The sarcoplasmic reticulum: an organized patchwork of specialized domains.

The sarcoplasmic reticulum (SR) of skeletal muscle cells is a convoluted structure composed of a variety of tubules and cisternae, which share a continuous lumen delimited by a single continuous membrane, branching to form a network that surrounds each myofibril. In this network, some specific domains basically represented by the longitudinal SR and the junctional SR can be distinguished. These domains are mainly dedicated to Ca(2+) homeostasis in relation to regulation of muscle contraction, with the longitudinal SR representing the sites of Ca(2+) uptake and storage and the junctional SR representing the sites of Ca(2+) release.

Pulse ENDOR and density functional theory on the peridinin triplet state involved in the photo-protective mechanism in the peridinin-chlorophyll a-protein from Amphidinium carterae.

The photoexcited triplet state of the carotenoid peridinin in the Peridinin-chlorophyll a-protein of the dinoflagellate Amphidinium carterae has been investigated by pulse EPR and pulse ENDOR spectroscopies at variable temperatures. This is the first time that the ENDOR spectra of a carotenoid triplet in a naturally occurring light-harvesting complex, populated by energy transfer from the chlorophyll a triplet state, have been reported. From the electron spin echo experiments we have obtained the information on the electron spin polarization dynamics and from Mims ENDOR experiments we have derived the triplet state hyperfine couplings of the alpha- and beta-protons of the peridinin conjugated chain.

Integrated computational strategies for UV/vis spectra of large molecules in solution.

In recent years, the margin of interaction between computational chemistry and most branches of experimental chemistry has increased at a fast pace. The experimental characterization of new systems relies on computational methods for the rationalization of structural, energetic, electronic and dynamical features. In particular, novel computational approaches allow accurate estimates of molecular parameters from spectroscopic optical observables, giving rise to synergic interactions between experimentalists and theoretically-oriented chemists.

On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl.

Electron spin resonance (ESR) measurements are highly informative on the dynamic behavior of molecules, which is of fundamental importance to understand their stability, biological functions and activities, and catalytic action. The wealth of dynamic information which can be extracted from a continuous wave electron spin resonance (cw-ESR) spectrum can be inferred by a basic theoretical approach defined within the stochastic Liouville equation formalism, i.e.

Accurate steady-state and zero-time fluorescence spectra of large molecules in solution by a first-principle computational method.

We report the first-principle calculation and analysis of the vibrationally resolved steady-state absorption and fluorescence spectra, and of the zero-time fluorescence spectrum of a sizable molecule, coumarin C153, in two different solvents. Our approach, bringing together the most recent developments in the fields of time-dependent density functional theory and of polarizable continuum solvent models, with an efficient method for the computation of vibrational contributions to transition intensities, allows a remarkable agreement with experiments, both concerning the line shapes and the solvatochromic and Stokes shifts. The method is also able to nicely describe the solvent relaxation effect on the fluorescence spectra, perfectly reproducing the energy shift between zero-time and steady-state fluorescence.

[Epidemiology of problems related to drugs and devices in nursing homes in various regions of Italy].

The premises, questions and methodological problems of a multicentre study aimed at describing the epidemiology of patients' problems that require a nursing intervention are described. The main points and methodological challenges are presented and discussed: (a.) the choice of focusing on patients cared for in Nursing homes and districts because a.

Nitration versus nitrosation chemistry of menthofuran: remarkable fragmentation and dimerization pathways and expeditious entry into dehydromenthofurolactone.

The reaction chemistry of menthofuran (1), a toxic furan terpenoid from various mint oils, with nitric acid and nitrous acid has been investigated. Treatment of 1 with nitric acid afforded a 1:1 mixture of the bisfuran derivatives 5 and 6, resulting from the unexpected cleavage of the furan into two carbonyl fragments (3-methylcyclohexanone and hydroxyacetone) and their subsequent trapping by unreacted 1. Under conditions of high dilution, the nitrofuran derivative 7 was formed instead as the major reaction product.

Unraveling the role of stereo-electronic, dynamical, and environmental effects in tuning the structure and magnetic properties of glycine radical in aqueous solution at different pH values.

