SciCombinator

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Concept: Covalent bond

161

Phytochrome photoreceptors in plants and microorganisms switch photochromically between two states, controlling numerous important biological processes. Although this phototransformation is generally considered to involve rotation of ring D of the tetrapyrrole chromophore, Ulijasz et al. (2010, Nature 463, 250-254) proposed that the A-ring rotates instead. Here, we apply MAS NMR to the two parent states of following studies of the 23-kDa GAF-domain fragment of phytochrome from Synechococcus OS-B'. Major changes occur at the A-ring covalent linkage to the protein as well as at the protein residue contact of ring D. Conserved contacts associated with the A-ring nitrogen rule out an A-ring photoflip, whereas loss of contact of the D-ring nitrogen to the protein implies movement of ring D. Although none of the methine bridges showed a chemical shift change comparable to those characteristic of the D-ring photoflip in canonical phytochromes, denaturation experiments showed conclusively that the same occurs in Synechococcus OS-B' phytochrome upon photoconversion. The results are consistent with the D-ring being strongly tilted in both states and the C15=C16 double bond undergoing a Z/E isomerization upon light absorption. More subtle changes are associated with the A-ring linkage to the protein. Our findings thus disprove A-ring rotation and are discussed in relation to the position of the D-ring, photoisomerization and photochromicity in the phytochrome family.

Concepts: Protein, Oxygen, Metabolism, Nitrogen, Group, Absorption, Covalent bond, Rotation

66

Glutathione S-transferase pi 1 (GSTP1), is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased glutathione (GSH). This data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at PLs C7-C8 olefin, while PLs C2-C3 olefin was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the x-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Angstrom resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; No covalent bond formation between hPL and GSTP1 was observed. Mass spectrometric (MS) analysis of reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting hPL is not membrane permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL:GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation.

Concepts: Cancer, Cell division, Chemical bond, Disulfide bond, Glutathione, Covalent bond, Electrophile, Pi bond

28

Immobilized Cu(OAc)(2) -bis(oxazolines) via hydrogen bonding by SBA-15 was applied to asymmetric Henry reaction, and good enantioselectivities were obtained (up to 83% ee) between 2-methoxybenzaldehyde and CH(3) NO(2) in isopropyl alcohol (iPrOH). The catalyst could be reused seven times without any obvious loss in enantioselectivity. For the first time, this facile and clean immobilization method is applied to the use of bis(oxazolines) complexes. Chirality 24:1092-1095, 2012. © 2012 Wiley Periodicals, Inc.

Concepts: Oxygen, Chemical reaction, Hydrogen, Hydrogenation, Carbon, Chemical bonding, Covalent bond, Isopropyl alcohol

28

We have computationally studied para-X-substituted phenols and phenolates (X = NO, NO(2) , CHO, COMe, COOH, CONH(2) , Cl, F, H, Me, OMe, and OH) and their hydrogen-bonded complexes with B(-) and HB (B = F and CN), respectively, at B3LYP/6-311++G** and BLYP-D/QZ4P levels of theory. Our purpose is to explore the structures and stabilities of these complexes. Moreover, to understand the emerging trends, we have analyzed the bonding mechanisms using the natural bond orbital scheme as well as Kohn-Sham molecular orbital (MO) theory in combination with quantitative energy decomposition analyses [energy decomposition analysis (EDA), extended transition state-natural orbitals for chemical valence (ETS-NOCV)]. These quantitative analyses allow for the construction of a simple physical model that explains all computational observations. © 2012 Wiley Periodicals, Inc.

Concepts: Scientific method, Electron, Oxygen, Molecule, Chemical bonding, Covalent bond, Molecular orbital, Molecular orbital theory

27

Herein we report a rational design strategy for tailoring intermolecular interactions to enhance room-temperature phosphorescence from purely organic materials in amorphous matrices at ambient conditions. The built-in strong halogen and hydrogen bonding between the newly developed phosphor G1 and the poly(vinyl alcohol) (PVA) matrix efficiently suppresses vibrational dissipation and thus enables bright room-temperature phosphorescence (RTP) with quantum yields reaching 24 %. Furthermore, we found that modulation of the strength of halogen and hydrogen bonding in the G1-PVA system by water molecules produced unique reversible phosphorescence-to-fluorescence switching behavior. This unique system can be utilized as a ratiometric water sensor.

