Evidence for the Formation of Pyrimidine Cations from the

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Evidence for the Formation of Pyrimidine Cations from the Sequential Reactions of Hydrogen Cyanide with the Acetylene Radical Cation Ahmed M. Hamid,† Partha P. Bera,*,‡,# Timothy J. Lee,*,‡ Saadullah G. Aziz,§ Abdulrahman O. Alyoubi,§ and M. Samy El-Shall*,† †

Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States NASA Ames Research Center, Moffett Field, California 94035, United States # Bay Area Environmental Research Institute, Petaluma, California 94952, United States § Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia ‡

S Supporting Information *

ABSTRACT: Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation in the gas phase at ambient temperature using the mass-selected variable temperature and pressure ion mobility technique. The formation and structures of the pyrimidine ion isomers are theoretically predicted via coupled cluster and density functional theory calculations. This ion−molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil.

SECTION: Environmental and Atmospheric Chemistry, Aerosol Processes, Geochemistry, and Astrochemistry

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varied organic chemistry.18−20 The diverse conditions of the nebula include surface densities given as Σ(r) = 2000/r g/cm2 and a thermal structure of the form T = 200r−1/2 K (r in au units), which ranges from 1000 to 2000 K near the early Sun to 10−100 K in the outer nebula, depending on the heliocentric distance and the height above the disk midplane.18−20 The wide ranges of temperatures and densities make solar nebulae uniquely suited for the formation of complex organics up to PAHs and polycyclic aromatic nitrogen-containing hydrocarbons (PANHs) from reactions involving acetylene, HCN, and isocyanide.8,20−22 Because molecules in outer space are subject to ionizing radiation and reaction rates of ion−molecule reactions may exceed by orders of magnitude those of gas-phase neutral reactions at the low interstellar temperatures (with the exception of fast radical−radical and radical−molecule reactions),23 ion chemistry becomes increasingly competitive to gas-phase neutral chemistry in cold ionizing environments.1,2,23 However, temperatures can be tens to even hundreds of degrees Kelvin in some star-forming regions.24 Because of the large ionization energy of HCN (IE = 13.6

itrogen-containing biomolecules and their precursors can arise in different environments by various mechanisms, including gas-phase ion−molecule reactions and gas/grain interactions in interstellar clouds and solar nebulae, in irradiated ices on dust grain surfaces, and solution biochemistry.1−7 The nitrogen in these molecules can be introduced by reactions of common astrochemical molecules such as hydrogen cyanide (HCN), which is the primary precursor involved in prebiotic synthesis and a possible precursor to the nitrogen heterocyclics that gave rise to biochemistry.8−10 HCN polymers have been shown to exist in solar system bodies such as meteorites, comets, and planets, in circumstellar envelopes, and even in Titan’s atmosphere.11−14 Moreover, HCN is formed in combustion processes, and therefore, HCN is likely to be involved in soot formation by both neutral and ionic reactions.15 To date, over 170 organic molecular species varying from simple radicals (e.g., CH) to complex molecules such as cyanopolyynes (e.g., HC11 N), organic molecules (e.g., acetylene, benzene, PAHs), C60, and C70 have been discovered in space.16 Unlike neutral pyrimidine, which has not been conclusively observed in the interstellar medium,17 there have been no astronomical searches for the pyrimidine cation in the environments in which it is most likely to exist. The solar nebula contains diverse environments suitable for rich and © 2014 American Chemical Society

Received: August 6, 2014 Accepted: September 9, 2014 Published: September 9, 2014 3392

