New insights into alpha-GalNAc-Ser motif: influence of hydrogen bonding versus solvent interactions on the preferred conformation

The structural features of the mucin-type simplest model, namely, the glycopeptide alpha-O-GalNAc-l-Ser diamide, have been investigated by combining NMR spectroscopy, molecular dynamics simulations, and DFT calculations. In contrast to previous reports, the study reveals that intramolecular hydrogen bonds between sugar and peptide residues are very weak and, as a consequence, not strong enough to maintain the well-defined conformation of this type of molecule. In fact, the observed conformation of this model glycopeptide can be satisfactorily explained by the presence of water pockets/bridges between the sugar and the peptide moieties. Additionally, DFT calculations reveal that not only the bridging water molecules but also the surrounding water molecules in the first hydration shell are essential to keep the existing conformation.     

Models of spherical shells as sources of Majumdar–Papapetrou type spacetimes

By starting with a seed Newtonian potential–density pair we construct relativistic thick spherical shell models for a Majumdar–Papapetrou type conformastatic spacetime. As a simple example, we considerer a family of Plummer–Hernquist type relativistic spherical shells. As a second application, these structures are then used to model a system composite by a dust disk and a halo of matter. We study the equatorial circular motion of test particles around such configurations. Also the stability of the orbits is analyzed for radial perturbation using an extension of the Rayleigh criterion. The models considered satisfying all the energy conditions.     

Newtonian Dynamics from the Principle of Maximum Caliber

The foundations of Statistical Mechanics can be recovered almost in their entirety from the principle of maximum entropy. In this work we show that its non-equilibrium generalization, the principle of maximum caliber (Jaynes, Phys Rev 106:620–630, 1957), when applied to the unknown trajectory followed by a particle, leads to Newton’s second law under two quite intuitive assumptions (both the expected square displacement in one step and the spatial probability distribution of the particle are known at all times). Our derivation explicitly highlights the role of mass as an emergent measure of the fluctuations in velocity (inertia) and the origin of potential energy as a manifestation of spatial correlations. According to our findings, the application of Newton’s equations is not limited to mechanical systems, and therefore could be used in modelling ecological, financial and biological systems, among others.     

Rapid access to ketones related to oleanolic and ursolic acids

We describe in this article a process with which to obtain different ketones related to oleanolic and ursolic acids from a natural source, Salvia canariensis L., with minimal use of chromatography columns. Amongst the isolated compounds was 12α-bromo-3-oxo-olean-13, 28-olide (3), which was fully characterised, including a characterisation of its molecular configuration by X-ray crystallographic analysis by 1 and 2-dimensional NMR techniques.     

Bidirectional Redox Molecular Switches: Electron-induced Cyclization and Cycloreversion Processes in Metacyclophanes

A reversible bidirectional ring-opening and ring-closing system triggered by electricity has been prepared by using metacyclophan-1-enes, a known thermo-photochromic molecular switch system.     

Controlling spin-spin network dynamics by repeated projective measurements

We show that coupled-spin network manipulations can be made highly effective by repeated projections of the evolving quantum states onto diagonal density-matrix states (populations). As opposed to the intricately crafted pulse trains that are often used to fine-tune a complex network's evolution, the strategy hereby presented derives from the "quantum Zeno effect" and provides a highly robust route to guide the evolution by destroying all unwanted correlations (coherences). We exploit these effects by showing that a relaxationlike behavior is endowed to polarization transfers occurring within a N-spin coupled network. Experimental implementations yield coupling constant determinations for complex spin-coupling topologies, as demonstrated within the field of liquid-state nuclear magnetic resonance.     

Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl–ThDP

In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions. The results allow to conclude that the reaction leading to the formation of L-ThDP occurs via a concerted mechanism, and during the nucleophilic attack on the pyruvate molecule, the ylide is in its AP form. The calculated activation barrier for the reaction is 19.2?kcal/mol, in agreement with the experimental reported value.     

Synthesis and functionalization of new polyhalogenated BODIPY dyes. Study of their photophysical properties and singlet oxygen generation

A theoretical and experimental study on the iodination of BODIPY dyes with different degrees of substitution has been developed. Polyhalogenated BODIPYs synthesized in this work are the first examples of this type of dyes with more than two halogen atoms in the BODIPY core and they can be selectively functionalized. Surprisingly, the position in which halogen is attached has a marked effect in the photophysical properties and modulates the fluorescence capacity of the resulting BODIPY. These iodinated BODIPYs are efficient singlet oxygen generators.     

A new estimate on the indirect Coulomb energy

Here we prove a new lower bound on the indirect Coulomb energy in quantum mechanics, in terms of the single particle density of the system. The new universal lower bound is an alternative to the classical Lieb–Oxford bound (with a smaller constant, C = 1.45 < C_LO = 1.68) but involving an additive kinetic energy term of the single particle density as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012