Flat corannulene: when a transition state becomes a stable molecule

Flat corannulene has been considered so far only as a transition state of the bowl-to-bowl inversion process. This study was driven by the prediction that substituents with strong steric repulsion could destabilize the bowl-shaped conformation of this molecule to such an extent that the highly unstable planar geometry would become an isolable molecule. To examine the substituents'' effect on the corannulene bowl depth, optimized structures for the highly-congested decakis(t-butylsulfido)corannulene were calculated. The computations, performed with both the M06-2X/def2-TZVP and the B3LYP/def2-TZVP methods (the latter with and without Grimme''s D3 dispersion correction), predict that this molecule can achieve two minimum structures: a flat carbon framework and a bowl-shaped structure, which are very close in energy. This rather unusual compound was easily synthesized from decachlorocorannulene under mild reaction conditions, and X-ray crystallographic studies gave similar results to the theoretical predictions. This compound crystallized in two different polymorphs, one exhibiting a completely flat corannulene core and the other having a bowl-shaped conformation.

The first flat metal-free corannulene derivative was predicted by computations and achieved by synthesis.     

Dynamic Interactions in Synthetic Receptors: A Guest Exchange Saturation Transfer Study

The accumulated knowledge regarding molecular architectures is based on established, reliable, and accessible analytical tools that provide robust structural and functional information on assemblies. However, both the dynamicity and low population of noncovalently interacting moieties within studied molecular systems limit the efficiency and accuracy of traditional methods. Herein, the use of a saturation transfer-based NMR approach to study the dynamic binding characteristics of an anion to a series of synthetic receptors derived from bambusuril macrocycles is demonstrated. The exchange rates of BF₄⁻ are mediated by the side chains on the receptor (100 s⁻¹<k_ex<5000 s⁻¹), which play a critical role in receptor-anion binding dynamics. The signal amplification obtained with this approach allows for the identification of different types of intermolecular interactions between the receptor and the anion, something that could not have been detected by techniques hitherto used to study molecular assemblies. These findings, which are supported by a computational molecular dynamic study, demonstrate the uniqueness and added value of this NMR method.     

Nucleus Independent Chemical Shift (NICS) at Small Distances from the Molecular Plane: The Effect of Electron Density

When close to the molecular plane, the behavior of nucleus independent chemical shift (NICS) as a function of the distance from the molecular plane deviates from its behavior at larger distances. By using a dense grid of NICS-probes (BQs) it is shown that, when close to the molecular plane, maximal (absolute) NICS values are obtained above the atoms. These maxima move towards the center as the grid is elevated until the (absolute) maximum NICS is obtained at the center and stay there when the grid is further elevated. It is shown that this behavior is a result of the current density, which is influenced by the electron density, according to the Biot-Savart law, which, in turn, causes the induced magnetic field measured by the NICS. It is thus concluded that if magnetic aromaticity is studied, the NICS calculations should be carried out at a large enough distance so that only the π-ring current affects the NICS. At distances ≥2 Å, NICS(r)_π,zz=A+B*C^r. Using non-linear correlation for obtaining A, B and C and extrapolate to NICS(1)_π,zz and NICS(1.7)_π,zz is recommended as measures for aromaticity.     

Real-Space Renormalization Estimates for Two-Phase Flow in Porous Media

We present a spatial renormalization group algorithm to handle immiscibletwo-phase flow in heterogeneous porous media. We call this algorithmFRACTAM-R, where FRACTAM is an acronym for Fast Renormalization Algorithmfor Correlated Transport in Anisotropic Media, and the R stands for relativepermeability. Originally, FRACTAM was an approximate iterative process thatreplaces the L × L lattice of grid blocks, representing the reservoir,by a (L/2) × (L/2) one. In fact, FRACTAM replaces the original L× L lattice by a hierarchical (fractal) lattice, in such a way thatfinding the solution of the two-phase flow equations becomes trivial. Thistriviality translates in practice into computer efficiency. For N=L ×L grid blocks we find that the computer time necessary to calculatefractional flow F(t) and pressure P(t) as a function of time scales as N^1.7 for FRACTAM-R. This should be contrasted with thecomputational time of a conventional grid simulator N^2.3. The solution we find in this way is an accurateapproximation to the direct solution of the original problem.     

Interpretation of Polarized Absorption and Emission Spectra of Molecules Incorporated in Stretched Polymer Films

Different methods for the interpretation of linear dichroic spectra of molecules incorporated in uniaxial matrices are discussed. A method based on the combination of both polarized absorption and emission measurements is described for the resolution of absorption and emission spectra into their different polarized components, and for the investigation of molecular distributions in the oriented matrix. The distributions of some planar molecules of different shapes incorporated in stretched polyethylene films are presented.     

Thermo-XRD-analysis of montmorillonite treated with 1,4-diaminoanthraquinone

Charcoals formed during the thermo-XRD-analysis of montmorillonite (MONT) complexes with the dye 1,4-diaminoanthraquinone (DAAQ) were investigated by using curve-fitting calculations. Five saturated dye solutions were prepared (i) in distilled water and (ii–v) in 0.1, 0.5, 1.0, and 2.0 molar HCl. Two series of dye-clay complexes were prepared by using clay suspensions of 0.6 %and of 0.006 % labeled first and second series, respectively. Five dye-clay complexes were prepared of each series by adding 25 mL of dye solution to 25 mL of clay suspension. There is no free dye in complexes of the first series, but those of the second series, which were synthesized with a high ratio between dye and clay, contain non-adsorbed dye even after five washings. Complexes of the first series are loaded with very small amounts of molecular and protonated DAAQ (5–24 mmol DAAQ per 100 g clay), and their spacings are 1.25–1.54 nm suggesting the presence of tactoids with protonated or molecular DAAQ lying parallel to the clay layers. No carbon analyses were performed to the second series complexes. In addition to tactoids with spacing of 1.32 nm, they contain tactoids with spacings of 1.81–1.96 nm, suggesting that intercalated DAAQ are lying perpendicular to the clay layers. Three types of intercalated charcoal are identified in both series during the thermal analysis, one type with a low thermal stability and two types with high thermal stabilities. Charcoals of the second series complexes preserve the geometry of the original complexes up to high temperatures.     

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer

Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics‐molecular mechanics approach with a recently developed semiempirical AM1‐SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C? H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important. © 2014 Wiley Periodicals, Inc.