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eV),25 we postulate that it can undergo sequential covalent addition, rather than charge transfer, onto small astrochemical ions such as acetylene (C2H2+•) to form biologically relevant ions such as pyrimidine (C4H4N2+•) and its isomers. Association of HCN with HCCH+• may produce a number of isomers of vinyl cyanide ion (C3H3N+•) via gas-phase ion− molecule reactions.26 The dissociation of pyrimidine ions also produces C3H3N+•.27 Pyrimidine and uracil were detected in meteorites, and laboratory experiments verified pyrimidine to be a possible source of uracil RNA bases under astrophysical conditions.28 However, no laboratory experiments have established any plausible mechanisms for the formation of pyrimidine from ion−molecule reactions involving the astrochemical molecules acetylene and HCN. Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation. The formation of pyrimidine ions by gas-phase ion−molecule reactions may lead to new pathways for the formation of complex biologically relevant compounds in space environments, such as the formation of uracil. For example, while it has been shown that uracil will form in irradiated water ices that have been seeded with pyrimidine,29 it has not been shown whether pyrimidine would need to form in the ice or whether it might form in the gas phase and then be incorporated into the ice. The sequential reactions of HCN with the acetylene radical cation were investigated using mass-selected ion mobility (MSIM) mass spectrometry.30−33 The instrument is described and shown schematically in Figure S1 (Supporting Information).30−33 In the experiments, acetylene ions, generated by electron impact ionization of acetylene vapor, are mass-selected using a quadrupole mass filter and injected into a drift cell containing HCN vapor or a mixture of HCN and helium at well-defined pressures and temperatures. Residence times of the various ions are measured by monitoring the signals corresponding to each ion as a function of time after injection into the drift cell. The reactant and product ions exiting the drift cell are analyzed and detected using a second quadrupole mass spectrometer. Figure 1 displays the mass spectra obtained following the injection of the C2H2+• ion into the drift cell containing He or HCN gas at higher pressures (0.6−0.9 Torr) and different temperatures (301−625 K). The injection of the mass-selected acetylene ion into 0.92 Torr of He (Figure 1a) shows only the C2H2+• parent ion with no fragmentation as a result of using low injection energy (11.2 eV, lab frame) below the dissociation energy of the acetylene ion. The ion reacts with HCN at room temperature by proton transfer and adduct formation to give H+(HCN) and C3H3N+•, respectively (Figure 1b), in agreement with previous studies.34,35 Because the addition channel is stabilized by third-body collisions, higher adducts such as C4H4N2+• (i.e., C2H2+• + 2HCN) are formed at higher pressures of HCN/He (0.74 Torr, Figure 1b and also see Figure S2, Supporting Information). Furthermore, association of one HCN molecule with the C4H4N2+• ion is observed at 303 K forming the C4H4N2+•(HCN) cluster (Figure 1b). Also, the proton-transfer channel (HCNH+) leads to the formation of the proton-bound dimer H+(HCN)2 (i.e., HCNH+NCH) at room temperature, as shown in Figure 1b. At higher temperatures (426 K), the noncovalent clusters C4H4N2+•(HCN) and H+(HCN)2 thermally dissociate (as expected) but not the C4H4N2+• ion, as shown in Figure 1c. This ion shows exceptional thermal stability as it survives at

Figure 1. Mass spectra of the C2H2+•/HCN reactions at different temperatures as indicated. The pressures (Torr) in the drift cell are (a) 0.92 He, (b) 0.14 HCN and 0.62 He, (c) 0.16 HCN and 0.74 He, and (d) 0.17 HCN and 0.60 He. The blue dots in (b), (c), and (d) represent the H+(HCN)n series with n = 1−2.

very high temperatures such as 625 K, as shown in Figure 1d. At this high temperature, only covalently bonded molecular ions are expected to survive because the cluster ions with typical binding energies in the range of 10−20 kcal/mol should thermally dissociate to the parent molecular ions.32 Therefore, the observation of both the C3H3N+• and C4H4N2+• ions at 625 K confirms the covalent bonding nature of these ions similar to the other observed ions at this temperature, such as protonated HCN and the H2O molecular ion (due to charge transfer ionization of water desorbed from the drift cell surface at 625 K). The results shown in Figure 1 suggest that sequential addition of two HCN molecules onto the acetylene ion at room temperature can lead to the formation of the covalently bonded C4H4N2+• ion (possibly pyrimidine+•) followed by noncovalent association of HCN molecules with the C4H4N2+• ion. To investigate the nature of bonding in the C4H4N2+•(HCN) cluster observed in Figure 1b, we determined the enthalpy and entropy changes for the HCN association with the C4H4N2+• ion using equilibrium thermochemical measurements.31,33 These thermochemical values are then compared to the corresponding values for the association of HCN with the actual pyrimidine radical cation measured under similar conditions.33 Figure 2a displays the mass spectra obtained for the association of HCN molecules with the C4H4N2+ ion at low temperatures. As the temperature decreases, the equilibrium distributions of the H+(HCN)n and C4H4N2+•(HCN)n clusters shift to higher n and up to five HCN molecules are observed to associate with each of the H+(HCN) and the C4H4N2+• ions at 185 K as shown in the bottom panel of Figure 2(a). Similar mass spectra are obtained for the association of the actual pyrimidine radical cation with HCN molecules at low temperatures, as shown in Figure 2b. The equilibrium reactions are represented by eqs 1 and 2 C4 H4N2+• + HCN ⇄ C4 H4N2+•(HCN) 3393

