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Ortiz and Seminario (J. Chem.Phys.2007, 127, 111106/1–3)proposed some years agoa simple and direct approach to obtain I/Vprofiles from the combination of ab initio equilibriumelectronic structure calculations and the uncertainty principle asan alternative or complementary tool to more sophisticated nonequilibriumGreen’s functions methods. In this work, we revisit the fundamentalsof this approach and reformulate accordingly the expression of theelectric current. By analogy to the spontaneous electron decay processin electron transitions, in our revision, the current is calculatedupon the relaxing process from the “polarized” stateinduced by the external electric field to the electronic ground state.The electric current is obtained from the total charge transferredthrough the molecule and the corresponding electronic energy relaxation.The electric current expression proposed is more general comparedwith the previous expression employed by Ortiz and Seminario, wherethe charge variation must be tested among different slabs of atomsat the contact. This new approach has been tested on benzene-1,4-dithiolateattached to different gold clusters that represent the contact withthe electrodes. Analysis of the total electron deformation densityinduced by the external electric voltage and properties associatedwith the electron deformation orbitals supports the conclusions obtainedfrom the I/Vprofiles. [ABSTRACT FROM AUTHOR]

The aim of this review is to describe the main physicochemical characteristics of diverse types of humic-metal-phosphate acid complexes. The effects of these complexes on phosphorus (P) fixation in soils with different pH values and physicochemical features and on plant phosphorus uptake are also discussed. Humic-metal-phosphate complexes have apparent stability constants in the same range as those of metal-humic complexes, in solutions with diverse pH and ionic-strength values. Likewise, the molecular-size distribution of humic-metal-phosphate complexes as a function of pH is similar to that of potassium or sodium humates and metal-humic complexes. Humic-metal-phosphate complexes are able to decrease phosphate fixation in soils and increase plant growth and phosphate uptake. Phosphorus fertilizers containing humic-metal-phosphate complexes proved to be efficient to improve plant growth and P uptake with respect to conventional fertilizers such as single superphosphate. The values of parameters related to plant phosphorus-utilization efficiency (PUt E) suggest that the regulation of root acquisition of phosphate from these complexes could involve the interregulation of a system for the optimization of metabolic P utilization in the shoot and another system involving stress responses of roots under phosphorus deficiency. [ABSTRACT FROM AUTHOR]

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(C6H4) nCH2Au ( n=1-5), Au2C(C6H4) nCAu2 ( n=1-5), and Au(C6H4) nAu ( n=1-5), respectively. The molecules were subjected to finite bias voltages ranging from 0 to 5 V. Analysis of the intramolecular electron transfer and electron delocalization revealed a completely opposite response to electric perturbation of pX2 in comparison with pX1 and pP. Thus, in pX2 the applied voltage causes an increase in the electron delocalization within the rings together with a large electron transfer and energetic stabilization. On the contrary, the same voltages partially destroy the electron delocalization in pX1 and pP, produce a large local electron polarization in the benzene rings, and a smaller energetic stabilization. These differences can be rationalized in terms of the role played by polarized valence bond structures in the total wave function. Theoretical estimation of the I/ V profiles indicates that pX2 chains are much better electronic conductors than pX1 and pP. [ABSTRACT FROM AUTHOR]

BACKGROUND: Previous studies showed that phosphate can be complexed by humic acids (HA) through stable metal (M) bridges (PMHA). We studied the thermodynamic properties of PMHA and their relationships with the ability of PMHA to both decrease soil P fixation and increase P availability for plants. With this aim, we studied the theoretical stability of PFeHA, PAlHA and PCaHA by molecular modelling methods in relation to the degree and intensity of P absorption in soils and the ability of plants to take up complexed P. RESULTS: A density functional theory (DFT) quantum chemical study enabled us to obtain stable structures for the three PMHA complexes in water solution. The theoretical stabilities (Δ G0) were consistent with that for apparent stability obtained by Scatchard method, PFeHA ≥ PAlHA > PCaHA, though the differences were clearer by the DFT method. Also the reduction of soil P fixation and the release of P from PMHA in the presence of an anionic resin confirmed the stability order of the different PMHA. Plant studies confirmed the ability of diverse plant species to take up both P and metal complexed in PMHA. CONCLUSION: The results indicated the potential efficiency of PMHA-based fertilizers to optimize P fertilization for crops cultivated in soils with high P fixation ability. Copyright © 2012 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Relations between aromaticity indices derived from chemical graph theory and those based on 6-center electron delocalization are investigated for a series of polybenzenoid hydrocarbons. Aromatic stabilization obtained by means of the effective scaled electron delocalization is highly correlated to the resonance energy, RE, obtained both from SCF MO calculations and conjugated ring circuits model. Local aromaticity of benzene rings is discussed using two different criteria, in one of them aromaticity is just given by the cyclic π-electron conjugation of the ring, whereas terms involving more than one ring are also considered in the other one. Indices derived from chemical graph theory and those obtained from the 6-center electron delocalization give rise to the same local aromaticity. Moreover, 6-center electron delocalization provides more quantitative information. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]

