Coincidence method for measuring the mass of neutral fragments emitted in a delayed fragmentation process from a singly charged molecule: Fragmentation pathway of adenine

We have studied by mass spectrometry the fragmentation pathways of a molecule of biological interest: adenine ${\mathrm{H}}_5{\mathrm{C}}_5{\mathrm{N}}_5\left(\mathrm{Ad}\right)$. The adenine molecules are ionized and excited in a single collision event mode with slow highly charged ${\mathrm{Ar}}^{8+}$ ions. A method based on the detection in coincidence of neutral and charged fragments has been developed for studying delayed fragmentation channels. The measured spectra show that the well-stated process, i.e., the successive emission of $\mathrm{HCN}$ fragments, is not the only fragmentation pathway. Although in the first fragmentation step the dominant channel is the emission of a neutral ${\mathrm{HCN}}^0(88\%)$, in the second fragmentation step the branching ratios for the delayed emission of an ${\mathrm{HCN}}^0$ and an ${\mathrm{H}}_2{\mathrm{CNCN}}^0$ from the intermediate parent ion ${\mathrm{H}}_4{\mathrm{C}}_4{\mathrm{N}}_4^{+}\left[\right(\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}]$ are surprisingly similar, 54% and 46%, respectively. As a consequence, the role of these two latter channels in the reversal process, i.e., the formation of adenine in gas phase, should be considered. Ab initio calculations of molecular energies show that the energy levels of these two fragmentation channels are very close. This is in qualitative agreement with the measured comparable branching ratios.

Figure 1

Structure of the adenine molecule and labeling of its constituents.

Figure 2

(Color online) Mapping of the equipotential lines for the extraction, acceleration, and focalization electric fields. The bold curve represents the field line along the trajectory of the ion. The number beside each circle denotes the time in $\mathrm{\mu }\mathrm{s}$ when an ${\mathrm{Ad}}^{+}$ ion passes through different regions. $0–0.4\mathrm{\mu }\mathrm{s}$: extraction field; $0.4–0.7\mathrm{\mu }\mathrm{s}$: acceleration field; $0.7–0.9\mathrm{\mu }\mathrm{s}$: cone; $1.1–1.9\mathrm{\mu }\mathrm{s}$: lens; $1.9–2.3\mathrm{\mu }\mathrm{s}$: steerers. The region between the lens and the steerers is a special region with small potential gradient and where the potential value is close to that applied on the TOF tube.

Figure 3

One-dimensional TOF fragmentation spectrum of singly charged adenine parent ions due to the impact of ${\mathrm{Ar}}^{8+}$. The events are selected by the detection of a scattered ${\mathrm{Ar}}^{7+}$ with the electron number criterion, $n=0$. The spectrum is calibrated in mass as shown in the upper scale.

Figure 4

Correlation spectrum between fragments resulting from the dissociation of a singly or doubly charged adenine parent ion. This spectrum was recorded without the electron number selection condition.

Figure 5

Expanded region of correlation spectrum around the spot ${\mathrm{Ad}}^{+}$ $(m=135)$. Crosses: correlated TOF of neutral and charged fragments simulated with the SIMION code for the delayed fragmentation channel ${\mathrm{Ad}}^{+}\to (\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}+\mathrm{HCN}$ in a time range $1.9–2.3\mathrm{\mu }\mathrm{s}$.

Figure 6

Expanded region around the spot $(\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}$ $(m=108)$. Two tails are observed. Crosses: simulation of the correlated TOF of the neutral and charged fragments for two delayed decay channels from the intermediate $(\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}$ parent ions. Tail A: reaction $(\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}\to (\mathrm{Ad}\text{−}2\mathrm{HCN}{)}^{+}+{\mathrm{HCN}}^0$, $108\to 81+27$. Tail B: reaction $(\mathrm{Ad}\text{−}\mathrm{HCN}{)}^{+}\to (\mathrm{Ad}\text{−}3\mathrm{HCN}{)}^{+}+{\mathrm{H}}_2{\mathrm{C}}_2{\mathrm{N}}_2^0$, $108\to 54+54$. Simulations have been performed for delay times, $1.7–2.0\mathrm{\mu }\mathrm{s}$ from the collision time.

Figure 7

Energy levels or fragmentation decay routes for ${\mathrm{Ad}}^{+}$.