Experimental and Theoretical Study of the Reactivity of Gold Nanoparticles Towards Benzimidazole‐2‐ylidene Ligands

The reactivity of benzimidazol‐2‐ylidenes with respect to gold nanoparticles (AuNPs) has been investigated using a combined experimental and computational approach. First, the grafting of benzimidazol‐2‐ylidenes bearing benzyl groups on the nitrogen atoms is described, and comparisons are made with structurally similar N‐heterocyclic carbenes (NHCs) bearing other N‐groups. Similar reactivity was observed for all NHCs, with 1) the erosion of the AuNPs under the effect of the NHC and 2) the formation of bis(NHC) gold complexes. DFT calculations were performed to investigate the modes of grafting of such ligands, to determine adsorption energies, and to rationalize the spectroscopic data. Two types of computational models were developed to describe the grafting onto large or small AuNPs, with either periodic or cluster‐type DFT calculations. Calculations of NMR parameters were performed on some of these models, and discussed in light of the experimental data.     

Replacement of Water Molecules in a Phosphate Binding Site by Furanoside‐Appended lin‐Benzoguanine Ligands of tRNA‐Guanine Transglycosylase (TGT)

The enzyme tRNA‐guanine transglycosylase has been identified as a drug target for the foodborne illness shigellosis. A key challenge in structure‐based design for this enzyme is the filling of the polar ribose‐34 pocket. Herein, we describe a novel series of ligands consisting of furanoside‐appended lin‐benzoguanines. They were designed to replace a conserved water cluster and differ by the functional groups at C(2) and C(3) of the furanosyl moiety being either OH or OMe. The unfavorable desolvation of Asp102 and Asp280, which are located close to the ribose‐34 pocket, had a significant impact on binding affinity. While the enzyme has tRNA as its natural substrate, X‐ray co‐crystal structures revealed that the furanosyl moieties of the ligands are not accommodated in the tRNA ribose‐34 site, but at the location of the adjacent phosphate group. A remarkable similarity of the position of the oxygen atoms in these two structures suggests furanosides as a potential phosphate isoster.     

A down-up chain with persistent labels on multifurcating trees

In this article, we propose to study a general notion of a down-up Markov chain for multifurcating trees with $n$ labeled leaves. We study in detail down-up chains associated with the $(\alpha ,\gamma )$-model of Chen et al. (Electron. J. Probab. 14 (2009), 400–430.), generalizing and further developing previous work by Forman et al. (arXiv:1802.00862, 2018; arXiv:1804.01205, 2018; arXiv:1809.07756, 2018; Random Struct. Algoritm. 54 (2020), 745–769; Electron. J. Probab. 25 (2020), 1–46.) in the binary special cases. The technique we deploy utilizes the construction of a growth process and a down-up Markov chain on trees with planar structure. Our construction ensures that natural projections of the down-up chain are Markov chains in their own right. We establish label dynamics that at the same time preserve the labeled alpha-gamma distribution and keep the branch points between the $k$ smallest labels for order $n^2$ time steps for all $k\ge 2$. We conjecture the existence of diffusive scaling limits generalizing the “Aldous diffusion” by Forman et al. (arXiv:1802.00862, 2018; arXiv:1804.01205, 2018; arXiv:1809.07756, 2018.) as a continuum-tree-valued process and the “algebraic $\alpha$-Ford tree evolution” by Löhr et al. (Ann. Probab. 48 (2020), 2565–2590.) and by Nussbaumer and Winter (arXiv:2006.09316, 2020.) as a process in a space of algebraic trees.