A synthetic mimic of protein inner space: buried polar interactions in a deep water-soluble host

A deep water-soluble cavitand was functionalized with a carboxylic acid directed toward the hydrophobic interior of the host. The buried salt-bridge interaction formed with a quinuclidium cationic guest was determined to be worth -3 kcal/mol using a free energy cycle. The strength of the interaction correlates well with buried salt bridges in proteins, indicating that the cavitand interior mimics the hydrophobic inner space of proteins.     

Photoregulated supramolecular hydrogels driven by polyradical interactions

Organic radical as a powerful tool has been extensively applied in synthetic chemistry. However, harnessing radical-mediated noncovalent interactions to fabricate soft materials remains elusive. Here we report a new category of supramolecular hydrogel system held by multiple radical-radical (polyradical) interactions, and its photosensitive cross-linking structure. A simple polyacrylamide with triarylamine (TAA) pendants is designed as the precursor. The TAA units in polymer can be converted into active TAA^•⁺ radical cations with light and further associate each other via TAA^•⁺‒TAA^•⁺ stacking interactions to form stable supramolecular network. Temporal control of the light irradiation dictates the degree of radical stacks, thus regulating the mechanical performance of the resulting hydrogel materials on-demand. Moreover, the reversible collapse of this hydrogels can be promoted by adding radical scavenger or exerting reduction voltage.     

Modification in structure, phase transition, and magnetic property of metallic gallium driven by atom-molecule interactions

The present work supports a novel paradigm in which the surface structure and stacking behavior of metallic gallium (Ga) were significantly influenced by the preparation process in the presence of organic small molecules (ethanol, acetone, dichloromethane, and diethyl ether). The extent of the effect strongly depends on the polarity of the molecules. Especially, a series of new atom-molecule aggregates consisting of metallic Ga and macrocyclic hosts (cyclodextrins, CDs) were prepared and characterized by various techniques. A comprehensive comparative analysis between free metallic Ga and the Ga samples obtained provides important and at present rare information on the modification in structure, phase transition, and magnetic property of Ga driven by atom-molecule interactions. First, there is a notable difference in microstructure and electronic structure between the different types of Ga samples. Second, differential scanning calorimetry analysis gives us a complete picture (such as the occurrence of a series of metastable phases of Ga in the presence of CDs) that has allowed us to consider that Ga atoms were protected by the shielding effect provided by the cavities of CDs. Third, the metallic Ga distributed in the aggregates exhibits very interesting magnetic property compared to free metallic Ga, such as the uniform zero-field-cooled and field-cooled magnetization processes, the enhanced responses in magnetization to temperature and applied field, and the fundamental change in shape of magnetic hysteresis loops. These significant changes in structural transformation and physical property of Ga provide a novel insight into the understanding of atom-molecule interactions between metallic atoms and organic molecules.     

Selective protein-protein interactions driven by a phenylalanine interface

Highly specific protein-protein interfaces have been the subject of considerable study for their potential utility in disrupting or interrogating cellular signaling and control networks. We report that coiled-coil sequences decorated with phenylalanine core residues fold into stable alpha-helical bundles and that these self-sort from similar peptide assemblies with aliphatic core side chains. For self-assembled ensembles derived from 30-residue monomeric peptides, the DeltaG of specificity is -1.5 kcal/mol, comparable with earlier self-sorting coiled-coil systems. Intriguingly, although this interface is constructed from canonical amino acids, it does not appear to have been exploited in native proteins.     

Hydrophobic side-chain interactions in a family of dimeric amide foldamers-potential alpha-helix mimetics

A series of new alpha-helix mimetics based on a benzamide scaffold and potentially able to disrupt protein-protein interactions have been synthesized and characterized by X-ray analysis. Inspection of the solid state structures of aromatic amide dimers confirmed that the molecules adopt a curved conformation with intramolecular H-bonding between the amide NH and the alkoxy oxygen of the neighboring aromatic fragment (d_NH…_O ∼ 2 Å). Adjacent dimer molecules are prone to form supramolecular assemblies due to both hydrophobic alkyl side-chain/side-chain interactions and intermolecular H-bonding.     

