The effects of solvation in the theoretical spectra of cationic dyes

We present a quantum-mechanical study on the solvent effects in the structure and electronic spectra of some cationic dyes: acridine orange, proflavine, safranine, neutral red, thionine and methylene blue. The geometry optimizations were carried out with the AM1 and DFT (with B3LYP functional) methods and the theoretical spectra of the dyes under study were obtained with Zindo time-dependent methods (TD–DFT and TD–HF). The solvation methodology adopted was the integral equation formulation (IEF) version of the polarizable continuum model (PCM).     

On a semiclassical interpretation of inter- and intramolecular interactions

The semiclassical models considered here are composed by charge distributions coming from ab initio quantum-mechanical calculations on actual molecular systems. These charge distributions interact with one another according to the laws of classical electrostatics. This article describes some results of a systematic examination of the performances of this model in a variety of cases, with the aim of putting in evidence the usefulness and the limits of this inherently approximate representation of chemical interactions. Intermolecular interactions are examined first; the test cases are interactions of neutral molecules with H⁺, Li⁺, and C1^?, and the formation of H-bonded complexes. Attention is paid mainly to the energetics of the processes; each interacting molecule is considered as a unique entity and classical molecular reactivity indexes (electrostatic potential V, polarization term P) are introduced to compute the interaction energy, to interpret the details of the interaction process, and then to elaborate on less expensive computational procedures. Intramolecular interactions are considered. Attention is paid to the question of defining chemical groups starting from SCF molecular wavefunctions. The transferability and conservation degree of groups derived from localized orbitals of actual molecules is examined in detail, taking as tests their ability to reproduce charge distribution, one-electron observables, and energy. The effect of classical fields on these groups is then examined, taking into consideration external fields originated either by a point charge or by a solvent, and internal fields deriving from substitution of chemical groups. The intergroup analysis is then extended to the case of bimolecular reaction acts by considering the whole system as a supermolecule. Approximate computational procedures able to reproduce the main features of these interactions are proposed and tested. All through the article the performances of the classical models are compared with ab initio SCF calculations (mainly of low or intermediate quality).     

A polarizable continuum model for molecules at diffuse interfaces

In this work we illustrate an extension of the polarizable continuum model to describe solvation effects on molecules at the interface between two fluid phases (liquid/liquid, liquid/vapor). This extension goes beyond the naive picture of the interface as a plane dividing two distinct dielectrics, commonly employed in continuum models. The main feature of the model is the use of a diffuse interface with an electric permittivity depending on the position. This characteristic clearly allows the study of simple interfaces as well as more complex membrane or multilayer structures. Moreover the smooth variation of the permittivity in the diffuse interface, in contrast to the sharp boundary between two regions, overcomes the numerical divergences due to charges placed at the boundary. The implementation of the model relies on the integral equation formalism, which allows one to calculate the reaction field acting on a molecule immersed in a dielectric environment once the proper Green's function is known. In the present case, such a Green's function is obtained numerically, allowing a large flexibility in the choice of the dielectric permittivity profile. The applications have been selected with the aim of illustrating the capabilities of the model; its present limitations are also discussed.     

Neutral organic lewis acids of π type

The interaction of some neutral acids of π type, bearing appropriate unsymmetrical substitutions at the C?C group with some selected bases (H₂O, NH₃, OH^?), is compared with that of the parent compound of a new set of neutral π acids, bearing symmetrical substitutions at the C?C group with the same bases. The analyses of the interaction energy, performed according to two decomposition schemes, with and without the counterpoise corrections, make clear the similarity of symmetrically and unsymmetrically substituted neutral organic acids.     

Solvation dynamics in acetonitrile: a study incorporating solute electronic response and nuclear relaxation

The solvent reorganization process after electronic excitation of a polar solute in a polar solvent such as acetonitrile is related mainly to the time evolution of the solute-solvent electrostatic interaction. Modern laser-based techniques have sufficient time resolution to follow this decay in real time, providing information to be confirmed and interpreted by theories and models. We present here a study aimed at the investigation of the different steps involved in the process taking place after a vertical S(0) --> S(1) excitation of a large size chromophore, coumarin 153 (C153), in acetonitrile, from both the solute and the solvent points of view. To do this, we use accurate quantum mechanical calculations for the solute properties within the polarizable continuum model (PCM) and classical molecular dynamics (MD) simulations, both equilibrium and nonequilibrium, for C153 in the presence of the solvent. The geometry of the solute is allowed to change in order to study the role of internal motions in the time-dependent solvation process. The solvent response function has been obtained from the simulation data and compared to experiment, while the comparison between equilibrium and nonequilibrium MD results for the solvation response confirms the validity of the linear response approximation in the C153-acetonitrile system. The MD trajectories have also been used to monitor the structure of the solvation shell and to determine its change in response to the change in the solute partial charges.     

