Exploring the Esterase Catalytic Activity of Minimalist Heptapeptide Amyloid Fibers.

This paper investigates the esterase activity of minimalist amyloid fibers composed of short seven-residue peptides, IHIHIHI (IH7) and IHIHIQI (IH7Q), with a particular focus on the role of the sixth residue position within the peptide sequence. Through computational simulations and analyses, we explore the molecular mechanisms underlying catalysis in these amyloid-based enzymes. Contrary to initial hypotheses, our study reveals that the twist angle of the fiber, and thus the catalytic site's environment, is not notably affected by the sixth residue.

Enhancing magneto-ionic effects in cobalt oxide films by electrolyte engineering.

Electric-field-driven ion motion to tailor magnetic properties of materials (magneto-ionics) offers much promise in the pursuit of voltage-controlled magnetism for highly energy-efficient spintronic devices. Electrolyte gating is a relevant means to create intense electric fields at the interface between magneto-ionic materials and electrolytes through the so-called electric double layer (EDL). Here, improved magneto-ionic performance is achieved in electrolyte-gated cobalt oxide thin films with the addition of inorganic salts (potassium iodide, potassium chloride, and calcium tetrafluoroborate) to anhydrous propylene carbonate (PC) electrolyte.

Atomistic fibrillar architectures of polar prion-inspired heptapeptides.

This article provides the computational prediction of the atomistic architectures resulting from self-assembly of the polar heptapeptide sequences NYNYNYN, SYSYSYS and GYGYGYG. Using a combination of molecular dynamics and a newly developed tool for non-covalent interaction analysis, we uncover the properties of a new class of bionanomaterials, including hydrogen-bonded polar zippers, and the relationship between peptide composition, fibril geometry and weak interaction networks. Our results, corroborated by experimental observations, provide the basis for the rational design of prion-inspired nanomaterials.

Enhanced Metallophilicity in Metal-Carbene Systems: Stronger Character of Aurophilic Interactions in Solution.

Metallophilicity is an essential concept that builds upon the attraction between closed shell metal ions. We report on the [M (bisNHC) ] (M=Au , Ag ; NHC=N-heterocyclic carbene) systems, which display almost identical features in the solid state. However, in solution the Au cation exhibits a significantly higher degree of rigidity owed to the stronger character of the aurophilic interactions.

Water Adsorption on MO (M = Ti, Ru, and Ir) Surfaces. Importance of Octahedral Distortion and Cooperative Effects.

Understanding metal oxide MO (M = Ti, Ru, and Ir)-water interfaces is essential to assess the catalytic behavior of these materials. The present study analyzes the HO-MO interactions at the most abundant (110) and (011) surfaces, at two different water coverages: isolated water molecules and full monolayer, by means of Perdew-Burke-Ernzerhof-D2 static calculations and ab initio molecular dynamics (AIMD) simulations. Results indicate that adsorption preferably occurs in its molecular form on (110)-TiO and in its dissociative form on (110)-RuO and (110)-IrO.

Intramolecular Photocycloaddition of 2(5 H)-Furanones to Temporarily Tethered Terminal Alkenes as a Stereoselective Source of Enantiomerically Pure Polyfunctionalyzed Cyclobutanes.

Allyloxymethyloxymethyl and 4-pentenoyloxymethyl substituents have been used as tethering groups to study the intramolecular [2 + 2] photocycloaddition of chiral 5-substituted 2(5 H)-furanones. The photoreactions proceed in good yield and provide the expected regio- and diastereoselective tricyclic compounds with complementary regioselectivity, which depends on whether the vinyl chain is attached to the furanone by an acetal or an ester linkage. Computational simulations agree with experimental observations and indicate that the origin of the different observed regioselectivity in the intramolecular photochemical reaction of lactones 5 and 6 arises from the relative stability of the initial conformers.

Reactivity of Metal Carbenes with Olefins: Theoretical Insights on the Carbene Electronic Structure and Cyclopropanation Reaction Mechanism.

Present work addresses the reactivity of several phenyl-substituted metal-carbene complexes with 4-methylstyrene by means of density functional theory OPBE simulations. Different paths that lead to cyclopropanation were explored and compared to the olefin metathesis mechanism. For this purpose, we chose four different catalysts: (i) the Grubbs second-generation olefin metathesis catalyst, (ii) a Grubs second-generation-like complex, in which ruthenium is replaced by iron, and (iii) two iron carbene complexes (a piano stool and a porphyrin iron carbene) that experimentally catalyze alkene cyclopropanation.

Drastic Effect of the Peptide Sequence on the Copper-Binding Properties of Tripeptides and the Electrochemical Behaviour of Their Copper(II) Complexes.

