Fast 3D shape screening of large chemical databases through alignment-recycling

Background  

Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.     

Synthesis of phosphorylated derivatives of isatin with sterically hindered phenol fragments

The synthesis of N-[dimethoxyphosphoryl-(3,5-di-tert-butyl-4-hydroxyphenyl)] methylisatins has been performed by the addition of isatin and 5-butylisatin to the double bond of dimethyl-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadienylidene)methylphosphonate. Subsequent functionalization of the compounds synthesized with thiosemicarbazide hydrochloride, 3-(3′,5′-di-tert-butyl-4′-hydroxyphenyl)propionic acid hydrazide, and isonicotinic acid. Hydrazide gave isatin derivatives containing several pharmacophore fragments. Each of them has the ability to the increase the antioxidant and biological activities of these compounds.     

Preparation and characterization of dense films of poly(amidoamine) dendrimers on indium tin oxide

Indium tin oxide (ITO) substrates were modified with a layer of poly(amidoamine) (PAMAM) dendrimers to change their surface properties and, in particular, the substrates' work function. The functionalization procedure involved the electrostatic adsorption of positively charged PAMAM dendrimers of generation five onto negatively polarized ITO surfaces. Three different PAMAM dendrimers were used: PAMAM-NH2 and PAMAM-OH with terminal amine and hydroxyl groups, respectively, as well as Q-PAMAM-NH2, which had been prepared from PAMAM-NH2 by quaternization of the dendrimer's terminal and internal amine groups with methyl iodide. The resulting organic films were analyzed by contact angle goniometry, X-ray photoelectron spectroscopy, ellipsometry, and Kelvin probe force microscopy to confirm the presence of a dense layer. A Langmuir isotherm was derived from surface densities of fluorescence-labeled PAMAM-NH2 dendrimers from which we deduced an equilibrium binding constant, K(eq), of (1.3 +/- 0.3) x 10(5) M(-1). Kelvin probe measurements of the contact potential difference revealed a high reduction of the work function from 4.9 eV for bare ITO to 4.3 eV for ITO with a dense film of PAMAM-NH2 of generation five. PAMAM-OH and Q-PAMAM-NH2 resulted in slightly smaller work function changes. This study illustrates that the work function of ITO can be tuned by adlayers composed of PAMAM dendrimers.     

Recognition of essential purines by the U1A protein

Background  

The RNA recognition motif (RRM) is one of the largest families of RNA binding domains. The RRM is modulated so that individual proteins containing RRMs can specifically recognize RNA targets with diverse sequences and structures. Understanding the principles governing this specificity will be important for the rational modification and design of RRM-RNA complexes.     

High-resolution Mn EXAFS of the oxygen-evolving complex in photosystem II: structural implications for the Mn4Ca cluster

The biological generation of oxygen by the oxygen-evolving complex in photosystem II (PS II) is one of nature's most important reactions. The recent X-ray crystal structures, while limited by resolutions of 3.2-3.5 A, have located the electron density associated with the Mn4Ca cluster within the multiprotein PS II complex. Detailed structures critically depend on input from spectroscopic techniques, such as EXAFS and EPR/ENDOR, as the XRD resolution does not allow for accurate determination of the position of Mn/Ca or the bridging and terminal ligand atoms. The number and distances of Mn-Mn/Ca/ligand interactions determined from EXAFS provide important constraints for the structure of the Mn4Ca cluster. Here, we present data from a high-resolution EXAFS method using a novel multicrystal monochromator that show three short Mn-Mn distances between 2.7 and 2.8 A and, hence, the presence of three di-mu-oxo-bridged units in the Mn4Ca cluster. This result imposes clear limitations on the proposed structures based on spectroscopic and diffraction data and provides input for refining such structures.     

A novel chelatofore functionalized spiropyran of the 2‐oxaindane series

A novel chelatofore functionalized spiropyran of the 2‐oxaindane series, namely 8‐formyl‐7‐hydroxy‐3′,3′‐dimethylspiro[2H‐chromene‐2,1′(3′H)‐2‐benzofuran], C₁₉H₁₆O₄, is reported. In the crystalline state, dimers are formed as a result of the π–π stacking of aromatic groups of the 2H‐chromene part of the molecule and C—H...O interactions. The C_spiro—O bond length in the pyran ring is 1.4558 (10) Å, which is longer than or equal to the bond length in thermo‐ and photochromic 2‐oxaindane spiropyrans synthesized previously, except for the 7,8‐benzo/6‐NO₂ derivative, in which this bond length is 1.465 (2) Å.     

New phosphonium salts based on 3-(diphenylphosphino)propanoic and ω-haloalkanoic acids

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