Parallel Jacobi–Davidson with block FSAI preconditioning and controlled inner iterations

The Jacobi–Davidson (JD) algorithm is considered one of the most efficient eigensolvers currently available for non‐Hermitian problems. It can be viewed as a coupled inner‐outer iteration, where the inner one expands the search subspace and the outer one reduces the eigenpair residual. One of the difficulties in the JD efficient use stems from the definition of the most appropriate inner tolerance, so as to avoid useless extra work and keep the number of outer iterations under control. To this aim, the use of an efficient preconditioner for the inner iterative solver is of paramount importance. The present paper describes a fresh implementation of the JD algorithm with controlled inner iterations and block factorized sparse approximate inverse preconditioning for non‐Hermitian eigenproblems in a parallel computational environment. The algorithm performance is investigated by comparison with a freely available software package such as SLEPc. The results show that combining the inner tolerance control with an efficient preconditioning technique can allow for a significant improvement of the JD performance, preserving a good scalability. Copyright © 2016 John Wiley & Sons, Ltd.     

Fast stereoselective reactions in electrosprayed Co(II)/neurotransmitter nanodroplets

Collision induced dissociation (CID) of the m/z 479 ion, formed by ESI of Co(NO3)2-CH3OH solutions with either pure (1S,2S)-(+)-N-methylpseudoephedrine or its mixtures with (1S,2R)-(+)- or (1R,2S)-(-)-ephedrine, provides compelling evidence for fast, stereoselective reactions in Co(II)/neurotrasmitter(s) aggregates during solvent evaporation of the ESI droplets.     

Molecular dynamics simulations of proteins and peptides: from folding to drug design

Computer simulations of proteins, lipids and nucleic acids at equilibrium have become essentially routine. However, the fact remains that complete sampling of conformational space continues to be a bottle-neck in the field. The challenge for the future is to overcome such problems and use computational approaches to understand recognition and spontaneous self-organization in biomolecular systems (folding, aggregation and assembly of complexes), processes that cannot be directly observed experimentally. In this review, examples illustrating the extent to which simulations can be used to understand these phenomena in biomolecular systems will be presented along with examples of methodological developments to increase our physical understanding of the processes. The study cases will cover the problems of peptide-receptor recognition and the use of the information obtained for the design of new non-peptidic ligands; the study of the folding mechanism of small proteins and finally the study of the initial stages of peptide self-aggregation.     

Single molecule magnets: from thin films to nano-patterns

Single molecule magnets (SMM) are a class of molecules exhibiting magnetic properties similar to those observed in conventional bulk magnets, but of molecular origin. SMMs have been proposed as potential candidates for several technological applications that require highly controlled thin films and patterns. Here we present an overview of the most important approaches for thin film growth and micro(nano)-patterning of SMM, giving special attention to Mn(12) based molecules. We present both conventional approaches to thin film growth (Langmuir-Blodgett, chemical approach, dip and dry, laser evaporation), patterning (micro-contact printing, deposition on patterned surface, moulding of homogeneous films) and new methods specifically developed for SMM (lithographically controlled wetting, lithographically controlled de-mixing).     

The reversible opening of water channels in cytochrome C modulates the heme iron reduction potential

Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanoseconds can bring to light unexpected events even for extensively studied biomolecules. This paper reports a combined computational/experimental approach that reveals the reversible opening of two distinct fluctuating cavities in Saccharomyces cerevisiae iso-1-cytochrome c. Both channels allow water access to the heme center. By means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical approach, the perturbed matrix method (PMM), that allows to reach long simulation times, changes in the reduction potential of the heme Fe(3+)/Fe(2+) couple induced by the opening of each cavity are calculated. Shifts of the reduction potential upon changes in the hydration of the heme propionates are observed. These variations are relatively small but significant and could therefore represent a tool developed by cytochrome c for the solvent driven, fine-tuning of its redox functionality.     

Reactivity of phosphonodithioato-dppt Ni(II) mixed ligand complexes with halogens: first example of a metal-coordinating tribromide anion

The first example of a metal complex containing a tribromide anion is presented and characterised by X-ray diffraction. Hybrid DFT calculations were used to investigate the nature of the bond in coordinating trihalides and the differences with the corresponding mono-halide complexes.     

Ligand Steric and Fluoroalkyl Substituent Effects on Enchainment Cooperativity and Stability in Bimetallic Nickel(II) Polymerization Catalysts

