Protein structural motif recognition via NMR residual dipolar couplings.

NMR residual dipolar couplings have great potential to provide rapid structural information for proteins in the solution state. This information even at low resolution may be used to advantage in proteomics projects that seek to annotate large numbers of gene products for entire genomes. In this paper, we describe a novel approach to the structural interpretation of dipolar couplings which is based on structural motif pattern recognition, where a predefined gapless structural template for a motif is used to search a set of residual dipolar couplings for good matches. We demonstrate the applicability of the method using synthetic and experimental data. We also provide an analysis of the statistical power of the method and the effects of order tensor frame orientation, motif size, and structural complexity on motif detection. Finally, we discuss remaining problems that must be overcome before the method can be used routinely to identify protein homologies.     

Asymmetric synthesis of 3,4-dihydrocoumarin motif with an all-carbon quaternary stereocenter via a Michael-acetalization sequence with bifunctional amine-thiourea organocatalysts

Asymmetric domino Michael-acetalization reactions of 2-hydroxynitrostyrene and 2-oxocyclohexanecarbaldehyde with a bifunctional thiourea-tertiary-amine organocatalyst, e.g., the Takemoto catalyst, followed by oxidation providing the 1',3-spiro-2'-oxocyclohexan-3,4-dihydrocoumarin having one all-carbon quaternary stereocenter with excellent diastereo- and enantioselectivities (up to >99% ee), are described. The structures and absolute configurations of the products were confirmed by X-ray analysis.     

Phenylated polyimides via bifunctional monomers

The synthesis of two phenylated bifunctional monomers, dimethyl 4-(4-(p-aminophenoxy)phenyl)-3,5,6-triphenylphthalate and dimethyl 4-(4-(4-(p-aminophenoxy)phenoxy)phenyl)-3,5,6-triphenylphthlate, was accomplished. Polymerization in solution or by a bulk polymerization procedure yielded a series of low molecular weight phenylated polyimides. The polymers were soluble in chlorinated hydrocarbons and exhibited thermal stabilities comparable to other polyimide systems.     

Extreme electronic modulation of the cofacial porphyrin structural motif

The synthesis, electrochemistry, and optical spectroscopy of an extensive series of cofacial bis[(porphinato)zinc(II)] compounds are reported. These species were synthesized using sequential palladium-catalyzed cross-coupling and cobalt-mediated [2+2+2] cycloaddition reactions. This modular methodology enables facile control of the nature of macrocycle-to-macrocycle connectivity and allows unprecedented modulation of the redox properties of face-to-face porphyrin species. We report the synthesis of 5,6-bis[(5',5'-10',20'-bis[4-(3-methoxy-3-methylbutoxy)phenyl]porphinato)zinc(II)]indane (1), 5,6-bis[(2'-5',10',15',20'-tetraphenylporphinato)zinc(II)]indane (2), 5-([2'-5',10',15',20'-tetraphenylporphinato]zinc(II))-6-[(5"-10',20'-bis[4-(3-methoxy-3-methylbutoxy)phenyl]porphinato)zinc(II)]indane (3), 5-([2'-5',10',15',20'-tetrakis(trifluoromethyl)porphinato]zinc(II))-6-[(5' '-10' ',20' '-bis[4-(3-methoxy-3-methylbutoxy)phenyl]porphinato)zinc(II)]indane (4), 5-(2'-5',10',15',20'-[tetrakis(trifluoromethyl)porphinato]zinc(II))-6-[(2'-5',10',15',20'-tetraphenylporphinato)zinc(II)]indane (5), 5,6-bis([2'-5',15'-diphenyl-10',20'-(trifluoromethyl)porphinato]zinc(II))indane (6), and 5,6-bis([2'-5',10',15',20'-tetrakis(trifluoromethyl)porphinato]zinc(II))indane (7); 4-7 define the first examples of cofacial bis[(porphinato)metal] compounds in which sigma-electron-withdrawing perfluoroalkyl groups serve as macrocycle substituents, while 2, 6, and 7 constitute the first such structures that possess a beta-to-beta linkage topology. Cyclic voltammetric studies show that the electrochemically determined HOMO and LUMO energy levels of these cofacial bis(porphinato) complexes can be lowered by 780 and 945 mV, respectively, relative to the archetypal members of this class of compounds; importantly, these orbital energy levels can be modulated over well-defined increments throughout these wide potentiometric domains. Analyses of these cofacial bis[(porphinato)metal] potentiometric data, in terms of the absolute and relative frontier orbital energies of their constituent [porphinato]zinc(II) building blocks, as well as the nature of macrocycle-to-macrocycle connectivity, provide predictive electronic structural models that rationalize the redox behavior of these species.     

Multi-purpose functionality for the structural elaboration of the piperazine-2,5-dione motif

Mild methods for controlled C- and N-alkylation of 3-benzyloxycarbonylpiperazine-2,5-diones are reported. The benzyloxylcarbonyl substituent can also serve as latent functionality for N-acyliminium ion formation and subsequent trapping enables installation of new carbon and/or heteroatom substituents.     

A common motif in G-protein-coupled seven transmembrane helix receptors

Summary G-protein-coupled receptors all share the seven transmembrane helix motif similar to bacteriorhodopsin. This similarity was exploited to build models for these receptors. From an analysis of a multi-sequence alignment of 225 G-protein-coupled receptors belonging to the rhodopsin-like superfamily, conclusions could be drawn about functional residues. Seven residues in the transmembrane regions are conserved throughout all aligned receptors. These residues cluster at the cytosolic side of the transmembrane helices and are for all rhodopsin-like G-protein-coupled receptors implied in signal transduction. An analysis of correlated mutations reveals a number of residues, both in the helices and in the cytosolic loops, that might be important in the signal transduction pathway in subfamilies of this receptor family.     

