Ab Initio Electronic, Magnetic, and Optical Properties of Fe Phthalocyanine on CrO(0001).

The organic molecules adsorbed on antiferromagnetic surfaces can produce interesting interface states, characterized by charge transfer mechanisms, hybridization of molecular-substrate orbitals, as well as magnetic couplings. Here, we apply an ab initio approach to study the adsorption of Fe phthalocyanine on stoichiometric CrO(0001). The molecule binds via a bidentate configuration forming bonds between two opposite imide N atoms and two protruding Cr ones, making this preferred over the various possible adsorption structures.

Self-Assembled Monolayers of N-Heterocyclic Olefins on Au(111).

Self-assembled monolayers (SAMs) of N-heterocyclic olefins (NHOs) have been prepared on Au(111) and their thermal stability, adsorption geometry, and molecular order were characterized by X-ray photoelectron spectroscopy, polarized X-ray absorption spectroscopy, scanning tunneling microscopy (STM), and density functional theory (DFT) calculations. The strong σ-bond character of NHO anchoring to Au induced high geometrical flexibility that enabled a flat-lying adsorption geometry via coordination to a gold adatom. The flat-lying adsorption geometry was utilized to further increase the surface interaction of the NHO monolayer by backbone functionalization with methyl groups that induced high thermal stability and a large impact on work-function values, which outperformed that of N-heterocyclic carbenes.

A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase.

The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations.

Coordination pattern, solution structure and DNA damage studies of the copper(II) complex with the unusual aminoglycoside antibiotic hygromycin B.

The aminoglycosidic antibiotic hygromycin B presents a peculiar chemical structure, characterized by two sugar rings joined via a spiro connection. The Cu(ii) complex of hygromycin B in water solution was characterized by (1)H-NMR, UV-Vis, EPR and CD spectroscopy, combined with potentiometric measurements. The spin-lattice relaxation enhancements were interpreted by the Solomon-Bloembergen-Morgan theory, allowing us to calculate copper-proton distances that were used to build a model of the complex by molecular mechanics and dynamics calculations.

Heteronuclear and homonuclear Cu2+ and Zn2+ complexes with multihistidine peptides based on zebrafish prion-like protein.

The homeostasis of metal ions, especially copper and zinc, is a major factor that may influence the prion diseases and the biological function of prion protein (PrP). The His-rich regions are basic sites for metal binding and antioxidant activity of the PrP structures. Animal prion-like proteins contain also His-rich domains, and their coordination chemistry may provide better insight into the chemistry and biology of PrP structures and related diseases.

Molecular dynamics study of the Cu2+ binding-induced "structuring" of the N-terminal domain of human prion protein.

In this work, we report molecular dynamics simulations on a fragment of the human prion protein spanning residues 31-120, with copper(II) bound to the repeat region in several ways corresponding to the known intra- and inter-repeat coordination modes, or to the metal site located at His111. The results of this study point to a different structuring tendency of the protein fragment depending on copper binding mode, with the highest degree of structuring in the case of intrarepeat Cu(II) coordination corresponding to high copper concentration.

Structural features of the Cu(II) complex with the rat Abeta(1-28) fragment.

The interaction between Cu(II) and the rat amyloid beta (1-28) fragment in micellar solutions at pH 7.5 was investigated by CD and NMR spectroscopy; the proton-copper distances were used in restrained molecular dynamics simulations to obtain a structural model of the Cu(II) complex.

Solution structures of cyclosporin a and its complex with dysprosium(III) in SDS micelles: NMR and molecular dynamics studies.

Cyclosporin A (CsA) is a cyclic naturally occurring peptide used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is due to the formation of a complex with cyclophilin A (Cyp), in which the cis 9MeLeu-10MeLeu amide bond of CsA assumes a trans conformation. The mechanism of the conformational inversion has not been delineated, but it has been postulated that metal ions binding induces a conformational change that enables CsA to bind Cyp.

NMR studies of the Zn2+ interactions with rat and human beta-amyloid (1-28) peptides in water-micelle environment.

Alzheimer's disease is a fatal neurodegenerative disorder involving the abnormal accumulation and deposition of peptides (amyloid-beta, Abeta) derived from the amyloid precursor protein. Here, we present the structure and the Zn2+ binding sites of human and rat Abeta(1-28) fragments in water/sodium dodecyl sulfate (SDS) micelles by using 1H NMR spectroscopy. The chemical shift variations measured after Zn2+ addition at T>310 K allowed us to assign the binding donor atoms in both rat and human zinc complexes.

Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site.

The solution structure of kanamycin A interacting with a ribosomal A-site fragment was solved by transferred-NOE techniques and found to agree with the structure of the complex observed in the crystal. Despite the fast exchange conditions found for the interaction, the bound form was identified by NOESY spectroscopy. At 600 MHz, NOE effects are only observed for the RNA-associated antibiotic.