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Figure 2. (a) Mass spectra obtained through thermochemistry measurements of the association reaction 1 upon injecting the mass-selected acetylene radical cation (C2H2+•) into a mixture of HCN and helium gases at different temperatures. The blue circles represent the protonated HCN cluster series [H+(HCN)n] with n = 1−5. The red squares represent the C4H4N2+•(HCN)n series with n = 1−5. (b) Mass spectra obtained through thermochemistry measurements of the association reaction 2 upon injecting the mass-selected pyrimidine radical cation (C4H4N2+•) into a mixture of HCN and helium gases at different temperatures.

pyrimidine+• + HCN ⇄ pyrimidine+•(HCN)

entropy changes associated with the formation of the C4H4N2+•(HCN) (−23.3 ± 2.5 cal/(mol K)) and the pyrimidine+•(HCN) (−28.9 ± 2.5 cal/(mol K)) complexes overlap within the experimental uncertainties around a ΔS° value of −26 cal/(mol K). However, the difference between the ΔS° values for the C4H4N2+•(HCN) and pyrimidine+•(HCN) complexes could suggest the presence of different distributions of structural isomers of the pyrimidine+•(HCN) complex under the experimental conditions of the thermochemical measurements (Figure S3, Supporting Information). As shown below, several different isomers of the noncovalent pyrimidine+•(HCN) complex having essentially the same binding energy can exist under the current experimental conditions. Therefore, the thermochemical equilibrium between the pyrimidine+• and the pyrimidine+•(HCN) ions is likely to involve different structural isomers of the pyrimidine+•(HCN) complex, and the measured entropy change should represent an average contributions from these isomers. We have performed ab initio quantum chemical computations to understand the gas phase formation of the pyrimidine radical cation via ion-molecule reactions. We optimized geometries of the precursors, intermediates, transition states, and products with the B3LYP36,37 density functional theory (DFT) method together with Dunning’s correlation-consistent valence triple-ζ basis set (cc-pVTZ).38 We employed the QChem 3.2 quantum chemistry package for all DFT computations.39 We obtained accurate energy differences using coupled cluster singles and doubles with perturbative triples [CCSD(T)]40 along with the cc-pVTZ basis set. The CCSD(T) calculations were performed using the MOLPRO 200841 quantum chemistry package.41 We have also performed

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The establishment of equilibrium is verified when (i) a constant ratio of the integrated intensity of the product to the reactant ions is maintained over the residence time of the ions at constant pressure and temperature and (ii) the arrival time distributions (ATDs) of the reactant and product ions are identical, indicating equal residence times as shown in Figure S3(a) and (b) (Supporting Information). When the equilibrium conditions are well-established, the equilibrium constant, Keq, can be measured using eq 3 Keq =

I[C4 H4N2+•(HCN)] I[C4 H4N2+•]PHCN

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where I[C4H4N2+•(HCN)] and I[C4H4N2+•] are the integrated intensities of the ATDs of the product and reactant ions of reaction 1, respectively, and PHCN is the pressure of HCN (in atmosphere) inside of the drift cell. The equilibrium constant, Keq, is measured at different temperatures, and from the slope and intercept of the van’t Hoff plot, ΔH° and ΔS° are obtained, respectively, as shown in Figure S3(c) (Supporting Information). The resulting −ΔH° (kcal/mol) and −ΔS° (cal/(mol K)) for the formation of C4H4N2+•(HCN) are 12.0 ± 0.8 and 23.3 ± 2.5, and those for pyrimidine+•(HCN) are 11.2 ± 0.8 and 28.9 ± 2.0, respectively. The similarity of the binding energies corresponding to the formation of the C4H4N2+•(HCN) and the pyrimidine+•(HCN) complexes provides direct evidence that the C4H4N2+• ion formed by the sequential reactions of two HCN molecules with the acetylene radical cation at room temperature has indeed a structure similar to that of the pyrimidine radical cation. The 3394