Colloid-colloid and colloid-wall interactions in driven suspensions

We investigate the nonequilibrium fluid structure mediated forces between two colloids driven through a suspension of mutually noninteracting Brownian particles as well as between a colloid and a wall in stationary situations. We solve the Smoluchowski equation in bispherical coordinates as well as with a method of reflections, both in linear approximation for small velocities and numerically for intermediate velocities, and we compare the results to a superposition approximation considered previously. In particular, we find an enhancement of the friction (compared to the friction on an isolated particle) for two colloids driven side by side as well as for a colloid traveling along a wall. The friction on tailgating colloids is reduced. Colloids traveling side-by-side experience a solute induced repulsion while tailgating colloids are attracted to each other.     

Atomic structure of a short alpha-helix stabilized by a main chain hydrogen-bond surrogate

Herein we report the 1.15 A X-ray crystal structure of a short alpha-helix in which the N-terminal i and i + 4 main chain hydrogen bond is replaced with a carbon-carbon bond. The structure shows that the hydrogen-bond surrogate (HBS) derived alpha-helix truly resembles the structure of canonical alpha-helices and provides unequivocal support for our helix nucleation strategy.     

FTIR studies of polar interactions in polymer blends

Specific interactions in binary blends of poly(vinyl chloride) (PVC) with ethylene–vinyl acetate copolymers (EVA) and ethylene-methyl acrylate copolymers (EMA) were investigated by observation of band shifts of the carbonyl absorption using ATR-FTIR spectroscopy at variable temperature. Blends of PVC with EVA and EMA could be prepared as heterogeneous, homogeneous or metastable homogeneous mixtures, depending on the copolymer composition. The miscible systems as well as the heterogeneous ones showed only very small or no band shifts. The metastable blends exhibited shifts of several wave numbers to lower values, which vanished at higher temperatures as the blends demixed. Strong interactions in the metastable blends could be related to good impact properties of the corresponding two-phase systems.     

NMR analysis of aromatic interactions in designed peptide beta-hairpins

Designed octapeptide beta-hairpins containing a central (D)Pro-Gly segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel beta-strands. Using a set of five peptide hairpins, aromatic interactions have been probed across antiparallel beta-sheets, in the non-hydrogen bonding position (Ac-L-Y-V-(D)P-G-L-Y/W-V-OMe: peptides 1 and 2), diagonally across the strands (Boc-Y/W-L-V-(D)P-G-W-L-V-OMe: peptides 3 and 6), and along the strands at positions i and i + 2 (Boc-L-L-V-(D)P-G-Y-L-W-OMe: peptide 4). Two peptides served as controls (Boc-L-L-V-(D)P-G-Y-W-V-OMe: peptide 5; Boc-L-Y-V-(D)P-G-L-L-V-OMe: peptide 7) for aromatic interactions. All studies have been carried out using solution NMR methods in CDCl(3) + 10% DMSO-d(6) and have been additionally examined in CD(3)OH for peptides 1 and 2. Inter-ring proton-proton nuclear Overhauser effects (NOEs) and upfield shifted aromatic proton resonances have provided firm evidence for specific aromatic interactions. Calculated NMR structures for peptides 1 and 2, containing aromatic pairs at facing non-hydrogen bonded positions, revealed that T-shaped arrangements of the interacting pairs of rings are favored, with ring current effects leading to extremely upfield chemical shifts and temperature dependences for specific aromatic protons. Anomalous far-UV CD spectra appeared to be a characteristic feature in peptides where the two aromatic residues are spatially proximal. The observation of the close approach of aromatic rings in organic solvents suggests that interactions of an electrostatic nature may be favored. This situation may be compared to the case of aqueous solutions, where clustering of aromatic residues is driven by solvophobic (hydrophobic) forces.     

