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Métodos de Cálculo de estructuras moleculares y aplicaciones.

We theoretically study and characterize a set of rhombus-shaped nanographenes of increasing size, or n-rhombenes, where n = 2–6, displaying zigzag edges leading to an enhancement of the (poly)radicaloid nature and the appearance of intrinsic magnetism as a function of n. Due to that system-dependent radicaloid nature, we employ spin-flip methods able to capture the challenging physics of the problem, thus providing accurate energy differences between high- and low-spin solutions. The theoretical predictions agree with the experimentally available magnetic exchange coupling for the recently synthesized 5-rhombene, as well as with the size at which the transition from a closed-shell to an open-shell ground-state solution occurs. We also investigate if standard DFT methods are able to reproduce the trend disclosed by spin-flip methods and if the results are highly dependent on the functional choice and/or the intrinsic spin contamination.

Curso que se imparte en la Universidad de Alicante, en el Máster de Ciencias de Materiales.

Fluctuation theorems allow one to obtain equilibrium information from nonequilibrium experiments. The probability distribution function of the relevant magnitude measured along the irreversible nonequilibrium trajectories is an essential ingredient of fluctuation theorems. In small systems, where fluctuations can be larger than average values, probability distribution functions often deviate from being Gaussian, showing long tails, mostly exponential, and usually strongly asymmetric. Recently, the probability distribution function of the van Hove correlation function of the relevant magnitude was calculated, instead of that of the magnitude itself. The resulting probability distribution function is highly symmetric, obscuring the application of fluctuation theorems. Here, the discussion is illustrated with the help of results for the heat exchanged during plastic deformation of aluminum nanowires, obtained from molecular dynamics calculations. We find that the probability distribution function for the heat exchanged is centrally Gaussian, with asymmetric exponential tails further out. By calculating the symmetry function we show that this distribution is consistent with fluctuation theorems relating the differences between two equilibrium states to an infinite number of nonequilibrium paths connecting those two states.

Numerous theoretical and experimental studies have attempted to determine the mechanisms of bacterial potassium channel selectivity (KcsA). However, there are still different aspects that remain uncovered. In this paper, we have built a model based on a selective filter (SF) for the KcsA, taking into account its structure and calculating the system interaction energy (cation–water–SF-fragment), using both sodium and potassium as cations. The results tell us which aspects could be responsible for the higher selectivity of the channel. All this reveals that there are two most important aspects: the dehydration of potassium in relation to sodium, and the environment where such dehydration occurs, in the entrance of the SF. Both semi-empirical and ab initio methods are applied to analyse and quantify the change of the interactions that take place when the cation K+ or Na+ crosses the SF.

Recent advances in the synthesis of stable organic (open-shell) polyradicaloids have opened their application as active compounds for emerging technologies. These systems typically exhibit small energy differences between states with different spin multiplicities, which are intrinsically difficult to calculate by theoretical methods. We thus apply here some DFT-based variants (FT-DFT, SF-DFT, and SF-TDDFT) on a test set of large and real-world molecules, as test systems for which such energy differences are experimentally available, also comparing systematically with RAS-SF results to infer if shortcomings of previous DFT applications are corrected. Additionally, we explore the spin–spin contribution to the ZFS tensor, of high interest for EPR spectroscopy, and derive the spatial extent of the corresponding (photoexcited) triplet state.

We investigate here the lowest‐energy (spin‐conserving) excitation energies for the set of He‐Ne atoms, with the family of nonempirical PBE, PBE0, PBE0‐1/3, PBE0‐DH, PBE‐CIDH, PBE‐QIDH, and PBE0‐2 functionals, after employing a wide variety of basis sets systematically approaching the basis set limit: def2‐nVP(D), cc‐pVnZ, aug‐cc‐pVnZ, and d‐aug‐cc‐pVnZ. We find that an accuracy (ie, mean unsigned error) of 0.3 to 0.4 eV for time‐dependent density functional theory (DFT) atomic excitation energies can be robustly achieved with modern double‐hybrid methods, which are also stable with respect to the addition of a double set of diffuse functions, contrarily to hybrid versions, in agreement with recent findings employing sophisticated multiconfigurational DFT methods.

