Two-dimensional semiconducting nanostructures based on single graphene sheets with lines of adsorbed hydrogen atoms

It is shown that lines of adsorbed hydrogen pair atoms divide the graphene sheet into strips and form hydrogen-based superlattice structures (2HG-SL). We show that the forming of 2HG-SL drastically changes the electronic properties of graphene from semimetal to semiconductor. The electronic spectra of "zigzag" (n,0) 2HG-SL is similar to that of (n,0) carbon nanotubes and have a similar oscillation of band gap with number n, but with non-zero minimal values. The composite dual-periodic (n,0)+(m,0) 2HG-SLs of "zigzag" strips are analyzed, with the conclusion that they may be treated as quasi-two-dimensional heterostructures. We also suggest an experimental way of fabricating hydrogen superlattices.Comment: 12 pages, 3 figure

The interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons

We have studied the interaction of polyaromatic hydrocarbons (PAHs) with the basal plane of graphite using thermal desorption spectroscopy. Desorption kinetics of benzene, naphthalene, coronene and ovalene at sub-monolayer coverages yield activation energies of 0.50 eV, 0.85 eV, 1.40 eV and 2.1 eV, respectively. Benzene and naphthalene follow simple first order desorption kinetics while coronene and ovalene exhibit fractional order kinetics owing to the stability of 2-D adsorbate islands up to the desorption temperature. Pre-exponential frequency factors are found to be in the range $10^{14}$-$10^{21} s^{-1}$ as obtained from both Falconer--Madix (isothermal desorption) analysis and Antoine's fit to vapour pressure data. The resulting binding energy per carbon atom of the PAH is $52\pm$5 meV and can be identified with the interlayer cohesive energy of graphite. The resulting cleavage energy of graphite is $61\pm5$~meV/atom which is considerably larger than previously reported experimental values.Comment: 8 pages, 4 figures, 2 table

Nanopercolation

We investigate through direct molecular mechanics calculations the geometrical properties of hydrocarbon mantles subjected to percolation disorder. We show that the structures of mantles generated at the critical percolation point have a fractal dimension $d_{f} \approx 2.5$. In addition, the solvent access surface $A_{s}$ and volume $V_{s}$ of these molecules follow power-law behavior, $A_{s} \sim L^{\alpha_A}$ and $V_{s} \sim L^{\alpha_V}$, where $L$ is the system size, and with both critical exponents $\alpha_A$ and $\alpha_V$ being significantly dependent on the radius of the accessing probing molecule, $r_{p}$. Our results from extensive simulations with two distinct microscopic topologies (i.e., square and honeycomb) indicate the consistency of the statistical analysis and confirm the self-similar characteristic of the percolating hydrocarbons. Due to their highly branched topology, some of the potential applications for this new class of disordered molecules include drug delivery, catalysis, and supramolecular structures.Comment: 4 pages, 5 figure

Conductance of Distorted Carbon Nanotubes

We have calculated the effects of structural distortions of armchair carbon nanotubes on their electrical transport properties. We found that the bending of the nanotubes decreases their transmission function in certain energy ranges and leads to an increased electrical resistance. Electronic structure calculations show that these energy ranges contain localized states with significant $\sigma$-$\pi$ hybridization resulting from the increased curvature produced by bending. Our calculations of the contact resistance show that the large contact resistances observed for SWNTs are likely due to the weak coupling of the NT to the metal in side bonded NT-metal configurations.Comment: 5 pages RevTeX including 4 figures, submitted to PR

Diamagnetic response of cylindrical normal metal - superconductor proximity structures with low concentration of scattering centers

We have investigated the diamagnetic response of composite NS proximity wires, consisting of a clean silver or copper coating, in good electrical contact to a superconducting niobium or tantalum core. The samples show strong induced diamagnetism in the normal layer, resulting in a nearly complete Meissner screening at low temperatures. The temperature dependence of the linear diamagnetic susceptibility data is successfully described by the quasiclassical Eilenberger theory including elastic scattering characterised by a mean free path l. Using the mean free path as the only fit parameter we found values of l in the range 0.1-1 of the normal metal layer thickness d_N, which are in rough agreement with the ones obtained from residual resistivity measurements. The fits are satisfactory over the whole temperature range between 5 mK and 7 K for values of d_N varying between 1.6 my m and 30 my m. Although a finite mean free path is necessary to correctly describe the temperature dependence of the linear response diamagnetic susceptibility, the measured breakdown fields in the nonlinear regime follow the temperature and thickness dependence given by the clean limit theory. However, there is a discrepancy in the absolute values. We argue that in order to reach quantitative agreement one needs to take into account the mean free path from the fits of the linear response. [PACS numbers: 74.50.+r, 74.80.-g]Comment: 10 pages, 9 figure

Surface Enhanced Second Harmonic Generation from Macrocycle, Catenane, and Rotaxane Thin Films: Experiments and Theory

Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest degree of order is observed in the case of macrocycle monolayers and the lowest in the case of rotaxane multilayers. The second harmonic generation activity is interpreted in terms of electric field induced second harmonic (EFISH) generation where the electric field is created by the substrate silver atoms. The measured second order nonlinear optical susceptibility for a rotaxane thin film is compared with that obtained by considering only EFISH contribution to SHG intensity. The electric field on the surface of a silver layer is calculated by using the Delphi4 program for structures obtained with TINKER molecular mechanics/dynamics simulations. An excellent agreement is observed between the calculated and the measured SHG susceptibilities.

