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2015 Annual Science Report

NASA Ames Research Center Reporting  |  JAN 2015 – DEC 2015

Computational Quantum Chemistry

Project Summary

We investigated the formation and functionalization of nitrogen substituted cyclic aromatic molecules such as the precursors of biomolecules, polycyclic aromatic hydrocarbons, and the feasibility of their detection via spectroscopic techniques.

4 Institutions
3 Teams
6 Publications
0 Field Sites
Field Sites

Project Progress

In the first reporting period of this project we have started investigations into the formation of nitrogenated polycyclic aromatic hydrocarbons (PANHs) and the precursors of biomolecules such as purine and pyrimidine, and their functionalization leading to nucleobases in the gas and condensed phases by accurate quantum chemistry methods. In a joint crossed molecular beam experiment and using computational quantum chemistry calculations we showed that PANHs can be synthesized in the cold dark molecular clouds. Dihydroisoquinoline – a nitrogen substituted polycyclic aromatic hydrocarbon – has been synthesized in the laboratory by exploiting a single collision condition between reaction partners pyridyl radical and 1,3-butadiene by our collaborators. By doing high accuracy coupled cluster singles and doubles including perturbative triples (and further including F12 corrections), along with large basis sets we showed that the reaction proceeds via a van der Waal’s complex that circumnavigates the entrance barrier (Figure 1), which indicates that it is plausible at the very low temperatures (10K) found in cold molecular clouds such as TMC-1. These results bode well for further investigations into the origin and identification of nitrogenated PAHs and related biomolecules, many of which are nitrogenated cyclic molecules, in interstellar molecular clouds.

Figure 1. Potential energy diagram for the reaction of ortho-pyridyl plus 1,3-butadiene. Energies for intermediates, transition states, and products are given relative to the reactants (in kJ mol-1) at the CCSD(T)-F12/6-311+G(2d,2p)+ZPVE at ωB97X/6-311+G* optimized geometries for sigma complex and associated TS, and CCSD(T)/6-311+G(2d,2p)+ZPVE at B3LYP/6-311+G* optimized geometries for the rest. The PES shows that the reaction is de-facto barrierless in the entrance channel, and that the dihydro(iso)quinoline is the exclusive product of the reaction between pyridyl radical and 1,3-butadiene.

Further work revolved around the investigations of formation of nucleobases thymine (Figure 2), uracil, and cytosine in mixed irradiated astrophysical ices containing pyrimidine. We found by quantum chemistry computation that all three can form in mixed molecular astrophysical ices. However, thymine can be produced by reactions between pyrimidine and hydroxyl and methyl radicals only with very limited efficiency, and only in the presence of a water matrix. The results indicate a limited role for thymine in prebiotic chemistry. Work is currently in progress to estimate the efficiency of similar chemistry producing the purine-based nucleobases, e.g. adenine and guanine.

Figure 2. Diagram illustrating the three pathways from pyrimidine 1 to thymine 6. Route 1 is two oxidations followed by a methylation, Route 2 is a methylation followed by two oxidation, and the Route 3 is oxidation, methylation, and oxidation.

Significant progress was made on the calculation of the spectroscopic properties of small as well as medium sized molecules. A framework for calculating the anharmonic vibrational spectra and rovibrational spectroscopic constants of polycyclic aromatic hydrocarbons (PAHs) was developed, and tested in collaboration with astronomers and experimentalists from the Dutch Astrochemistry Network (DAN). The initial study focused on the “linear” PAH molecules naphthalene, anthracene, and tetracene. As an example of how the calculations compare to experiment for tetracene, see Figure 3. Additionally, the possible importance of charged molecular clusters in certain astrophysical environments was investigated with two studies on the OCHCO+ and NNHNN+ molecular cations. State of the art electronic structure methods were employed to investigate their potential energy surfaces and to predict their rovibrational spectroscopic constants and spectra.

Figure 3. Full IR spectrum of tetracene calculated using two methods, harmonic (top) and anharmonic (middle), compared with Ar matrix isolation spectrum at T ≈ 10 K (bottom). A selected region is shown with the relative intensities increased by a factor of four. The greyed out lines in the matrix-isolation spectrum are water contamination.

The excited electronic states and electronic spectra of PANH and PAH anions, which may be important in the photo-irradiated regions of the interstellar medium, were investigated. These studies complement our earlier studies of the electronic spectra of PAH and PANH neutral and cationic systems. Anions are relatively rare in most astrophysical environments, but given the size of PAH and PANH molecules, it is known that anions will be more stable and in many cases even support stable excited electronic states. Our studies confirmed these expectations, especially for the PANH molecules.