On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis.

The permeation of dioxin-like pollutants, namely, chlorinated dibenzodioxins and dibenzofurans, through lipid membranes has been simulated using classic molecular dynamics (CMD) combined with the umbrella sampling approach. The most toxic forms of chlorinated dibenzodioxin and dibenzofuran, 2,3,7,8-tetrachloro-p-dibenzodioxin (TCDD) and 2,3,7,8-tetrachlorodibenzofuran (TCDF), and a dioleyl-phosphatidylcholine (DOPC) lipid membrane of 50 Å wide have been chosen for our study. The free energy profile shows the penetration process is largely favoured thermodynamically (ΔG ≈ -12 kcal/mol), with a progressively decrease of the free energy until reaching the energy minima at distances of 8 Å and 9.

Confinement on the optical response in h-BNCs: Towards highly efficient SERS-active 2D substrates.

Several experimental and theoretical studies have shown that 2D hybrid structures formed by boron, nitrogen and carbon atoms (h-BNCs) possess a highly tunable linear and non-linear optical responses. Recent advances towards the controlled synthesis of these unique structures have motivated an important number of experimental and theoretical work. In this work, the confinement on the optical response induced by boron-nitride (BN) strings in h-BNC 2D structures is investigated using time-dependent density functional theory (TDDFT) and electron density response properties.

The effect of spin polarization on the electron transport of molecular wires with diradical character.

Some of the most promising materials for application in molecular electronics and spintronics are based on diradical chains. Herein, the proposed relation between increasing conductance with length and diradical character is revisited using ab initio methods that account for the static electron correlation effects. Electron transmission was previously obtained from restricted single determinant wavefuntions or tight-binding approximations, which are unable to account for static correlation.

Assessing the Reversed Exponential Decay of the Electrical Conductance in Molecular Wires: The Undeniable Effect of Static Electron Correlation.

An extraordinary new family of molecular junctions, inaccurately referred to as "anti-Ohmic" wires in the recent literature, has been proposed based on theoretical predictions. The unusual electron transport observed for these systems, characterized by a reversed exponential decay of their electrical conductance, might revolutionize the design of molecular electronic devices. This behavior, which has been associated with intrinsic diradical nature, is reexamined in this work.

Anti-ohmic single molecule electron transport: is it feasible?

Hitherto, only molecular wires with a regular ohmic behavior in which the electric conductance decreases with the wire length have been synthesized. Implementation of molecular conductors with reversed conductance/length trend (anti-ohmic) might revolutionize the field of molecular electronics, allowing the development of electronic devices with extraordinary properties. It is for this reason that, recently, theoretical efforts have been focused on this topic and different structures have been proposed to show reversed conductance/length behavior on the basis of density functional theory non-equilibrium Green function approach (DFT-NEGF) and models.

A computational study of the interaction of graphene structures with biomolecular units.

Due to the great interest that biochemical sensors constructed from graphene nanostructures have raised recently, in this work we analyse in detail the electronic factors responsible for the large affinity of biomolecular units for graphene surfaces using ab initio quantum chemical tools based on density functional theory. Both finite and periodic graphene structures have been employed in our study. Whereas the former allows the analysis of the different energy components contributing to the interaction energy separately, the periodic structure provides a more realistic calculation of the total adsorption energy in an extended graphene surface and serves to validate the results obtained using the finite model.

Understanding conductivity in molecular switches: a real space approach in octaphyrins.

In recent years, expanded porphyrins have emerged as a promising class of π-conjugated molecules that display unique electronic, optical and conformational properties. Several expanded porphyrins can switch between planar and twisted conformations, which have different photophysical properties. Such a change of topology involves a Hückel-Möbius aromaticity switch in a single molecule and it can be induced by solvent, pH and metallation.

Tunable aromaticity in bicalicenes.

The unusual aromatic stability of cyclic bicalicene has been suggested to come from a tetraionic structure, where positive and negative charges are located on the cyclopropene and cyclopentadiene rings, respectively. Energetic, magnetic, geometric and electron delocalization analysis performed on a series of bicalicene derivatives, incorporating different electron donating and withdrawing groups, and electrically perturbed bicalicene structures provide additional proof of the role played by this tetraionic structure in the aromatic stability of bicalicene. In this work the aromatic stabilization is chemically and electrically tuned, enhancing or disrupting the electron delocalization and aromatic stability of the cyclopropene and cyclopentadiene rings by increasing or decreasing their corresponding charges.

Theoretical study of the adsorption of aromatic units on carbon allotropes including explicit (empirical) DFT dispersion corrections and implicitly dispersion-corrected functionals: the pyridine case.

The suitability of implicitly dispersion-corrected functionals, namely the M06-2X, for the determination of interaction energies and electron polarization densities in adsorption studies of aromatic molecules on carbon allotropes surfaces is analysed by comparing the results with those obtained using explicit dispersion through Grimme's empirical corrections. Several models of increasing size for the graphene sheet together with one-dimensional curved carbon structures, (5,5), (6,6) and (7,7) armchair single-walled nanotubes, and two-dimensional curved carbon structures, C60 fullerene, have been considered as substrates in this work, whereas pyridine has been chosen as an example for the adsorbed aromatic molecule. Comparison with recent experimental estimations of the adsorption energy and calculations using periodic boundary conditions on a supercell of 72 carbon atoms indicates that a finite model containing ninety six carbon atoms (C96) approaches quite well the adsorption on a graphene sheet.

Revisiting the Calculation of I/V Profiles in Molecular Junctions Using the Uncertainty Principle.

Ortiz and Seminario (J. Chem. Phys.

Analyzing the electric response of molecular conductors using "electron deformation" orbitals and occupied-virtual electron transfer.

The concept of "electron deformation orbitals" (EDOs) is used to investigate the electric response of conducting metals and oligophenyl chains. These orbitals and their eigenvalues are obtained by diagonalization of the deformation density matrix (difference between the density matrices of the perturbed and unperturbed systems) and can be constructed as linear combinations of the unperturbed molecular orbitals within "frozen geometry" conditions. This form of the EDOs allows calculating the part of the electron deformation density associated to an effective electron transfer from occupied to virtual orbitals (valence to conduction band electron transfer in the band model of conductivity).

Aromaticity of closed-shell charged polybenzenoid hydrocarbons.

The aromatic stabilization of closed-shell charged polybenzenoid hydrocarbons (PBHs) has been scrutinized by means of energetic and magnetic aromaticity criteria and by direct measures of electron delocalization. Thus, topological resonance energies and their circuit contributions, ring current maps, and multicenter delocalization indices have been calculated for a series of 18 polybenzenoid cations containing from 3 to 10 benzene rings. All calculations indicate that the closed-shell cations have a similar degree of aromaticity compared to that of the corresponding closed-shell neutral PBHs.

Electronic properties of p-xylylene and p-phenylene chains subjected to finite bias voltages: a new highly conducting oligophenyl structure.

Recently, experimental and theoretical determination of electric currents induced by finite bias voltages in p-xylylene chains attached to gold contacts revealed higher conductance of these systems in comparison with p-phenylene homologous chains. To gain more insight into the conducting properties of these oligophenyl structures, ab initio studies were carried out on the electronic properties of two different p-xylylene-like chains (pX1 and pX2) and the p-phenylene (pP) chain attached to gold contacts, with molecular formulas AuCH2 (C6 H4 )n CH2 Au (n=1-5), Au2 C(C6 H4 )n CAu2 (n=1-5), and Au(C6 H4 )n Au (n=1-5), respectively. The molecules were subjected to finite bias voltages ranging from 0 to 5 V.