A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1-18, Z=1-118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtaine...
a Structures of compounds that exhibit an increase in basicity due to the assistance of an auxiliary group which is part of the same network of covalent bonds as the basic site. b A rotaxane and a catenane which display an increase in basicity due to the mechanical bond between the subunit...
The computed reaction pathway also shows a TS in which the sugar-phosphate bond is being broken (C1-OP = 2.2 Å) and the sugar-Asn30 bond is being formed (C1-N = 2.1 Å) (Fig. 5c and Supplementary Table 3). Simultaneously, the proton of the imide hydroxyl group...
In addition to the vdW, electrostatic, and H-bond interactions, few scoring functions also include the intramolecular energy of ligands. Because the ligand conformations vary considerably between the bound and unbound states, the ligands usually acquire a strain energy after docking. Several scoring ...
(labelled W1 and W2). At P1 site, the lactam forms a hydrogen bond with H163-A. At P2 site, the side chain of Leu slips extremely into the hydrophobic S2 subsite. At P3 site, the side chain of Val gets exposed to solvent and exhibits tolerance of this site to a wide range of ...
(Beedle et al.2016). This modification is well-known as a trigger of protein misfolding, in addition to potentially leading to the formation of a disulfide bond that protects the Ig domain fold. The intramolecular S–S bond leads to stiffening of the Ig domain segments (Ainavarapu et al....
Amolecular graphis given by nodes and edges that represent atoms and bonds, respectively. Often nodes and edges are labeled with atom and bond properties. Obviously, molecular graphs are undirected. The number of edges connecting each node is limited by the number of covalent bonds an atom can ...
intensity, or the wavelength vs. amplitude, of fluctuation functions. It is generally accepted, on the other hand, that the temperature increase causes a decrease in the global average of the hydrogen bond probability in pure H2O. A question arises immediately whether the temperature increase ...
The LINCS algorithm38 was applied to constrain the covalent bonds with hydrogen atoms. The time step of the simulations was set to 2 fs. The interactions above 10 Å were regarded as nonbond. To determine whether a hydrogen bond exists between a peptide and a protein in the MD ...
We use SCFBio (http://www.scfbio-iitd.res.in/software/drugdesign/lipinski.jsp) web tool for evaluating their Lipinski rule satisfaction of drug likeness properties (including molecular weight, number of hydrogen donor and acceptor bonds, rotatable bond, octanol/water partition coefficient or LogP...