Using molecular dynamics simulations to identify the key factors responsible for chiral recognition by an amino acid-based molecular micelle

Molecular dynamics (MD) simulations were used to investigate the binding of six chiral compounds to the amino acid-based molecular micelle (MM) poly-(sodium undecyl-(L)-leucine-leucine) or poly(SULL). The MM investigated is used as a chiral selector in capillary electrophoresis. The project goal was to characterize the chiral recognition mechanism in these separations and to move toward predictive models to identify the best amino acid-based MM for a given separation. Poly(SULL) was found to contain six binding sites into which chiral compounds could insert. Four sites had similar sizes, shapes, and electrostatic properties. Enantiomers of alprenolol, propranolol, 1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, 1,1′-bi-2-naphthol, chlorthalidone, or lorazepam were separately docked into each binding pocket and MD simulations with the resulting intermolecular complexes were performed. Solvent-accessible surface area calculations showed the compounds preferentially associated with binding sites where they penetrated into the MM core and shielded their non-polar atoms from solvent. Furthermore, with five of the six compounds the enantiomer with the most favorable free energy of MM association also experienced the most favorable intermolecular hydrogen bonding interactions with the MM. This result suggests that stereoselective intermolecular hydrogen bonds play an important role in chiral discrimination in separations using amino acid-based MMs.GRAPHICAL ABSTRACT     

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

A flexible protein-peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexibility of protein side chains was as important as ligand flexibility for successful protein-peptide docking. On the basis of mean field theory, a transferable potential was designed to evaluate distance-dependent protein-ligand interactions and atomic solvation energies. The potential parameters were developed using a self-consistent process based on only 10 known complex structures. The effectiveness of each intermediate potential was judged on the basis of a Z score, approximating the gap between the energy of the native complex and the average energy of a decoy set. The Z score was determined using experimentally determined native structures and decoys generated by docking with the intermediate potentials. Using 6600 generated decoys and the Z score optimization criterion proposed in this work, the developed potential yielded an acceptable correlation of R(2) = 0.77, with binding free energies determined for known MHC I complexes (Class I Major Histocompatibility protein HLA-A(*)0201) which were not present in the training set. Test docking on 25 complexes further revealed a significant correlation between energy and dRMS, important for identifying native-like conformations. The near-native structures always belonged to one of the conformational classes with lower predicted binding energy. The lowest energy docked conformations are generally associated with near-native conformations, less than 3.0 Angstrom dRMS (and in many cases less than 1.0 Angstrom) from the experimentally determined structures.     

NOTE: Synthesis and Characterization of a Poly(acrylamide) with Pendant 1,4-piperazine-2,5-dione Moieties via Post-polymerization Cyclization

A poly(acrylamide) was synthesized from N ^α -Boc-N ^? -acrolyl-l-lysylglycine methyl ester via radical polymerization. This polymer typically had Mn ～ 100,000 g/mol, Mw ～ 300,000 g/mol, and a T_g of 93°C. Removal of Boc with TFA and cyclization with DABCO? in DMSO at 65°C afforded a soluble piperazinedione-containing polymer that had a T_g of 157°C and thermal stability up to 300°C. These results demonstrate a viable and efficient synthetic route to piperazinedione-containing polyacrylamides of high molecular weight. Related polymers that incorporate substituted indane moieties could be useful high T_g materials for fabrication of LC and NLO devices.     

PHOSPHORUS-CONTAINING AMINOCARBOXYLIC ACIDS. COMMUNICATION IV.1 A CONVENIENT METHOD OF PHOSPHONIC ACIDS SYNTHESIS

Abstract

The communication is concerned with the synthesis of phosphonic aminocarboxylic acids by phosphorylation of diethyl ω-halogen alkyl acetamidomalonates with tris(trimethylsilyl) phosphite, followed by alcoholysis and acid hydrolysis of the resulting intermediate esters.     

