A complete shape characterization for molecular charge densities represented by Gaussian-type functions

An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB₂ molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian-type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two-dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two-dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.     

Chalcogenide Exchange Reaction of [RGa(μ3-Te)]4 with Elemental Sulfur and Selenium: A Density Functional Theory Study

Thermodynamic and mechanistic features of the chalcogen exchange reaction between [RGa( ₃-Te)]₄ and elemental sulfur or selenium have been studied employing density functional theory (DFT) calculations using the BL3YP basis set and Stuttgart pseudopotentials. For [MeGa( ₃-E)]₄ (E=S, Se, Te) the correlation between the calculated parameters and diffraction data for their isolable analogs is greater than 98%. Each step of the conversion of [MeGa( ₃-Te)]₄ to [MeGa( ₃-E)]₄ via [Me₄Ga₄( ₃-Te)_4–x ( ₃-E) _x ] (E=S, Se) is predicted to occur as a series of isolated reactions. The entropy change for each chalcogen exchange is small in magnitude and corresponds to the degree of cage distortion within the cubane molecules. Calculations performed on [MeGa( ₃-Te)]₄...S₈ and [MeGa( ₃-Te)]₄-S suggest that an increase in electrophilicity of the gallium next to a surface bound tellurium may result in nucleophilic cage opening for which intermediate structures are calculated.     

Gold(III) complexes with imidazole,benzoxazole, purine and pyrimidine derivatives

Summary The synthesis and characterization of Au^III complexes with several heterocyclic ligands are reported. The compounds have general formula [AuX₃(L)], where L =N-methylimidazole (N-MeIz),N-ethylimidazole (N-EtIz),N-propylimidazole (N-PrIz), benzoxazole (BO), 2-methylbenzoxazole (2-MeBO), 2,5-dimethylbenzoxazole (2,5-diMeBO), 2-amino-pyrimidine (2-APm), 4(6) -hydroxy-pyrimidine [4(6)-hydrPm] or hypoxanthine (Hypox) and X = Cl or Br. Elemental analysis, conductivity measurements and spectral studies were used for the characterization of the complexes. A square-planar geometry withN-bonded heterocyclic ligands is suggested.     

An algebraic method that includes Gibbs minimization for performing phase equilibrium calculations for any number of components or phases

The most widely used technique for performing phase equilibria calculations is the K-value method (equality of chemical potentials). This paper proposes a more efficient algorithm to achieve the results that includes Gibbs minimization when we know the number of phases. Using the orthogonal derivatives, the tangent plane equation and mass balances, it is possible to reduce the Gibbs minimization procedure to the task of finding the solution of a system of non-linear equations. Such an operation is easier and faster than finding tangents or areas, and appears to converge as fast as the K-value method. Examples illustrate application of the new technique to two and three phases in equilibrium for binary and ternary mixtures.     

Single wall carbon nanotubes density of states: comparison of experiment and theory

We study the electronic structure of a variety of single wall carbon nanotubes and report density of states obtained with the Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation and hybrid PBE0 approximation of density functional theory using Gaussian orbitals and periodic boundary conditions. PBE gives very good results for metallic tubes but the addition of a portion of exact exchange in the hybrid PBE0 functional worsens the agreement between experiment and theory. On the other hand, the PBE0 hybrid significantly improves the theoretical predictions (compared to PBE) for semiconducting tubes.     

Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.     

A catalyst-free synthesis of asymmetric diaryl ketones from aryltins

A series of diaryl ketones have been synthesized in good yields (40-78%) through the catalyst-free reaction of trimethylarylstannanes with aroyl chlorides in chlorobenzene as solvent. In addition, an attractive feature is that these reactions are completely regioselective making possible the synthesis of diarylketones which are not usually available under the influence of the directing forces of the substituents present in the aromatic ring. Also, the reaction conditions are mild enough to be applied to acid sensitive molecules.     

Effect of branching and confinement on star-branched polymeric systems

The effect of confinement, number of branches (functionality), and size of the molecules on various properties as a function of temperature of star-branched polymers confined between two walls was studied using Monte Carlo simulations with the parallel tempering technique. The coil-to-globule transition and the liquidlike to solidlike transition, similar to those observed for linear chains, were characterized in all systems by changes in the heat capacity, internal energy, and radius of gyration. The transitions were also characterized by the most probable isomeric structure at a given temperature. The radius of gyration of the star polymers was smaller than the values of linear chains when the number of arms f increased. For star chains with more than f=5 arms the values of the radius of gyration, and therefore the size of the molecules, were similar for every condition of confinement studied, especially at higher temperatures. As confinement was increased, the difference in the radius of gyration of linear chains and star polymers became even larger. The coil-to-globule transition temperatures shifted to higher temperatures as the size of the chains and the number of arms in a molecule were increased. Effects of confinement were higher on the properties of the system at the smallest separations (less than twice the monomer diameter), where the coil-to-globule transition shifted to lower temperatures. The liquidlike to solidlike transition was present at almost the same temperature for different conditions of confinement, chain size, and number of arms. The behavior of the systems for separations between the walls greater than five bead diameters was similar to the behavior in the unconfined case. Hence, no considerable effect of confinement was found above this separation.     

Ultrasensitive small molecule fluorogenic probe for human heparanase

Heparanase (HPA) is a critical enzyme involved in the remodeling of the extracellular matrix (ECM), and its elevated expression has been linked with diseases such as various types of cancer and inflammation. The detection of heparanase enzymatic activity holds tremendous value in the study of the cellular microenvironment, and search of molecular therapeutics targeting heparanase, however, no structurally defined probes are available for the detection of heparanase activity. Here we present the development of the first ultrasensitive fluorogenic small-molecule probe for heparanase enzymatic activity via tuning the electronic effect of the substrate. The probe exhibits a 756-fold fluorescence turn-on response in the presence of human heparanase, allowing one-step detection of heparanase activity in real-time with a picomolar detection limit. The high sensitivity and robustness of the probe are exemplified in a high-throughput screening assay for heparanase inhibitors.

Heparanase, a critical enzyme involved in the remodeling of the extracellular matrix, activates a disaccharide probe HADP to give a strong fluorescence signal.