Structural-topological preferences and protonation sequence of aliphatic polyamines: a theoretical case study of tetramine trien

Abstract

A large set of lowest and medium energy conformers of aliphatic tetramine trien was used to uncover structural-topological preferences of poliamines. Numerous common structural features among HL and H 2 L tautomers were identified, e.g., H-atoms of protonated functional groups are always involved in intramolecular NH•••N interactions and they result in as large and as many as possible rings in lowest energy conformers. Largest, 11-membered, rings stabilize a molecule most and they appeared to be strain free whereas 5-memebred-rings were most strained (all formed. In contrast to HF, the overall performance of B3LYP was found satisfactory for the purpose of the study; it reproduced MP2 results well.

A unified molecular‐wide and electron density based concept of chemical bonding

“…Polyamines are extremely flexible molecules and often unexpected BPs are found in equilibrium structures 22 . Molecular graphs of protonated triethylenetetramine ( trien , HL) of (i) the lowest energy conformer (LEC; HL‐1) and (ii) the second lowest energy HL‐2 (with Δ E = E HL‐2 − E HL‐1 = 0.70 kcal/mol) found at the MP2 level are shown in Figure 1.…”

Competition reaction-based prediction of polyamines’ stepwise protonation constants: a case study involving 1,4,7,10-tetraazadecane (2,2,2-tet)

“…It was necessary to employ MMFF(aq) because the sets of LECs discovered in the gas phase (using MMFF) were significantly different. This was done by a systematic variation of the torsional angle of each rotatable bond as described previously [40] with slight modifications implemented in the case of 3,2,3-tet (see PART 1 of the SI for a full description of the conformational search procedure used). We have also performed conformational search on the same ligands with explicitly added four water molecules which were placed (i) randomly in relation to their orientation toward a backbone structure of a ligand, but (ii) quite evenly along a molecule; for illustration, free ligands with water molecules are shown in Figure 1.…”

“…To this effect, we took advantage of having a large data bank from previous work [40] where hundreds of 2,2,2-tet conformers were fully optimised in Gaussian. A thorough inspection of the optimisation profiles generated for all tautomers of protonated forms of 2,2,2-tet revealed that in order to predict 'safely' the set of lowest energy conformers needed for the purpose of this study it would be sufficient to implement a pre-optimisation operation which involves terminating the optimisation process after 20 steps -for details see PART 4 in the SI.…”

“…We reported recently the first extensive conformational analysis of protonated polyamines using trien as a case study [40] and showed that the developed protocol was able to identify representative sets of LECs. These were used to predict %-fraction of each tautomeric form of the singly and doubly protonated trien which were in good agreement with experimental data obtained from the 13 C NMR spectrometry.…”

“…Usefulness of that conformational search protocol and the CRn methodology in predicting four protonation constants of highly negatively charged molecules [12,13] have motivated us to undertake this investigation where four stepwise protonation constants of 2,2,2-tet will be predicted using 1,5,8,12-tetraazadodecane (3,2,3-tet) as a reference molecule. As far as we could establish, this is the first attempt to combine the two methodologies we referred to above [12,40]. Hence, we have selected tetramines of similar structures for which experimental values are known as this allowed us verification of theoretically predicted…”