Search results for "bonding"
showing 10 items of 996 documents
Compensation of steric demand by cation–π interactions, cobaltocenium cations as guests in tetraurea calix[4]arene dimers
2003
The affinities of ferrocene (2) and the cobaltocenium cation (3+), which have roughly the same size and differ in their charge, towards the inner cavity of the dimeric capsule formed by tetraurea calix[4]arene (1) were studied in C2D4Cl2 solutions. While 3+, which occupies more than 75% of the internal volume of the dimer, is readily encapsulated this is not the case for 2. This is probably due to cation-pi interactions, which operate only between 3+ and the aromatic rings of the calix[4]arene dimer. We found that the affinity of the cobaltocenium cation is higher than that of the tropylium cation (4+) and is only 2-3 times less than that of the tetraethylammoniun cation (5+). From the vari…
Two dimensional self-assembly of bis-acylureas having various functional end groups.
2011
We present the synthesis and morphology study of thirteen bis-acylurea molecules with various functional end groups. The bis-acylureas have two acylurea groups, -NH-CO-NH-CO-, divided by a pentamethylene spacer, -(CH(2))(5)-, and two symmetric functional end groups, such as, aliphatic, benzyl, mono- and bi-thiophenyl, sulfur-containing, and propargyl (HC[triple bond]CCH(2)-) moieties. The bis-acylureas were synthesized by the coupling reactions of ureas with pimeloyl chloride or pimelic acid. Upon cooling from hot isotropic solutions, the bis-acylureas spontaneously form supermolecules. In the cases of aliphatic, benzyl, mono- and bi-thiophenyl functional groups, two dimensional supramolecu…
Energy interactions in amyloid-like fibrils from NNQQNY.
2014
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of t…
Crystal structure of 4-[(adamantan-1-yl)amino]naphthalene-1,2-dione
2019
The title compound, an example of a stable 1,2-naphthoquinone, illustrates steric buttressing of the adamantanyl group.
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
2004
The chicken avidin gene belongs to an extended gene family encoding seven avidin-related genes (AVRs), of which only avidin is expressed in the chicken. The sequences of AVR4 and AVR5 are identical and the common protein (AVR4) has been expressed both in insect and bacterial systems. The recombinant proteins are similarly hyperthermostable and bind biotin with similarly high affinities. AVR4 was crystallized in the apo and biotin-complexed forms and their structures were determined at high resolution. Its tertiary and quaternary structures are very similar to those of avidin and streptavidin. Its biotin-binding site shows only a few alterations compared with those of avidin and streptavidin…
Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment
2019
Photodynamic therapy is a promising approach to treat a variety of superficial tumors and other diseases. One of its major limitations arises from its dependence on molecular oxygen, which decreases the efficiency of the therapy in hypoxia conditions commonly developed by solid tumors. The present contribution reveals the molecular mechanism of a modified thymine bearing a nitroimidazole substituent, a photosensitizer able to produce highly harmful interstrand cross-links in the DNA double strand after irradiation selectively in absence of oxygen. The mechanism is resolved at a fully atomistic and electronic level relying on quantum mechanics (CASPT2, coupled-cluster, DFT, and TD-DFT method…
A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation.
2007
Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein−solvent and solvent−solvent hydrogen bonding have been analyzed and compared to the ones in trehalose−water and sucrose−water systems (Proteins 2005, 59, 291−302). Results help in rationalizing, at a molecular level, the effects of homologues disaccharides on protein structure/dynamics experimentally observed. Furthermore, the effectiveness of disaccharides in bioprotection in terms of peculiar protein−matrix coupling is also discussed.
Crystal structure ofp-toluenesulfonylmethyl isocyanide
2015
The molecule of the commercially available title compound, C9H9NO2S, has crystallographically imposed mirror symmetry, the mirror plane passing through the isocyanide group and thepara-C atoms, the methyl C atom and the S atom of the methyl 4-tolyl sulfone moiety. In the crystal, C—H...O hydrogen-bond interactions link the molecules into chains running parallel to thebaxis.
Influence of theZ/EIsomerism on the Pathway Complexity of a Squaramide‐Based Macrocycle
2020
The rising interest on pathway complexity in supramolecular polymerization has prompted the finding of novel monomer designs able to stabilize kinetically trapped species and generate supramolecular polymorphs. In the present work, the exploitation of the Z/E (geometrical) isomerism of squaramide (SQ) units to produce various self-assembled isoforms and complex supramolecular polymerization pathways in methylcyclohexane/CHCl3 mixtures is reported for the first time. This is achieved by using a new bissquaramidic macrocycle (MSq) that self-assembles into two markedly different thermodynamic aggregates, AggA (discrete cyclic structures) and AggB (fibrillar structures), depending on the solven…
Geminal Imidazolium Salts: A new Class of Gelators
2012
The gelling behavior of some geminal diimidazolium salts was investigated in solvents differing in polarity and hydrogen bond donor ability. The used salts, namely the 3,3'-di-n-decyl-1,1'(1,4-phenylenedimethylene)diimidazolium dibromide [p-Xyl-(decim)(2)][Br](2) (1), the 3,3'-di-n-dodecyl-1,1'(1,4-phenylenedimethylene)diimidazolium dibromide [p-Xyl-(dodecim)(2)][Br](2) (2), and the 3,3'-di-n-dodecyl-1,1'(1,4-phenylenedimethylene)diimidazolium ditetrafluoroborate [p-Xyl-(dodecim)(2)][BF(4)](2) (3), differ in the alkyl chain length and in the anion properties, such as size, shape, and coordination ability. In all cases in which gelation process was observed, the obtained gels were characteri…