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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. [ABSTRACT FROM AUTHOR]

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic‐structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage‐gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case. [ABSTRACT FROM AUTHOR]

We extend for the first time a quantum mechanical energy decomposition analysis scheme based on deformation electron densities to a hybrid electrostatic embedding quantum mechanics/molecular mechanics framework. The implemented approach is applied to characterize the interactions between cisplatin and a dioleyl-phosphatidylcholine membrane, which play a key role in the permeation mechanism of the drug inside the cells. The interaction energy decomposition into electrostatic, induction, dispersion and Pauli repulsion contributions is performed for ensembles of geometries to account for conformational sampling. It is evidenced that the electrostatic and repulsive components are predominant in both polar and non-polar regions of the bilayer. [ABSTRACT FROM AUTHOR]

The affinity of graphene and white graphene sheets by dioxin‐like pollutants was compared by means of high‐level quantum chemical calculations. 2,3,7,8‐tetrachloro‐p‐dibenzodioxin (TCDD) and 2,3,7,8‐tetrachlorodibenzofuran (TCDF) were chosen as prototypes of dioxin‐like pollutants with high toxicological activity. Large interaction energies were obtained both in graphene and white graphene surfaces, contrary to other previous works using the graphene surface only. The interactions clearly differed in the relative weight of inductive and dispersion forces, being the former more important in white graphene. Leaving thermal effects out, the stacking adsorption was energetically favored over the perpendicular in graphene whereas no difference was found in white graphene. Due to the low water solubility of dioxin‐like pollutants very small differences were obtained between gas phase and solution adsorption enthalpies. Including thermal effects, perpendicular adsorption was found to be both energetically and entropically favored over stacking at 298 K. The adsorption free energies reflected a larger affinity by white graphene than graphene by around 2–5 kcal·mol−1. Therefore, boron nitride 2D surfaces are expected to perform better than carbon 2D surfaces as adsorbents for dioxin‐like pollutants in line with recent experimental works on water contaminants. [ABSTRACT FROM AUTHOR]

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 results. [ABSTRACT FROM AUTHOR]

The Clar Goblet, the first radical bowtie nanographene proposed by Erich Clar nearly 50 years ago, was recently synthesized. Bowtie nanographenes present quasi‐degenerate magnetic ground states, which make them so elusive as unique. A thorough analysis is presented of the spin‐state energetics of Clar Goblet and bowtie nanographenes by a battery of existing and novel ab initio procedures ranging from density functional theory to complete active space Hamiltonians. With this, it was proven that π radicals of bowtie nanographenes sit on BP (Benzo[cd]Pyrene) moieties driven by their local aromaticity, a purely chemical concept, which confers global stability to the whole structure. Besides, a novel Pauli energy densities analysis provided a visual intuitive explanation for this preference. These findings allow envisioning that analogous bowtie nanographenes with arbitrary polyradical character are not only feasible at the molecular scale but will share Clar Goblet's peculiar properties. [ABSTRACT FROM AUTHOR]

The partition of the multicenter electron delocalization indices and the nucleus independent chemical shift indices into alpha and beta contributions in open-shell systems has been performed. In general it is shown that a full understanding of aromaticity in these systems cannot be achieved by restricting the calculations to the global properties but by dissecting these properties into α and β terms. The 4n+2- and 4n-aromaticity rules for singlet and triplet annulenes, respectively, reduce to a general aromaticity rule when the α and β terms are studied separately. This new rule allows us to extend the concept of conflicting aromaticities to radical systems that are simultaneously α-aromatic and β-antiaromatic or vice versa. The existence of such systems is demonstrated here by means of multicenter electron delocalization indices and nucleus independent chemical shifts. Finally, the global aromatic/antiaromatic character of these radical systems is estimated by means of aromatic stabilization energy, which is shown to be either slightly positive or slightly negative, thus reflecting the small aromatic/antiaromatic character of these radicals and reinforcing the conclusions obtained with aromaticity indices. [ABSTRACT FROM AUTHOR]

The analysis of previously reported shortcomings of the condensed Fukui functions obtained making use of the quantum theory of atoms in molecules indicates these drawbacks are due to the inadequacy of the definition employed to compute them and not to the partitioning. A new procedure, which respects the mathematical definition and solves these problems, is presented for the calculation of condensed Fukui functions for atomic basins defined according to the quantum theory of atoms in molecules. It is tested in a set of 18 molecules, which includes the most controversial reported cases. [ABSTRACT FROM AUTHOR]

