Mechanisms of the Formation of Adenine,Guanine, and Their Analogues in UV-Irradiated

Mixed NH3:H2O Molecular Ices Containing Purine

Partha P. Bera,1,2,* Tamar Stein,3,4,* Martin Head-Gordon,3,4 and Timothy J. Lee1

Abstract

We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase ana-logues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H2O:NH3 iceseeded with precursor purine by using ab initio and density functional theory computations. Our quantumchemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl andamino radicals, together with water and ammonia, explains the experimentally obtained products in an inde-pendent study. The relative abundances of these products appear to largely follow from relative thermodynamicstabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pureammonia ice, where cations are promptly neutralized by free electrons from NH3 ionization. Amine groupaddition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is muchmore abundant due to higher abundance of H2O. The amino group is preferentially attached to the 6 position,giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position,leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2position depending on the first substitution. Given that H2O is far more abundant than NH3 in the experi-mentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to bethe most abundant bi-substituted photoproducts. Key Words: Astrophysical ice—Abiotic organic synthesis—Nucleic acids—Origin of life—RNA world. Astrobiology 17, 771–785.

1. Introduction

Anumber of pathways for the formation of life onEarth have been suggested (Lazcano and Miller, 1996;

Orgel, 2004; Miller and Cleaves, 2006). They involve pre-biotic chemical transformations, eventually leading to com-plex biomolecules that are capable of self-replicating andundergoing evolution. Theories about an extraterrestrial de-livery of biogenic molecules to early Earth have been putforward (Chyba et al., 1990). If such extraterrestrial deliveryis responsible for the formation of the first biomolecules andlife on Earth, then insight into such processes can be obtainedby studying the molecular composition and evolution on thesurfaces of meteorites and comets similar to those that fre-quently fall on Earth. A number of well-studied meteorites,such as Murchison, are known to harbor molecules that are ofbiological importance (Kvenvolden et al., 1970; Mullie and

Reisse, 1987; Cooper et al., 2001). Among these moleculesare amino acids, sugars, and nucleic acids that are an inte-gral part of DNA and RNA as well as proteins. Our focus inthis paper is solely on the possible formation pathways forthe purine-based nucleobases adenine and guanine, and theiranalogues.

Nucleic acids can be made of the two types of nitro-genated cyclic aromatic hydrocarbons or N-heterocycles:purine and pyrimidine. Nitrogenated heterocycles have longbeen searched for within the gaseous interstellar media, indense and diffuse clouds, but their presence has never beenconfirmed (Simon and Simon, 1973; Kuan et al., 2004).Pyrimidine (C4H4N2), a nitrogenated monocyclic molecule,has not been observed in the interstellar media in the gasphase either, despite an extensive search (Charnley et al.,2005). Yet the formation of pyrimidine cation via ion-molecule reactions has been shown to occur in the gas phase

1NASA Ames Research Center, Moffett Field, Mountain View, California.2Bay Area Environmental Research Institute, Petaluma, California.3University of California, Berkeley, California.4Lawrence Berkeley National Laboratory, Berkeley, California.*These authors contributed equally to this research.

ASTROBIOLOGYVolume 17, Number 8, 2017ª Mary Ann Liebert, Inc.DOI: 10.1089/ast.2016.1614

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(Hamid et al., 2014). Formation of purine, a pentamer ofHCN, by the combination of five hydrogen cyanide mole-cules has been predicted to be very exothermic and istherefore unlikely to happen in isolation (Roy et al., 2007).

Nitrogenated cyclic molecules have been, however,identified in meteorites (Folsome et al., 1971; Stoks andSchwartz, 1979; Callahan et al., 2011). The nucleobasesadenine, guanine, cytosine, and uracil were extracted fromthe well-known Murchison and Murray carbonaceous chon-drites (Stoks and Schwartz, 1979) and have been proved tobe of extraterrestrial origin (Hayatsu, 1964; Hayatsu et al.,1975; Shapiro, 1999; Nelson et al., 2001; Martins et al.,2008). Together with nucleic acids, amino acids (Kvenvol-den et al., 1970), and other organic compounds of biologicalinterest, have been found in the meteoritic samples (Croninand Pizzarello, 1997; Dworkin et al., 2001). Whether theyare synthesized in the gas phase and delivered to the surfaceof the grains or were synthesized on the cold grain surfacesdue to photoprocessing is not known. It has been shown,however, that once delivered on the surfaces of grains, thesebiomolecule precursors can be further photoprocessed intolarger, more complex molecules. A plausible pathway fortheir formation is via the photoprocessing by cosmic radi-ation of the ices accumulated on the surfaces of grains.These ices are known to contain volatile organic moleculessuch as H2O, CH3OH, CO, CO2, NH3, CH4 (Gibb et al.,2004; Dartois, 2005), as well as larger molecules such asPAHs and nitrogenated heterocycles (Sandford et al., 2004).

