How the electron-deficient cavity of heterocalixarenes recognizes anions: insights from computation.

We have quantum chemically analyzed the bonding mechanism behind the affinity of various heterocalixarenes for anions with a range of geometries and net charges, using modern dispersion-corrected density functional theory (DFT-D3BJ). The purpose is to better understand the physical factors that are responsible for the computed affinities and thus to develop principles for a more rational design of anion receptors. Our model systems comprise heterocalixarenes 1-4 as hosts, which are characterized by different bridging heteroatoms (O, N, S) as well as the anionic guests Cl-, Br-, I-, BF4-, CH3CO2-, H2PO4-, HSO4-, NCS-, NO3-, PF6-, and SO42-. We use various analysis schemes (EDA, NCI, and NBO) to elucidate the interactions between the calixarene cavity and the anions to probe the importance of the different bonding modes (anion-π, lone-pair electron-π, σ-complexes, hydrogen bonds, and others) of the interactions. Electrostatic interactions appear to be dominant for heterocalixarenes with oxygen bridges whereas orbital interactions prevail in the case of nitrogen and sulfur bridges. Dispersion interactions are however in all cases non-negligible.

Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins.

N ε-Methylation of lysine residues in histones plays an essential role in the regulation of eukaryotic transcription. The 'highest' methylation mark, N ε-trimethyllysine, is specifically recognised by N ε-trimethyllysine binding 'reader' domains, and undergoes demethylation, as catalysed by 2-oxoglutarate dependent JmjC oxygenases. We report studies on the recognition of the closest positively charged N ε-trimethyllysine analogue, i.e. its trimethylphosphonium derivative (KPme3), by N ε-trimethyllysine histone binding proteins and Nε-trimethyllysine demethylases. Calorimetric and computational studies with histone binding proteins reveal that H3KP4me3 binds more tightly than the natural H3K4me3 substrate, though the relative differences in binding affinity vary. Studies with JmjC demethylases show that some, but not all, of them can accept the phosphonium analogue of their natural substrates and that the methylation state selectivity can be changed by substitution of nitrogen for phosphorus. The combined results reveal that very subtle changes, e.g. substitution of nitrogen for phosphorus, can substantially affect interactions between ligand and reader domains / demethylases, knowledge that we hope will inspire the development of highly selective small molecules modulating their activity.

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond.

Invited for this month's cover are the groups of Prof. Dr. Teodorico C. Ramalho (Federal University of Lavras and University Hradec Kralove) and Prof. Dr. F. Matthias Bickelhaupt (Vrije Universiteit Amsterdam and Radboud University). The cover picture shows the key message of their work, that is, the covalency of the chalcogen bonds, in an elegantly simple and attractive manner. To that end, the chalcogen bonds are represented by schematic 3D structures of the bond donor D2 Ch and the bond acceptor A- , and their attractive interaction in green. Then, a colorful molecular orbital (MO) diagram where the HOMO-LUMO mixing is represented by the mixing of red (HOMO) and blue (LUMO) into purple (MO) is presented. Read the full text of their Full Paper at 10.1002/open.202000323.

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond.

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.

Trends and anomalies in H-AH(n) and CH(3)-AH(n) bond strengths (AH(n) = CH3, NH2, OH, F).

Along the series of H-AH(n) bonds, with AH(n) = CH(3), NH(2), OH, and F, the bond dissociation energies show a steady increase as can be expected from the increasing difference in electronegativity along this series. However, in the same series for CH(3)-AH(n) the bond strength first decreases from CH(3)-CH(3) to CH(3)-NH(2) and only thereafter increases again along CH(3)-NH(2), CH(3)-OH and CH(3)-F. To understand the origin of the apparent anomaly occurring for the trend in C-A bond strengths, we have analyzed the bonding mechanism in H-AH(n), CH(3)-AH(n) and other model systems, using density functional theory at BLYP/TZ2P. We recover that increasing electronegativity difference across a bond causes an increasing stability. But we also find that the nature of the bond changes qualitatively for AH(n) = CH(3) due to the saturation of A with hydrogens. The need of the methyl group to adopt an umbrella shaped geometry plays a key role in the difference between bonds with CH(3)* and other second period AH(n)* radicals.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins.

A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation-π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain. These results have implications in rational drug design by specifically targeting the aromatic cage of readers of trimethyllysine.

Direct detection of the mercury-nitrogen bond in the thymine-Hg(II)-thymine base-pair with (199)Hg NMR spectroscopy.

We have observed the 1-bond (199)Hg-(15)N J-coupling ((1)J((199)Hg,(15)N) = 1050 Hz) within the Hg(II)-mediated thymine-thymine base pair (T-Hg(II)-T). This strikingly large (1)J((199)Hg,(15)N) is the first one for canonical sp(2)-nitrogen atoms, which can be a sensitive structure-probe of N-mercurated compounds and a direct evidence for N-mercuration.