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harmonic vibrational frequency calculations using B3LYP to confirm the nature of minima and transition states. Successive association of two HCN molecules with HCCH+• leads to the formation of C4H4N2+•, which has the same molecular formula as pyrimidine, but it can also be any of the other cyclic or acyclic isomers of pyrimidine+•. The first step of the reaction was previously investigated,26 and 16 low-energy (under 50 kcal/mol) isomers of the C3H3N+• ion have been found following a thorough search of the potential energy surface (PES). Expectedly, the association process for this ion− molecule reaction is barrierless. The direct association of HCCH+• and HCN leads to two isomers that are trans and cis forms of the HCCHNCH+• structural formula and are 16.95 and 17.03 kcal/mol above the C3H3N+• global minimum, respectively.26 The explicit structures of these two isomers are given in Figure S4 (Supporting Information). These two isomers have one H atom on each of the carbon atoms and none on the nitrogen and, therefore, have a suitable CCNC framework to serve as a starting point for the formation of the pyrimidine molecule.26 For later discussion, we label the atoms in the CCNC framework as C4C3N2C1; therefore, for example, “C1” is the terminal C atom that is bonded to the N atom. Other isomers that are lower in energy than the two (HCCHNCH+•) isomers mentioned above have a different carbon/nitrogen framework and have either more or less hydrogen atoms on each carbon. Thus, these isomers will require a significant activation energy in order to isomerize to HCCHNCH+•, as has been shown previously.42 In Figure 3, the relative energetic positions of the intermediates and the transition states on the PES that connects HCN and C3H3N+• with pyrimidine and pyrazine ions are shown. Figure S5 (Supporting Information) shows the optimized geometries of the reactants, intermediates, transition states, and products. The energy difference between the pyrimidine ion and the separated HCN and HCCHNCH+• species is 77.5 kcal/mol. An approaching HCN molecule can attach with C3H3N+• in a number of places depending on the spatial orientation of its approach. The nitrogen atom of HCN can attach with the C1 carbon of HCCHNCH+•, leading to a molecule (intermediate A, Figure 3) with a formula of CHCHNCHNCH+• that is 71.7 kcal/mol above the pyrimidine ion. This isomer then goes through a transition state a (Figure 3), which is 72.8 kcal/mol above the pyrimidine ion, to cyclize into the pyrimidine cation. The transition state a is thus only 1.1 kcal/mol above the intermediate A. This is route A in Figure 3 (and Figure S5, Supporting Information). Second, the carbon atom from the HCN molecule can attach to the C4 carbon of HCCHNCH+• and make a CC bond to form an isomer with the structural formula NCHCHCHNCH +• (intermediate B), which is 38.9 kcal/mol above the pyrimidine ion. This isomer can also lead to a pyrimidine ion upon cyclization through transition state b (Figure 3), which is only 1.4 kcal/mol above intermediate B. This is route B (Figure S5, Supporting Information). Intermediate B is more stable relative to intermediate A. The nitrogen atom of the HCN molecule can attack the C4 carbon atom of HCCHNCH+• and produce a stable minimum HCNCHCHNCH+• (intermediate C), which is 41.7 kcal/mol above the pyrazine ion and 46.5 kcal/mol above the pyrimidine ion. Intermediate C cyclizes to form a pyrazine ion through transition state c (Figure 3), which is 7.5 kcal/mol above C. This is route C. A fourth possibility exists in which the carbon atom on the HCN molecule attaches to the C1 carbon on the HCCHNCH+• molecule. We found that the

