Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

Abstract

The bonding energies of proton-bound homodimers BH(+)B were measured by ion mobility equilibrium studies and calculated at the DFT B3LYP/6-311++G** level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°(dissoc)) of the proton-bound dimers (BH(+)B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°(dissoc) for (1,3-diazine)2H(+), i.e., (pyrimidine)2H(+) and (3-F-pyridine)2H(+) are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°(dissoc) for the pyrimidine(·+)(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine)2H(+), (pyridine)2H(+), (2-F-pyridine)2H(+), (3-F-pyridine)2H(+), (2,6-di-F-pyridine)2H(+), (4-F-pyridine)2H(+), (1,3-diazine)2H(+), (1,4-diazine)2H(+), (1,3,5-triazine)2H(+), and (pentafluoropyridine)2H(+) are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH(+)B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4 (meta or para) positions, the lowest energy rotamers are T-shaped with the planes of the two rings rotated by 90° about the hydrogen bond, while the planar rotamers are weakened by repulsion between the ortho hydrogen atoms of the two rings. Conversely, in ortho-substituted (1,2-diazine)2H(+) and (2-F-pyridine)2H(+), attractive interactions between the ortho (C-H) hydrogen atoms of one ring and the electronegative ortho atoms (N or F) of the other ring are stabilizing, and increase the protonated dimer binding energies by up to 4 kcal/mol. In all of the dimers, rotation about the hydrogen bond can involve a 2-4 kcal/mol barrier due to the relative energies of the rotamers.

Interactions of Nucleic Acid Bases with Temozolomide. Stacked, Perpendicular, and Coplanar Heterodimers

“…Auguring well for our own data above, these authors found good agreement between their experimental measurements and calculated data. Prior work has extended as well to radical cation dimers − where both experimental and calculated data have shown that both stacked and perpendicular arrangements can occur in homo and heterodimers of aromatics. These geometries can at times be quite competitive in terms of energy, as for example in the case of the naphthalene/benzene dimer.…”

Morphological self-assembly of enantiopure allenes for upstanding chiral architectures at interfaces

“…It has to be mentioned, however, that both monomer and dimer signals indicate the presence of protonated species, which could contribute to the dimerisation preference. 14 For a better understanding of this assembly tendency, we investigated the agglomeration behaviour of unprotonated species via molecular dynamics (MD) simulations starting from 100 individual molecules in a volume corresponding to 10 À4 M concentration (for details, see ESI †). After several ns-long simulations at 200 K we found a high probability for the formation of supramolecular dimers (Fig.…”

Growth kinetics and formation mechanisms of complex organics by sequential reactions of acetylene with ionized aromatics

“…The mechanisms of the nitrogen incorporation in the PAH ions are important in understanding the ion chemistry in a nitrogen rich atmosphere such as that of Titan [9,13,[58][59][60][61]. DFT calculations indicate that substitution of a carbon atom with nitrogen in the benzene cation ring leads to lowering or eliminating the barrier to the acetylene addition [46][47][48][49][50][51][52][53][54]. These predictions are experimentally verified by the observation of fast sequential reactions of acetylene with the pyridine and pyrimidine cations [26].…”

“…1). The details of the instrument can be found in several publications [25,26,38,47] and only a brief description of the experimental procedure is given here. The molecular ions benzonitrile (C 7 H 5 N + , m/z 103), phenylacetylene (C 8 H 6 + , m/z 102), or styrene (C 8 H 8 + , m/z 104) were generated by 50 eV EI ionization following the supersonic beam expansion of the corresponding vapor mixture consisting of 0.1-0.2% of the organic vapor (benzonitrile, Fig.…”

“…This level of theory has been proven to yield sufficiently accurate and reliable results on similar systems [26,47,49,50]. The geometry optimizations and energy calculations were done using the fairly large 6-311++G** basis set which includes d-type and p-type polarization functions on nonhydrogen and hydrogen atoms, respectively and also have all electrons included [51].…”