Materese et al. (2017) studied the photoprocessing ofpurine in astrophysical ices in the laboratory. In their ex-periments, they deposited a mixture of H2O, NH3, and pu-rine (relative abundances of approximately 1:0.1:10-3) on asubstrate cooled to *15 K. At the same time, the growingice was irradiated with UV light (Lyman a at 121.6 nm, i.e.,10.2 eV, and a broadband continuum centered at 160 nm)in order to simulate astrophysical photoprocessing. After1–2 days of irradiation, samples were analyzed usinggas-chromatographic (GC-MS) techniques. In a companionpaper, Materese et al. (2017) presented their experi-mental findings. These authors found that 2-aminopurine,6-aminopurine (adenine), 2,6-diaminopurine, hypoxanthine,xanthine, isoguanine, and guanine are formed in identifi-able quantities. Previously, it was found that irradiation ofpyrimidine in analogously prepared ices produced uracil,cytosine, and thymine (though only small quantities of thelatter after elevated doses of radiation), and their formationmechanisms were studied (Nuevo et al., 2009, 2012, 2014;Bera et al., 2010; Sandford et al., 2015).

In the present study, we used electronic structure calcu-lations to explore the pathways by which doped purine couldbe aminated and hydroxylated in the irradiated NH3:H2Oexperimental ices. We investigated the physical processesthat may occur under the experimental conditions, theintermediates that may be generated, and the possible re-actions that they may undergo. The results constitute reac-tion pathways leading from irradiated reactants to a rangeof products, independent of experimental input. We thencompared the computational results with those obtainedfrom the experiments. With the experiments characteriz-ing many (though not all) key products of photoprocessingof purine in astrophysical ices, our computational resultsmay help unravel the preferred reaction pathways and the

preference for some products over others. We consider theroles played by the physical conditions such as UV irradi-ation and condensed phase environment in this transforma-tion in order to gain insight into the nature of thephotochemical transformations that occur on cold grainsurfaces or small Solar System objects such as asteroids andcomets.

2. Methods

Structures and relative energies of the reactants, inter-mediates, and products were calculated using density func-tional theory, the most widely used class of electronic structuremethods. Specifically, geometry optimizations were carriedout by using the B3LYP functional (Lee et al., 1988; Becke,1993) with the cc-pVDZ basis set. Higher-accuracy relativeenergies of the structures were calculated with oB97M-V, arange-separated hybrid meta-GGA functional (Mardirossianand Head-Gordon, 2016) with the cc-pVQZ basis set. oB97M-V has been established as very accurate for noncovalent in-teractions, as well as thermochemistry, barrier heights, andmore across the main group elements. Moreover, as a range-separated functional, it reduces the self-interaction error (Chaiand Head-Gordon, 2009; Kronik et al., 2012) and thus issuitable for the description of radical cations.

To model the effect of the extended ice environment, weused the conductor-like solvent model C-PCM (Barone andCossi, 1998) from the class of polarizable continuum model(PCM) (Tomasi et al., 2005). Specifically, we employed animplementation (Lange and Herbert, 2010a, 2010b) thatensures continuous potential energy surfaces, as a functionof molecular geometry changes. In this model, the bulk isrepresented as a polarizable medium characterized by itsdielectric constant e. It is expected that the solvent dielectricwill better represent the condensed phase and enable us tostudy the effect of the solvent. In the PCM calculations, thegeometries were first re-optimized with the solvent model,again by using B3LYP/cc-pVDZ. Single-point PCM ener-gies were then calculated at the oB97M-V/cc-PVQZ levelof theory. We used e = 78.39 for the dielectric constant ofwater for all calculations (Weast, 1989).

All calculations were done using the Q-Chem 4 quantumchemistry program package (Shao et al., 2015).

3. Results

Under the direct influence of UV irradiation, organicmolecules undergo a number of physical and chemicalchanges. Ultraviolet irradiation of purine will generally leadto electronic excitation into excited states, simultaneousexcitation of vibrational and rotational modes, and ioniza-tion to create cations and free electrons. The excess energyin excited states and/or ions will potentially lead to isomeri-zation and photofragmentation. Irradiation of the ices mayalso produce various reactive species—ions and radicals—such as OH and NH2 in H2O and NH3 ices, respectively, orboth in a mixed molecular ice. It can also produce elec-tronically excited solvent molecules that either dissociate intofragments or release energy collisionally and radiatively.