The synthesis and characterization of two neutrally charged bimetallic Ni(II) ethylene polymerization catalysts, {2,7-di-[2,6-(3,5-di-methylphenylimino)methyl]1,8-naphthalenediolato}-bis-Ni(II) (methyl)(trimethylphosphine) [(CH(3) )FI(2) -Ni(2) ] and {2,7-di-[2,6-(3,5-di-trifluoromethyl-phenylimino)methyl]-1,8-naphthalenediolato}-bis-Ni(II) (methyl)(trimethyl-phosphine) [(CF(3) )FI(2) -Ni(2) )], are reported. The diffraction-derived molecular structure of (CF(3) )FI(2) -Ni(2) reveals a Ni???Ni distance of 5.8024(5)??. In the presence of ethylene and Ni(COD)(2) or B(C(6) F(5) )(3) co-catalysts, these complexes along with their monometallic analogues [2-tert-butyl-6-((2,6-(3,5-dimethylphenyl)phenylimino)methyl)-phenolate]-Ni(II) -methyl(trimethylphosphine) [(CH(3) )FI-Ni] and [2-tert-butyl-6-((2,6-(3,5-ditrifluoromethyl-phenyl)phenylimino)methyl)phenolato]-Ni(II) -methyl-(trimethylphosphine) [(CF(3) )FI-Ni], produce polyethylenes ranging from highly branched M(w) =1400 oligomers (91?methyl branches per 1000?C) to low branch density M(w) =92?000 polyethylenes (7?methyl branches per 1000?C). In the bimetallic catalysts, Ni???Ni cooperative effects are evidenced by increased product polyethylene branching in ethylene homopolymerizations (～3× for (CF(3) )FI(2) -Ni(2) vs. monometallic (CF(3) )FI-Ni), as well as by enhanced norbornene co-monomer incorporation selectivity, with bimetallic (CH(3) )FI(2) -Ni(2) and (CF(3) )FI(2) -Ni(2) enchaining approximately three- and six-times more norbornene, respectively, than monometallic (CH(3) )FI-Ni and (CF(3) )FI-Ni. Additionally, (CH(3) )FI(2) -Ni(2) and (CF(3) )FI(2) -Ni(2) exhibit significantly enhanced thermal stability versus the less sterically encumbered dinickel catalyst {2,7-di-[(2,6-diisopropylphenyl)imino]-1,8-naphthalenediolato}-bis-Ni(II) (methyl)(trimethylphosphine). The pathway for bimetallic catalyst thermal deactivation is shown to involve an unexpected polymerization-active intermediate, {2,7-di-[2,6-(3,5-di-trifluoromethyl-phenylimino)methyl]-1-hydroxy,8-naphthalenediolato-Ni(II) (methyl)-(trimethylphosphine).     

Applications of dewetting in micro and nanotechnology

Dewetting is a spontaneous phenomenon where a thin film on a surface ruptures into an ensemble of separated objects, like droplets, stripes, and pillars. Spatial correlations with characteristic distance and object size emerge spontaneously across the whole dewetted area, leading to regular motifs with long-range order. Characteristic length scales depend on film thickness, which is a convenient and robust technological parameter. Dewetting is therefore an attractive paradigm for organizing a material into structures of well-defined micro- or nanometre-size, precisely positioned on a surface, thus avoiding lithographical processes. This tutorial review introduces the reader to the physical-chemical basis of dewetting, shows how the dewetting process can be applied to different functional materials with relevance in technological applications, and highlights the possible strategies to control the length scales of the dewetting process.     

pH-sensitive ligand for luminescent quantum dots

We developed a strategy to switch the luminescence of semiconductor quantum dots with chemical stimulations. It is based on the photoinduced transfer of either energy from CdSe-ZnS core-shell quantum dots to [1,3]oxazine ligands or electrons from the organic to the inorganic components. The organic ligands incorporate a dithiolane anchoring group, an electron-rich indole, and a 4-nitrophenylazophenoxy chromophore in their molecular skeleton. Their adsorption on the surface of the quantum dots results in partial luminescence quenching. Electron transfer from the indole fragment to the nanoparticles is mainly responsible for the decrease in luminescence intensity. Upon addition of base, the [1,3]oxazine ring of the ligands opens to generate a 4-nitrophenylazophenolate chromophore, which absorbs in the range of wavelengths where the quantum dots emit. This transformation activates an energy-transfer pathway from the excited nanoparticles to the ligands. In addition, the oxidation potential of the ligand shifts in the negative direction, improving the efficiency of electron transfer. The overall result is a decrease in the luminescence quantum yield of 83%. Addition of acid also opens the [1,3]oxazine ring of the ligands. However, the resulting 4-nitrophenylazophenol does not absorb in the visible region and cannot accept energy from the excited nanoparticles. Furthermore, the oxidation potential shifts in the positive direction, lowering the electron-transfer efficiency. In fact, the luminescence quantum yield increases by 33% as a result of this transformation. These changes are fully reversible and can be exploited to probe the pH of aqueous solutions from 3 to 11. Indeed, our sensitive quantum dots adjust their luminescence in response to variations in pH within this particular range of values. Thus, our general design strategy can eventually lead to the development of pH-sensitive luminescent probes for biomedical applications based on the unique photophysical properties of semiconductor quantum dots.     

Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution

Assessment of the perturbed matrix method (PMM) ability in reproducing valence UV absorption spectra is carried out on two model systems: 1,2,3-triazine in methanol solution and uracil in water solution. Results show that even using the simplest definition of the quantum center, i.e. the portion of the system explicitly treated quantum mechanically, PMM provides rather good results. This paper further confirms the possibility of using PMM as a theoretical-computational tool, complementary to other methodologies, for addressing the electronic properties in molecular systems of high complexity.