The binding and electrochemical properties of the complexes Cu -HAH, Cu -HWH, Cu -Ac-HWH, Cu -HHW, and Cu -WHH have been studied by using NMR and UV/Vis spectroscopies, CV, and density functional calculations. The results obtained highlight the importance of the peptidic sequence on the coordination properties and, consequently, on the redox properties of their Cu complexes. For Cu -HAH and Cu -HWH, no cathodic processes are observed up to -1.

Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis.

Senile plaques are extracellular deposits found in patients with Alzheimer's Disease (AD) and are mainly formed by insoluble fibrils of β-amyloid (Aβ) peptides. The mechanistic details about how AD develops are not fully understood yet, but metals such as Cu, Zn, or Fe are proposed to have a non-innocent role. Many studies have also linked the non biological metal aluminum with AD, a species whose concentration in the environment and food has been constantly increasing since the industrial revolution.

Multiple Condensation Reactions Involving Pt(II) /Pd(II) -OH2 , Pt-NH3 , and Cytosine-NH2 Groups: New Twists in Cisplatin-Nucleobase Chemistry.

The coordination chemistry of the antitumor agent cisplatin and related complexes with DNA and its constituents, that is, the nucleobases, appears to be dominated by 1:1 and 1:2 adducts of the types cis-[Pta2 (nucleobase)X] and cis-[Pta2 (nucleobase)2 ] (a=NH3 or amine; a2 =diamine or diimine; X=Cl, OH or OH2 ). Here, we have studied the interactions of the putative 1:1 adducts cis-[Pta2 (1-MeC-N3)(OH2 )](2+) (with a=NH3 , a2 =2,2'-bpy (2,2'-bipyridine), 1-MeC=model nucleobase 1-methylcytosine) with additional cis-[Pt(NH3 )2 (OH2 )2 ](2+) or its kinetically superior analogues [Pd(en)(OH2 )2 ](2+) (en=ethylenediamine) and [Pd(2,2'-bpy)(OH2 )2 ](2+) . Depending upon the conditions applied different compounds of different nuclearity are formed.

Dioxygen activation in the Cu-amyloid β complex.

We investigate, by means of density-functional theory, the binding of dioxygen to Cu(I)-amyloid β (Aβ), one of the first steps in the oxidation of ascorbate by dioxygen. Cu, Aβ, ascorbate and dioxygen are all present in the synapse during neurodegeneration, when the above species can trigger an irreversible oxidative stress inducing the eventual death of neurons. The binding of dioxygen to Cu(I) is possible and its role in dioxygen activation of Cu ligands and of residues in the first coordination sphere is described in atomic detail.

Coordination properties of a metal chelator clioquinol to Zn(2+) studied by static DFT and ab initio molecular dynamics.

Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials.

Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models.

Alzheimer's disease (AD) is a neurological disease of confusing causation with no cure or prevention available. The definitive diagnosis is made postmortem, in part through the presence of amyloid-beta plaques in the brain tissue, which can be done with the small molecule thioflavin-T (ThT). Plaques are also found to contain elevated amounts of metal ions Cu(ii) and Zn(ii) that contribute to the neurotoxicity of amyloid-beta (Aβ).

3D structures and redox potentials of Cu2+-Aβ(1-16) complexes at different pH: a computational study.

Oxidative stress induced by redox-active metal cations such as Cu(2+) is a key event in the development of Alzheimer's disease. A detailed knowledge of the structure of Cu(2+)-Aβ complex is thus important to get a better understanding of this critical process. In the present study, we use a computational approach that combines homology modeling with quantum-mechanics-based methods to determine plausible 3D structures of Cu(2+)-Aβ(1-16) complexes that enclose the different metal coordination spheres proposed experimentally at different pH values.

Mixed adenine/guanine quartets with three trans-a2 Pt(II) (a=NH(3) or MeNH(2)) cross-links: linkage and rotational isomerism, base pairing, and loss of NH(3).

Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross-linked by three linear metal moieties such as trans-a2 Pt(II) (with a=NH3 or MeNH2 ) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)}2 ][(ClO4 )6 ]⋅3H2 O (1) (with 9-EtA=9-ethyladenine and 9-MeGH=9-methylguanine) was crystallized from water and found to adopt a flat Z-shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9-MeGH, a meander-like construct, trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)2 }][(ClO4 )6 ]⋅[(9-MeGH)2 ]⋅7 H2 O (2) is formed, in which the two extra 9-MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1.

DFT study on the recovery of Hoveyda-grubbs-type catalyst precursors in enyne and diene ring-closing metathesis.

DFT (B3LYP-D) calculations have been used to better understand the origin of the recovered Hoveyda-Grubbs derivative catalysts after ring-closing diene or enyne metathesis reactions. For that, we have considered the activation process of five different Hoveyda-Grubbs precursors in the reaction with models of usual diene and enyne reactants as well as the potential precursor regeneration through the release/return mechanism. The results show that, regardless of the nature of the initial precursor, the activation process needs to overcome relatively high energy barriers, which is in agreement with a relatively slow process.

