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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 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]

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 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 concept of 'electron deformation orbitals' (EDOs) is used to investigate the electric response of conducting metals and oligophenyl chains. These orbitals and their eigenvalues are obtained by diagonalization of the deformation density matrix (difference between the density matrices of the perturbed and unperturbed systems) and can be constructed as linear combinations of the unperturbed molecular orbitals within 'frozen geometry' conditions. This form of the EDOs allows calculating the part of the electron deformation density associated to an effective electron transfer from occupied to virtual orbitals (valence to conduction band electron transfer in the band model of conductivity). It is found that the 'electron deformation' orbitals pair off, displaying the same eigenvalue but opposite sign. Each pair represents an amount of accumulation/depletion of electron charge at different molecular regions. In the oligophenyl systems investigated only one pair contributes effectively to the charge flow between molecular ends, resulting from the promotion of electrons from occupied orbitals to close in energy virtual orbitals of appropriate symmetry and overlapping. Analysis of this pair along explains the differences in conductance of olygophenyl chains based on phenyl units. © 2014 Wiley Periodicals, Inc. [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]

Fertilizers based on phosphate-metal-humate complexes are a new family of compounds that represents a more sustainable and bioavailable phosphorus source. The characterization of this type of complex by using solid 31P NMR in several fertilizers, based on single superphosphate (SSP) and triple superphosphate (TSP) matrices, yielded surprising and unexpected trends in the intensity and fine structure of the 31P NMR peaks. Computational chemistry methods allowed the characterization of phosphate-calcium-humate complexes in both SSP and TSP matrices, but also predicted the formation of a stable sulfate-calcium-humate complex in the SSP fertilizers, which has not been described previously. The stability of this complex has been confirmed by using ultrafiltration techniques. Preference towards the humic substance for the sulfate-metal phase in SSP allowed the explanation of the opposing trends that were observed in the experimental 31P NMR spectra of SSP and TSP samples. Additionally, computational chemistry has provided an assignment of the 31P NMR signals to different phosphate ligands as well as valuable information about the relative strength of the phosphate-calcium interactions within the crystals. [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]

Chemical reactivity descriptors are derived within the framework of the pair density functional theory. These indices provide valuable information about bonding rearrangements and activating mechanisms upon electrophilic or nucleophilic reactions. Indices derived and tested in this work represent nonlocal counterparts of the local reactivity indices derived in the context of conceptual density functional theory (CDFT) and frequently used in reactivity studies; the Fukui function, the local softness and the dual descriptor. In this work, we show how these nonlocal indices provide a quantum chemical basis to explain the success of qualitative resonance models in chemical reactivity predictions. Also, local information is implicitly contained as CDFT indices are obtained by simple integration. As illustrative examples, we have considered in this work the Markovnikov's rule, the reactivity of enolate anion, the nucleophilic conjugate addition to α,β-unsaturated compounds and the electrophilic aromatic substitution of benzene derivatives. The densities used in this work were obtained with Hartree-Fock, Kohn-Sham DFT, and singles and doubles configuration interaction (CISD) approaches. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Thermodynamic stability of metal-aminoacid complexes in water is discussed in terms of the Gibbs free energy of water-ligand exchange processes, and the electronic stabilizing factors thoroughly investigated by means of 1-electron and 2-electron density properties. Hexacoordinated complexes formed between iron cations and glycine molecules acting as monodentate or bidentate ligands have been chosen as targets for the current study. Results agree with experimental findings, and complexes formed with bidentate ligands are found to be more stable than those formed with monodentate ones. The larger the number of the coordinated glycine molecules the more stable is the complex. Fe(III) complexes are more stable than Fe(II) ones, but differences are small and the Fe3+/Fe2+ exchange process appears to be energetically feasible for these complexes. Formation of the second glycine-iron interaction involving the amino nitrogen in the bidentate ligands is enthalpycally unfavorable but takes place due to the large entropy rise of the process. The larger stability of Fe(III) complexes is due however to the balance between energetic and solvation terms, which is favorable to these complexes. Electron density properties account satisfactorily for the electronic energy changes along the complex formation in terms of ligand-metal electron transfer and covalent bond orders. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [ABSTRACT FROM AUTHOR]

The multicenter bond indices (MCI), recently proposed as quantitative measures of cyclic delocalization in aromatic systems, have been applied to characterize the differences in the nature of the electron reorganization in a series of allowed and forbidden electrocyclic reactions of linear neutral polyenes of general formula CnHn+2 and related charged systems of formula CnHn+2(+) and CnHn+2(-) for n ranging from 4 to 7. The proposed methodology, which is based on the monitoring of the variation of the extent of cyclic delocalization along the concerted reaction paths, is shown to be completely consistent with the empirical Evans/Dewar classification anticipating aromatic transition states for allowed and anti-aromatic transition states for forbidden electrocyclic reactions. Although the study reports the results of the analysis of electron reorganization just for the above-mentioned particular class of electrocyclic reactions, the proposed approach is completely general and its conclusions remain valid for any pericyclic reaction. Copyright © 2009 John Wiley & Sons, Ltd. [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]

The concept of transmission channel plays a key role in the theory of molecular conductors. They are usually constructed from one‐electron functions (molecular spin orbitals) in the extensively employed LCAO‐MO method. Thus, the electric conductance can be obtained from the transmission matrix, whose diagonalization leads to a set of transmission eigenchannels. In this work, it is shown how using the time‐energy uncertainty relation approach, the electron transport can be also analysed in terms of coupled transmission channels. Here, the transmission channels are constructed in terms of electron deformation orbitals (EDOs), which in turn arise from linear combinations of occupied and unoccupied one‐electron functions. These transmission channels allow linking the electric conduction in molecular junctions with the traditional interpretation in mesoscopic systems, where the electron transport occurs by promotion of electrons from the valence to the conduction bands. Moreover, they lead to an expression of the electric conductance within the Landauer formalism, with the conductance given by the product of the quantum conductance and a transmission function. Transmission channels of junctions formed by polycyclic aromatic chains attached to gold atoms are analysed in detail. Symmetry rules for the MOs involved in these channels are established, giving rise to a straightforward method for the analysis of the transport ability in molecular systems. Symmetry allowed occupied and unoccupied MOs combine to form electron transport channels on the action of an external electric perturbation. These channels provide an interpretation of the electron transport in molecules similar to that given by the band theory in mesoscopic systems, where the electron transport occurs by promotion of electrons from the valence to the conduction band. [ABSTRACT FROM AUTHOR]