The design of advanced N-doped carbon materials towards oxygen reduction reaction (ORR) catalysis is only possible if the nature of the active sites is fully understood. There is an important piece of research seeking to overcome this challenge through experimental or theoretical results. However, the combination of both approaches is necessary to deepen the knowledge about this subject. This work presents excellent agreement between experimental results and computational models, which provides evidence of the nature of the most active sites in N-doped carbon materials. N-doped carbon materials have been experimentally obtained through double stage treatment of polyaniline in distinct atmospheres (both oxygen-containing and inert atmospheres) at different temperatures (800–1200 °C). According to temperature programmed desorption (TPD), Raman spectroscopy, N2-adsorption isotherms at −196 °C and X-ray photoelectron spectroscopy (XPS), this synthesis method results in the selective formation of nitrogen species, without significant changes in structural order or porosity. ORR catalytic tests evidence the highly efficient catalysis, with platinum-like performance in terms of the current density and onset potential, of N-doped carbon materials selectively containing graphitic-type nitrogen species. Computational chemistry, through DFT calculations, shows that edge-type graphitic nitrogen is more effective towards ORR catalysis than pyridinic, pyrrolic, pyridonic, oxidized and basal-type graphitic nitrogen species.

We briefly present some of the most modern and outstanding non-conventional density-functional theory (DFT) methods, which have largely broadened the field of applications with respect to more traditional calculations. The results of these ongoing efforts reveal that a DFT-inspired solution always exists even for pathological cases. Among the set of emerging methods, we specifically mention FT-DFT, OO-DFT, RSX-DFT, MC-PDFT, and FLOSIC-DFT, complementing the last generation of existing density functionals, such as local hybrid and double-hybrid expressions.

P-postmodified polyaniline was obtained by reacting phosphorus trichloride (PCl3) and chlorodiphenylphosphine (PPh2Cl) and polyaniline (PANI), under mild conditions. The reaction was found to be very selective, as only the imine groups were involved in the P-functionalization, and efficient as well, affording a P-loading of 3 at.% and 5 at.% for PPh2Cl and PCl3, respectively. All the polymers were characterized by different techniques and the results were endorsed by theoretical calculations. Experimental and Density Functional Theory results proved that the reaction occurs through the imine groups and the phosphorus atoms, generating NP bonds. The electrochemical properties of the NP modified materials were evaluated and the catalytic activity towards oxygen reduction reaction was measured. It was found that a high concentration of phenyl groups from PPh2Cl (about 3 at.%) affected negatively the activity of the catalyst since they prevented the access of the oxygen molecules to the catalytic active sites. However, a lower amount of PPh2 groups (1 at.%) or the use of PCl3 avoided this hindrance and resulted in an improved catalytic activity with respect to pristine PANI.

Zigzag edges of neutral armchair–oriented Graphene Nano–Ribbons show states strongly localized at those edges. They behave as free radicals that can capture electrons during processing, increasing ribbon's stability. Thus, charging and its consequences should be investigated. Total energy calculations of finite ribbons using spin–polarized Density Functional Theory (DFT) show that ribbon's charging is feasible. Energies for Pariser-Parr-Pople (PPP) model Hamiltonian are compatible with DFT allowing the study of larger systems. Results for neutral ribbons indicate: i) the fundamental gap of spin–polarized (non–polarized) solutions is larger (smaller) than experimental data, ii) the ground state is spin–polarized, a characteristic still not observed experimentally. Total energy of GNRs decreases with the number of captured electrons reaching a minimum for a number that mainly depends on zigzag–edges size. The following changes with respect to neutral GNRs are noted: i) the ground state is not spin–polarized, ii) fundamental gap is in-between that of spin–polarized and non–polarized solutions of neutral ribbons, iii) while in neutral ribbons valence and conduction band onsets vs. the fundamental gap, linearly and symmetrically approach mid–gap with slope 0.5, charging induces Fermi level pinning, i.e., the slopes of the valence and conduction bands being about 0.1 and 0.9, in agreement with experiment.

