Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis

We demonstrate the application of the transition manifold framework to the late-stage fibrillation process of the NFGAILS peptide, a amyloidogenic fragment of the human islet amyloid polypeptide (hIAPP). This framework formulates machine learning methods for the analysis of multi-scale stochastic systems from short, massively parallel molecular dynamical simulations. We identify key intermediate states and dominant pathways of the process. Furthermore, we identify the optimally timescale-preserving reaction coordinate for the dock-lock process to a fixed pre-formed fibril and show that it exhibits strong correlation with the mean native hydrogen-bond distance. These results pave the way for a comprehensive model reduction and multi-scale analysis of amyloid fibrillation processes. Graphic Abstract

Chiral recognition in bicyclic guanidines

A theoretical study of chiral recognition in bicyclic guanidines has been carried out by means of B3LYP/6-31+G(d,p) DFT calculations. A series of complexes between protonated 4,8-dimethyl-1,5,7-triazabicyclodecene (DTBD) and 2,5-disubtituted chiral cyclopentanones have been evaluated for chiral recognition, both in the gas phase and in benzene solution as per the polarizable continuum model (PCM) and analyzed by AIM and NBO methodologies. An inversion in the sense of chiral recognition has been observed between gas phase and solvated results for cyclopentanone complexes. Among the different correlations found (i.e. between electron density, hydrogen bond distance, second-order perturbation energy), a linear correlation has been established between the chiral recognition energy and different molecular parameters.

Competition of hydrogen-bond acceptors for the strong carboxyl donor

A database study on the competition of hydrogen-bond acceptors for the strong carboxyl donor in crystals is reported. The relative success in attracting this donor is determined for 34 types of acceptor (O, N, S, halogen and π acceptors), and a correlation between the success in competition and the average hydrogen-bond distance is established.

Infrared studies of water in crystalline hydrates: K2HgCl4.H2O

Infrared spectra of polycrystalline K2HgCl4.H2O at different degrees of deuteration were recorded, in the 4000–250 cm−1 region, at temperatures between liquid-nitrogen and 130 °C. The spectra confirm the existence of a single type of water molecule, engaged in two equivalent hydrogen bonds. The value of 2548 cm−1 for the isolated O—D stretching frequency leads to an estimate of 3.25(3) Å for the O … Cl hydrogen-bond distance, in excellent agreement with the results of X-ray and neutron diffraction. Dynamic coupling is appreciable for stretch, bend, and librational fundamentals but is weaker than in CuCl2.2H2O or K2CuCl4.2H2O, in which the water molecules in the crystal are more tightly bonded.A number of corrected values are reported of isolated O—D stretching frequencies in hydrates studied previously.