Atomistic Simulation Study of Cu0.327Ni0.673 Alloys: from Solid Solution to Phase Segregation

We present a combined Monte‐Carlo/molecular dynamics study of a Cu_0.327Ni_0.673 alloy system. On the basis of nearest‐neighbor coordination number analyses atomic clustering and phase segregation is explored. Along this line, free energy profiles are calculated and separated into entropic and energetic contributions. The competition of both terms was found in accordance to the experimental phase diagrams (phase separation of the solid solution below about 600 Kelvin). Two independent simulation runs were performed. At 1000 Kelvin the observed configurations correspond to solid solutions exhibiting a weak tendency to cluster atoms of identical species. At room temperature the energetic favoring of atomic separation is clearly dominant and leads to the formation of Ni‐rich and Cu‐rich domains. The latter are separated by interfacial regions whose width ranges from 0.5 to 1 nanometers.     

Persicamidines—Unprecedented Sesquarterpenoids with Potent Antiviral Bioactivity against Coronaviruses

A new family of highly unusual sesquarterpenoids (persicamidines A–E) exhibiting significant antiviral activity was isolated from a newly discovered actinobacterial strain, Kibdelosporangium persicum sp. nov., collected from a hot desert in Iran. Extensive NMR analysis unraveled a hexacyclic terpenoid molecule with a modified sugar moiety on one side and a highly unusual isourea moiety fused to the terpenoid structure. The structures of the five analogues differed only in the aminoalkyl side chain attached to the isourea moiety. Persicamidines A–E showed potent activity against hCoV-229E and SARS-CoV-2 viruses in the nanomolar range together with very good selectivity indices, making persicamidines promising as starting points for drug development.     

New Silver Tellurates – The Crystal Structures of a Third Modification of Ag2Te2O6 and of Ag4TeO5

Single crystals of a third modification of Ag₂Te₂O₆ (denoted as Ag₂Te₂O₆–III) and of Ag₄TeO₅ have been obtained as minor by‐products during hydrothermal phase formation experiments in the system Ag‐Hg‐Te‐O. The crystal structure of Ag₂Te₂O₆–III (P2₁/c, Z = 4, a = 6.4255(10), b = 6.9852(11), c = 13.204(2) Å, β = 90.090(3)°, 1885 independent reflections, R[F² > 2σ(F²)] = 0.0334, wR2(F² all) = 0.0817) comprises tellurium in oxidation states +IV and +VI and is topologically related to the structure of the Ag₂Te₂O₆–I modification, which consists of similar layers and interjacent layers of Ag⁺ cations. Ag₄TeO₅ (C2/c, Z = 8, a = 16.271(2), b = 6.0874(10), c = 11.4373(16) Å, β = 106.730(10)°, 2372 independent reflections, R[F² > 2σ(F²)] = 0.0288, wR2(F² all) = 0.0737) is made up of a layer‐like arrangement of isolated [Te^VI₂O₁₀] double octahedra and of Ag⁺ cations situated both in layers parallel and inside the layers of the anionic moieties.     

Synthetic Activators of Cell Migration Designed by Constructive Machine Learning

Constructive machine learning aims to create examples from its learned domain which are likely to exhibit similar properties. Here, a recurrent neural network was trained with the chemical structures of known cell-migration modulators. This machine learning model was used to generate new molecules that mimic the training compounds. Two top-scoring designs were synthesized, and tested for functional activity in a phenotypic spheroid cell migration assay. These computationally generated small molecules significantly increased the migration of medulloblastoma cells. The results further corroborate the applicability of constructive machine learning to the de novo design of druglike molecules with desired properties.     

Understanding Refractive Index Changes in Homologous Series of Unbranched Organic Compounds Based on Beer's Law

Changes of the refractive index for homologous series of hydrocarbons are usually plotted versus the density. While there is a clear linear dependence for alkanes and alkenes, the linearity deteriorates for homologous series with functional groups involving heteroatoms. The slope can even become negative, e. g., for carboxylic acids. For gaining a deeper understanding and to establish a more general correlation, we reinvestigate the corresponding theories starting with the Newton-Laplace, Gladstone-Dale and the Lorentz-Lorenz rules. We revisit the concept of molar refractivity pioneered by Landolt and Brühl and show that it is closely connected with a twin of Beer's law. We conclude that the refractive index of homologues series should better be plotted versus the molar concentration of the main UV-chromophore, the C−H bond, which actually causes the refractive index changes. This new approach is not limited to alkanes and alkenes but holds for homologous series with functional groups including heteroatoms.     

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.     

Temperature dependence and resonance assignment of 13C NMR spectra of selectively and uniformly labeled fusion peptides associated with membranes

HIV-1 and influenza viral fusion peptides are biologically relevant model fusion systems and, in this study, their membrane-associated structures were probed by solid-state NMR (13)C chemical shift measurements. The influenza peptide IFP-L2CF3N contained a (13)C carbonyl label at Leu-2 and a (15)N label at Phe-3 while the HIV-1 peptide HFP-UF8L9G10 was uniformly (13)C and (15)N labeled at Phe-8, Leu-9 and Gly-10. The membrane composition of the IFP-L2CF3N sample was POPC-POPG (4:1) and the membrane composition of the HFP-UF8L9G10 sample was a mixture of lipids and cholesterol which approximately reflects the lipid headgroup and cholesterol composition of host cells of the HIV-1 virus. In one-dimensional magic angle spinning spectra, labeled backbone (13)C were selectively observed using a REDOR filter of the (13)C-(15)N dipolar coupling. Backbone chemical shifts were very similar at -50 and 20 degrees C, which suggests that low temperature does not appreciably change the peptide structure. Relative to -50 degrees C, the 20 degrees C spectra had narrower signals with lower integrated intensity, which is consistent with greater motion at the higher temperature. The Leu-2 chemical shift in the IFP-L2CF3N sample correlates with a helical structure at this residue and is consistent with detection of helical structure by other biophysical techniques. Two-dimensional (13)C-(13)C correlation spectra were obtained for the HFP-UF8L9G10 sample and were used to assign the chemical shifts of all of the (13)C labels in the peptide. Secondary shift analysis was consistent with a beta-strand structure over these three residues. The high signal-to-noise ratio of the 2D spectra suggests that membrane-associated fusion peptides with longer sequences of labeled amino acids can also be assigned with 2D and 3D methods.