Cation-anion interactions and polar structures in the solid state

Complicated structures where oxygen and fluorine are found together in one framework, where deviations from Pauling's second crystal rule (PSCR) are expected, often result in structures with important physical properties. The [NbOF5]2- anion and therefore all the individual Nb-O and Nb-F bonds are ordered in noncentrosymmetric KNaNbOF5 and centrosymmetric CsNaNbOF5. The Na/K- and Na/Cs-O/F interactions in these phases, in particular the expected deviations from PSCR and the bond valence model, reveal the essential role of the small potassium cations in the acentric packing of the [NbOF5]2- anion. KNaNbOF5 crystallizes in the orthorhombic and polar space group Pna21 (No. 33) with lattice constants a = 11.8653(11) A, b = 5.8826(6) A, c = 8.1258(8) A, and Z = 4, while CsNaNbOF5 crystallizes in the orthorhombic space group Pbcn (No. 60) with lattice constants a = 8.3155(7), b = 13.3176(11), c = 11.1314(9), and Z = 8.     

Molecular sieve valves driven by adsorbate-adsorbate interactions: hysteresis in permeation of microporous membranes

A recently derived mesoscopic framework describing activated micropore diffusion is employed to explore system criticality in microporous membranes under nonequilibrium conditions. Rapid exploration of parameter space, possible with this continuum framework, elucidates a novel temperature-induced ignition and extinction of the molecular flux under a macroscopic gradient in pressure (chemical potential). Deviation from equilibrium like phase behavior (i.e., shifting and narrowing of phase envelopes and double hysteresis) derives from asymmetry of the coupled boundaries of the nonequilibrium membrane. We confirm this new phase behavior, akin to "opening" and "closing" of a molecular valve, via gradient kinetic Monte Carlo simulations of thin one-dimensional and three-dimensional systems. The heat of adsorption, strength of adsorbate-adsorbate intermolecular forces, and chemical potential gradient are all shown to control 'valve' actuation, suggesting potential implications in chemical sensing and novel diffusion control.     

Specific interactions in complexes formed by polythiophene derivatives bearing polar side groups and plasmid DNA

The interaction between plasmid DNA and polythiophene derivatives bearing substituents with polar groups has been examined using electrophoresis assays, and both UV-Vis and CD spectroscopies. Results clearly indicate that such conducting polymers form stable adducts with DNA, even although the interactions strongly depend on the chemical constitution of the polymers. Furthermore, digestion assays with EcoRI and BamHI evidence that the polymers form specific interactions with the DNA, protecting the target nucleotide sequences of these restriction enzymes. On the other hand, UV-Vis and CD spectra show that the interactions induce a fast and very significant exposition of the nitrogen bases, which is consequence of the structural alterations induced in the circular DNA. These results have been compared with those previously reported for polypyrrole, poly(3,4-ethylenedioxythiophene) and poly(3-methylthiophene). Finally, a model based on the intercalation of the conducting polymer between the two DNA strands has been proposed.     

Cation-cation interactions between uranyl cations in a polar open-framework uranyl periodate

Novel open-framework alkali metal uranyl periodates, having the formula A[(UO2)3(HIO6)(OH)(O)(H2O)].1.5H2O (A = Li, Na, K, Rb, Cs), have been prepared through mild hydrothermal synthesis. These isostructural compounds contain distorted UO7 pentagonal bipyramids that are linked through a uranyl (UO22+) to uranyl cation-cation interaction. This interaction arises from a single axial uranyl oxygen coordinating at an equatorial site of an adjacent uranyl unit. These uranium oxide polyhedra are further bound by IO6 distorted octahedra creating an open-framework structure whose channels contain the alkali metal cations.     

Band shape in vibrational spectra and interactions of polar molecules in liquids

The structure and shape of bands in the Raman vibrational spectra of polar molecules in liquids are analyzed. The possibility of using these data to examine interactions of molecules as well as their vibrational and orientational dynamics is shown. Translated from Zhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 270–281, March–April, 1997.