Aziridines as a structural motif to conformational restriction of azasugars

In order to investigate the hypothesis that the glycosidase inhibitor isofagomine was bound to alpha- or beta-glucosidase in a 1,4B conformation, a number of bicyclic aziridines that adopt the 1,4B or B1,4 conformations were synthesised and investigated. (1R)-2-endo,3-exo-2,3-Dihydroxy-4-endo-4-hydroxymethyl-6- azabicyclo[3.1.0]hexane (5) and its N-methyl and N-benzyl analogues and (1S)-2-exo-3-endo-2,3-dihydroxy-4- endo-4-hydroxymethyl-6-azabicyclo-[3.1.0]hexane (6) were synthesised. The aziridines 5 and 6 were found to be weak or not inhibitors of alpha-glucosidase, beta-glucosidase and alpha-fucosidase.     

Gold-mediated bifunctional modification of oligosaccharides via a three-component coupling reaction

An efficient modular approach for single-site incorporation of two independent functionalities (amines and alkynes) into aldehyde-containing oligosaccharides concurrently by using a one-pot gold-mediated three-component coupling reaction in aqueous medium under mild conditions has been developed.     

3-Bromotetrazine: labelling of macromolecules via monosubstituted bifunctional s-tetrazines

We report the synthesis and first characterisation of the novel chemical probe 3-bromotetrazine and establish its reactivity towards nucleophiles. This led to the synthesis of several novel classes of 3-monosubstituted s-tetrazines. A remarkable functional group selectivity is observed and is utilised to site-selectively functionalise different complex molecules. The stability of 3-bromotetrazine under the reaction conditions facilitated the development of a protocol for protein functionalisation, which enabled a “minimal”, bifunctional tetrazine unit as a bio-orthogonal handle for inverse electron demand Diels–Alder reactions. Additionally, a novel tetrazine-based chemical probe was developed and its application in the context of thiol-targeted natural product isolation and labelling of mammalian cells is demonstrated.

3-Bromotetrazine selectively labels small and macromolecules up to proteins and can then be used as a fluorophore or as a bio-orthogonal handle for downstream functionalisation.     

Assembly kinetics of nanocrystals via peptide hybridization

The assembly kinetics of colloidal semiconductor quantum dots (QDs) on solid inorganic surfaces is of fundamental importance for implementation of their solid-state devices. Herein an inorganic binding peptide, silica binding QBP1, was utilized for the self-assembly of nanocrystal quantum dots on silica surface as a smart molecular linker. The QD binding kinetics was studied comparatively in three different cases: first, QD adsorption with no functionalization of substrate or QD surface; second, QD adsorption on QBP1-modified surface; and, finally, adsorption of QBP1-functionalized QD on silica surface. The surface modification of QDs with QBP1 enabled 79.3-fold enhancement in QD binding affinity, while modification of a silica surface with QBP1 led to only 3.3-fold enhancement. The fluorescence microscopy images also supported a coherent assembly with correspondingly increased binding affinity. Decoration of QDs with inorganic peptides was shown to increase the amount of surface-bound QDs dramatically compared to the conventional methods. These results offer new opportunities for the assembly of QDs on solid surfaces for future device applications.     

Rhombimines-cyclic tetraimines of trans-1,2-diaminocyclohexane shaped by the diaryl ether structural motif

[reaction: see text] Rhombimines, chiral macrocyclic tetraimines, are preferentially formed because of the structural bias in the reaction of aromatic ether-linked dialdehydes with enantiomerically pure trans-1,2-diaminocyclohexane.     

Ionic polymers as a new structural motif for high-energy-density materials

Energetic materials have been used for nearly two centuries in military affairs and to cut labor costs and expedite laborious processes in mining, tunneling, construction, demolition, and agriculture, making a tremendous contribution to the world economy. Yet there has been little advancement in the development of altogether new energetic motifs despite long-standing research efforts to develop superior materials. We report the discovery of new energetic compounds of exceptionally high energy content and novel polymeric structure which avoid the use of lead and mercury salts common in conventional primary explosives. Laboratory tests indicate the remarkable performance of these Ni- and Co-based energetic materials, while DFT calculations indicate that these are possibly the most powerful metal-based energetic materials known to date, with heats of detonation comparable with those of the most powerful organic-based high explosives currently in use.     

Synthesis of Fischer type-carbene complexes containing a coordinated thioimidate structural motif

This paper describes a tandem strategy to synthesize a series of new Fischer carbene complexes [(CO)(4)M[double bond, length as m-dash]C[N-(CH(2))(4)-]CH[double bond, length as m-dash]C(NRR')(SR'); M = Cr, W; R = Ar, R' = Me, -(CH(2))(2)-] with a thioimide or thiazoline fragment, in which the sulfur or nitrogen atom is coordinated to a metal center, depending on the nature of alkylating groups included as R'. We have trapped by protonation the proposed intermediate as the thioamide 12 [(CO)(5)W[double bond, length as m-dash]C[N-(CH(2))(4)-]CH(2)C(S)NHPh], which reveals the pathway of this reaction.     

具有聚酰胺结构特征的有机非线性光学材料的分子设计

有机非线性光学材料具有非共振系数大,响应时间短,光损伤阈值高等优点,是当前材料科学的重要前沿课题之一,[1-2].目前主要采用改变取代基性质和共轭长度等方法来优化非线性光学极化率和透光性之间的关系[3-4].本文设计了一种新的结构,即在共轭链上含有多个交替排列的供电基团(D)和吸电基团(A),运用量子化学方法研究了这种聚酰胺分子的结构,非线性光学性质和电子光谱,发现它们的非线性光学系数随链长增大,而电子吸收波段并不发生红移.