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 number of surrounding BN strings (NBN) necessary to “isolate” the optical modes of a carbon nanoisland (nanographene) from the remaining substrate has been characterized in two different nanoisland models: benzene and pyrene. It was found that for NBN ≥ 3 the excitation wavelengths of the optically active modes remain constant and the changes in the transition densities, the ground to excited state density differences and their associated electron deformation orbitals are negligible and strongly confined within the carbon nanoisland. Using a water molecule as model system, Raman enhancement factors of 10^6 for the water vibrational modes are obtained when these electromagnetic “hot spots” are activated by an external electromagnetic field. The high tunability of the optical absorption bands of nanographenes through changes in size and morphology makes h-BNCs be perfect materials to construct platforms for surface enhancement Raman spectroscopy (SERS) for a wide range of laser sources.Xunta de Galicia | Ref. GRC2019/2

Can aromaticity enhance the electron transport in molecular wires?

An interesting debate has been recently raised around the role played by aromaticity in the electron transport ability of molecular wires. Normally, it is associated to destructive interference effects, so that the more aromatic the wire the less conductor. This rule was observed experimentally in a series of homologous wires containing ring units of different aromaticity, but theoretical calculations and other recent experiments demonstrate the rule cannot be generalized and depends, for instance, in the type of molecule-electrode contact. However, neither chemical explanation nor qualitative rules were given yet to allow predicting the specific behavior of different molecular junctions. In this work, using series of polymeric molecular wires of different length and formed by different aromatic units, it is proven how it is possible to change from an expected destructive to a constructive interference effect of the aromaticity in the electron transport. Thus, aromaticity may be also employed to enhance the electron transport in a molecular wire. A chemical explanation to the experimental and theoretical observations is given and a simple way of tuning the response of a molecular wire to an external electric voltage by increasing/decreasing its aromaticity and changing its type of molecule-electrode contact is provided.Xunta de Galicia | Ref. GRC2015/01

Simulating the detection of dioxin-like pollutants with 2D surface-enhanced Raman spectroscopy using h-BNC substrates

The ability of 2D hybrid structures formed by boron, nitrogen and carbon atoms (h-BNCs) to act as potential substrates for the surface-enhanced Raman spectroscopy (SERS) detection of dioxin-like pollutants is theoretically analyzed. The strong confinement and high tunability of the electromagnetic response of the carbon nanostructures embedded within the h-BNC sheets point out that these hybrid structures could be promising for applications in optical spectroscopies, such as SERS. In this work, two model dioxin-like pollutants, TCDD and TCDF, and a model h-BNC surface composed of a carbon nanodisk of ninety-six atoms surrounded by a string of borazine rings, BNC96, are used to simulate the adsorption complexes and the static and pre-resonance Raman spectra of the adsorbed molecules. A high affinity of BNC96 for these pollutants is reflected by the large interaction energies obtained for the most stable stacking complexes, with dispersion being the most important contribution to their stability. The strong vibrational coupling of some active modes of TCDF and, specially, of TCDD causes the static Raman spectra to show a ”pure” chemical enhancement of one order of magnitude. On the other hand, due to the strong electromagnetic response of BNC96, confined within the carbon nanodisk, the pre-resonance Raman spectra obtained for TCDD and TCDF display large enhancement factors of 108 and 107, respectively. Promisingly, laser excitation wavelengths commonly used in SERS experiments also induce significant Raman enhancements of around 104 for the TCDD and TCDF signals. Both the strong confinement of the electromagnetic response within the carbon domains and the high modulation of the resonance wavelengths in the visible and/or UV region in h-BNCs should lead to a higher sensitivity than that of graphene and white graphene parent structures, thus overcoming one of the main disadvantages of using 2D substrates for SERS applications.Xunta de Galicia | Ref. GRC2019/2

Deciphering the Chemical Basis of Fluorescence of a Selenium-Labeled Uracil Probe when Bound at the Bacterial Ribosomal A-Site

We unveil in this work the main factors that govern the turn-on/off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. Whereas the constraint into an “in-plane” conformation of the two rings of the fluorophore is the main driver for the observed turn-on fluorescence emission in the presence of the antibiotic paromomycin, the electrostatics of the environment plays a minor role during the emission process. Our computational strategy clearly indicates that, in the absence of paromomycin, the probe prefers conformations that show a dark S1 electronic state with participation of nπ* electronic transition contributions between the selenium atom and the π-system of the uracil moiety

