Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• tools are applied to each of the simulation trajectories and this process was streamlined by using Galaxy workflows. The conformations of the antigens were analyzed using root-mean-square deviation, end-to-end distance, Ramachandran plots, and hydrogen bonding analysis. Additionally, RMSF and clustering

• solution and bound to antibody) were also measured. A standard hydrogen-bonding analysis using MDAnalysis and VMD was carried out with the default angle cut-off and distance cut-off. A cluster analysis of the peptide portion of the antigen was carried out (Figure 5) using TTClust [42]. The clusters were

• (Figures S4 and S5 in Supporting Information File 1), the bound Tn-antigen is able to stay resident in the dominant conformation without regularly flipping to other conformations. Hydrogen bonding The specifics of intermolecular interactions can also be considered, and here we utilized a hydrogen-bonding

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• the neighbouring adsorption site. This helps in understanding the nonstatistical pattern formation for this surface–adsorbate system and hints toward an inclusion of dispersion attraction as another determining factor for surface adsorption. Keywords: bonding analysis; cyclooctyne; density functional

Direct estimate of the internal π-donation to the carbene centre within N-heterocyclic carbenes and related molecules

• Diego M. Andrada,
• Nicole Holzmann,
• Thomas Hamadi and
• Gernot Frenking

Beilstein J. Org. Chem. 2015, 11, 2727–2736, doi:10.3762/bjoc.11.294

• calculations and with an energy decomposition analysis. The investigated molecules include N-heterocyclic carbenes (NHCs), the cyclic alkyl(amino)carbene (cAAC), mesoionic carbenes and ylide-stabilized carbenes. The bonding analysis suggests that the carbene centre in cAAC and in diamidocarbene have the

• weakest X→p(π) π-donation while mesoionic carbenes possess the strongest π-donation. Keywords: bonding analysis; N-heterocyclic carbenes; π-donation; Introduction Since the isolation and unambiguous characterization of imidazol-2-ylidene by Arduengo in 1991 [1], the chemistry of stable singlet carbenes

• –acceptor bonds was investigated by an energy decomposition analysis (EDA) which was developed by Morokuma [88] and by Ziegler and Rauk [89][90]. The bonding analysis focuses on the instantaneous interaction energy ∆Eint of a bond A–B between two fragments A and B in the particular electronic reference