Nature of cationic poly(propylenimine) dendrimers in aqueous solutions as studied using versatile indicator dyes

Aqueous solutions of four cationic poly(propylenimine) low-generation dendrimers of different architecture and hydrophobicity have been examined as media for acid-base reactions of indicator dyes. The cationic dendrimers in solution can be considered as oligomers of cationic polyelectrolytes, or surfactant-like species, able to form micelles through self-association or sometimes even as unimolecular micelles. The dendrimers influence the ionization constants, tautomeric equilibria, and absorption/emission/excitation spectra of indicator dyes. The p K a values of the majority of the indicator dyes decrease in dendrimer solutions, often by 1-2 p K a units, similar to effects registered in micellar solutions of cationic surfactants. Analogously, the shifts of absorption band maxima indicate that the microenvironments of the dyes bound to the dendrimers are less polar than in water. However, some spectral effects denote the specificity of the dendrimers. The greatest difference between the dendrimers and spherical surfactant micelles is revealed by kinetic processes, especially of bromophenol blue alkaline fading in a dendrimer solution but not in a micellar surfactant solution. Within the dendrimer series, the most significant differences were observed for substances possessing n-dodecyl tails on the one hand and those without such hydrophobic portions on the other. For the last-named, the decrease in p K a's of indicators, band shifts of their anions, and in particular displacement of tautomeric equilibria compared with aqueous solutions are much smaller than for more hydrophobic dendrimers.     

Experimentally-based recommendations of density functionals for predicting properties in mechanically interlocked molecules

Mechanically interlocked molecules (rotaxanes and catenanes) have already revolutionized molecular electronics and have the promise of a similar impact in other areas of nanotechnology, ranging from nanoactuators to in vivo drug nanocarriers. However, it would be most useful to have quantitative criteria for predicting structures, binding, and excitation energies for use in designing molecules with mechanical bonds. We assess here the use of density functional theory (DFT) to a noncovalently bound complex and find that no density functional is fully satisfactory. However, we find that the new M06-suite of density functionals, which include attractive medium-range interactions, leads to dramatic improvements in the structures (error of 0.04 A in the interplanar distances for M06-L compared to 0.42 A for B3LYP) and excitation energies (within 0.08 eV for TD-M06-HF without empirical correction compared to 2.2 eV error for TD-B3LYP). However, M06 predicts the complex to be too strongly bound by 22.6 kcal mol(-1) (B3LYP leads to too weak a bond by 29 kcal mol(-1)), while current empirical FF DREIDING is too weakly bound by only 15 kcal mol(-1).     

Sandwich-type tetranuclear lanthanide complexes with cucurbit[6]uril: from molecular compounds to coordination polymers

Sandwich-type lanthanide complexes with macrocyclic ligand cucurbit[6]uril (C 36H 36N 24O 12, CB[6]) were synthesized under hydrothermal conditions from aqueous solutions of lanthanide(III) bromides, CB[6], and 4-cyanopyridine. According to X-ray analysis (Ln = La, Pr, Dy, Ho, Er, and Yb), the compounds with different structural types of lanthanide cores have a common fragment where the tetranuclear hydroxo complex is sandwiched between two macrocycles {(IN@CB[6])Ln 4(mu 3-OH) 4(IN@CB[6])} (6+) (IN = isonicotinate). The photoluminescence (for Ln = Eu) and Fourier transform ion cyclotron resonance mass spectra (for Ln = Pr, Dy, and Er) were studied. The compounds are used for the first time as precursors for the synthesis of lanthanide-silver heterometallic coordination polymers. The chainlike crystal structure of polymers (Ln = La, Pr, and Dy) is constituted by the sandwich complexes linked via the coordination of IN nitrogen atoms to the silver atoms.     

Ascospiroketals A and B, unprecedented cycloethers from the marine-derived fungus Ascochyta salicorniae

Chemical investigation of the marine-derived fungus Ascochyta salicorniae led to the isolation of two novel natural products, ascospiroketals A (1) and B (2). From a biosynthetic standpoint, the compounds possess new ring systems. [structure: see text].     

