Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules

In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some “rules of thumb” have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.     

Crystal,electronic structure and hydrogenation properties of the Mg5.57Ni16Ge7.43 cluster phase with a new type of polyhedron

The ternary germanide Mg_5.57Ni₁₆Ge_7.43 (cubic, space group Fmm, cF116) belongs to the structural family based on the Th₆Mn₂₃-type. The Ge1 and Ge2 atoms fully occupy the 4a (mm symmetry) and 24d (m.mm) sites, respectively. The Ni1 and Ni2 atoms both fully occupy two 32f sites (.3m symmetry). The Mg/Ge statistical mixture occupies the 24e site with 4m.m symmetry. The structure of the title compound contains a three-core-shell cluster. At (0,0,0), there is a Ge1 atom which is surrounded by eight Ni atoms at the vertices of a cube and consequently six Mg atoms at the vertices of an octahedron. These surrounded eight Ni and six Mg atoms form a [Ge1Ni₈(Mg/Ge)₆] rhombic dodecahedron with a coordination number of 14. The [GeNi₈(Mg/Ge)₆] rhombic dodecahedron is encapsulated within the [Ni₂₄] rhombicuboctahedron, which is again encapsulated within an [Ni₃₂(Mg/Ge)₂₄] pentacontatetrahedron; thus, the three-core-shell cluster [GeNi₈(Mg/Ge)₆@Ni₂₄@Ni₃₂(Mg/Ge)₂₄] results. The pentacontatetrahedron is a new representative of Pavlyuk's polyhedra group based on pentagonal, tetragonal and trigonal faces. The dominance of the metallic type of bonding between atoms in the Mg_5.57Ni₁₆Ge_7.43 structure is confirmed by the results of the electronic structure calculations. The hydrogen sorption capacity of this intermetallic at 570 K reaches 0.70 wt% H₂.     

Complete Einstein Metrics are Geodesically Rigid

We prove that every complete Einstein (Riemannian or pseudo-Riemannian) metric g of nonconstant curvature is geodesically rigid: if any other complete metric has the same (unparametrized) geodesics with g, then the Levi-Civita connections of g and coincide.     

Crystal chemistry and physical properties of the ternary compounds REBC (RE = Ce,Pr, Nd)

The ternary rare-earth metal boride carbides REBC (RE = Ce, Pr, Nd) were prepared by melting mixtures of the elements and subsequent annealing at temperatures between 1270 K and 1570 K. Their crystal structures were refined from single crystal X-ray diffraction data. They crystallize in the LaBC-type structure (space group P2₁2₁2₁, Z = 20); CeBC: a = 8.5021(5) Å, b = 8.5217(7) Å, c = 12.3834(7) Å, R1 = 0.033 (wR2 = 0.059) for 2838 reflections with I_o > 2σ(I_o); PrBC: a = 8.4478(5) Å, b = 8.4719(8) Å, c = 12.325(1) Å, R1 = 0.031 (wR2 = 0.063) for 2564 reflections with I_o > 2σ(I_o); NdBC: a = 8.370(1) Å, b = 8.392(1) Å, c = 12.253(3) Å, R1 = 0.035 (wR2 = 0.086) for 4275 reflections with I_o > 2σ(I_o). The structure consists of a three-dimensional framework of rare-earth metal atoms resulting from the stacking of slightly corrugated two-dimensional square nets, leading to voids filled with B₅C₅ finite chains. The magnetism of the compounds PrBC and NdBC is characterized by the onset of ferromagnetism with Curie temperatures around 10 K and 8 K, respectively. The reduced effective paramagnetic moment μ_eff ≈ 1.8 μ_B as well as the weak magnetization at 6 K, 5 T is discussed.     

Grafting of Polyfluorene by Surface‐Initiated Suzuki Polycondensation

Graft work : The first surface‐initiated and site‐specific palladium‐catalyzed Suzuki polycondensation that allows selective grafting and patterning of semiconducting and emissive poly[9,9‐bis(2‐ethylhexyl)fluorene] ( 1 ) at room temperature is developed (see scheme). The pattering is demonstrated by AFM (see image).

     

Nonequatorial circular orbits of spinning particles in the Schwarzschild–de Sitter background

In this paper analytical solutions of the Mathisson–Papapetrou equations that describe nonequatorial circular orbits of a spinning particle in the Schwarzschild–de Sitter background are studied, and the role of the cosmological constant is emphasized. It is shown that generally speaking a highly relativistic velocity of the particle is a necessary condition of motion along this type of orbits, with an exception of orbits locating close to the position of the static equilibrium, where low velocities are possible as well. Depending on the correlation between the spin orientation of the particle and its orbital velocity some of the possible nonequatorial circular orbits exist due to the repulsive action on the particle caused by the spin–gravity coupling and the others are caused by the attractive action. Here values of the energy of the particle on the corresponding orbits are also analyzed.     

Formation of Polymer Nanolayers with Special Properties at Polymer Surfaces

A principal possibility of the utilization of polymer peroxides for the modification of polymer surfaces that provides an immobilization of the tailored quantity of peroxide groups at them has been established. The processes of polymer surface activation with following “grafting from” or “grafting to” utilizing immobilized peroxide groups has been studied using a FTIR-ATR spectroscopy, ellipsometry and measurements of contact angles. The proposed technique of polymer surface activation is based on the universal ability of carbon chain polymer to participate the free radical reactions.