Performance of ab initio and density functional methods for conformational equilibria of CnH2n+2 alkane isomers (n=2-8)

Conformational energies of n-butane, n-pentane, and n-hexane have been calculated at the CCSD(T) level and at or near the basis set limit. Post-CCSD(T) contribution were considered and found to be unimportant. The data thus obtained were used to assess the performance of a variety of density functional methods. Double-hybrid functionals like B2GP-PLYP and B2K-PLYP, especially with a small Grimme-type empirical dispersion correction, are capable of rendering conformational energies of CCSD(T) quality. These were then used as a `secondary standard' for a larger sample of alkanes, including isopentane and the branched hexanes as well as key isomers of heptane and octane. Popular DFT functionals like B3LYP, B3PW91, BLYP, PBE, and PBE0 tend to overestimate conformer energies without dispersion correction, while the M06 family severely underestimates GG interaction energies. Grimme-type dispersion corrections for these overcorrect and lead to qualitatively wrong conformer orderings. All of these functionals also exhibit deficiencies in the conformer geometries, particularly the backbone torsion angles. The PW6B95 and, to a lesser extent, BMK functionals are relatively free of these deficiencies. Performance of these methods is further investigated to derive conformer ensemble corrections to the enthalpy function, $H_{298}-H_0$, and the Gibbs energy function, ${\rm gef}(T)\equiv - [G(T)-H_0]/T$, of these alkanes. While $H_{298}-H_0$ is only moderately sensitive to the level of theory, ${\rm gef}(T)$ exhibits more pronounced sensitivity. Once again, double hybrids acquit themselves very well.Comment: J. Phys. Chem. A, revised [Walter Thiel festschrift

Atomic Scale Modelling of Two-Dimensional Molecular Self-Assembly on a Passivated Si Surface

International audienceThe self-assembly of two-dimensional (2D) molecular structures on a solid surface relies on the subtle balance between non covalent intermolecular and molecule-surface forces. The energetics of 2D molecular lattices forming different patterns on a passivated semiconductor surface are here investigated by a combination of atomistic simulation methods. Density-functional theory provides structure and charges of the molecules, while metadynamics with empirical forces provides a best guess for the lowest-energy adsorption sites of single molecules and dimers. Subsequently, molecular dynamics simulations of extended molecular assemblies with empirical forces yield the most favorable lattice structures at finite temperature and pressure.The theoretical results are in good agreement with scanning tunneling microscopy observations of self-assembled molecular monolayers on a B-doped Si(111) surface, thus allowing to rationalize the competition of long-range dispersion forces between the molecules and the surface. Such a result demonstrates the interest of this predictive approach for further progress in supramolecular chemistry on semiconductor surface

CheS-Mapper - Chemical Space Mapping and Visualization in 3D

Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis

Preliminarno ispitivanje antimikotskog i citotoksičnog djelovanja derivata cikloalkil[b]tiofena PLS-DA analizom

A series of 2-[(arylidene)amino]-cycloalkyl[b]thiophene-3-carbonitriles (2a-x) was synthesized by incorporation of substituted aromatic aldehydes in Gewald adducts (1a-c). The title compounds were screened for their antifungal activity against Candida krusei and Criptococcusneoformans and for their antiproliferative activity against a panel of 3 human cancer cell lines (HT29, NCI H-292 and HEP). Forantiproliferative activity, the partial least squares (PLS) methodology was applied. Some of the prepared compounds exhibited promising antifungal and proliferative properties. The most active compounds for antifungal activity were cyclohexyl[b]thiophene derivatives, and forantiproliferative activity cycloheptyl[b]thiophene derivatives, especially 2-[(1H-indol-2-yl-methylidene)amino]-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carbonitrile (2r), which inhibited more than 97 % growth of the three cell lines. The PLS discriminant analysis (PLS-DA)applied generated good exploratory and predictive results and showed that the descriptors having shape characteristics were strongly correlated with the biological data.Koristeći supstituirane aromatske aldehide u Gewaldovim aduktima 1a-c sintetizirani su derivati 2-[(ariliden)amino]-cikloalkil[b]tiofen-3-karbonitrila (2a-x). Ispitano je antimikotsko djelovanje tih spojeva na gljivice Candida krusei i Criptococcus neoformans te antiproliferativno djelovanje na tri humane tumorske stanične linije (HT29, NCI H-292 i HEP). Za antiproliferativno djelovanje primijenjena je metoda parcijalnih najmanjih kvadrata (PLS) koristeći softverski program Pentacle. Neki od ispitanih spojeva pokazuju obećavajuće antimikotsko i antiproliferativno djelovanje. Najjače antimikotsko djelovanje imaju cikloheksil[b]tiofen derivati, a najjače antiproliferativno djelovanje cikloheptil[b]tiofen derivati, posebice 2-[(1H-indol-2-il-metiliden)amino]-5,6,7,8-tetrahidro-4H-ciklohepta[b]tiofen-3-karbonitril (2r), koji inhibira više od 97 % rast svih triju ispitivanih staničnih linija. Primijenjena PLS diskriminirajuća analiza dala je dobre istraživačke i prognostičke rezultate i pokazala da deskriptori dobro koreliraju s biološkim rezultatima