A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution

A procedure to partition the GEPOL molecular surface into tesserae that respects the molecular symmetry constraints is presented. Using this method it is possible to build a solvent reaction field for the Polarizable Continuum Model with the same symmetry of the nuclear potential. Several applications are reported and discussed to evaluate the performance of this new procedure. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1262–1272, 2001     

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.     

A semiparametric Bayesian generalized linear mixed model for the reliability of Kevlar fibers

We analyze the reliability of NASA composite pressure vessels by using a new Bayesian semiparametric model. The data set consists of lifetimes of pressure vessels, wrapped with a Kevlar fiber, grouped by spool, subject to different stress levels; 10% of the data are right censored. The model that we consider is a regression on the log‐scale for the lifetimes, with fixed (stress) and random (spool) effects. The prior of the spool parameters is nonparametric, namely they are a sample from a normalized generalized gamma process, which encompasses the well‐known Dirichlet process. The nonparametric prior is assumed to robustify inferences to misspecification of the parametric prior. Here, this choice of likelihood and prior yields a new Bayesian model in reliability analysis. Via a Bayesian hierarchical approach, it is easy to analyze the reliability of the Kevlar fiber by predicting quantiles of the failure time when a new spool is selected at random from the population of spools. Moreover, for comparative purposes, we review the most interesting frequentist and Bayesian models analyzing this data set. Our credibility intervals of the quantiles of interest for a new random spool are narrower than those derived by previous Bayesian parametric literature, although the predictive goodness‐of‐fit performances are similar. Finally, as an original feature of our model, by means of the discreteness of the random‐effects distribution, we are able to cluster the spools into three different groups. Copyright © 2012 John Wiley & Sons, Ltd.     

Absorption spectroscopy of toluene pyrolysis

Toluene pyrolysis in high temperature/high pressure argon atmosphere has been studied in a conventional diaphragm-type shock tube. The investigated ranges of temperature and pressure were 1500–2300 K and 8–13 bar, respectively. Extinction measurements in the near infrared have been carried out to follow the formation of carbonaceous particulate (soot). Pyrolysis products were optically characterized by absorption measurements in the wavelength range 300–800 nm, with high time/spectral resolution. The application of Tauc analysis to the absorption spectra allowed to identify three levels of energy gap; they have been attributed to carbonaceous structures with 3–5 and 7–9 fused aromatic rings, and to soot particles.     

The theoretical study of predissociation in diatomics. the case of the O2 B' 3Σ−u state

The predissociation of excited O₂ has been studied theoretically with the aid of a simple model describing the Rydberg-valence crossing which occurs in the B and B' ³Σ^?_u states. Calculations of the decay rates have been performed by means of a method described previously. The energy shifts caused by the interaction of a discrete state with the dissociative continuum have been computed by the Fano method. Isotopic effects and the dependence of decay rates and energy shifts on the minimum energy gap between the adiabatic curves have been emphasized.     

A preliminary ab initio investigation of the fate of the oxirane cation after vertical ionization of the oxirane molecule

A set of significant sections of the lowest energy hypersurfaces of the oxirane cation C₂H₄O⁺ are presented and discussed with the purpose of investigating the most probable rearrangement pathways following the initial ionization process. It is shown that the most important geometrical parameters involved in such processes are the ∠COC valence angle and the torsional angle of the two CH₂ groups. The most favoured rearrangement processes involve the second vertical ionization state from which it is possible to pass to a more stable open planar form via a conrotatory torsion of the two CH₂ groups and a moderate energy barrier. Other rearrangement processes involving a linear form are still possible. The calculations have been performed using a CI procedure starting from the molecular orbital space of the neutral parent molecule.     

On the ab initio geometry optimization of molecular solutes

We present several variants of methods for the automatic search of optimum geometries of solutes via ab initio SCF procedures. The physical meaning of geometry optimization in solution is discussed. Advantages and disadvantages of the different variants are shown making use of calculations on the HF dimer with different basis sets, supplemented by information on the computational times. Suggestions for the most convenient strategies (which in part depend on the nature of the solute) are also done.     

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.     

Ab initio molecular electrostatic potentials

The ab initio isopotential map of guanine is given and compared to that of adenine. It shows that in contrast to the situation in adenine, the most basic site of guanine is N₇ with a secondary potential minimum at O₆. These results as well as those concerning the secondary out-of-plane attractive regions over the NH₂ group and C₈ H bonds of the two molecules are discussed in connection with the available experimental knowledge concerning the bonding of alkylating carcinogens and mutagens.     

A theoretical description of thetrans-cis conversion in the lowest excited states of diimide

The lowest excited states of the diimide molecule have been calculated by three different SCF-type methods, the performances of which are analyzed in regard to the prediction of geometries and energies. The calculations have been performed with two basis sets (STO-3G and 4-31G) both supplemented with more diffuse functions on the N atoms. Lowest energy pathways for thetrans-cis interconversion in the various states are presented for the three calculation methods and for the two basis sets.