doi:10.1016/j.ijms.2007.02.016 
Copyright © 2007 Elsevier B.V. All rights reserved.
Cytosine neutral molecules and cation–radicals in the gas-phase Structures, energetics, ion chemistry, and neutralization–reionization mass spectrometry
aDepartment of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, United States
bDepartment of Chemistry, University of Akron, Akron, OH, United States
Received 18 August 2006;
revised 2 February 2007;
accepted 20 February 2007.
Available online 5 March 2007.
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Abstract
Gas-phase cytosine molecules and cation–radicals represent a complex system of several nearly isoenergetic tautomers within each group. Computational methods differ in ordering the relative enthalpies of neutral cytosine tautomers. At our highest level of theory, CCSD(T)/aug-cc-pVTZ calculations find an enol form, anti-2-hydroxy-4-aminopyrimidine (2), to be the most stable neutral tautomer in the gas-phase, followed by its rotamer, syn-2-hydroxy-4-aminopyrimidine (3), the canonical oxo-form, 4-amino-1,2-dihydropyrimidin-2(1H)-one (1), imino-forms, 2-oxo-4-iminodihydro(1H,3H)pyrimidine (4 and 5), and another oxo-form, 4-amino-dihydropyrimidin-2(3H)-one (6). Other tautomers, such as anti-anti, syn-syn and syn-anti-2-hydroxy-4-iminodihydro(3H,4H)pyrimidines (7–9), are less stable. The adiabatic ionization energies of the major cytosine tautomers have been calculated to be 8.71, 8.64, 8.62, 8.58, 8.64, and 8.31 eV for 1, 2, 3, 4, 5, and 6, respectively. Cytosine cation–radicals show very close relative energies that increase in the order of 6
+ (most stable) <2+ ≈ 3+ < 4+ ≈ 7+ ≈ 1+ < 5+. In addition, distonic ions having radical centers at C-5 (10+) and C-6 (11+ are found as low-energy isomers of 1+–7+. Metastable cytosine cation–radicals undergo ring-cleavage dissociations by eliminations of CO (major) and HN
CO (minor). The energetics of these and other higher-energy dissociations, including the pertinent transition states, have been established by high-level ab initio and density functional theory calculations and plausible mechanisms have been proposed. Collisional neutralization of cytosine cation–radicals with trimethylamine and dimethyldisulfide as electron donors forms stable molecules that are detected as cation–radicals following collisional reionization. The dissociations observed upon neutralization–reionization mainly include ring-cleavages followed by loss of NCO, HNCO, and formation of C2H3N, C2H2N, and CO neutral fragments that are assigned to ion dissociations following reionization.
Keywords: Cytosine tautomers; Cytosine cation–radicals; Ionization energies; Neutralization–reionization; Ab initio calculations
Fig. 1. B3LYP/6-31 + G(d,p) optimized structures of cytosine tautomers 1–9. Bond lengths in angstroms.
Fig. 2. Relative free energies (
, top panel) and equilibrium molar fractions (lower panel) of cytosine tautomers 1–4 in the gas-phase as a function of temperature. The relative energies were from CCSD(T)/aug-cc-pVTZ single-point calculations. Full circles: 1; open circles: 2; full triangles: 3; open triangles: 4.
Fig. 3. B3LYP/6-31+G(d,p) optimized structures of cytosine cation–radicals 1+–7+. Bond lengths in angstroms.
Fig. 4. B3LYP/6-31+G(d,p) optimized structures of dissociation intermediates. Bond lengths in angstroms.
Fig. 5. Tandem mass spectra of [cytosine]+ obtained as kinetic energy scans. (a) Metastable-ion spectrum. (b) Collisionally-activated dissociation (He) mass spectrum. (c) Neutralization–reionization mass spectrum.
Fig. 6. Collisionally-activated dissociation mass spectrum of [cytosine]+ obtained as a B/E linked scan. Inset shows the standard 70 eV electron ionization mass spectrum of cytosine [57].
Fig. 7. B3LYP/6-31+G(d,p) optimized structures of transition states for ion isomerizations and dissociation. Bond lengths in angstroms.
Fig. 9. (a) Neutralization (CH3SSCH3)/reionization (O2) mass spectrum of [cytosine]+. (b) Neutralization (CH3SSCH3)/neutral collisional activation (He)/reionization (O2) mass spectrum of [cytosine]+.
Table 1.
Relative energies of cytosine tautomers
a In units of kJ mol
−1 at 0 K and including B3LYP/6-31+G(d,p) zero-point vibrational energy corrections.
b Single-point energies on B3LYP/6-31+G(d,p) optimized geometries.
c Effective energies from linear basis set extrapolation:
E[CCSD(T)/large basis set ≈
E[CCSD(T)/small basis set] +
E[MP2/large basis set] −
E[MP2/small basis set].
d Single-point energies on MP2(FULL)/6-31+G(d,p) optimized geometries.
e E(B3-MP2) = 0.5{
E[B3LYP] +
E[MP2]}.
f From ref. Trygubenko et al.
[52].
Table 2.
Cytosine ionization and recombination energies
a Adiabatic ionization energies in units of electronvolt at 0 K including B3LYP/6-31+G(d,p) ZPVE corrections.
b Vertical ionization energies.
c Vertical recombination energies in cation–radicals.
Table 3.
Relative and dissociation energies of cytosine cation–radicals
a In units of kJ mol
−1 at 0 K including B3LYP/6-31+G(d,p) zero-point vibrational energy corrections.
b Relative to
1+ unless specified otherwise.
c From single-point calculations using spin-projected PMP2 energies.
d Effective energies from linear basis set extrapolation:
E[CCSD(T)/large basis set ≈
E[CCSD(T)/small basis set] +
E[MP2/large basis set] −
E[MP2/small basis set].
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