Energy-directed tree search: an efficient systematic algorithm for finding the lowest energy conformation of molecules

We present a new systematic algorithm, energy-directed tree search (EDTS), for exploring the conformational space of molecules. The algorithm has been designed to reliably locate the global minimum (or, in the worst case, a structure within 4 kJ mol(-1) of this species) at a fraction of the cost of a full conformational search, and in this way extend the range of chemical systems for which accurate thermochemistry can be studied. The algorithm is inspired by the build-up approach but is performed on the original molecule as a whole, and objectively determines the combinations of torsional angles to optimise using a learning process. The algorithm was tested for a set of 22 large molecules, including open- and closed-shell species, stable structures and transition structures, and neutral and charged species, incorporating a range of functional groups (such as phenyl rings, esters, thioesters and phosphines), and covering polymers, peptides, drugs, and natural products. For most of the species studied the global minimum energy structure was obtained; for the rest the EDTS algorithm found conformations whose total electronic energies are within chemical accuracy from the true global minima. When the conformational space is searched at a resolution of 120 degrees , the cost of the EDTS algorithm (in its worst-case scenario) scales as 2(N) for large N (where N is the number of rotatable bonds), compared with 3(N) for the corresponding systematic search.     

Efficient peptide coupling involving sterically hindered amino acids

Hindered amino acids have been introduced into peptide chains by coupling N-(Cbz- and Fmoc-alpha-aminoacyl)benzotriazoles with amino acids, wherein at least one of the components was sterically hindered, to provide compounds 3a-e, (3c +3 c'), 5a-d, (5a + 5a'), 6a-c, (6b + 6b'), 8a-c, 9a-e, 10a-d, and (10a + 10a') in isolated yields of 41-95% with complete retention of chirality as evidenced by NMR and HPLC analysis. The benzotriazole activation methodology is a new route for the synthesis of sterically hindered peptides. (Note: compound numbers written within brackets represent diastereomeric mixtures or racemates; compound numbers without brackets represent enantiomers.).     

Fumed silica – rheological additive for adhesives,resins, and paints

Fumed silica, a synthetic silicon dioxide, is a powerful rheological additive for resins and paints to introduce thixotropy or even a yield point. The rheological effectiveness of fumed silica is based on its ability to form percolating networks which immobilize large volumes of liquid. By a combination of advanced rheological experiments, spectroscopical investigations, and quantum chemical calculations it could be demonstrated that the formation and stability of the silica network is strongly influenced by particle-resin interactions. The results can be used to develop comprehensive models, which explain the rheological performance of different grades of fumed silica in different resins.     

Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter

Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl⁻ anion and a proton (H⁺), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu_in and Glu_ex.     

4-Azidocinnoline—Cinnoline-4-amine Pair as a New Fluorogenic and Fluorochromic Environment-Sensitive Probe

A new type of fluorogenic and fluorochromic probe based on the reduction of weakly fluorescent 4-azido-6-(4-cyanophenyl)cinnoline to the corresponding fluorescent cinnoline-4-amine was developed. We found that the fluorescence of 6-(4-cyanophenyl)cinnoline-4-amine is strongly affected by the nature of the solvent. The fluorogenic effect for the amine was detected in polar solvents with the strongest fluorescence increase in water. The environment-sensitive fluorogenic properties of cinnoline-4-amine in water were explained as a combination of two types of fluorescence mechanisms: aggregation-induced emission (AIE) and excited state intermolecular proton transfer (ESPT). The suitability of an azide–amine pair as a fluorogenic probe was tested using a HepG2 hepatic cancer cell line with detection by fluorescent microscopy, flow cytometry, and HPLC analysis of cells lysates. The results obtained confirm the possibility of the transformation of the azide to amine in cells and the potential applicability of the discovered fluorogenic and fluorochromic probe for different analytical and biological applications in aqueous medium.