Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Synthesis and structural characterization of cationic rhenium(V) and technetium(V) dioxo complexes containing four N-heterocyclic carbene ligands

Cationic dioxorhenium and dioxotechnetium complexes of the composition [MO(2)(L(1))(4)](+) (L(1) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene) have been prepared from various starting materials and studied spectroscopically and by X-ray crystallography. The metal-carbon distances range from 2.216(4) to 2.232(4) A indicating mainly sigma-bonding.     

Temperature-dependent crystal structure of the isopropanol clathrate of Dianin's compound

The title compound undergoes two order-disorder transitions between 15 and 299 K, dictated by ordering of the guest molecules in the host cages, and resulting in three related crystal structures. We anticipate behaviour of this kind to be widespread, and speculate that the concept of "the crystal structure" for individual Dianin's clathrates may be elusive.     

The Site‐Assembly Determines Catalytic Activity of Nanoparticles

Heterogeneous catalysts are often designed as metal nanoparticles supported on oxide surfaces. Here, the relation between particle morphology and reaction kinetics is investigated by scaling relation kinetic Monte Carlo simulations using CO oxidation over Pt nanoparticles as a model reaction. We find that different particle morphologies result in vastly different catalytic activities. The activity is strongly affected by kinetic couplings between sites, and a wide site distribution generally enhances the activity. The present study highlights the role of site‐assemblies as a concept that, in addition to isolated active sites, can be used to understand catalytic reactions over nanoparticles.     

Exceptions and counterexamples: Understanding Abel's comment on Cauchy's Theorem

It may seem odd that Abel, a protagonist of Cauchy's new rigor, spoke of “exceptions” when he criticized Cauchy's theorem on the continuity of sums of continuous functions. However, when interpreted contextually, exceptions appear as both valid and viable entities in the early 19th century. First, Abel's use of the term “exception” and the role of the exception in his binomial paper is documented and analyzed. Second, it is suggested how Abel may have acquainted himself with the exception and his use of it in a process denoted critical revision is discussed. Finally, an interpretation of Abel's exception is given that identifies it as a representative example of a more general transition in the understanding of mathematical objects that took place during the period. With this interpretation, exceptions find their place in a fundamental transition during the early 19th century from a formal approach to analysis toward a more conceptual one.