On a possible catalytic effect of water on some nucleophilic substitution reactions in “Inert” solvents

Ab initio SCF MO LCAO calculations with the 4-31G basis set on the ten most stable complexes involving H₂O, HF, HC1, F^– and Cl^– have been examined in order to verify whether there is some evidence supporting the hypothesis that water can act as a catalyst for some nucleophilic substitution reactions performed in inert solvents with hydrogen halides as nucleophile agents (e.g. the formation of halohydrins from epoxides). Energetic considerations and an analysis of the electrostatic contribution to the reactivity of the H₂O-HX adduct seem to support this hypothesis.     

Bayesian estimation of relaxation times T(1) in MR images of irradiated Fricke-agarose gels

The authors present a novel method for processing T(1)-weighted images acquired with Inversion-Recovery (IR) sequence. The method, developed within the Bayesian framework, takes into account a priori knowledge about the spatial regularity of the parameters to be estimated. Inference is drawn by means of Markov Chains Monte Carlo algorithms. The method has been applied to the processing of IR images from irradiated Fricke-agarose gels, proposed in the past as relative dosimeter to verify radiotherapeutic treatment planning systems. Comparison with results obtained from a standard approach shows that signal-to noise ratio (SNR) is strongly enhanced when the estimation of the longitudinal relaxation rate (R1) is performed with the newly proposed statistical approach. Furthermore, the method allows the use of more complex models of the signal. Finally, an appreciable reduction of total acquisition time can be obtained due to the possibility of using a reduced number of images. The method can also be applied to T(1) mapping of other systems.     

Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models

In this paper, a computational strategy, based on DFT calculations at the M06-2X level, combined with the polarizable continuum model, the Hessian matrix reconstruction method and the Partial hessian vibrational approach is applied to evaluate inter- and intra-layer vibrational couplings between hydrogen bonded and stacked DNA base pairs. The present work demonstrates that this computational scheme can effectively predict and interpret the vibrational couplings of nucleic acids in solution. The effect of the environment described in a cluster or in a continuum manner is necessary in order to improve the agreement with the experimental values.     

The Fluorophore 4′,6‐Diamidino‐2‐phenylindole (DAPI) Induces DNA Folding in Long Double‐Stranded DNA

DAPI (4′,6‐diamidino‐2‐phenylindole) is a widely used fluorescent dye, whose complicated binding features to DNAs and RNAs have been the object of debates and are still not fully understood. In this study, different approaches were employed, including binding equilibrium measurements (spectrofluorometry), melting experiments (spectrophotometry), viscometric measurements, circular dichroism, and T‐jump kinetic analyses; all data concur in shedding light on the complex mechanistic aspects of the binding mode of DAPI to natural DNA. Conditions are found that induce the mode of the DAPI/DNA interaction to change from groove binding to intercalation. Moreover, it is observed, for the first time, that DAPI is able to induce the formation of a rather compact polymer–dye adduct under particular conditions. The results suggest that this form is a folded or coiled DNA structure stabilized by DAPI dye bridges.     

New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model

We present recent developments in the symmetry implementation of the Polarizable Continuum Model (PCM). The structure of the matrix, which defines the PCM solvent response, is examined, and we demonstrate how this matrix can be transformed to a block diagonal form where each block belongs to different irreducible representations of the molecular point group. This development is especially important at the Multi-configurational Self-Consistent Field (MCSCF) level where symmetry is needed to avoid problems with symmetry breaking in the wave function and facilitate the optimization of electronic excited states. Moreover, although only the totally symmetric part of the solvent interaction is needed for energy calculations, in response or perturbation theory calculations of molecular properties, other irreps play an important role and the classification of solvent interaction terms by irrep is, therefore, desirable. In addition, the use of symmetry reduces the computational cost. The implementation presented here is illustrated with a series of calculations of absorption and emission processes in solution on the diazines pyrazine, pyrimidine, and pyridazine. These calculations allow us to illustrate both formal aspects of the implementation such as the choice of active spaces based on orbital symmetry as well as practical aspects such as the speed-up of the calculation.     

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.     

D0–D6 States Counting and GW Invariants

We describe a correspondence between the Donaldson?CThomas invariants enumerating D0?CD6 bound states on a Calabi?CYau 3-fold and certain Gromov?CWitten invariants counting rational curves in a family of blowups of weighted projective planes. This is a variation on a correspondence found by Gross?CPandharipande, with D0?CD6 bound states replacing representations of generalised Kronecker quivers. We build on a small part of the theories developed by Joyce?CSong and Kontsevich?CSoibelman for wall-crossing formulae and by Gross?CPandharipande?CSiebert for factorisations in the tropical vertex group. Along the way we write down an explicit formula for the BPS state counts which arise up to rank 3 and prove their integrality. We also compare with previous ??noncommutative DT invariants?? computations in the physics literature.