Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile

Abstract

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH(+)(H2O) consistent with the formation of a weak carbon-based CH(δ+)··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH(+)··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH(+)(CH3OH) and pyrimidineH(+)(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4(●+) ion by weak CH(δ+)··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4(●+)(H2O)(n-1) + H2O → C4N2H3(●) + (H2O)(n)H(+) and C4N2H5(+)(H2O)(n-1) + H2O → C4N2H4 + (H2O)(n)H(+) are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5(+)(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.

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

“…For example, for re- The B3LYP/6-311++G * * method has been previously used to accurately compute (within 1.5 kcal/mol) binding energies of complexes involving ionized benzene and nitrogen heterocyclic molecules similar to the present systems. 34,36 This trend continues in the present study not only in the calculations of binding energies but also the proton affinities as evident from the excellent agreement between the calculated and the experimental values listed in Table I. The calculated lowest energy isomer of the proton-bound pyrimidine dimer at the B3LYP/6-311++G * * level has a T-shape geometry with a H-bond distance of 1.6 Å as shown in Figure 4.…”

Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

“…The details of the instrument can be found in several publications and only a brief description of the experimental procedure is given here. 8,17,21 In the experiments, the molecular ions of pyridine (C 5 H 5 N + • ), pyrimidine (C 4 H 4 N 2 + • ) are formed by electron impact ionization using electron energy of 60-70 eV following the supersonic expansion of 40 psi (2.8 bars) of ultra-high pure helium seeded with about 1%-4% of pyridine or pyrimidine vapor through a pulsed supersonic nozzle (500 μm) to the vacuum source chamber with 10 −7 mbar pressure. In order to form the H + pyridine (C 5 H 5 NH + ), 10% H 2 in helium was used as carrier gas.…”

“…4,15,16 Ionized aromatics containing N heteroatoms such as the pyridine and the pyrimidine radical cations can also participate in hydrogen bonding interactions. 20,21 The hydration of these ions has been investigated both experimentally and theoretically. 20,21 However, no data exist on the interactions of these ions with HCN in spite of their importance in biology and origin of life.…”

“…20,21 The hydration of these ions has been investigated both experimentally and theoretically. 20,21 However, no data exist on the interactions of these ions with HCN in spite of their importance in biology and origin of life. Here, we present the first study of the stepwise association of HCN with the pyridine (C 5 NH 5 + • ) and pyrimidine (C 4 N 2 H 4 + • ) radical cations and protonated pyridine (C 5 NH 5 )H + .…”

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

“…These experiments can identify the chains of reactions leading to the formation of PAHs and PANHs found in soot, combustion, organic aerosols, interstellar clouds, and meteorites [16][17][18][19][20][21][22][23][24][25][26][27]. They can also provide detailed information on the reactivity, kinetics, growth mechanisms, energy barriers, and structures of large organic ions as well as on their complexes with associated solvent molecules in different environments [28][29][30].…”