On the direct calculation of the time evolution of excited molecular states in the presence of nonadiabatic interactions

The possibility is explored of calculating the time evolution of a given initial molecular state, in the presence of sufficiently strong nonadiabatic interactions, with a fully quantum-mechanical approach. Two methods are presented. The first one is based on the determination of the molecular eigenstates, with expansion of the nuclear wavefunctions on a Hermite basis. The second method is based on the Padé 1,1 approximation of the time evolution operator and on a finite difference representation of the time-dependent nuclear wavefunctions. Both methods are applied to simple models of a diatomic molecule.     

Configuration-interaction calculations for the ground state of OF2, NO 2 − , CN−: Canonical orbitals and exclusive orbitals

The C.I. method is applied to already published double- SCF wave functions for OF₂, NO ₂ ^– and CN^–. All doubly excited configurations are considered. The second order approximation values presented for those cases are compared with the exact energy values in some minor cases. An attempt has been made to improve the rate of convergency of the process by transforming the canonical SCF occupied orbitals into localized ones and the virtual canonical orbitals into a particular type of localized orbitals. These latter show also an intuitively acceptable spatial conformation.

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Zusammenfassung Die CI Methode wird auf bereits bekannte Doppel-Zeta-SCF-Wellenfuntionen für die Systeme OF₂, NO ₂ ^– und CN^– angewandt. Dabei werden alle doppelt angeregten Konfigurationen berücksichtigt. Um die Konvergenz zu verbessern, werden versuchsweise die kanonischen und besetzten SCF-Orbitale in lokalisierte Orbitale und die virtuellen kanonischen Orbitale in einen besonderen Typ von lokalisierten Orbitalen transformiert. Die letzteren zeigen eine besonders geeignete räumliche Anpassung.

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Résumé Pour un calcul de intéraction de configurations, comprenant toutes le configurations à double excitation, on a employé des fonctions d'onde SCF sur une base doublée. Pour le calcul complet on a essayé des formules d'approximation, qu'on a pu vérifier avec le calcul exact sur des cas réduits.Pour améliorer la vélocité de convergence du procés on a transformé les orbitales canoniques SCF en orbitales localisées et aprés on a construit, selon un procedé particulier, des orbitales virtuelles localisées qui montrent une conformation dans l'espace qui est intuitivement satisfaisante.

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Work supported by the Consiglio Nazionale delie Ricerche.     

Detection of a stable nitroxide during chemical depolymerization of heparin

The use of low-molecular-weight heparins (LMWHs) has become common, since compared to unfractionated heparin (UFH), they have a much longer plasma half-life and lower incidence of side effects. LMWHs are derived from the depolymerization of UFH, obtained either chemically, physically or enzymatically. We employed electron spin resonance (ESR) spectroscopy to study the depolymerization of UFH by copper in the presence of hydrogen peroxide. A stable nitroxide radical was detected. This could be generated by the hydroxyl radical attack either to the N-SO⁻₃ group or to free amino groups present in the UFH preparation.     

Spatially resolved (semi)quantitative determination of iron (Fe) in plants by means of synchrotron micro X-ray fluorescence

Iron (Fe) is an essential element for plant growth and development; hence determining Fe distribution and concentration inside plant organs at the microscopic level is of great relevance to better understand its metabolism and bioavailability through the food chain. Among the available microanalytical techniques, synchrotron μ-XRF methods can provide a powerful and versatile array of analytical tools to study Fe distribution within plant samples. In the last years, the implementation of new algorithms and detection technologies has opened the way to more accurate (semi)quantitative analyses of complex matrices like plant materials. In this paper, for the first time the distribution of Fe within tomato roots has been imaged and quantified by means of confocal μ-XRF and exploiting a recently developed fundamental parameter-based algorithm. With this approach, Fe concentrations ranging from few hundreds of ppb to several hundreds of ppm can be determined at the microscopic level without cutting sections. Furthermore, Fe (semi)quantitative distribution maps were obtained for the first time by using two opposing detectors to collect simultaneously the XRF radiation emerging from both sides of an intact cucumber leaf.