Thioflavin-T excimer formation upon interaction with amyloid fibers.

The molecular mechanism of the Thioflavin-T (Th-T) binding to amyloids remains unknown. By combining experimental analysis of Th-T excitation and emission spectra with theoretical calculations we suggest that Th-T fluorescence changes upon interaction with amyloids may arise from the formation of an excimer with an oblique angle of ~120 degrees.

Insights on the binding of Thioflavin derivative markers to amyloid-like fibril models from quantum chemical calculations.

Thioflavin-T (ThT) is one of the most widely used dyes for staining and identifying amyloid fibrils, which share a common parallel in register β-sheet structure. Unfortunately, ThT is a charged molecule, which limits its ability to cross the blood brain barrier and its use as an efficient dye for in vivo detection of amyloid fibrils. For this reason, several uncharged ThT derivatives have been designed and their binding properties to Aβ fibrils studied by fluorescence assays.

Three dimensional models of Cu(2+)-Aβ(1-16) complexes from computational approaches.

Elucidation of the coordination of metal ions to Aβ is essential to understand their role in its aggregation and to rationally design new chelators with potential therapeutic applications in Alzheimer disease. Because of that, in the last 10 years several studies have focused their attention in determining the coordination properties of Cu(2+) interacting with Aβ. However, more important than characterizing the first coordination sphere of the metal is the determination of the whole Cu(2+)-Aβ structure.

Pt(II) coordination to N1 of 9-methylguanine: why it facilitates binding of additional metal ions to the purine ring.

The preparation and X-ray crystal structure analysis of {trans-[Pt(MeNH(2))(2)(9-MeG-N1)(2)]}⋅{3 K(2)[Pt(CN)(4)]}⋅6 H(2)O (3 a) (with 9-MeG being the anion of 9-methylguanine, 9-MeGH) are reported. The title compound was obtained by treating [Pt(dien)(9-MeGH-N7)](2+) (1; dien=diethylenetriamine) with trans-[Pt(MeNH(2))(2)(H(2)O)(2)](2+) at pH 9.6, 60 °C, and subsequent removal of the [(dien)Pt(II)] entities by treatment with an excess amount of KCN, which converts the latter to [Pt(CN)(4)](2-).

Structures and stabilities of Fe2+/3+ complexes relevant to Alzheimer's disease: an ab initio study.

Iron is one of the most abundant metals found in senile plaques of post mortem patients with Alzheimer's disease. However, the interaction mode between iron ions and β-amyloid peptide as well as their precise affinity is unknown. In this study we apply ab initio computational methodology to calculate binding energies of Fe(2+/3+) with the His13-His14 sequence of Aβ, as well as other important ligands such as His6 and Tyr10.

Mechanistic insights into ring-closing enyne metathesis with the second-generation Grubbs-Hoveyda catalyst: a DFT study.

The full catalytic process (precatalyst activation, propagating cycle and active-species interconversion) of the ring-closing enyne metathesis (RCEYM) reaction of 1-allyloxy-2-propyne with the Grubbs-Hoveyda complex as catalyst was studied by B3LYP density functional theory. Both the ene-then-yne and yne-then-ene pathways are considered and, for the productive catalytic cycle, the feasibility of the endo-yne-then-ene route is also explored. Calculations predict that the ene-then-yne and yne-then-ene pathways proceed through equivalent steps, the only major difference being the order in which they take place.

Computational calculations of pKa values of imidazole in Cu(II) complexes of biological relevance.

The imidazole ring is part of the lateral chain of histidine. One of the main features of this amino acid is the ability to coordinate copper, especially Cu(2+), because of the intermediate base nature of its imidazole ring, which has a great biological relevance. Proteins such as cytochrome c oxidase, a crucial enzyme in the respiratory chain, and β-amyloid peptide, implicated in the pathology of Alzheimer's disease, are examples of proteins containing histidines in their coordination sphere.

The role of exact exchange in the description of Cu(2+)-(H(2)O)(n) (n = 1-6) complexes by means of DFT methods.

This paper analyses the behavior of different density functionals in the description of the most stable structures of Cu(2+)-(H(2)O)(n) complexes (n = 1-6). From n = 3 to n = 6, different coordination numbers of the metal cation were considered. The structures and energies of the complexes were theoretically determined by means of density functional methods that include different amounts of exact exchange: the BLYP functional (0% of exact exchange), the B3LYP functional (20% of exact exchange), the MPWB1K functional (44% of exact exchange), and BHLYP functional (50% of exact exchange).