H2O possesses a large photodissociation cross section inthe UV-wavelength range (Engel et al., 1992) of the H2 UVsource employed experimentally (Materese et al., 2017).NH3 possesses a non-negligible dissociation cross section

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and dissociates into NH2 and H around 181 nm (Suto andLee, 1983; Nakajima et al., 1991). Furthermore, hydroxylradicals can abstract hydrogen from NH3 and produce NH2

radicals (Stuhl, 1973; Monge-Palacios et al., 2013). Insummary, hydroxyl (OH) and amino (NH2) radicals arepotentially produced in the ices by the following processes:

H2Oþ hm! Hcþ cOH (1)

NH3þ hm! Hcþ cNH2 (2)

H2Oþ hm! H2Ocþþ e� (3)

NH3þ hm! NH3cþþ e� (4)

NH3þ cOH! cNH2þH2O (5)

Of the above-mentioned photoprocesses, all channels but (3)seem open under Lyman a irradiation. Radicals and ions canalso be generated from purine itself via the following pro-cesses:

Puþ hm! Pu½ �þcþ e� (6)

Puþ hm! Pu=H

� �cþHc (7)

where [Pu/H]� designates a radical formed by the cleavage ofa C–H bond on the purine ring.

The main question of interest is identifying the secondarypathways by which hydroxyl and amino substituted purinederivatives are formed from the parent neutral moleculesand the radicals and ions that are formed in the primaryphotoinduced processes discussed above. Furthermore,ionization energy of NH3 is 10.02 eV, which is low enoughfor Lyman a (121.6 eV, *10.2 eV) to ionize it to NH3

+. ButStuhl (1973) and Monge-Palacios et al. (2013) showed thathydroxyl radical abstracts hydrogen atoms from NH3 toproduce NH2 easily (reaction 5 in the manuscript). As H2Ois 10 times more abundant than NH3 in the experimentalconditions, hydroxyl radicals would be produced in largequantities, which would produce NH2 radicals. The processwould augment the primary NH2 formation process via di-rect dissociation. Therefore, we believe that NH2 would bethe most dominant nitrogenous attacking group, althoughthe possibilities of reactions with NH3

+ cannot be ruled out.In Fig. 1, we present a summary of the stepwise substitutionof NH2 and OH groups on the purine ring. Here, we enu-merate some of the main possible reaction channels. First,neutral purine can react with neutral H2O or NH3, or withthe corresponding OH and NH2 radicals. Second, purinecations can likewise react with H2O or NH3, or the OH orNH2 radicals. Third, purine radicals (that have lost a Hatom) can recombine with either OH or NH2 radicals. Otherchannels are also possible.

PuþH2O! Pu=H-OH� �

þH2 (8)

PuþNH3 ! Pu=H-NH2

� �þH2 (9)

Puþ cOH! Pu=H-OH� �

þHc (10)

Puþ cNH2 ! Pu=H-NH2

� �þHc (11)

PucþþH2O! Pu=H-OH� �

þH2þ (12)

PucþþNH3 ! Pu=H-NH2

� �þH2

þ (13)

Pucþþ cOH! Pu=H-OH� �

þHþ (14)

Pucþþ cNH2 ! Pu=H-NH2

� �þHþ (15)

Pu=Hcþ cOH! Pu=H-OH� �

(16)

Pu=Hcþ cNH2 ! Pu=H-NH2

� �(17)

Neutral–neutral reactions (8 and 9) between H2O (or NH3)and purine are expected to be several orders of magnitudeslower than reactions involving radicals or cations, because oftheir high activation barriers, particularly in cold ice matrices.Thus, it is reasonable to assume that the chemistry in theseices is going to be dominated by the reactions of OH and NH2

radicals with ionized, radical or neutral purine, and itsderivatives.

We studied the neutral purine and hydroxyl radical (andamine radical) pathways (10 and 11) and found that theaddition of the hydroxyl (or the amino) radical to purine,leading to radical intermediates, is endothermic due to theloss of aromaticity. This result, in our view, makes channels10 and 11 unlikely relative to some of the other possibilitiesdiscussed below. The overall reactions, after H atom loss toyield neutral substituted products, are exothermic.

Purine cations are likely to be formed in the irradiatedmixed molecular ices (primary channel 6) as the UV lamppossesses enough energy to ionize purine. Purine cation canundergo an addition reaction with nucleophilic H2O or NH3

(secondary channels 12 and 13). This reaction is exothermicin the entrance channel, as well as barrierless, so this initialstep is likely to proceed. Consider reaction with the watermolecule as an example:

PucþþH2O! Pu-OH2½ �cþ (18)

Furthermore, this reaction is likely under a relatively lowradiation flux because it requires only one primary photo-product to proceed. Completion of the reaction involveselimination of a proton and an H atom (or conceivably H2

+�)to make the final hydroxylated or aminated products fromthe initial intermediates. Therefore, channels 12 and 13 in-volve multiple steps as seen in Fig. 2. One of these steps, theloss of the H atom from the intermediates, is associated witha large reaction barrier and therefore will be unlikely tooccur directly. This barrier would be lowered and possiblyentirely removed if the H atom is later abstracted by anotherradical, R (H or OH or NH2):

Pu-OH2½ �cþþRc! Pu-OH½ �þþRH (19)

Finally, proton abstraction would yield the final product ina third reaction:

