Low‐Barrier Hydrogen Bonds in Negative Thermal Expansion Material H 3 [Co(CN) 6 ]

Electron density and thermal motion of diamond at elevated temperatures

The electron density and thermal motion of diamond are determined at nine temperatures between 100 K and 1000 K via synchrotron powder X-ray diffraction (PXRD) data collected on a high-accuracy detector system. Decoupling of the thermal motion from the thermally smeared electron density is performed via an iterative Wilson-Hansen-Coppens-Rietveld procedure using theoretical static structure factors from density functional theory (DFT) calculations. The thermal motion is found to be harmonic and isotropic in the explored temperature range, and excellent agreement is observed between experimental atomic displacement parameters (ADPs) and those obtained via theoretical harmonic phonon calculations (HPC), even at 1000 K. The Debye temperature of diamond is determined experimentally to be Θ_D = 1883 (35) K. A topological analysis of the electron density explores the temperature dependency of the electron density at the bond critical point. The properties are found to be constant throughout the temperature range. The robustness of the electron density confirms the validity of the crystallographic convolution approximation for diamond in the explored temperature range.

Synchrotron X-ray Electron Density Analysis of Chemical Bonding in the Graphitic Carbon Nitride Precursor Melamine

Melamine is a precursor and building block for graphitic carbon nitride (g-CN) materials, a group of layered materials showing great promise for catalytic applications. The synthetic pathway to g-CN includes a polycondensation reaction of melamine by evaporation of ammonia. Melamine molecules in the crystal organize into wave-like planes with an interlayer distance of 3.3 Å similar to that of g-CN. Here we present an extensive investigation of the experimental electron density of melamine obtained from modelling of synchrotron radiation X-ray single-crystal diffraction data measured at 25 K with special focus on the molecular geometry and intermolecular interactions. Both intra- and interlayer structures are dominated by hydrogen bonding and π-interactions. Theoretical gas-phase optimizations of the experimental molecular geometry show that bond lengths and angles for atoms in the same chemical environment (C-N bonds in the ring, amine groups) differ significantly more for the experimental geometry than for the gas-phase-optimized geometries, indicating that intermolecular interactions in the crystal affects the molecular geometry. In the experimental crystal geometry, one amine group has significantly more sp3 -like character than the others, hinting at a possible formation mechanism of g-CN. Topological analysis and energy frameworks show that the nitrogen atom in this amine group participates in weak intralayer hydrogen bonding. We hypothesize that melamine condenses to g-CN within the layers and that the unique amine group plays a key role in the condensation process.

Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond

Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.

Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study

Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.

Responsive Four-Coordinate Iron(II) Nodes in FePd(CN)4

Metal node design is crucial for obtaining structurally diverse coordination polymers (CPs) and metal-organic frameworks with desirable properties; however, Fe^II ions are exclusively six-coordinated. Herein, we present a cyanide-bridged three-dimensional (3D) CP, FePd(CN)₄ , bearing four-coordinate Fe^II ions, which is synthesized by thermal treatment of a two-dimensional (2D) six-coordinate Fe^II CP, Fe(H₂ O)₂ Pd(CN)₄ ⋅4 H₂ O, to remove water molecules. Atomic-resolution transmission electron microscopy and powder X-ray and neutron diffraction measurements revealed that the FePd(CN)₄ structure is composed of a two-fold interpenetrated PtS topology network, where the Fe^II center demonstrates an intermediate geometry between tetrahedral and square-planar coordination. This four-coordinate Fe^II center with the distorted geometry can act as a thermo-responsive flexible node in the PtS network.