1H and 13C NMR study of the complex formed by copper(II) with the nucleoside antibiotic sinefungin.

Sinefungin (SFG) is an antifungal and antiparasitic nucleoside antibiotic composed by ornithine and adenosine moieties both having the potential to bind copper(II). NMR studies performed at physiological pH have shown that the alpha-amino and the carboxylate groups in the ornithine unit are the preferred donor sites for Cu(II) binding. On the contrary, at acidic pH, Cu(II) complexation starts from adenosine nitrogen being the alpha-amino group still protonated and not available for metal binding.

Tandem repeat-like domain of "similar to prion protein" (StPrP) of Japanese pufferfish binds Cu(II) as effectively as the mammalian protein.

The main structural domains of prion proteins, in particular the N-terminal region containing characteristic amino acid repeats, are well conserved among different species, despite divergence in primary sequence. The repeat region seems to play an important role, as verified by pathogenicity only observed in organisms having repeats composed of eight residues. In this work three different peptides belonging to the tandem repeat region of StPrP-2 from the Japanese pufferfish Takifugu rubripes have been considered; the coordination modes and conformations of their complexes with Cu(II) have been investigated by using potentiometric titrations, spectroscopic data, and restrained molecular dynamics simulations.

1H and 13C-NMR and molecular dynamics studies of cyclosporin a interacting with magnesium(II) or cerium(III) in acetonitrile. Conformational changes and cis-trans conversion of peptide bonds.

Cyclosporin A (CsA) is an important drug used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is related to the inhibition of T-cell activation through binding with the proteins Cyclophilin (Cyp) and, subsequently, Calcineurin (CN). In the complex with its target (Cyp), CsA adopts a conformation with all trans peptide bonds and this feature is very important for its pharmacological action.

Structure and stability of the CuII complexes with tandem repeats of the chicken prion.

Prion protein (PrP) misfolding is one of the pivotal issues in understanding the rudiments of neurodegenerative disorders. The conformational change of mammalian cellular PrP to scrapie PrP is caused by an unknown agent, but there is reasonable evidence supporting the key role of copper ions in this process. The structure of the avian PrP was found to be very similar to the mammalian protein, although there is only 30% homology in the secondary structure.

Fine tuning the structure of the Cu2+ complex with the prion protein chicken repeat by proline isomerization.

The interaction between the single hexarepeat unit of chicken prion protein [ChPrP(54-59)] and Cu(II) was investigated by NMR, finding different coordination modes for the trans/trans and cis/trans isomers.

SIMQUADNMR: a program for simulation and interpretation of multiple quantum-filtered NMR spectra of quadrupolar nuclei.

In this paper, we present a computer program which simulates NMR multiple quantum-filtered spectra of quadrupolar nuclei as a function of physical parameters, of the type of experiment and experimental conditions. The program works by solving relaxation theory equations for the given system, and it can be useful in order to plan the ideal conditions to set up specific experiments or to give a physical interpretation of experimental results. The program allows to independently follow the dependence of individual coherences and relaxation rates as a function of up to 50 parameters regarding the physical properties of the system under investigation, sample conditions and instrumental setup making it an helpful tool also for teaching purposes.

NMR structural model of the interaction of herbicides with the photosynthetic reaction center from Rhodobacter sphaeroides.

The interaction of the herbicides acifluorfen and paraquat with the photosynthetic reaction center from Rhodobacter sphaeroides has been studied by NMR relaxation measurements. Interaction in aqueous solution has been demonstrated by evaluating motional features of the bound form through cross-relaxation terms of protons at fixed distances on the herbicides. Contributions to longitudinal nonselective relaxation rates different from the proton-proton dipolar relaxation were inferred, most probably due to paramagnetic effects originating from the high-spin nonheme Fe(II) ion in the reaction center.

NMR and EPR structural delineation of copper(II) complexes formed by kanamycin A in water.

The complexes formed by kanamycin A at three different pH values (5.5, 7.4 and 12.

The structure of the Ce(III)-angiotensin II complex as obtained from NMR data and molecular dynamics calculations.

Angiotensin II is shown by nuclear magnetic resonance (NMR) to form a complex in water at pH 4.0 with cerium(III), the ideal paramagnetic probe for Ca(2+). Paramagnetic shifts induced by the metal were used for the determination of dissociation constant and complex stoichiometry.

Metallochaperones and metal-transporting ATPases: a comparative analysis of sequences and structures.

A comparative structural genomic analysis of a new class of metal-trafficking proteins can provide insights into the intracellular chemistry of reactive cofactors such as copper and zinc. Starting from the sequences of the metallochaperone Atx1 and from the first soluble domain of the copper-transporting ATPase Ccc2, both from yeast, a search on the available genomes was performed using a homology criterion and a metal-binding motif x'-x"-C-x'''-x''''-C. By limiting ourselves to 20% identity with any of the proteins found, several soluble copper-transport proteins were identified, as well as soluble domains of membrane-bound ATPases.