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. Broken Symmetry Unrestricted Kohn-Sham Density Functional Theory (BS-UKS-DFT) in combination with electron transport analysis based on electron deformation orbitals (EDOs) reflects an exponential decay of the electrical conductance with length. Also, other important effects such as quantum interference are correctly accounted for, leading to a decrease of the conductance as the diradical character increases. As a proof-of-concept, the electrical conductance obtained from BS-UKS-DFT and CASSCF(2,2) wavefunctions were compared in diradical graphene strips in the frame of the pseudo-π approach, obtaining very similar resultsXunta de Galicia | Ref. GRC2019/2

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. Since the diradical character arises from a near-degeneracy of the frontier orbitals, the employment of a multireference approach is mandatory. CASSCF calculations on a set of nanowires based on polycyclic aromatic hydrocarbons (PAHs) demonstrate that, in the frame of an appropriate multireference treatment, the ground state of these systems shows the expected exponential decay of the conductance. Interestingly, these calculations do evidence a reversed exponential decay of the conductance, although now in several excited states. Similar results have been obtained for other recently proposed candidates to "anti-Ohmic" wires. These findings open new horizons for possible applications in molecular electronics of these promising systems.Xunta de Galicia | Ref. GRC2019/24Agencia Estatal de Investigación | Ref. PGC2018-095953-B-I0

Aromaticity of closed-shell charged polybenzenoid hydrocarbons

Abstract: 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. All cations investigated display a large degree of electronic delocalization in the ring, accompanied by significant aromatic stabilization and a strong diatropic peripheral electron current. Graph theoretical models describe perfectly the aromatic features of these hydrocarbon fragments, showing how they can be understood as a superposition of specific neutral PBHs. The large aromatic character of these systems suggests they may be relatively stable upon formation at combustion conditions, like those given in the interstellar medium. It has been postulated that closed-shell fragments of PBHs may play an important role in the photoluminescent phenomenon known as extended red emission

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 9.5 Å from the centre of the membrane for, respectively, TCDD and TCDF. At the centre of the membrane, both molecules display subtle local maxima with free energy differences of 0.5 and 1 kcal/mol with respect to the energy minima for TCDD and TCDF, respectively. Furthermore, the intermolecular interactions between the molecules and the lipid membrane have been characterized at the minima and the local maxima using hybrid quantum mechanics/molecular mechanics energy decomposition analysis (QM/MM-EDA). Total interaction energies of −17.5 and −16.5 kcal/mol have been found at the energy minima for TCDD and TCDF, respectively. In both cases, the dispersion forces govern the molecule-membrane interactions, no significant changes have been found at the local maxima, in agreement with the classical free energy profile. The small differences found in the results obtained for TCDD and TCDF point out that the adsorption and diffusion processes through the cell membrane are not related to the different toxicity shown by these pollutants

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 topological models. From the previous works, it can be stated that an anti-ohmic molecular wire must display a very small HOMO–LUMO gap and a reversed bond alternation pattern in the case of polyenes and related conjugated systems. In this work, the pursuit of a mechanism by which the anti-ohmic electron transport may arise was carried out by studying the paradigmatic anti-ohmic p-xylylene chain (pX2) at the DFT level in combination with topological models. It has been found that the electron transport in the anti-ohmic regime is favored by a long-range superexchange mechanism, which, contrary to what is expected, is reinforced by the increase in the length of the chain. Moreover, strong links between anti-ohmic character in molecular wires and one-dimensional topological insulator models have been established. Due to the small HOMO–LUMO gap predicted at DFT level, the anti-ohmic character has been put to the proof using a multireference scenario. Preliminary results point out to the presence of different ohmic and anti-ohmic electronic states. In the particular case of pX2 the anti-ohmic states do not correspond to the ground state. These findings require a reconsideration of previous studies on the reversed conductance/length behavior using single reference methodologies.Xunta de Galicia | Ref. GRC2015/017Ministerio de Economia, Industria y Competitividad | Ref. CTQ2015-65790-