The implementation of the n-center electron delocalization indices, n-DIs, and n-order electron localization indices, n-LIs, within the framework of the quantum theory of atoms in molecules, QTAIM, is performed. n-DIs are shown to be very useful to study the local aromaticity in monocyclic and polycyclic compounds. Total and π n-DIs from n = 4 to 7 were computed for a series of typical 4, 5, 6, and 7-center aromatic and antiaromatic rings. For n ≥ 5 the π n-DI accounts for the 95% of the total n-DI and can be employed alone to measure the aromaticity. A scaling factor on the n-DIs is required in order to compare the aromaticity of [5c-6e] and [6c-6e] rings, the same correction allows to estimate the relative aromatic stabilization of polycyclic compounds using the sum of its values for individual rings. This is called Effective Scaled Electron Delocalization, ESED. The comparison with other aromaticity indices reflects a good correlation between ESED and both resonance energies, and HOMA indices. The most important differences between scaled π n-DIs and NICS(0) indices are found for compounds that contain rings with different number of centers or π electrons. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]

[Display omitted] • -Strong optical confinement is achieved in carbon nanoislands of h-BNCs. • -Carbon nanoislands retain the main electronic features of their isolated counterparts –h. • -BNCs are of potential application for surface enhanced Raman spectroscopy. 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 (N BN) 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 N BN ≥ 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. [ABSTRACT FROM AUTHOR]

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. [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]

The aromaticity of a representative sample of pro-aromatic radicals and its nitro, amino, hydroxyl and imine substituted derivatives has been analysed by means of multicenter delocalization indices (MCI) and nuclear-independent chemical shifts (NICS). Because of their radical character, these compounds may exhibit conflicting α/β aromaticity, so that the contribution of α and β electrons to the MCI and NICS has been analysed separately and their values qualitatively interpreted in terms of the 2n+1/2n rule. All the monocyclic radicals investigated show conflicting α/β aromaticity. Thus, significant MCI values have been found for one of the spin components, whereas negligible values, even slightly negative, have been obtained for the other spin component. NICS indices confirm the aromatic character reflected by the MCIs and clearly show the antiaromatic or non-aromatic character of the other spin components. The same has been found for the donor rings of the bicyclic pro-aromatic radicals investigated, whereas all the fused benzene rings of these radicals show a clear aromatic character in both spin components. Substitutions at the donor carbon position by strong deactivating groups provoke a small increase of the aromatic character in the aromatic spin components and a significant decrease of the antiaromatic character in the antiaromatic spin components whereas activating groups have little effect., (© 2025 Wiley-VCH GmbH.)

One of the challenges for the realization of molecular electronics is the design of nanoscale molecular wires displaying long-range charge transport. Graphene nanoribbons are an attractive platform for the development of molecular wires with long-range conductance owing to their unique electrical properties. Despite their potential, the charge transport properties of single nanoribbons remain underexplored. Herein, we report a synthetic approach to prepare N-doped pyrene-pyrazinoquinoxaline molecular graphene nanoribbons terminated with diamino anchoring groups at each end. These terminal groups allow for the formation of stable molecular graphene nanoribbon junctions between two metal electrodes that were investigated by scanning tunneling microscope-based break-junction measurements. The experimental and computational results provide evidence of long-range tunneling charge transport in these systems characterized by a shallow conductance length dependence and electron tunneling through >6 nm molecular backbone.