Pu-OH½ �þþH2O! Pu=H-OH� �

þH3Oþ (20)

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Pathway A on Fig. 2 is a nucleophilic substitution path-way that proceeds via secondary reactions 14 and 15 be-tween purine radical cation and OH radical (or NH2 radical).The ionization of an electron from purine’s p-electron sys-tem leaves a hole in the aromatic system. The charge islikely to be primarily on the less electronegative carbonatoms. A radical NH2 or OH group can then attack one ofthe two carbon atoms (C2 or C6) on the six-membered ar-omatic ring, or the C8 carbon atom on the five-membered ring.Addition to the nitrogen atoms on the ring is also theoreticallypossible. This channel is most likely to proceed in high radi-ation conditions as it requires simultaneous presence of tworeactive intermediates derived from the primary photochemical

pathways. It has been shown that a reaction between a poly-cyclic aromatic hydrocarbon and hydroxyl is exothermic andbarrierless in the entrance channel (Ricca and Bauschlicher,2000).

Figure 2, pathway B shows the intermediates associatedwith reactions 18–20. The radical cation complex, 18, afterH2O addition (Fig. 2B) loses a hydrogen atom and a protonin stepwise fashion (concerted H2

+ loss is unlikely) to yieldhydroxypurine. This may happen by H abstraction (19),followed by H+ loss (20); it can also occur in the reverseorder. Note that there are two places from which H (or H+)can be abstracted—either from CH at the sp3 site or fromH2O as seen from Fig. 2. Our calculations suggest that H is

FIG. 1. A reaction scheme indicating the amino and hydroxyl group substitutions on the purine ring. Horizontal arrowsindicate hydroxyl group substitutions, while the vertical arrows indicate amino group substitutions. Quantum chemicalcalculations indicate that 2-hydroxypurine and adenine are the most favorable singly substituted photoproduct, and xan-thine, isoguanine, guanine, and 2,6-diaminopurine are the most favorable doubly substituted photoproducts.

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abstracted first with the help of an OH radical to form aclosed-shell cationic intermediate. This intermediate thenundergoes proton loss with the help of the surrounding H2Omolecules, similar to pathway A.

Previously, while studying similar mechanisms in-volving the pyrimidine (C4H2N2) molecules, we found theionic pathway to be the most important and efficient one(Bera et al., 2010; Sandford et al., 2015). Nucleobases areknown to undergo a number of bond-breaking and structuraltransformations due to ionizing radiation (Bera and Schae-fer, 2005; Lind et al., 2006). Henceforth, in this paper wewill be discussing the results involving the cationic path-ways (coming from 14 and 15 directly, or from 12 and 13indirectly). We further discuss the likelihood of the ionicmechanism in mixed molecular ices over other types ofmechanisms in Section 4.

Dehydrogenated purine radicals (Pu/H) generated by CHor NH bond breaking in purine can undergo reaction withOH or NH2 radicals to make hydroxylated or aminatedproducts (16 and 17). We found that these types of reactionscan directly produce the products and are exothermic.However, because they require the simultaneous presence oftwo reactive species produced from the primary radiativeprocesses, they will only be important when the concen-tration of such species becomes similar to the parent species.Of course, H atoms generated from H2O and NH3 can reactwith Pu/H to regenerate neutral purine under high radiationexposure. Those H atoms can also react with purine neutralto produce hydrogenated purine.

OH radical could further oxidize products of oxidation ofpurine and lead to the formation of doubly oxidized prod-ucts. This could occur following ionization of the mono-hydroxy product (as in channel 21), or without (channel 22):

Pu=H�OH� �þ

cþ cOH! Pu=H=H �OHð Þ2� �

þHþ (21)

Pu=H�OHþ cOH! Pu=H �OHð Þ2� �

c

! Pu=H=H �OHð Þ2� �

þHc(22)

The above ion-radical and radical-molecule reactions aregenerally fast and typically barrierless in the entrancechannel. It was shown earlier that the proton loss from theprotonated intermediates in aqueous media is spontaneous(Bera et al., 2016).

We explored these mechanisms to discern whetherthe reactions between these reactants leading to the func-tionalized products are favorable and whether the formationof adenine and guanine is favored over other plausibleproducts. We also explored the catalytic activity of the H2O,NH3, and mixed molecular ices. These quantum chemicaldata were used to interpret the laboratory experimental results.