Figure 3. Reaction of HCCHNCH+• and HCN is shown; energy (kcal/mol) is at the CCSD(T)/cc-pVTZ level of theory. (b) Association complexes between HCN and the pyrimidine ion; distances are in Å at the UMP2/cc-pVTZ level of theory. The HCCH+ + HCN reaction is reported in ref 26.

intermediate, HCCHNCHCHN+•, formed via this route automatically undergoes either a hydrogen rearrangement or cyclization to a pyrazine ion and, therefore, does not represent a minimum on the PES. Thus, only one of the two possible routes starting from the HCCHNCH+• ion leads to the pyrazine ion via an intermediate, but the pyrazine ion can also form via the secondary route (the fourth possible reaction) directly. In Table S1 (Supporting Information), the absolute and relative energies of the intermediates and transition states using B3LYP and CCSD(T) with the cc-pVTZ basis set are presented. The pyrimidine ion is the lowest in energy. The pyrazine ion is 4.8 kcal/mol above the pyrimidine ion at the CCSD(T) level of theory. The intermediates A, B, and C are 71.7, 38.9, and 46.5 kcal/mol above the pyrimidine ion, respectively. In Figure S6 (Supporting Information), the optimized geometric structures of the pyrimidine ion and the pyrazine ion at the B3LYP/cc-pVTZ level of theory are presented. Both molecules are planar and have C2v symmetry. The lowest-energy intermediate is B and the transition state is b in these associative processes. This pathway also has the lowest barrier to form the pyrimidine ion. All of the intermediates and transition states are energetically below the separated reactants. Furthermore, the lowest-energy pathway leads to the pyrimidine ion (Figure 3) and not its isomer pyrazine ion. It may also be noted that there are two routes that lead to the pyrimidine ion as opposed to only one that leads to its isomer pyrazine ion. The other pathway to the formation of the pyrazine ion does not form an intermediate and competes with 3395

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in which the HCN molecule is attached to the pyrimidine ion from the side and is pointing directly toward the hydrogen on the C5 carbon atom on pyrimidine. The binding energy for complex 3 is 10.4 (B3LYP) and 11.3 kcal/mol (ωB97X). For all three complexes described above, the HCN molecule forms a H-bond with its N atom acting as a hydrogen acceptor to the hydrogen atom located at the different positions on the pyrimidine ion, although there will also be a charge-dipole component to the overall binding energy. The fourth and most interesting complex is one in which the HCN molecule is attached perpendicular to the molecular plane of the pyrimidine ion (complex 4). The binding energy for this complex is 10.2 and 12.5 kcal/mol at the B3LYP/cc-pVTZ and ωB97X/ccpVTZ levels of theory, respectively. It is clear that both the B3LYP and ωB97X functionals give similar binding energies for the four pyrimidine+•(HCN) complexes using the cc-pVTZ basis set. These binding energies are also similar to the recently published33 M06-2X45/6-311++G(d,p) structural calculations of the pyrimidine+•(HCN)n clusters with n = 1−4 that show that the binding energies of complexes 2 and 4 are 11.2 and 12.7 kcal/mol, respectively, at this level of theory.33 To improve the accuracy of the calculations for the pyrimidine+•(HCN) complexes, we computed binding energies using the CCSD(T)-F12/aug-cc-pVTZ method (using geometries optimized at the UMP2/cc-pVTZ level). At this level of theory, the calculated binding energies (ZPVE-corrected) for complexes 1−4 are 13.1, 12.9, 12.8, and 13.4 kcal/mol, respectively. Again, the binding energies of all four isomers are similar to each other and are in good agreement with the experimental −ΔH° value (12.0 ± 0.8 kcal/mol) for the formation of the C4H4N2+•(HCN) complex. Therefore, on the basis of the different levels of computations that we used, it can be concluded that the binding energies of all four isomers of the pyrimidine+•(HCN) complex are similar to each other, and moreover, they are quite similar to the energies determined by the experimental van’t Hoff plots (Figure S3(c), Supporting Information) for both the C4H4N2+•(HCN) complex formed by the sequential reactions of two HCN molecules with the acetylene radical cation at room temperature (12.0 ± 0.8 kcal/ mol) and the actual pyrimidine+•(HCN) complex (11.2 ± 0.8 kcal/mol). Experiments are currently underway in our laboratory to investigate the reactions of the pyrazine ion with HCN and to measure the binding energy of the noncovalent pyrazine+•(HCN) complex for comparison with the pyrimidine+•(HCN) complex. These experiments could provide additional information regarding the possible formation of the pyrazine ion from the sequential reactions of HCN with the acetylene radical cation. In conclusion, from the joint experimental and theoretical work undertaken in this study, we find that under the gas phase ionizing conditions in space, a mixture of acetylene and HCN reacts to synthesize pyrimidine molecules via ion−molecule reactions. By matching the binding energies of HCN with the pyrimidine ion obtained by theoretical and experimental methods, we identify the covalently bonded C4H4N2+• mass fragment to be the pyrimidine ion. Although neutral pyrimidine has not been conclusively identified in the ISM, pyrimidine ion formation cannot be ruled out solely based on the nondetection of the neutral. This ion−molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil.

