Analysis of the interaction energy in the Cu+-H2O and Cl−-H2O systems,with CP corrections to the BSSE of the separate terms,and MC simulations of the aqueous systems with and without CP corrections

The interaction energyE of the systems Cu⁺-H₂O and Cl^–-H₂O has been computed over a wide range of distances and orientations with the MINI-1 basis set in the SCF approximation. The interaction energy has been decomposed according to the Kitaura-Morokuma scheme, with and without counterpoise (CP) corrections to the basis set superposition error. The importance of this correction is analysed by its effect upon Monte Carlo calculations of the Cu⁺-water and Cl^–-water systems, using two-body potentials without and with CP corrections. The effect of CP corrections on theE analysis is similar to that found in other systems of analogous composition (of the general type ion plus neutral ligands), but with significant differences in the details. The effect of the CP corrections to the interaction potential, and then on the results of the Monte Carlo simulations, is small for the Cu⁺ ion, but remarkable for the Cl^– ion.     

Robust mean–variance hedging via G-expectation

In this paper we study mean–variance hedging under the $G$-expectation framework. Our analysis is carried out by exploiting the $G$-martingale representation theorem and the related probabilistic tools, in a continuous financial market with two assets, where the discounted risky one is modeled as a symmetric $G$-martingale. By tackling progressively larger classes of contingent claims, we are able to explicitly compute the optimal strategy under general assumptions on the form of the contingent claim.     

On the active site of mononuclear B1 metallo β-lactamases: a computational study

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called ‘3H’ and ‘DCH’ sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum–classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.     

Increasing structural and functional complexity in self-assembled coordination cages

Progress in metallo-supramolecular chemistry creates potential to synthesize functional nano systems and intelligent materials of increasing complexity. In the past four decades, metal-mediated self-assembly has produced a wide range of structural motifs such as helicates, grids, links, knots, spheres and cages, with particularly the latter ones catching growing attention, owing to their nano-scale cavities. Assemblies serving as hosts allow application as selective receptors, confined reaction environments and more. Recently, the field has made big steps forward by implementing dedicated functionality, e.g. catalytic centres or photoswitches to allow stimuli control. Besides incorporation in homoleptic systems, composed of one type of ligand, desire arose to include more than one function within the same assembly. Inspiration comes from natural enzymes that congregate, for example, a substrate recognition site, an allosteric regulator element and a reaction centre. Combining several functionalities without creating statistical mixtures, however, requires a toolbox of sophisticated assembly strategies. This review showcases the implementation of function into self-assembled cages and devises strategies to selectively form heteroleptic structures. We discuss first examples resulting from a combination of both principles, namely multicomponent multifunctional host–guest complexes, and their potential in application in areas such as sensing, catalysis, and photo-redox systems.

This review highlights recent strategies towards the rational synthesis of metallo-supramolecular multicomponent systems, the implementation of functionality and the challenge to create multifunctional assemblies in non-statistical fashion.     

Dynamics of some piecewise smooth Fermi-Ulam models

We find a normal form which describes the high energy dynamics of a class of piecewise smooth Fermi-Ulam ping pong models. Depending on the value of a single real parameter, the dynamics can be either hyperbolic or elliptic. In the first case, we prove that the set of orbits undergoing Fermi acceleration has zero measure but full Hausdorff dimension. We also show that for almost every orbit, the energy eventually falls below a fixed threshold. In the second case, we prove that, generically, we have stable periodic orbits for arbitrarily high energies and that the set of Fermi accelerating orbits may have infinite measure.     

Fermi Acceleration in Anti-Integrable Limits of the Standard Map

We consider a dynamical system on the semi-infinite cylinder which models the high energy dynamics of a family of mechanical models. We provide conditions under which we ensure that the set of orbits undergoing Fermi acceleration has measure zero.     

New insight into the IR-spectra/structure relationship in amyloid fibrils: a theoretical study on a prion peptide

Molecular-level structural information on amyloid aggregates is of great importance for the understanding of protein-misfolding-related deseases. Nevertheless, this kind of information is experimentally difficult to obtain. In this work, we used molecular dynamics (MD) simulations combined with a mixed quantum mechanics/molecular mechanics theoretical methodology, the perturbed matrix method (PMM), in order to study the amide I' IR spectrum of fibrils formed by a short peptide, the H1 peptide, derived from residues 109 through 122 of the Syrian hamster prion protein. The PMM/MD approach allows isolation of the amide I' signal arising from any desired peptide group of the polypeptide chain and quantification of the effect of the excitonic coupling on the frequency position. The calculated single-residue signals were found to be in good agreement with the experimental site-specific spectra obtained by means of isotope-labeled IR spectroscopy, providing a means for their interpretation at the molecular level. In particular, our results confirm the experimental hypothesis that residues ala117 are aligned in all strands and that the alignment gives rise to a red shift of the corresponding site-specific amide I' mode due to strong excitonic coupling among the ala117 peptide groups. In addition, our data show that a red shift of the amide I' band due to strong excitonic coupling can also occur for amino acids adjacent in sequence to the aligned ones. Thus, a red shift of the signal of a given isotope-labeled amino acid does not necessarily imply that the peptide groups under consideration are aligned in the β-sheet.     

PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results

Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete analysis of results obtained by the principal docking programs. To this aim, we developed PacDOCK, a freely available and user-friendly web server that comprises a collection of tools for positional distance-based and interaction-based analysis of docking results, which can be provided in several file formats. PacDOCK allows a complete analysis of molecular docking results through root mean square deviation (RMSD) calculation, molecular visualization, and cluster analysis of docked poses. The RMSD calculation compares docked structures with a reference structure, also when atoms are randomly labelled, and their conformational and positional differences can be visualised. In addition, it is possible to visualise a ligand into the target binding pocket and investigate the key receptor–ligand interactions. Moreover, PacDOCK enables the clustering of docking results by identifying a restrained number of clusters from many docked poses. We believe that PacDOCK will contribute to facilitating the analysis of docking results to improve the efficiency of computer-aided drug design.