A recently developed extended Lagrangian model employing localized basis functions and nonperiodic boundary conditions (GLOB/ADMP) was applied to the radicals issuing from the homolytic breaking of the C(alpha)-H(alpha) bond of glycine in aqueous solution at different pH values. Although the modifications of the structure and the magnetic properties of these species induced by the solvent are qualitatively reproduced by a static discrete-continuum model, magnetic parameters are further tuned by short-time dynamical effects (solute vibrations and solvent librations). The results delivered by GLOB/ADMP simulations for both hyperfine tensors and g-tensors are in remarkable agreement with their experimental counterparts, allowing a reliable disentanglement of the overall observables into well-defined contributions.

Isotopomeric conformational changes in the anisole-water complex: new insights from HR-UV spectroscopy and theoretical studies.

Resonance enhanced multiphoton ionization and rotationally resolved S1<--S0 electronic spectra of the anisole-2H2O complex have been obtained. The experimental results are compared with high level quantum mechanical calculations and with data already available in the literature. Quite surprisingly, the equilibrium structure of the anisole-2H2O complex in the S0 state shows some non-negligible differences from that of the isotopomer anisole-1H2O complex.

Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case.

By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face pi-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S(1))(2). TD-PBE0, TD-LC-omegaPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al.

On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: the anisole-ammonia 1:1 complex.

State-of-the-art spectroscopic and theoretical methods have been exploited in a joint effort to elucidate the subtle features of the structure and the energetics of the anisole-ammonia 1:1 complex, a prototype of microsolvation processes. Resonance enhanced multiphoton ionization and laser-induced fluorescence spectra are discussed and compared to high-level first-principles theoretical models, based on density functional, many body second order perturbation, and coupled cluster theories. In the most stable nonplanar structure of the complex, the ammonia interacts with the delocalized pi electron density of the anisole ring: hydrogen bonding and dispersive forces provide a comparable stabilization energy in the ground state, whereas in the excited state the dispersion term is negligible because of electron density transfer from the oxygen to the aromatic ring.

Calculated spectroscopic and electric properties of the alkali metal-ammonia complexes from Kn-NH3 to Frn-NH3 (n=0,+1).

The newly developed Stuttgart small-core scalar relativistic pseudopotentials for the alkali metals are used to study spectroscopic and electric properties of the heavier alkali metal-ammonia complexes from K(n)-NH(3) to Fr(n)-NH(3) (n=0,+1) at the second-order Moller-Plesset (MP2) and coupled cluster [CCSD(T)] levels of theory. Equilibrium geometries and dissociation energies computed at the MP2 level are in reasonable agreement with their CCSD(T) counterparts, whereas for the dipole polarizabilities MP2 is not performing well overestimating significantly electron correlation effects. The bond distances increase monotonically with increasing mass of the metal atom as relativistic effects are small in these systems.

Toward effective and reliable fluorescence energies in solution by a new state specific polarizable continuum model time dependent density functional theory approach.

A state specific (SS) model for the inclusion of solvent effects in time dependent density functional theory (TD-DFT) computations of emission energies has been developed and coded in the framework of the so called polarizable continuum model (PCM). The new model allows for a rigorous and effective treatment of dynamical solvent effects in the computation of fluorescence and phosphorescence spectra in solution, and it can be used for studying different relaxation time regimes. SS and conventional linear response (LR) models have been compared by computing the emission energies for different benchmark systems (formaldehyde in water and three coumarin derivatives in ethanol).

Unraveling solvent-driven equilibria between alpha- and 3(10)-helices through an integrated spin labeling and computational approach.

In this work we present an effective and flexible computational approach, which is the result of an ongoing development in our groups, allowing the complete a priori simulation of the ESR spectra of complex systems in solution. The usefulness and reliability of the method are demonstrated on the very demanding playground represented by the tuning of the equilibrium between 3(10)- and alpha-helices of polypeptides by different solvents. The starting point is the good agreement between computed and X-ray diffraction structures for the 3(10)-helix adopted by the double spin-labelled heptapeptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe.

Halogen bonds between 2,2,6,6-tetramethylpiperidine-N-oxyl radical and CxHyFzI species: DFT calculations of physicochemical properties and comparison with hydrogen bonded adducts.

Structural, thermodynamic, and magnetic properties of adducts between the 2,2,6,6-tetramethylpiperidine-N-oxyl radical and representative hydrogen and halogen bond donors in solution have been investigated by an integrated computational tool including hybrid density functionals and discrete-continuum solvent models. From a quantitative point of view, the computed values show a fair agreement with experiment when environmental effects are taken into the proper account. From a more general point of view, our analysis points out a number of analogies, but also some difference, between hydrogen and halogen bond, which have been interpreted in terms of the various effects tuning thermodynamic and spectroscopic parameters.