The sum-over-states (SOS) method allows the computation of polarizabilities and hyperpolarizabilities additively from the contributions of different electronic excited states in a given molecule or cluster. Subsequent analysis of the main excited configurations contributing to the relevant excited states allows characterizing the orbitals involved in the linear and nonlinear optical response. Unfortunately, the chemically relevant information that can be obtained by SOS is hindered by a series of methodological and computational drawbacks. Among these drawbacks, we can highlight the high computational cost, problems arising from nonconvergent series and errors caused by the inaccurate description of excitation energies and/or higher excited state matrix elements. For this reason, coupled-perturbed schemes are currently widely used to determine the NLO potential of molecules and materials. However, such a choice limits the amount of intuitive chemical information that, on the other hand, can be retrieved by a successful SOS computation. In this work, we present and discuss a novel computational strategy that offers the means to extract the useful chemical insights from a coupled-perturbed calculation at almost negligible extra computational cost providing a transparent picture about orbital contributions to the properties of interest. The proposed method is based on the generation and further analysis of field-induced orbitals, FIOs, from the analytic or numerical derivatives of the dipole moment. Orbital symmetry rules are derived using group theory and the method is tested for a series of small and medium size systems. [ABSTRACT FROM AUTHOR]

The increasing miniaturization of devices creates the need for adequate power sources and direct methanol fuel cells (DMFC) are a strong option in the various possibilities under current development. DMFC catalysts are mostly based on platinum, for its outperformance in three key areas (activity, selectivity and stability) within methanol oxidation framework. However, platinum poisoning with products of methanol oxidation led to the use of alloys. Ruthenium-platinum alloys are preferred catalysts active phases for methanol oxidation from an industrial point of view and, indeed, ruthenium itself is a viable catalyst for this reaction. In addition, the route of methanol decomposition is crucial in the goal of producing H2 from water reaction with methanol. However, the reaction pathway remains elusive and new approaches, namely in computational methods, have been ensued to determine it. This article reviews the various recent theoretical approaches for determining the pathway of methanol decomposition, and systematizes their validation with experimental data, within methodological context. [ABSTRACT FROM AUTHOR]

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. In addition, qualitative relations between interaction energy and electron polarization upon adsorption have been established using the finite model. In this work, we have analysed thermodynamically stable adsorption complexes formed by glycine, melamine, pyronin cation, porphine, tetrabenzoporphine and phthalocyanine with a 2D structure of ninety six carbons and periodic structures formed by cells of fifty and seventy two carbons. Differences in the electrostatic, Pauli repulsion, induction and dispersion energies among aromatic and non-aromatic molecules, charged and non-charged molecules and H–π and stacking interactions have been thoroughly analysed in this work. [ABSTRACT FROM AUTHOR]

The ability of different carbon allotropes surfaces as potential substrates for enhanced Raman spectroscopy is analysed theoretically and the factors responsible of the Raman-enhancing mechanism deeply scrutinised. Our analysis is based on the partition of the Raman tensor into molecule and surface terms, which leads to three different contributions to the Raman activity ('molecule', 'surface' and 'intermolecular'). Both static and pre- resonance conditions are considered in our analysis of the Raman spectra of pyridine adsorbed on model planar and curved surfaces and the three contributions to the Raman activity obtained separately. At static conditions, there is a general decrease in the Raman activity of vibrational modes associated to the molecule, proportional to the strength of the molecule-surface interaction. This stems from a reduction of the polarizability of pyridine upon its adsorption on the carbon surface. Under pre-resonance conditions, the surface contributes significantly to the Raman activity of the pyridine vibrational modes, even if the electronic transition involves exclusively energy levels from the surface. This is because of small vibrational couplings between molecular and surface modes which are negligible in metallic surface-like silver. It suggests also the possibility of finding similar effects in metallic surface built from lighter atoms like silicon or aluminium. [ABSTRACT FROM AUTHOR]

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. Analysis of the interaction energy components reveals that the M06-2X functional accounts for most of the dispersion energy implicitly, followed far by wB97X and B3LYP, whereas B97 and BLYP do not differ too much from HF. It has been found that M06-2X corrects only the energy component associated to dispersion and leaves the rest, electrostatic, Pauli and induction "unaltered" with respect to the other DFT functionals investigated. Moreover, only the M06-2X functional reflects the effect of dispersion on the electron polarization density, whereas for the remaining functionals the polarization density does not differ too much from the HF density. This makes the former functional more suitable a priori for the calculation of electron density related properties in these adsorption complexes. [ABSTRACT FROM AUTHOR]