Multiply charged complexes bound by noncovalent interactions have been previously described in the literature, although they were mostly focused on organic and main group inorganic systems. In this work, we show that similar complexes can also be found for organometallic systems containing transition metals and deepen in the reasons behind the existence of these species. We have studied the structures, binding energies, and dissociation profiles in the gas phase of a series of charged hydrogen-bonded dimers of metallocene (Ru, Co, Rh, and Mn) derivatives isoelectronic with the ferrocene dimer. Our results indicate that the carboxylic acid-containing dimers are more strongly bonded and present larger barriers to dissociation than the amide ones and that the cationic complexes tend to be more stable than the anionic ones. Additionally, we describe for the first time the symmetric proton transfer that can occur while in the metastable phase. Finally, we use a density-based energy decomposition analysis to shine light on the nature of the interaction between the dimers.

Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, namely, electrostatic, Pauli, and polarization, for cationic, anionic, and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires sizable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wave function by means of a larger basis set and the introduction of polarization into the MM region through a polarizable force field do not translate to a faster convergence with the QM region size, but they lead to better results for the different interaction energy components. The results obtained in this work provide insight into the effect of each energy component on the convergence of the solute-solvent interaction energy with the QM region size. This information can be used to improve the MM FFs and embedding schemes employed in QM/MM calculations of solvated systems.

Herein, it is shown how anion recognition in highly polar solvents by neutral metal-free receptors is feasible when multiple hydrogen bonding and anion-π interactions are suitably combined. A neutral aromatic molecular tweezer functionalized with azo groups is shown to merge these two kinds of interactions in a unique system and its efficiency as an anion catcher in water is evaluated using first-principles quantum methods. Theoretical calculations unequivocally prove the high thermodynamic stability in water of a model anion, bromide, captured within the tweezer's cavity. Thus, static calculations indicate anion-tweezer interaction energies within the range of covalent or ionic bonds and stability constants in water of more than 10 orders of magnitude. First-principles molecular dynamics calculations also corroborate the stability through the time of the anion-tweezer complex in water. It shows that the anion is always found within the tweezer's cavity due to the combination of the tweezer-anion interactions plus a hydrogen bond between the anion and a water molecule that is inside the tweezer's cavity.

Several measures of aromaticity including energetic, magnetic, and electron density criteria are employed to show how aromatic stabilization can explain the stability sequence of hydroporphyrins, ranging from porphin to octahydroporphin, and their preferred hydrogenation paths. The methods employed involve topological resonance energies and their circuit energy effects, bond resonance energies, multicenter delocalization indices, ring current maps, magnetic susceptibilities, and nuclear-independent chemical shifts. To compare the information obtained by the different methods, the results have been put in the same scale by using recently proposed approaches. It is found that all of them provide essentially the same information and lead to similar conclusions. Also, hydrogenation energies along different hydrogenation paths connecting porphin with octahydroporphin have been calculated with density functional theory. It is shown by using the methods mentioned above that the relative stability of different hydroporphyrin isomers and the observed inaccessibility of octahydroporphin both synthetically and in nature can be perfectly rationalized in terms of aromaticity., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The presence of intramolecular hydrogen bond (IHB) in beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals was investigated using the QTAIM topological study on UB3LYP/6-311++G(2d,2p) charge densities. Only one of the two conformers of beta-hydroxyethylperoxy radical which were previously considered to present IHB displays a bond critical point (BCP) associated to an IHB. Furthermore, the atomic energies and electron populations indicate no evidence of IHB in the second conformer. Nevertheless, very small differences in molecular energies were obtained using several one-step and multi-step methods (G3, G3B3) between both conformers. No BCP is found between the hydroxyl hydrogen and the oxygen in the most stable conformer or in the transition state for the dissociation path of beta-hydroxyethoxy radical. However, a BCP is formed in the last steps of this path, thereby yielding H-bonded products.

The existence of the orbital interaction presented in the literature as being the cause for the stabilisation of the Z,Z configuration of Ph-S-N=S=N-S-Ph (1) and its derivatives in the crystal phase, has been investigated. The results of theoretical calculations at the DFT/B3LYP/6-311+G* level of theory suggest that such a stabilising interaction might not exist or be extremely weak and that packing forces must be the main cause of the observed Z,Z configuration in the solid. To reach this conclusion structural and energetic parameters were combined to study the bonding in these -S-N=S=N-S- systems. For the analogous Ph-Se-N=S=N-Se-Ph (2) in particular the isomeric equilibrium in solution found in the variable-temperature 77Se NMR spectrum indicates that, in the gas phase or in solution, the observed Z,Z configuration is not stabilised to a greater extent than the Z,E configuration.