Through a study of the thermal degradation of poly(diethylene glycol terephthalate) and poly ethylene isophthalate), it was found that diethylene glycol and isophthalate units promoted thermal degradation through increased chain flexibility and more favourable bond angles, respectively.
Structure inserts show (left-hand side) the location of the non-favourable torsion angles, outliers (red) and allowed (blue), and (right-hand side) a B -factor putty representation for the single structure refined with phenix.refine.refine
In case of GlcNAc(4S) and GlcNAc 6S), the strong interaction between sulfate groups and hydrogens of the hydroxyl groups defines the most favourable ω dihedral angle conformation.
For the sulfated GalNAc derivatives, the positions of Na+ ions are crucial for the selection of the most energetically favourable ω dihedral angle conformation.
Rotamer conformations were assigned using the Dunbrack backbone-dependent rotamer library in PyMOL (http://www.pymol.org), variable architectures were explored and assessed using Molprobity [ 31], checking for clashes, favourable Φ-Ψ angles and side-chain positions.
Herein, a chlorine atom shows very favourable distance (336 pm) and σ hole angle (160.4°) to the sulfur of methionine.
We set the search range from 40° to 90°, referring to the results in the previous chapter that low-angle fault planes are not favourable.
None of the options for closing the angle between the lines presented a favourable option to the British commander: any manoeuvre to bring ships closer would limit their firing ability to their bow guns, and potentially expose their decks to raking or enfilading fire from the enemy ships.
Figure 6A,B shows that high-energy conformations, as indicated by for example non-favourable Ramachandran φ,ψ-angle combinations, occurred transiently and were concentrated in regions of structural flexibility.
