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A new hierarchical method to determine molecular similarity is introduced. The goal of this method is to detect if a pair of molecules has the same structure by estimating a rigid transformation that aligns the molecules and a correspondence function that matches their atoms. The algorithm firstly detect similarity based on the global spatial structure. If this analysis is not sufficient, the algorithm computes novel local structural rotation-invariant descriptors for the atom neighborhood and uses this information to match atoms. Two strategies (deterministic and stochastic) on the matching based alignment computation are tested. As a result, the atom-matching based on local similarity indexes decreases the number of testing trials and significantly reduces the dimensionality of the Hungarian assignation problem. The experiments on well-known datasets show that our proposal outperforms state-of-the-art methods in terms of the required computational time and accuracy.
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We present a density functional theory (DFT) study aimed at understanding the injection and recombination processes that occur at the interface between PbS QDs and TiO2 oxide nanoparticles with different morphologies. The calculated injection rates fall in the picosecond timescale in good agreement with the experiments. In addition, our simulations show that the (101) facet of TiO2 more favourably accommodates the QD, resulting in stronger electronic couplings and faster electron injections than the (001) surfaces. Despite this, the (101) slab is also more prone to faster electron recombination with the valence band of the QD, which can lead to overall lower injection efficiencies than the (001) surface.
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Inspired by their geometrical perfection, intrinsic beauty, and particular properties of polyhedranes, a series of carbo-cages is proposed in silico via density functional theory computations. The insertion of alkynyl units into the C-C bonds of polyhedranes results in a drastic lowering of the structural strain. The induced magnetic field shows a significant delocalization around the three-membered rings. For larger rings, the response is paratropic or close to zero, suggesting a nonaromatic behavior. In the carbo-counterparts, the values of the magnetic response are shifted with respect to their parent compounds, but the aromatic/nonaromatic character remains unaltered. Finally, Born-Oppenheimer molecular dynamics simulations at 900 K do not show any drastic structural changes up to 10 ps. In the particular case of a carbo-prismane, no structural change is perceived until 2400 K. Therefore, although carbo-cages have enthalpies of formation 1 order of magnitude higher than those of their parent compounds, their future preparation and isolation should not be discarded, because the systems are kinetically stable, explaining why the similar systems like carbo-cubane have already been synthesized.
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ZnO has attracted a great deal of research as a potential replacement of TiO2 for dye-sensitized solar cells (DSSCs), owing to the unique combination of interesting electronic properties (i.e., high electron mobility) and structural richness. Here, we present a DFT/TDDFT study about the interaction of the prototypical N3 and N719 Ru(II) sensitizers on ZnO models to understand some of the atomistic details that are crucial to the dye/semiconductor interaction. We pay particular attention to the adsorption mode of the sensitizer and to the effect of the complexation on the electronic structure of the dye. The sensitizers are predicted to strongly interact with the ZnO surface. In particular, the interaction is strengthened when three dye carboxylic groups are involved in the adsorption. Moreover, if the anchoring group bears a proton, the adsorption is predicted to be dissociative. The charge density donation from the dye to the semiconductor raises the valence and conduction band edges of the latter, in such a way that the optical gap of ZnO widens. Proton transfer from the dye to the semiconductor balances the charge donation effect and restores the electronic levels of the noninteracting fragments. The impact of dye/semiconductor interaction on the adsorbed dye optical properties is then discussed.
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Motivated by the recent experiments by Wang et al. (Angew. Chem., Int. Ed. 2012, 51, 6154-6157), in which the alkylamine-capped magic-size (CdSe)13 has been isolated for the first time, we report on the computational modeling of the putative low-lying isomers of (CdSe)13, both bare and ligand-protected. According to Density Functional Theory (DFT) calculations, the core@cage configuration Se@Cd13Se12, consisting of a Se atom incarcerated in the center of a puckered Cd13Se12 cage, lies lower in energy than fullerene- and wurtzite-like structures. Methylamine-capped nanoclusters present average bond energies per ligand of about 20 kcal mol(-1), while bond energy decomposition schemes show this interaction to be mostly electrostatically-driven. The computed Time-Dependent-DFT (TDDFT) spectrum of the lowest-lying methylamine-protected (CdSe)13 isomer essentially coincides with the experiment, with a notable blueshift of the absorption features induced by the ligands. The LUMO has been found to be the acceptor orbital for all the lowest-lying electronic excitations, in both the bare and methylamine-capped clusters, which could explain the narrow emission profiles inherent in semiconductor nanostructures. In addition, the attachment of pyridine and aniline molecules has been evaluated. Interestingly, the molecular orbitals of these aromatic amines located on the edges of the valence and conduction bands may act as trap states, in agreement with experimental evidences. In the particular case of pyridine molecules, unoccupied orbitals intrude into the HOMO-LUMO gap of the cluster.
