Determining concentration depth profiles in fluorinated networks by means of electric force microscopy

By means of electric force microscopy, composition depth profiles were measured with nanometric resolution for a series of fluorinated networks. By mapping the dielectric permittivity along a line going from the surface to the bulk, we were able to experimentally access to the fluorine concentration profile. Obtained data show composition gradient lengths ranging from 30 nm to 80 nm in the near surface area for samples containing from 0.5 to 5 wt. % F, respectively. In contrast, no gradients of concentration were detected in bulk. This method has several advantages over other techniques because it allows profiling directly on a sectional cut of the sample. By combining the obtained results with x-ray photoelectron spectroscopy measurements, we were also able to quantify F/C ratio as a function of depth with nanoscale resolution.     

Solid state structure and absolute configuration of filifolinol acetate

Careful reevaluation of the 1H and 13C NMR spectroscopic data of filifolinol acetate (4) led to the reassignment of the C-10 and C-11 signals, as well as the gem-dimethyl signals. Single crystal X-ray analysis provided an independent structural confirmation of 4, and comparison of the experimental vibrational circular dichroism spectrum with calculations performed using density functional theory provided the absolute configuration of this 3H-spiro-1-benzofuran-2,1'-cyclohexane and related molecules.     

Influence of the alkyl and alkoxy side chains on the electronic structure and charge-transport properties of polythiophene derivatives

Density Functional Theory has been used to study the structural, electronic and charge-transport properties of two regio-regular head-to-tail polythiophene derivatives, i.e. poly(3-hexyl-thiophene), P3HT, and poly(3-oxyhexyl-thiophene), P3OHT. The effect of substituents on the electronic structure was analyzed by means of bandwidth, bandgap, effective mass, total and partial densities of states and crystal orbital overlap populations. Electronic couplings were estimated from band diagrams as the splitting of the valence band. The neutral and cationic states of isolated oligomers were optimized using the supercell approximation. The hole-transfer rates and mobilities were evaluated according to Marcus's theory. Results provide a compelling illustration of the effect of side chains on the crystal packing, electronic structure and charge-transport properties. Thus, the hole mobility calculated for the alkyl derivative was 0.15 cm(2) V(-1) s(-1) (experimental mobility is 0.10 cm(2) V(-1) s(-1)), while the alkoxy derivative has a theoretical mobility of 0.49 cm(2) V(-1) s(-1). The obtained results hopefully could motivate experimentalists to try out P3OHT for an improved charge carrier mobility.     

NCIPLOT: a program for plotting non-covalent interaction regions

Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/~yang/software.htm.     

Synthesis of novel chromene scaffolds for adenosine receptors

A one-pot procedure was developed for the synthesis of novel 3-[amino(methoxy)methylene]-2-oxo-3,4-dihydro-2H-chromen-4-yl)-3-cyanoacetamides and chromeno[3,4-c]pyridine-1-carbonitriles from the reaction of 2-oxo-2H-chromene-3-carbonitriles and cyanoacetamides. These chromene derivatives were identified as new scaffolds for adenosine receptors and the hits 3a, 3c, 5a, and 5b were found.     

Potent "clicked" MMP2 inhibitors: synthesis, molecular modeling and biological exploration

A new series of MMP2 inhibitors is described, following a fragment-based drug design approach. One fragment containing an azide group and a well known hydroxamate Zinc Binding Group in a α-sulfone, α-tetrahydropyrane scaffold, has been synthesized. Water-LOGSY, STD and competition-STD experiments indicate that this fragment binds to the active site of the enzyme. A click chemistry reaction was used to connect the azide to lipophilic alkynes selected to interact selectively with the S1' subunit of MMP2, as shown by docking and molecular dynamic experiments of the designed compounds. The most potent compounds 18 and 19 displayed an IC(50) of 1.4 and 0.3 nM against MMP2 respectively, and showed negligible activity towards MMP1 and MMP7, two metalloproteinases which have a shallow S1' subsite. Compound 18 also showed a promising selectivity profile against some antitarget metalloproteinases, such as MMP8, and considerably less activity against MMP14 (IC(50) = 65 nM), and MMP9 (IC(50) = 98 nM), other MMPs characterized by having a deep S1' pocket and, therefore, more similar to MMP2.     