In Fig. 1, we present a summary of the stepwise substi-tution of NH2 and OH groups on the purine ring leading toimportant singly and doubly substituted products. The hor-izontal arrows refer to the hydroxyl (OH) group substitution,and the vertical arrows refer to the amino (NH2) groupsubstitution on the ring. After the first OH substitution onthe six-membered ring, oxidized purines such as hypoxan-thine (6-hydroxypurine) and 2-hydroxypurine (also knownas purinol) are produced. An additional hydroxyl substitu-tion at the C2 position would lead to xanthine (2,6,-dihydroxypurine). Both hypoxanthine and xanthine havebeen detected in the experimental samples produced fromthe UV irradiation of H2O:purine and H2O:NH3:purinemixed molecular ices (Materese et al., 2017). An NH2

group substitution to hypoxanthine leads to the formation

FIG. 2. Mechanisms of OH (A) and H2O (B) addition to purine radical cation. In A, the first step is the addition ofhydroxyl with purine cation followed by the loss of a proton assisted by H2O molecule(s). In B, the first step is the additionof H2O with purine radical cation followed by the loss of a hydrogen atom and proton in a stepwise manner.

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of guanine, while an NH2 group substitution to 2-hydroxypurine leads to the formation of isoguanine. AnNH2 group substitution either to the 2 or the 6 positionfirst on the purine ring gives 2-aminopurine or adenine (6-aminopurine), respectively. A second NH2 group additionon adenine on the six-membered purine ring leads to theformation of 2,6-diaminopurine. A hydroxyl group additionto adenine gives isoguanine, and hydroxyl group addition to2-aminopurine produces guanine. 2,6-Diaminopurine, gua-nine, and isoguanine were all detected in the experimentalsamples after irradiation of purine in mixed molecular ices(Materese et al., 2017). In the following sections, we ex-plore these reactions stepwise via the reaction mechanismsdescribed above.

3.1. Step 1: First substitution

3.1.1. Amine group substitution to purine. An NH2

group can attach barrierlessly with the carbon framework ofthe purine cation to form three intermediates (see Fig. 3).

The 2(2H)-aminopurine and 6(6H)-aminopurine cations(labeled 3b and 3a in Fig. 3) are 57.8 and 54.0 kcal/molbelow the reactants, respectively. The 8(8H)-aminopurinecation (labeled 3c in Fig. 3) is the lowest-energy interme-diate, 68.2 kcal/mol below the reactants, namely a bare pu-rine cation, H2O, and an NH2 radical. In other words, the8(8H)-aminopurine molecule has a larger proton affinitybecause it preserves the aromaticity of the six-memberedring compared to the proton affinities of the 2- and the6-aminopurine when the proton attaches with the carbonframework. A proton will be lost to produce 2-, 6-, and the8-aminopurine. Such a purely gas phase loss of the proton isenergetically unfavorable, as the energies of the products arehigher than the isolated reactants devoid of H2O. When aH2O molecule was explicitly included, and the proton wasallowed to be abstracted by an H2O molecule, the combinedenergy of the products and a H3O+ falls below that of thereactants and the intermediates, as seen in Fig. 3. This sit-uation is similar to pyrimidine oxidation, where we foundthat the reaction requires the presence of multiple H2O

FIG. 3. A reaction diagram for the cationic mechanism of amino group substitution to purine starting from purine cation,NH2 and H2O as reactants on the left, arbitrarily set to zero kcal/mol. The structures in the square brackets are those of theintermediates and, on the right, are those of the products. The black numbers were calculated using oB97M-V/aug-cc-pVQZ in the gas phase, and the red numbers were calculated assuming a condensed phase environment, using a PCM.

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molecules that can take the proton away from the chargedintermediates (Bera et al., 2010). Adenine, 6-aminopurine,is the lowest-energy product at about 73.1 kcal/mol belowthe reactants. 2-Aminopurine is slightly above adenine,followed by 8-aminopurine, which is an even higher-energystructure. Adenine is the most likely amine product after thefirst amino group addition to purine and is only synthesizedin the presence of a mixed H2O-NH3 ice.

Allowing this reaction step to take place in a condensedphase environment reveals interesting insights about thisprocess. The reactants, purine cation, the hydroxyl radical,and one molecule of H2O were treated using a modifiedpolarized continuum model with a dielectric to model thebulk water. The charged closed shell intermediates andthe neutral products plus the hydronium ions were treatedthe same way, and their energies are given in Fig. 3. The rednumbers were calculated for the reactants, intermediates,and products in the presence of the solvent. The presence ofthe solvent lowers the energies of the reactants, intermedi-ates, and products but not by equal amounts. The combinedenergy of the reactants (purine cation, H2O and NH2 radical)was chosen as the zero in Fig. 3. The three cationic inter-mediates 2-, 6-, and 8-aminopurine cations are 54.0, 50.7,and 62.8 kcal/mol below the reactants, respectively. Theyare relatively less stabilized with respect to the reactants inthe solvent than in the gas phase. This means that the re-actants are slightly more stabilized by the solvent than theintermediates. The final products 2-, 6-, and 8-aminopurinesare 97.3, 99.7, and 95.9 kcal/mol below the reactants, re-spectively, which shows that the products are much moresolvent-stabilized compared to the intermediates. The rela-tive energy lowering of the products due to solvation isapproximately 30 kcal/mol. Gas phase calculations revealthat in this case only one H2O molecule is necessary tomake this reaction favorable. The solvent phase calculationsfurther establish the gas phase observations—that in thepresence of H2O, the forward reaction is feasible, as shownin Fig. 3.