Concepts: DNA, Oxygen, Water, Hydrogen, Atom, Carbon, Chemical bonding, Covalent bond

27

A new ternary dithulium hexacobalt icosastannide, Tm2.22Co6Sn20, and a new quaternary thulium dilithium hexacobalt icosastannide, TmLi2Co6Sn20, crystallize as disordered variants of the binary cubic Cr23C6 structure type (cF116). 48 Sn atoms occupy sites of m.m2 symmetry, 32 Sn atoms sites of .3m symmetry, 24 Co atoms sites of 4m.m symmetry, eight Li (or Tm in the case of the ternary phase) atoms sites of -3 symmetry and four Tm atoms sites of m-3m symmetry. The environment of one Tm atom is an 18-vertex polyhedron and that of the second Tm (or Li) atom is a 16-vertex polyhedron. Tetragonal antiprismatic coordination is observed for the Co atoms. Two Sn atoms are enclosed in a heavily deformed bicapped hexagonal prism and a monocapped hexagonal prism, respectively, and the environment of the third Sn atom is a 12-vertex polyhedron. The electronic structures of both title compounds were calculated using the tight-binding linear muffin-tin orbital method in the atomic spheres approximation (TB-LMTO-ASA). Metallic bonding is dominant in these compounds, but the presence of Sn-Sn covalent dumbbells is also observed.

Concepts: Electron, Quantum mechanics, Molecule, Atom, Chemical bond, Metal, Covalent bond, Atomic number

27

Surface covalent organic frameworks (SCOFs), featured by atomic thick sheet with covalently bonded organic building units, are promised to possess unique properties associated with reduced dimensionality, well-defined in-plane structure, and tunable functionality. Although a great deal of efforts has been made to obtain SCOFs with different linkages and building blocks via both “top-down” exfoliation and “bottom-up” on surface synthesis approaches, the obtained SCOFs generally suffer a low crystallinity, which impedes the understanding of intrinsic properties of the materials. Herein, we demonstrate a self-limiting solid-vapor interface reaction strategy to fabricate highly ordered SCOFs. The coupling reaction is tailored to take place at the solid-vapor interface by introducing one precursor via vaporization to the surface pre-loaded with the other precursor. Following this strategy, highly ordered honeycomb SCOFs with imine linkage are obtained. The controlled formation of SCOFs in our study shows the possibility to a rational design and synthesis of SCOFs with desired functionality.

Concepts: Chemical reaction, Atom, Covalent bond, Genetic linkage, Intrinsic and extrinsic properties, Electronics terms

27

In recent years, various dipeptidyl peptidase IV (DPP-4) inhibitors have been released as therapeutic drugs for type 2 diabetes in many countries. In spite of their diverse chemical structures, no comparative studies of their binding modes in the active site of DPP-4 have been disclosed. We determined the co-crystal structure of vildagliptin with DPP-4 by X-ray crystallography and compared the binding modes of six launched inhibitors in DPP-4. The inhibitors were categorized into three classes on the basis of their binding subsites: (i) vildagliptin and saxagliptin (Class 1) form interactions with the core S1 and S2 subsites and a covalent bond with Ser630 in the catalytic triad; (ii) alogliptin and linagliptin (Class 2) form interactions with the S1' and/or S2' subsites in addition to the S1 and S2 subsites; and (iii) sitagliptin and teneligliptin (Class 3) form interactions with the S1, S2 and S2 extensive subsites. The present study revealed that the additional interactions with the S1', S2' or S2 extensive subsite may increase DPP-4 inhibition beyond the level afforded by the fundamental interactions with the S1 and S2 subsites and are more effective than forming a covalent bond with Ser630.

Concepts: Electron, Atom, Sociology, Hydrogen bond, Enzyme inhibitor, Covalent bond, Dipeptidyl peptidase-4, Development of dipeptidyl peptidase-4 inhibitors

27

Chitosan grafted with polymethyl methacrylate (PMMA-g-CS) was prepared via a free-radicals polymerization technique as a carrier for enzyme immobilization. α-Chymotrypsin (CT), as an enzyme model in this study, was immobilized onto the prepared PMMA-g-CS via covalent bonding. Calcium alginate (CA) beads were developed for encapsulating PMMA-g-CS-CT to produce PMMA-g-CS-CT/CA composite beads. Morphology and size of PMMA-g-CS particles were investigated by TEM and found to be in the nanoscale. The structure and surface morphology of the beads before and after immobilization process were characterized by FT-IR and SEM, respectively. Both the bound CT content and relative activity of immobilized enzyme were measured. A higher retained activity (about 97.7%) obtained for the immobilized CT at pH 9 for 24h. The results indicated that immobilized CT maintained excellent performance even after 25 reuses and retained 75% from its original activity after 60 days of storage at 25°C.

Concepts: Electron, Enzyme, Atom, PH, Covalent bond, Ionic bond, Immobilized enzyme, Calcium alginate

27

Based on the recently proposed super valence bond model, in which superatoms can compose superatomic molecules by sharing valence pairs and nuclei for shell closure, the 23c-14e bi-icosahedral Au(23)((+9)) core of Au(38)(SR)(24) is proved to be a superatomic molecule. Molecular orbital analysis reveals that the Au(23)((+9)) core is an exact analogue of the F(2) molecule in electronic configuration. Chemical bonding analysis by the adaptive natural density partitioning method confirms the superatomic molecule bonding framework of Au(38)(SR)(24) in a straightforward manner.

Concepts: Electron, Oxygen, Molecule, Atom, Chemical bond, Covalent bond, Molecular orbital theory, Valence bond theory