Confinement of halide ions within homologous inverse coordination hosts; modification of halide-ion selectivity

The structures of a series of spherical host-guest complexes [{MeE(PPh)(3)Li(4)·3thf}(4)(μ(4)-X)](-) (E = Al, [1X](-); E = Ga, [2X](-); E = In, [3X](-)) reveal that changing the halide ions (X = Cl, Br, or I) within their central tetrahedral Li(4) sites has negligible effect on the structural parameters.     

High yield synthesis and reactivity of a phosphinidene bridged dimolybdenum complex

Protonation of [Mo2Cp2(mu-H)(mu-PHR*)(CO)4] (Cp = eta5-C5H5, R* = 2,4,6-C6H2tBu3) with HBF4.OEt2 gives the hydridophosphinidene complex [Mo2Cp2(mu-H)(mu-PR*)(CO)4]BF4, which is easily deprotonated with H2O to give the known phosphinidene complex [Mo2Cp2(mu-PR*)(CO)4] in 95% yield. Reaction of the latter with I2 gives the unsaturated phosphinidene complex [Mo2Cp2I2(mu-PR*)(CO)2], which exhibits an intermetallic distance of 2.960(2) A. Irradiation of solutions of [Mo2Cp2(mu-PR*)(CO)4] with UV light gives a mixture of the triply bonded [Mo2Cp2(mu-PR*)(mu-CO)2] and the hydridophosphido derivative [Mo2Cp2(mu-H){mu-P(CH2CMe2)C6H2tBu2}(CO)4] as major species. The latter complex results from an intramolecular C-H bond cleavage from a tBu group and has been characterized by spectroscopy and an X-ray study. Irradiation in the presence of HCC(p-tol) results in the insertion of the alkyne into the Mo-P bond to give [Mo2Cp2{mu-eta1:eta2,kappa-C(p-tol)CHPR*}(CO)4] structurally characterized through an X-ray study.     

Stereochemical memory in the temperature-dependent photodenitrogenation of bridgehead-substituted DBH-type azoalkanes: inhibition of inverted-housane formation in the diazenyl diradical through the mass effect (inertia) and steric hindrance

The photochemical denitrogenation of the cyclopentene-annelated DBH-type azoalkanes 1 has been examined in solution as a function of bridgehead substitution and temperature. For all derivatives, namely, the unsubstituted 1a(H/H), monomethyl 1b(Me/H) dimethyl 1c(Me/Me), monophenyl 1d(Ph/H), and diphenyl 1e(Ph/Ph), the temperature-dependent ratio of syn and anti housanes 2 provides experimental support for a competition between the singlet (high temperature) and triplet (low temperature) reaction channels in the direct photolysis. The syn/anti ratio of the housanes 2 depends on the extent and type of bridgehead substitution; the amount of the anti diastereomer (retention) follows the order Ph > Me > H, and double substitution is more effective than single. This stereochemical memory is interpreted in terms of the mass effect (inertia) of the substituents and steric interaction (size) between the substituents at the bridgehead and the methylene bridge during the deazetation step of the transient diazenyl diradical conformations (1)DZ (exo-ax) and (1)DZ (exo-eq). These conformers are impulsively generated upon decay of the (1)(n,pi)-excited azoalkane, a trajectory assessed through computational work. The new mechanistic feature disclosed by the unprecedented anti stereoselectivity (retention) is the intervention of a puckered 1,3-cyclopentanediyl singlet diradical (1)DR as product bifurcation step, whose conformational relaxation to the planar species (loss of stereochemical memory) is encumbered by bridgehead substitution.