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The rational design of ligand molecules has earned lots of attention as an elegant means to tailor the electronic and optical properties of semiconductor quantum dots (QDs). Aromatic dithiocarbamate molecules, in particular, are known to greatly influence the optoelectronic properties of CdSe QDs, red-shifting the absorption features and enhancing the photoluminescence. Here, we present an integrated computational study, which combines ab initio molecular dynamics and excited state calculations including thousands of excitations, aimed at understanding the impact of this kind of surface ligand on the optoelectronic properties of CdSe QDs. We demonstrate that the valence electronic states of the dithiocarbamate molecules, mostly localized in the anchoring moiety, are responsible for the red-shift of the absorption features of capped CdSe QDs. Ligands develop interfacial electronic states close to the band edges of the CdSe, which enhance the absorption features of the QD and might open new channels for the radiative decay from the excited state, improving optical emission. Hybridized QD/ligand states could also funnel interfacial charge transfer between the inorganic core and surface molecules, a process that lies at the heart of many photovoltaic and photocatalytic devices. This work may pave the way toward the design of new capping ligands that, adsorbed on the QD surface, could provide control over the optoelectronic properties of the semiconductor core.
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We investigate the photoinduced dipole (PID) phenomenon, which holds enormous potential for the optimization of quantum dot-sensitized solar cells (QDSSCs), by means of first-principles electronic structure calculations. We demonstrate that the sensitization of the TiO2 substrate with core/shell QDs produces almost no changes in the ground state but decisively improves the performance upon photoexcitation. In particular, the maximum attainable VOC is predicted to increase by â¼25 meV due to two additive effects: (i) the displacement of the photoexcited hole away from the TiO2 surface and (ii) the interfacial electrostatic interaction established between the TiO2-injected electrons and the holes residing in the QD core. We believe that this work, explaining the mechanisms by which PID cells deliver better efficiencies, paves the way for the design of new QDSSCs with improved efficiencies.
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In this work, we build a benchmark data set of geometrical parameters, vibrational normal modes, and low-lying excitation energies for MX quantum dots, with M = Cd, Zn, and X = S, Se, Te. The reference database has been constructed by ab initio resolution-of-identity second-order approximate coupled cluster RI-CC2/def2-TZVPP calculations on (MX)6 model molecules in the wurtzite structure. We have tested 26 exchange-correlation density functionals, ranging from local generalized gradient approximation (GGA) and hybrid GGA to meta-GGA, meta-hybrid, and long-range corrected. The best overall functional is the hybrid PBE0 that outperforms all other functionals, especially for excited state energies, which are of particular relevance for the systems studied here. Among the DFT methodologies with no Hartree-Fock exchange, the M06-L is the best one. Local GGA functionals usually provide satisfactory results for geometrical structures and vibrational frequencies but perform rather poorly for excitation energies. Regarding the CdSe cluster, we also present a test of several basis sets that include relativistic effects via effective core potentials (ECPs) or via the ZORA approximation. The best basis sets in terms of computational efficiency and accuracy are the SBKJC and def2-SV(P). The LANL2DZ basis set, commonly employed nowadays on these types of nanoclusters, performs very disappointingly. Finally, we also provide some suggestions on how to perform calculations on larger systems keeping a balance between computational load and accuracy.
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ZnS and CdS small nanoclusters have been predicted to trap alkali metals and halogen atoms. However would this kind of nanocompounds be able to encapsulate dianions and dications? This would be very interesting from an experimental point of view, since it would allow the isolation of such divalent ions. Moreover, the resulting endohedral complexes would serve as building blocks for new cluster-assembled materials, with enhanced stability arising from the electrostatic interaction between the incarcerated ions. In this work we have studied the structure and stability of (X@(CdS)i)(±2) with X = Be, Mg, Ca, O, S, Se and i = 9, 12, 15, 16 on the basis of Density Functional Theory and Quantum Molecular Dynamics simulations. Most of the nanoclusters are found to trap both chalcogen and alkaline earth atoms. Furthermore, the chalcogen doped clusters are calculated to be both thermodynamically and thermally stable. However, only a few of alkaline earth metal doped structures are predicted to be thermally stable. Therefore, the charge of the dopant atom appears to be crucial in the endohedral doping. Additionally, the absorption spectra of the title compounds have been simulated by means of Time Dependent Density Functional Theory (TDDFT) calculations. The calculated optical features show a blueshift with respect to the bulk CdS wurtzite. Furthermore, doping modifies notably the optical spectra of nanoclusters, as the absorption spectra shift to lower energies upon encapsulation.
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The potential energy surface of the hypothetical NaMgAlSiPSCl system (heavy periodane) is exhaustively analyzed via the gradient embedded genetic algorithm (GEGA) in combination with density functional theory (DFT) computations. The electronegativity differences among the elements in both the second and third rows of the periodic table indicate that low-energy heavy periodane structures are obtained when highly electronegative and electropositive elements are bound together, but the global minimum of the heavy periodane system is completely different to its second-row analog (LiBeBCNOF).