Finally, we note that there are certainly other intermedi-ates that are possible, which is consistent with discussiongiven earlier on alternative mechanistic paths. Ammonia canform a complex with purine cation directly at the C2, C6, orC8 positions. Another radical (e.g., OH) can abstract H fromeither the sp3 CH bond or from NH3. The latter processyields intermediates 3a, 3b, and 3c, but the former processwill produce lower-energy intermediates due to the basicityof amines. These protonated aminopurines may also be ac-cessible by proton migration from 3a, 3b, and 3c.

3.1.2. Hydroxyl group addition to purine. In aH2O:NH3:purine mixed molecular ice, of course, the hy-droxylation process is in competition with the amination inthe first step. The H2O:NH3 ratio is approximately 10:1 inthe experiments that have been recently carried out (Ma-terese et al., 2017); hence, the OH radicals generated fromH2O will have a higher probability to oxidize purine first.We examined the energies of the hydroxylation process byfollowing a cationic mechanism. OH attack on the purinecation can occur at three different carbon atoms and produce2(2H)-, 6(6H)-, and 8(8H)-hydroxypurine ion intermediates,as seen in Fig. 4 (labeled as 4b, 4a, and 4c, respectively).These intermediates lose a proton to form the products.

8-Hydroxypurine cation is the lowest-energy intermediate,69.3 kcal/mol below the reactants, followed by the 2-hydroxypurine cation and the 6-hydroxypurine cation, 60.9and 53.9 kcal/mol below the reactants, respectively. Al-lowing an H2O molecule to explicitly abstract the pro-ton from the intermediates creates hydronium ion (H3O+)and three products: 2-hydroxypurine, 6-hydroxypurine, and8-hydroxypurine, 77.2, 76.2, and 74.4 kcal/mol below thecombined energy of the reactants, respectively (Fig. 4). The2-hydroxypurine is the most favorable isomer if one followsa pure gas phase mechanism among the three mono-hydroxylated products examined in Fig. 4.

An interesting difference from the hydroxylation of py-rimidine molecule is that it is relatively easier to deprotonatethe hydroxypurine cationic intermediates. In the case ofpyrimidine hydroxylation (Bera et al., 2010), multiple H2Omolecules, that is, a condensed phase–like environment,were necessary for hydroxylation to proceed. In the case ofpurine, we see that only one H2O molecule is enough for thereaction to proceed. As shown below, however, the reactionstill proceeds more readily in the ice matrix rather than inthe gas phase via a purely bimolecular process.

In the condensed phase, the energies of the intermedi-ates 8(8H)-hydroxypurine, 2(2H)-hydroxypurine, and 6(6H)-hydroxypurine cations (4c, 4b, and 4a, respectively, inFig. 4) are 65.7, 59.7, and 55.2 kcal/mol below the reac-tants, respectively. The three products 2-hydroxypurine,6-hydroxypurine, and 8-hydroxypurine, along with theH3O+, are 104.1, 103.4, and 100.3 kcal/mol below the re-actants, respectively. The products are stabilized by about30 kcal/mol in the condensed phase due mainly to chargedelocalization in the water matrix. In the gas phase, thecharge is more localized on the purine cation. The con-densed phase calculations prove that the H2O matrix helpsabstract the proton from the intermediate and facilitate thereaction. The relative energy ordering of the three productsstays the same in both the gas phase and condensed phasecalculations.

In the second step below, we will examine the amine andhydroxyl group addition to the preferred products after thefirst step.

3.2. Step 2: Second substitution

Following the amine and hydroxyl group additions to thepurine ring, the process may continue, and further substi-tution of amine or hydroxyl groups may take place. In thefollowing section we address the addition of NH2 to 2- and6-hydroxypurine and OH to 2- and 6-aminopurine. Wesubsequently consider amine group addition to monoami-nopurine and hydroxyl group addition to hydroxypurine.

3.2.1. Amino group addition to 2- and 6-hydroxy-purine(s). Following mechanisms similar to those we in-vestigated in the previous steps, we investigate the reactionsof the 6-hydroxypurine and 2-hydroxypurine cations withthe NH2 radical in Fig. 5. In Fig. 5, the combined energy ofthe 6-hydroxypurine radical cation, NH2 radical, and H2O isset to be zero. All the other species’ energies are plottedwith respect to this zero energy. The 2-hydroxypurine cationis 6.3 kcal/mol below the energy of the 6-hydroxypurinecation. The energies and the structures of the intermediates

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and products that originate from the 2-hydroxypurine cationare depicted in blue in Fig. 5. The cationic intermediates,produced after nucleophilic attack of the NH2 radical on 6-hydroxypurine cation, are 46.9 and 65.8 kcal/mol below thereactants (colored black in Fig. 5). Upon proton loss to anearby water molecule, the two products, guanine and 8-amino-6-hydroxypurine, are 63.9 and 58.3 kcal/mol belowthe reactants, respectively. Guanine (along with H3O+) isbelow the reactants and the proton-attached intermediate(5a) in terms of energy; the other intermediate (5b) is belowthe deprotonated product by 7.5 kcal/mol.

