Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed

Prompt K_short production in pp collisions at sqrt(s)=0.9 TeV

The production of K_short mesons in pp collisions at a centre-of-mass energy of 0.9 TeV is studied with the LHCb detector at the Large Hadron Collider. The luminosity of the analysed sample is determined using a novel technique, involving measurements of the beam currents, sizes and positions, and is found to be 6.8 +/- 1.0 microbarn^-1. The differential prompt K_short production cross-section is measured as a function of the K_short transverse momentum and rapidity in the region 0 < pT < 1.6 GeV/c and 2.5 < y < 4.0. The data are found to be in reasonable agreement with previous measurements and generator expectations.Comment: 6+18 pages, 6 figures, updated author lis

Theoretical studies of halocarbene cycloaddition selectivities : A new interpretation of negative activation energies and entropy control of selectivity

Ab initio RHF calculations with the 3–21G basis set have been carried out on cycloadditions of CF2 and CCl2 with ethylene. Although p-complex intermediates are predicted for both reactions at this level, MP2/3-21G calculations imply that there are no complexes in reactions of CCl2 or more reactive carbenes with ethylene or substituted alkenes. Nevertheless, negative activation energies can be observed, since ?G reaches a maximum due to the increase in —T?S for these bimolecular reactions. The apparent “entropy control” for reactive carbenes results from the rapid decrease in ?H. As the reactivity of the alkene increases, the transition state shifts to an earlier point on the free energy surface, where —T?S‡ is lower, but ?H‡ is higher than for less reactive alkenes. Model potentials are developed for ?H and —T?S which reproduce experimental behavior, without the assumption of intermediates

Lost and found: Helminths infecting invasive raccoons introduced to Italy

North American raccoons (Procyon lotor) have been introduced to several European countries, where they may represent a sanitary threat as hosts of several pathogens such as the zoonotic ascarid Baylisascaris procyonis. We carried out parasitological analysis on raccoons introduced to Italy to verify whether the species had carried along B. procyonis or any other gastro-intestinal helminths that may threaten humans, livestock or native wildlife. We examined 64 raccoons culled in Northern Italy during control activities and 3 roadkills opportunistically sampled from a separate population located in central Italy. Helminths were collected from the gastro-intestinal tract through standard parasitological techniques and identified based on a combination of morphology and molecular methods. Overall, examined raccoons showed a poor parasitic fauna, with almost 30% of individuals free of any helminth infection. The most prevalent species were the nematodes Strongyloides procyonis (26.9%), Aonchotheca putorii (25.4%) and Porrocaecum sp. (19.4%). Plagiorchis sp. trematodes were also common (13.4%), whereas cestodes were scarcely represented. With the exception of S. procyonis introduced from North America, all the other identified taxa have either a Eurasian or a wide Holarctic distribution. Despite not finding any B. procyonis in the examined raccoons, passive surveillance for this parasite should be implemented, especially in Tuscany, since the limited host sample examined in the present survey does not allow to exclude its presence

Ionization potentials, electron affinities, and molecular orbitals of 2-substituted norbornadienes. Theory of 1,2 and homo-1,4 carbene cycloaddition selectivities

The ionization potentials, electron affinities, and π orbital shapes of 2-substituted norbornadienes have been determined by photoelectron spectroscopy, electron-transmission spectroscopy, and ab initio molecular orbital calculations, respectively. The deductions made about the electronic structures of 2-methoxy-, (trimethylsiloxy)-, chloro-, cyano-, (methoxycarbonyl)-, and phenylnorbornadienes permit a detailed interpretation of the reactivities and selectivities observed experimentally in carbene cycloadditions to these molecules. A substituent at C-2 of norbornadiene not only affects the 2-3 π bond but also influences the 5-6 π bond due to through-space interactions between π orbitals. The orbital energy changes and polarization induced by 2-substituents provide a compelling rationale of the variations in 1,2 and homo-1,4 cycloadditions of carbenes to these species, and confirm the electrophilic nature of both of these cycloadditions.</p

Dipole stabilization of α-heteroatom carbanions: theory and experiment

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