspaper prepared by chemical and physical activation

Adsorption properties of activated carbons prepared from waste newspaper by chemical and physical activation were investigated using water vapor, ammonia, methane, and methylene blue (MB) as adsorbents. The water vapor adsorption isotherms show type V behavior and the maximum vapor adsorption of the chemically and physically activated products is about 1050 and 450 ml/g, respectively. The higher water vapor adsorption of the chemically activated products is attributed to the higher specific surface area (S(BET)) and greater hydrophilic activity (arising from the surface oxygen-containing functional groups) than in the physically activated products. The adsorption of ammonia and methane was measured by temperature-programmed desorption (TPD). NH(3) adsorption is found to be higher in the chemically activated product than in the physically activated product while methane adsorption is slightly higher in the physically activated products even though these have lower S(BET) values. In the MB adsorption, the chemically activated products show higher adsorption (390 mg/g) than the physically activated product. These results are suggested to be related to the surface characteristics.     

Imaging mass spectrometry of gold nanoparticles in a tissue section as an immunohistochemical staining mass probe

For analysis of low abundance peptides in a tissue section, immunohistochemical staining through antibody‐antigen interaction is a usual technique. The antibody is conjugated with a probe moiety that aids in highly sensitive detection. Gold nanoparticles, which show excellent chemical stability and variation of surface modifications, are expected to act as a sensitive mass probe to desorb gold ions (Au⁺, Au₂⁺, Au₃⁺) that are distinguishable from fragment ions from organic molecules. Here, green fluorescent proteins (GFP) in a tissue section of a transgenic zebrafish were detected by the gold mass probe conjugated with antibodies. Due to the efficient ionization and desorption of gold ions, imaging mass spectrometry of Au₂⁺ ions indicated the distribution of gold nanoparticles stained in a tissue section, and the mass signal distribution was consistent with the area where the GFP‐expressing cells were distributed. Conventional immunofluorescence techniques showed intense autofluorescence that come from intrinsic fluorophores in the tissue section. In contrast, the gold nanoparticles acted as an immunostaining mass probe that displayed significantly lower background signals.     

Acidity distribution of carboxyl groups in Loy Yang brown coal: its analysis and the change by heat treatment

Brown coals have a considerable number of acidic functional groups of which the main component is carboxyl groups, and the acidity has a wide distribution. In this paper, changes of the acidity distribution were examined by aqueous titration when brown coal was heat-treated to control its acidity distribution. For Loy Yang brown coal from Australia dried at 50 degrees C under vacuum (LY50), the acid dissociation constant, Ka, was distributed over a wide pKa range between 2 and 9. Then, using Gaussian functions, the acidity distribution was divided into four groups, which were characterized by average pKa values: average pKa value of 3.8 (hereafter referred to as Group A), 5.2 (Group B), 6.8 (Group C), and 8.3 (Group D). Among them, Groups A, B, and C were assigned to carboxyl groups. From the changes of the number of carboxyl groups when brown coal was heat-treated up to 400 degrees C, it was found that the way of decrease was different among these acidic groups. The decrease of the amount of carboxyl groups in Group C was significant, and at 325 degrees C most of them disappeared. On the other hand, the carboxyl groups in Group A remained even at a high temperature of 400 degrees C. We estimated approximately the structures around carboxyl groups for LY50 and their structural changes by heat treatment using the known pKa values for simple carboxylic acids and the pKa values calculated by the MOPAC program for complicated carboxylic acids.     

Determination of alkylphenols and alkylphenol polyethoxylates by reversed-phase high-performance liquid chromatography and solid-phase extraction

A simple, accurate and reproducible reversed-phase high-performance liquid chromatography (HPLC) method was developed for the separation and characterisation of alkylphenols (APs) and alkylphenol polyethoxylates (APEOs), using a C18 octadecyl silica (ODS) column. APs and each APEO oligomer were separated successfully within a reasonable time without gradient elution. An excellent resolution was obtained, even for mixtures of APs and low EO number APEOs, which are otherwise difficult to separate using conventional normal-phase HPLC methods. This method, combined with solid-phase extraction, was highly applicable for the simultaneous determination of alkylphenols and alkylphenol ethoxylates in real samples.     