a hydrogen-transfer pathway leading to a different (noncyclic) product [CH2CHNCHCN]+. Route C, which leads to a pyrazine ion, has a larger transition energy barrier (relative to B). Therefore, pyrimidine ion formation via route B should be the preferred pathway from an energy consideration perspective. However, in C3H3N+ (HCCHNCH+), the C1 atom carries a net positive charge. Therefore, a nucleophilic attack by the nitrogen lone pair of HCN on the C1 carbon of C3H3N+ leading to intermediate A (and eventually pyrimidine) may cause the reaction to proceed via route A. Thus, it is likely that both pyrimidine and pyrazine will form, but from thermodynamic considerations and considerations of the long-range character of the PES, pyrimidine would seem to be favored. Pyrimidine and pyrazine ions formed are internally “hot” due to the excess energy from multiple bond formation. In the experimental drift cell, this excess energy can be dissipated by third-body collisions with a helium carrier gas. In the ISM however, such collisions are rarer. However, energy dissipation may occur via radiative processes, such as rotational and vibrational relaxation, or by expulsion of a hot hydrogen atom or proton from the product. Additionally, one needs to remember that the time scale for formation of molecules is much longer in the ISM. It is important to note that the cyclic aromatic framework is stable and robust and thus can be longlived in the ISM.43 The experimental results indicate that the binding energies of HCN with C4H4N2+• and with the pyrimidine ion are quite similar to each other. We performed several ab initio quantum chemistry computations to characterize the nature of association products and binding energies of HCN molecule with a pyrimidine ion. We found four (pyrimidine)+•HCN complexes, as shown in Figure 4.

Figure 4. Association complexes between HCN and the pyrimidine ion; distances between the nearest atoms are given in Å.

The first pyrimidine+•(HCN) complex (complex 1) is one in which the HCN molecule is in the same plane as the pyrimidine ion and is pointing toward the hydrogen atom on the C4 carbon on pyrimidine. The binding energy (the difference between the energy of the complex and the energy of isolated pyrimidine ion and HCN molecule) of this complex is 11.5 and 12.5 kcal/mol at the B3LYP/cc-pVTZ and ωB97X44 /cc-pVTZ levels of theory, respectively. Complex 2 is one in which the HCN molecule is again in the same plane as the pyrimidine ion and pointing directly toward the hydrogen atom at the C2 carbon atom. The binding energy of this complex is 11.2 (B3LYP) and 12.3 kcal/mol (ωB97X). Complex 3 is one 3396

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ASSOCIATED CONTENT

S Supporting Information *

The experimental setup of the MSIM system (Figure S1), effect of third-body collisions on the addition channel (Figure S2), arrival time distributions and van’t Hoff plots (Figure S3), optimized geometries, and relative and total energies of the reactants, intermediates, transition states, and products (Figures S4 and S5 and Table S1) are reported. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected] (M.S.E.). *E-mail: [email protected] (P.P.B.). *E-mail: [email protected] (T.J.L.). Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by the National Science Foundation (CHE-0911146). P.P.B. and T.J.L. gratefully acknowledge the support from the NASA Laboratory Astrophysics Carbon in the Galaxy consortium grant (NNH10ZDA001N).

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REFERENCES

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