Enhanced half-metallicity in edge-oxidized zigzag graphene nanoribbons.

We present a comprehensive theoretical study of the electronic properties and relative stabilities of edge-oxidized zigzag graphene nanoribbons. The oxidation schemes considered include hydroxyl, lactone, ketone, and ether groups. Using screened exchange density functional theory, we show that these oxidized ribbons are more stable than hydrogen-terminated nanoribbons except for the case of the etheric groups.

Interplay of intrinsic, environmental, and dynamic effects in tuning the EPR parameters of nitroxides: further insights from an integrated computational approach.

The role of stereoelectronic, environmental, and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of a prototypical nitroxide spin probe has been investigated by an integrated computational approach based on extended Lagrangian molecular dynamics and discrete-continuum solvent models. Trajectories were generated in two protic solvents as well as in the gas phase for reference; structural analysis of the dynamics, and comparison with optimized solute-solvent clusters, allowed for the identification of the prevailing solute-solvent hydrogen-bonding patterns and helped to define the strategy for the computation of magnetic parameters. This was performed in a separate step, on a large number of frames, by a high-level DFT approach coupling the PBE0 hybrid functional with a tailored basis set and with proper account of specific and bulk solvent effects.

Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations.

A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (S(B)) delocalized over several nucleobases, excited-state geometry optimization indicates that S(B) subsequently evolves into a state in which the excitation is localized on a single base.

Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution.

The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky rotation of the normal modes and the effect of thermal excitation. The method automatically selects the relevant vibronic contributions to the spectrum, independently of their frequency, and it is able to provide fully converged spectra with moderate computational times, both in vacuo and in solution. By describing the electronic states in the frame of the density functional theory and its time-dependent extension, they computed the room temperature absorption spectra of coumarin C153 and trans-stilbene in cyclohexane and the phosphorescence spectrum of porphyrazine in gas phase, showing that the method is fast and efficient.

Evidence for sevenfold coordination in the first solvation shell of Hg(II) aqua ion.

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C2 symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species.

Effective method to compute Franck-Condon integrals for optical spectra of large molecules in solution.

The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky [Acta Physicochim. URSS 7, 551 (1937)] rotation of the normal modes. The method automatically selects the relevant vibronic contributions to the spectrum, independent of their frequency, and it is able to provide fully converged spectra with a quite modest computational time, both in vacuo and in condensed phase.

Ab initio modeling of CW-ESR spectra of the double spin labeled peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe in acetonitrile.

In this work we address the interpretation, via an ab initio integrated computational approach, of the CW-ESR spectra of the double spin labeled, 310-helical, peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe dissolved in acetonitrile. Our approach is based on the determination of geometric and local magnetic parameters of the heptapeptide by quantum mechanical density functional calculations taking into account solvent and, when needed, vibrational averaging contributions. The system is then described by a stochastic Liouville equation for the two electron spins interacting with each other and with two 14N nuclear spins, in the presence of diffusive rotational dynamics.

Chemical, pulse radiolysis and density functional studies of a new, labile 5,6-indolequinone and its semiquinone.

The chemical and spectroscopic characterization of 5,6-indolequinones and their semiquinones, key transient intermediates in the oxidative conversion of 5,6-dihydroxyindoles to eumelanin biopolymers, is a most challenging task. In the present paper, we report the characterization of a novel, relatively long-lived 5,6-indolequinone along with its semiquinone using an integrated chemical, pulse radiolytic, and computational approach. The quinone was obtained by oxidation of 5,6-dihydroxy-3-iodoindole (1a) with o-chloranil in cold ethyl acetate or aqueous buffer: it displayed electronic absorption bands around 400 and 600 nm, was reduced to 1a with Na2S2O4, and reacted with o-phenylenediamine to give small amounts of 3-iodo-1H-pyrrolo[2,3-b]phenazine (2).

Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water.

The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart.

Electronic structure and stability of semiconducting graphene nanoribbons.

We present a systematic density functional theory study of the electronic properties, optical spectra, and relative thermodynamic stability of semiconducting graphene nanoribbons. We consider ribbons with different edge nature including bare and hydrogen-terminated ribbons, several crystallographic orientations, and widths up to 3 nm. Our results can be extrapolated to wider ribbons providing a qualitative way of determining the electronic properties of ribbons with widths of practical significance.