Isospecific copolymerization of styrene and a styrene‐terminated polyisoprene macromonomer with the Ni(acac)2/MAO catalyst

The copolymerization of styrene (St) with a styrene‐terminated polyisoprene macromonomer (SIPM) by a nickel(II) acetylacetonate [Ni(acac)₂] catalyst in combination with methylaluminoxane (MAO) was investigated. A SIPM with a high terminal degree of functionalization and a narrow molecular weight distribution was used for the copolymerization of St. The copolymerization proceeded easily to give a high molecular weight graft copolymer. After fractionation of the resulting copolymer with methyl ethyl ketone, the insoluble part had highly isotactic polystyrene in the main chain and polyisoprene in the side chain. Lowering the MAO/Ni molar ratio and the polymerization temperature were favorable to producing isospecific active sites. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1241–1246, 2000     

Polymerization of methyl methacrylate with nickelocene‐methylaluminoxane catalyst

The polymerization of methyl methacrylate (MMA) catalyzed with cyclopentadienylnickel‐methylaluminoxane (Cp₂Ni‐MAO) was investigated. Polymerization readily proceeds with this catalyst, and the resulting polymer is rich in syndiotactic content. The effects of the MAO/Ni system on the polymerization activity of MMA were observed, and it was found that only small amounts of MAO are required to reach high polymerization activity.     

Construction of arene-fused-piperidine motifs by asymmetric addition of 2-trityloxymethylaryllithiums to nitroalkenes: the asymmetric synthesis of a dopamine D1 full agonist, A-86929

The straightforward methodology for the construction of chiral arene-fused-piperidine motifs using a highly enantioselective addition of 2-trityloxymethylaryllithiums to cyclic and acyclic nitroalkenes has been developed. The versatility of the process was highlighted by the first asymmetric synthesis of a dopamine D1 full agonist, A-86929.     

Efficient synthesis of (±)-γ-lycorane employing stereoselective conjugate addition to nitroolefin

(±)-γ-Lycorane 3 was synthesized in 52% overall yield via seven steps from 5 by employing the highly stereoselective nitro-Michael cyclization of 5 to 9 and diastereoselective conjugate addition of aryllithium to a nitroolefin 10 as two key steps.     

Colloidal crystallization of thermo-sensitive gel spheres of poly (<Emphasis Type="Italic">N</Emphasis>-isopropyl acrylamide). Influence of gel size

Influence of the gel size on the morphology, phase diagram, and reflection spectroscopy of the colloidal crystals of thermo-sensitive gel spheres, poly (N-isopropylacrylamide) (pNIPAm), was discussed by adding the data of two gel samples of pNIPAm(400–5) and pNIPAm(600–5) of 412 nm (at 25 °C) and 220 nm (at 45 °C) and of 517 nm (at 20 °C) and 294 nm (at 45 °C), respectively. Colloidal single crystals formed, but not so large compared with the giant crystals of small pNIPAm gels reported previously. The suspensions even with ion-exchange resins were turbid and hard to observe the single crystals clearly with the naked eyes as gel size increased. The critical concentration of melting decreased sharply as the suspensions were deionized with coexistence of the mixtures of cation- and anion-exchange resins. The critical concentration increased as the gel size increased and/or dispersion temperature increased. Density of the gel spheres increased as their size increased. These results demonstrated that the colloidal crystallization takes place by the extended electrical double layers formed around the gel spheres in addition of the excluded volume effect of the gels. Contribution of the electrical double layers on the crystallization increased sharply as temperature increased and gel concentration decreased, respectively. The contribution also increased slightly as sphere size increased, when comparison was made at the same gel concentration in wt.%. The present work clarified that the colloidal interfaces, which are inevitable for the formation of the electrical double layers, are formed between the water phase and gel spheres, though the gel spheres contain a lot of water molecules at the inner sphere region.