Some of the intermediates associated with NH2 attack onthe 2-hydroxypurine cation include structure 5c (-66.9 kcal/mol), 5d (-44.5 kcal/mol), and a rearranged form of 5d at97.3 kcal/mol below the reactants. The unusually low energyof the latter intermediate, which is isoguanine protonated atthe amine group (5e), relative to the other intermediatesstems from the proton having moved from the carbon atom

(C6) to the amine group, giving the nitrogen atom a formalpositive charge. This is also the structure that results fromdirect attack of NH3 at the C6 position of 2-hydroxypurinecation. Similar rearrangements of intermediates 5a, 5b, and5c are possible and, because of the relatively high basicity ofamines, should also be significantly lower in energy. Uponloss of a proton, the lowest-energy intermediate producesisoguanine with energy 66.7 kcal/mol below reactants, andthe other intermediate produces the 8-amino-2-hydroxyl-purine with relative energy of -59.7 kcal/mol. The mono-hydroxylated purines prefer to attach an amine group on thesix-membered ring. 2-Hydroxypurine, which is the preferredproduct at the first hydroxylation step (Fig. 5), producesisoguanine, and 6-hydroxypurine produces guanine afteramine group addition.

In the condensed phase, the combined energies of thereactants, that is, 6-hydroxypurine cation (or 2-hydroxypurinecation), OH radical, and one H2O molecule calculated in the

FIG. 4. A reaction diagram for the cationic mechanism of hydroxyl group substitution to purine starting from purinecation, OH and H2O as reactants on the left, arbitrarily set to zero kcal/mol. The structures in the square brackets are those ofthe intermediates and, on the right, are those of the products. The black numbers were calculated using oB97M-V/aug-cc-pVQZ in the gas phase, and the red numbers were calculated assuming a condensed phase environment, using a PCM.

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presence of the solvent, have been again set to zero. Rel-ative energies of the intermediates (OH group attachedcationic intermediates and H2O) and the products (mono-amino monohydroxy purine and H3O+) are also plotted inFig. 5. As for the gas phase, one of the intermediates (5e) isunusually stabilized due to the movement of the proton fromcarbon to the NH2 group. The products are lower in energycompared to the reactants as well as the intermediates ex-cept for that one case in which the proton has moved.The loss of the proton from the C6 carbon, however, is

energetically feasible and likely driven by the large gasphase proton affinity of isoguanine.

3.2.2. Hydroxyl group addition to 2- and 6-aminopurine(s).Starting from 2-aminopurine and 6-aminopurine cation, amonohydroxylation produces four cationic intermediates.The two intermediates, 2(2H)-hydroxy-6-aminopurine and8(8H)-hydroxyl-6-aminopurine (labeled 6a and 6b in Fig. 6)produced from the 6-aminopurine and hydroxyl radical, are41.1 and 65.3 kcal/mol below reactants (colored black).

FIG. 5. A reaction diagram for the cationic mechanism of amino group substitution to 2-hydroxypurine and 6-hydroxypurine starting from their cations, NH2 and H2O as reactants on the left, arbitrarily set to zero kcal/mol. Thestructures in the square brackets are those of the intermediates and, on the right, are those of the products. The blacknumbers were calculated in the gas phase at the oB97M-V/aug-cc-pVQZ level of theory, and the red numbers werecalculated assuming a condensed phase environment, using a PCM.

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The intermediates 6c and 6e (colored blue) produced fromthe 2-aminopurine cation and OH radical are 71.2 and87.1 kcal/mol below the reactants. These energies arelower than the product energies as seen in Fig. 6. The twoproducts produced from the monohydroxy-2-aminopurineintermediates are guanine, which is 51.5 kcal/mol belowthe reactants, and 8-hydroxy-2-aminopurine, which is41.5 kcal/mol below the reactants. The products associ-ated with the 6-aminopurine are isoguanine, which is54.3 kcal/mol below the reactants, and 8-hydroxy-6-aminopurine, which is 43.5 kcal/mol below the reactants.

In this case, although well below the reactants, theproducts are not below the intermediates when only onewater molecule is involved. A water environment istherefore necessary to deprotonate the intermediates andproduce the products. Again, the monoaminated purinesprefer to attach a hydroxyl group to the six-memberedring and especially either on the 2 or the 6 carbons. Iso-guanine is slightly more energetically favored over gua-nine. Both isoguanine and guanine can be found in theexperimental samples, isoguanine being more abundantthan guanine.