[EN] Zigzag edges of neutral armchair–oriented Graphene Nano–Ribbons show states strongly localized at those edges. They behave as free radicals that can capture electrons during processing, increasing ribbon's stability. Thus, charging and its consequences should be investigated. Total energy calculations of finite ribbons using spin–polarized Density Functional Theory (DFT) show that ribbon's charging is feasible. Energies for Pariser-Parr-Pople (PPP) model Hamiltonian are compatible with DFT allowing the study of larger systems. Results for neutral ribbons indicate: i) the fundamental gap of spin–polarized (non–polarized) solutions is larger (smaller) than experimental data, ii) the ground state is spin–polarized, a characteristic still not observed experimentally. Total energy of GNRs decreases with the number of captured electrons reaching a minimum for a number that mainly depends on zigzag–edges size. The following changes with respect to neutral GNRs are noted: i) the ground state is not spin–polarized, ii) fundamental gap is in-between that of spin–polarized and non–polarized solutions of neutral ribbons, iii) while in neutral ribbons valence and conduction band onsets vs. the fundamental gap, linearly and symmetrically approach mid–gap with slope 0.5, charging induces Fermi level pinning, i.e., the slopes of the valence and conduction bands being about 0.1 and 0.9, in agreement with experiment.

The successful use of graphene nanoribbons (GNRs) in a variety of applications in nanoelectronics depends not only on reliable control of their forbidden gaps, but also on the understanding of the effects that contacts to leads may have on their conductance G. By combining Landauer's formalism and a simplified version of the embedded cluster method, G through suspended 9-AGNR has been calculated as a function of energy (sample bias) and the strength of the contact between the ribbon and leads attached to both zigzag edges. Green's functions of contacted ribbons have been derived from HF nonspin polarized solutions of the Pariser-Parr-Pople Hamiltonian. It is shown that the G associated with the two quasidegenerate states around the Fermi level, which are strongly localized at the zigzag edges, equals a conductance quantum G0 for very weak leads-ribbon coupling, decreasing to zero as that coupling increases. At the Fermi level G is zero for small coupling, increasing up to G0 for a value of coupling that depends on the GNR length, and, finally, decreasing to zero for large coupling. Conductance through other energies, starting at G=0 for no coupling, increases with coupling to the electrodes up to near one quantum at a pace that may appreciably depend on the particular molecular orbital. These results illustrate the difficulties that may be found in exploring practical uses of GNRs.

Recent interest in the absorption and photo-luminescence properties of a molecule with an envisioned optoelectronic use, such as TPD (N,N′-diphenyl-N,N′-bis(3-methylphenyl)-(1,1′-biphenyl)-4,4′-diamine), prompted us to apply Density Functional Theory (DFT) and Time-Dependent DFT methods to obtain theoretical results in agreement with experimental findings. Based on these benchmark results, we tackled in a further step the study of a set of molecules derived from the triphenylamine moiety, trying thus to relate their structures with their expected behavior in optical devices. Therefore, we analyzed several key properties for it, like the Stokes shift (important for laser applications), or their absorption and emission spectra which, together with the energies of frontier molecular orbitals, help to determine their optical behavior.

Organic light emitting diodes (OLEDs) are current-driven devices that utilize light emission from excited states of molecules.(1) Operating OLEDs involves charge injection from the anode and the cathode into the adjacent organic layers, transport of injected charge carriers through the organic layers, and exothermic recombination of holes and electrons to generate electronically excited states of molecules. Subsequent deactivation of molecules produces electroluminescence (EL) that goes out of the device. Attaining high quantum efficiency for EL requires: (i) efficient charge injection from both electrodes into the adjacent organic layers at low drive voltage, (ii) charge balance, and (iii) confinement of charge carriers within the emitting layer to increase the probability of emissive recombination. The insertion of hole-acceptor and electron-acceptor layers between the electrodes and the emitting layer substantially increases efficiency. A multilayer structure of OLED’s consists of the emitting layer sandwiched between hole- and electron-acceptor layers that in turn are in contact with the metallic anode and cathode, respectively. Amorphous molecular materials have been proven to show several characteristics that qualify them as excellent materials to be used in OLED’s.(1) Their most remarkable feature is that, due to their homogeneous and isotropic properties, they form smooth thin films, allowing uniform contact with the metallic electrodes and between organic layers. An issue concerning nomenclature is here worthy of comment. As stated above, device operation involves three main processes, namely, charge injection, charge transport, and light emission. Although in this work we will only focus on the first, we shall also use the accepted terminology of hole- or electron-transporters, being aware of the fact that the correct one would be “acceptors” instead of ‘transporters” (investigating their transport performance(2) would require considering also carrier mobi