Laponite assisted dispersion of carbon nanotubes in water

The ability of Laponite to stabilize aqueous suspensions of multiwalled carbon nanotubes (MWCNTs) was investigated with the help of analytical centrifugation, microscopic image analysis, and measurements of electrical conductivity of hybrid Laponite+MWCNT suspensions. The impact of nanotube concentration C(n) (0.0025-0.5 wt%) and Laponite/MWCNTs ratio X (varied within 0-1 wt/wt) on the properties of Laponite+MWCNT hybrid suspensions was discussed. It was observed that sonication of MWCNTs at critical minimal concentration of Laponite X(c)≈0.25±0.05 resulted in efficient dispersion and formation of stabilized suspensions of individual nanotubes. The stabilization of nanotubes in the presence of Laponite was explained by adsorption of Laponite particles and formation of a hydrophilic charged shell on the surface of nanotubes. Increase of MWCNT concentration above the critical value resulted in percolation and formation of spatially extended electrically conductive networks of particles.     

Structure and hydrolysis of the U(IV), U(V), and U(VI) aqua ions from ab initio molecular simulations

Ab initio molecular dynamics simulations at 300 K, based on density functional theory, are performed to study the hydration shell geometries, solvent dipole, and first hydrolysis reaction of the uranium(IV) (U(4+)) and uranyl(V) (UO(2)(+)) ions in aqueous solution. The solvent dipole and first hydrolysis reaction of aqueous uranyl(VI) (UO(2)(2+)) are also probed. The first shell of U(4+) is coordinated by 8-9 water ligands, with an average U-O distance of 2.42 ?. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 ?, respectively. The simulated EXAFS of U(4+) matches well with recent experimental data. The first shell of UO(2)(+) is coordinated by five water ligands in the equatorial plane, with the average U═O(ax) and U-O distances being 1.85 ? and 2.54 ?, respectively. Overall, the hydration shell structure of UO(2)(+) closely matches that of UO(2)(2+), except for small expansions in the average U═O(ax) and U-O distances. Each ion strongly polarizes their respective first-shell water ligands. The computed acidity constants (pK(a)) of U(4+) and UO(2)(2+) are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24, respectively. The predicted pK(a) value of UO(2)(+) is 8.5.     

Efficient electroformation of supergiant unilamellar vesicles containing cationic lipids on ITO-coated electrodes

Giant unilamellar vesicles (GUVs) represent a versatile in vitro system widely used to study properties of lipid membranes and their interaction with biomacromolecules and colloids. Electroformation with indium tin oxide (ITO) coated coverslips as electrodes is a standard approach to GUV production. In the case of cationic GUVs, however, application of this approach leads to notorious difficulties. We discover that this is related to aging of ITO-coated coverslips during their repeated use, which is reflected in their surface topography on the nanoscale. We find that mild annealing of the ITO-coated surface in air reverts the effects of aging and ensures efficient reproducible electroformation of supergiant (diameter > 100 μm) unilamellar vesicles containing cationic lipids.     

In situ molecular spectroscopic evidence for CO2 intercalation into montmorillonite in supercritical carbon dioxide

The interaction of anhydrous supercritical CO(2) (scCO(2)) with both kaolinite and ~1W (i.e., close to but less than one layer of hydration) calcium-saturated montmorillonite was investigated under conditions relevant to geologic carbon sequestration (50 °C and 90 bar). The CO(2) molecular environment was probed in situ using a combination of three novel high-pressure techniques: X-ray diffraction, magic angle spinning nuclear magnetic resonance spectroscopy, and attenuated total reflection infrared spectroscopy. We report the first direct evidence that the expansion of montmorillonite under scCO(2) conditions is due to CO(2) migration into the interlayer. Intercalated CO(2) molecules are rotationally constrained and do not appear to react with waters to form bicarbonate or carbonic acid. In contrast, CO(2) does not intercalate into kaolinite. The findings show that predicting the seal integrity of caprock will have complex dependence on clay mineralogy and hydration state.     

Synthesis of 7-Alkoxyquinolines,Coumarins, and Resorufins

Synthesis of the title compounds by treatment of the sodium salts of 7-quinolinol, 7-hydroxycoumarin, and resorufin with alkyl halides is described.