The uncatalyzed, thermal N-inversion reactions were studied of pyrimidin-4(3H)-imine (PMI), pyridin-2(1H)-imine (PYI), and 1H-purine-6(9H)-imine (PUI). Relevant regions of the potential energy surfaces were explored with second-order Møller-Plesset perturbation theory (MP2(full)/ 6-31G(d)) and with coupled cluster theory (CCSD/6-31G(d), CCSD/6-31+G(d)). The thermochemistry of stationary structures was evaluated at the MP2 level and their energies also were computed at the levels CCSD(T)/6-311+G(d,p) and CCSD(T)/6-311+G(2df,2p) and with structures optimized at lower CCSD levels. The best estimates for the (E)-preference free enthalpies ΔG298(Z vs. E) are 2.6 (PMI), 2.3 (PYI), and 6.0 (PUI) kcal/mol and for the free enthalpies of activation ΔG298(Z → E) they are 21.6 (PMI), 21.1 (PYI) and 19.7 (PUI) kcal/mol. Nonplanar N-inversion transition state (ITS) structures occur along enantiomeric reaction paths and stationary structures for in-plane N-inversion correspond to second-order saddle points (SOSP) on the potential energy surface. The deformation energy ΔEdef = E(SOSP) - E(ITS) is less than 0.5 kcal/mol for PMI and PUI, but it is as high as ΔEdef ≈ 2 kcal/mol for PYI. The detailed study of structures and electronic structures along the entire N-inversion path of the isomerization (Z)-PMI ⇆ (E)-PMI revealed a remarkable stabilization due to asymmetry in the ascent region from the (E)-isomer to ITS. Structures in this region of the potential energy surface allow best for additional bonding overlaps in the HOMO, and this amidine effect predicts lower N-inversion barriers in analogous imines with (Z)-preference energies. The discussion of the halogen-bonded aggregate PMI·ClCH3 exemplifies that the asymmetry in N-inversion paths is retained and perhaps even enhanced in chlorinated solvents of low polarity.