We theoretically discuss here the relationships between the structure of recently synthesized nanorings, dubbed as cyclo-2,7-pyrenylene (CPY) and formed upon bending and bonding a finite number of pyrene units until self-cyclation, and a set of chemically relevant properties such as the induced structural and energetical strain, the electronic and optical properties, or the response to charge injection, as well as their transport mechanism through a concerted migration of charge-carriers. We also compare these properties, and their evolution with the number of pyrene-linked units, with those obtained for the closely related cycloparaphenylene (CPP) compounds, trying to disclose the underlying structure–property guidelines. To do it, we always employ dispersion-corrected DFT methods to systematically include the key effects affecting all the properties tackled. A correct match with some available experimental results, for the [4]CPY compound (the only one synthesized so far), anticipates the accuracy of the calculations done for the rest of compounds. Finally, since this kind of systems are envisioned as possible precursors for the fine-tuned and controlled synthesis of carbon nanotubes, we also address the stability of the dimers found in their crystalline structure, and the associated cohesive energy, which may drive the synthesis of the corresponding nanotubes after an adequate dehydrogenation reaction.

The competition between Na+ and K+ with a protein for water was investigated by using Density Functional Theory (DFT) calculations. The optimized potential energy curves have been made in the DFT, together with balanced basis sets of split valence Def2-SV(P). Initially, calculations were done in order to know the organization of the hydration shell of the sodium and potassium ions, when up to sixteen molecules of water are added. The results indicate the structure and stability of these cations with water clusters. Then, this knowledge was used for the analysis of the hydrated protein when potassium or sodium cations approach them, showing that cation has a dehydration process more favorable energetically, and indicating for which cation, potassium or sodium is the competition with the protein for water more favorable.

Well dispersed iron catalysts were synthesized in silica (Fe0.0XSiO2) by a one-step synthesis procedure. These materials were tested in the propylene epoxidation reaction with gaseous O2. The influence of the iron metal loading on the iron incorporation and distribution in the support (both influenced by the synthetic procedure) were thoroughly studied (conversion, generation and selectivity). Electron Microscopy and UltraViolet–Visible (UV–VIS), Raman and Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy techniques were used to analyze the iron distribution in the catalysts and to probe its incorporation into the silica framework. In situ FTIR was also used to analyze the interaction between propylene and iron-based catalysts. Computational calculations considering a single-site iron catalyst incorporated into the silica structure show a possible interaction between O2 and the incorporated iron atom and the olefin bond and the acidic proton neighboring the iron species which favor the reaction between the two molecules near the iron atom.

Cycloparaphenylenes (CPPs) are nanosized structures with unique isolated and bulk properties, and are synthetic targets for the template-driven bottom-up synthesis of carbon nanotubes. Thus, a systematic understanding of the supramolecular order at the nanoscale is of utmost relevance for molecular engineering. In this study, it is found that intramolecular noncovalent (dispersion) interactions must be taken into account for obtaining accurate estimates of the structural and optoelectronic properties of [n]CPP compounds, and their influence as the number of repeat units increases from n=4 to n=12 is also analyzed, both in the gas phase and in solution. The supramolecular self-assembly, for which both intra- and intermolecular noncovalent interactions are relevant, of [6]CPP is also investigated by calculating the binding energies of dimers taken along several crystal directions. These are also used to estimate the cohesive energy of the crystal, which is compared to the value obtained by means of dispersion-corrected DFT calculations using periodic boundary conditions. The reasonable agreement between both computational strategies points towards a first estimate of the [6]CPP cohesive energy of around 50 kcal mol−1.

Detailed electronic structure calculations of picene clusters doped by potassium modeling the crystalline K3picene structure show that while two electrons are completely transferred from potassium atoms to the lowest-energy unoccupied molecular orbital of pristine picene, the third one remains closely attached to both material components. Multiconfigurational analysis is necessary to show that many structures of almost degenerate total energies compete to define the cluster ground state. Our results prove that the 4s orbital of potassium should be included in any interaction model describing the material. We propose a quarter-filled two-orbital model as the most simple model capable of describing the electronic structure of K-intercalated picene. Precise solutions obtained by a development of the Lanczos method show low-energy electronic excitations involving orbitals located at different positions. Consequently, metallic transport is possible in spite of the clear dominance of interaction over hopping.

Electron donor-acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this work, we study EDA complexes of carbon dioxide with ketones using several ab initio and Density Functional Theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.