FIG. 6. A reaction diagram for the cationic mechanism of amino group substitution to 2-aminopurine and 6-aminopurinestarting from their cations, OH and H2O as reactants on the left, arbitrarily set to zero kcal/mol. The structures in the squarebrackets are those of the intermediates and, on the right, are those of the products. The black numbers were calculated usingthe oB97M-V/aug-cc-pVQZ level of theory, in the gas phase, and the red numbers were calculated assuming a condensedphase environment, using a PCM.

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When examining the reaction by the condensed phasecalculations, we again keep the reactants 2-aminopurine and6-aminopurine cations, OH radical, and H2O as the startingpoint. The monohydroxy-monoaminopurines are products,along with H3O+. The products are again stabilized by about30 kcal/mol compared to the gas phase due to the H2Osolvent effect. The intermediates remain more or less at thesame level as in the gas phase. Three out of the four prod-ucts are below the energies of the intermediates shown inFig. 6 in the condensed phase.

One intermediate [derived from 6d by proton migrationfrom C6 to C5 but not shown in Fig. 6 (6e)] shows largerstabilization and is 83.5 kcal/mol below the reactants. This isdue to allowing the structure to pucker slightly in the gasphase. This intermediate (plus a H2O) has energy comparableto the product guanine and H3O+. Other lower-energy pro-tonated intermediates are possible if solvent-assisted protonmigration is feasible from the site of hydroxyl attack to anamine site, which is more basic. This yields amine-protonatedguanine or isoguanine, and so on. The icy environment couldfacilitate such proton shuttling. Finally, both in the gas phaseand in the condensed phase calculations, we find that iso-guanine has a lower energy relative to guanine. The relativeenergy ordering of the products also remains the same.

3.2.3. Amine group non-addition in pure ammonia ice.When the experiments were performed in a pure ammoniaice, no products were observed, except for perhaps a traceamount of adenine (Materese et al., 2017). These results aresimilar to the pyrimidine irradiation in pure ammonia ices.This lack of product formation is in sharp contrast to theamounts of products produced in the mixed H2O and NH3

molecular ices and pure H2O ices. The UV source used forthe irradiation (10.2 eV) is enough to ionize NH3 to its cation(gas phase threshold is 10.1 eV), as well as to photolyze it toyield NH2 radicals (NH2) as discussed earlier. A reactionmechanism could be imagined in which a purine radicalcation reacts with the amine (NH2) radical to produce initialintermediates, which lose a proton to the neighboring NH3

molecules to produce the products and NH4+ ion. This reac-

tion sequence is plausible since the proton affinity of NH3 islarge, 211 kcal/mol (Czako et al., 2008), and there are 10 NH3

molecules to each purine molecule in the pure NH3 ices. Lackof experimentally detected products in the pure ammoniaice, however, suggests that some characteristic of the am-monia ice precludes this pathway.

Indeed, in a similar ice experiment, Cuylle et al. (2012)showed that, in Lyman a irradiated ammonia ice seededwith pyrene, its anions are exclusively produced as a resultof free electrons generated by ionization of NH3, and thefact that the ratio of NH3 to pyrene was large (5000:1). Onthe other hand, in water ices (also 5000:1 ratio), pyrenecations are produced presumably by direct ionization, asLyman a does not ionize water molecules; therefore, strayfree electrons are not available. In mixed H2O and NH3

ices, when keeping the ice:pyrene ratio at 5000:1, the re-sults depended on the relative abundances of H2O and NH3.Under conditions similar to the experiments we are mod-eling (H2O:NH3 ratio is 10:1), anion signal was quenched,and only pyrene cations were produced.

Purine has a larger electron affinity than pyrene and,hence, would exclusively yield purine anions in Lyman a

irradiated NH3 ice experiments. A reaction of the purineanion with NH2, or other radicals, or formation of a coor-dination complex with NH3, would be unfavorable froman electrostatic point of view. This is presumably the rea-son that that product formation was not observed in exper-imental studies of purine in NH3 ice (Materese et al., 2017).In a mixed ice with H2O:NH3 ratio of 10:1, we expect thecations of purine to be present, and the cationic reactionmechanism would yield all the products that have beenpredicted in this work or seen by the experiments.

4. Discussion

Interestingly, we find that the amine group preferentiallybinds at the 6 position on the purine ring, while the hydroxylgroup prefers the 2 position. As a consequence, adenineis the thermodynamically preferred monoaminated product,and 2-hydroxypurine is the monohydroxylated preferredproduct. In Fig. 1, the upward or the left paths seem to be theway forward after the first step.

Both NH2 and OH radicals are very effective nucleo-philes. From our calculations, we do not observe muchdifference in reaction energies for the reaction of purinewith either NH2 or OH. Both the set of monoaminated andmonohydroxylated products are expected to form after thefirst set of substitutions. Based on thermodynamics, the firstNH2 substitution leads to adenine, while the first OH sub-stitution leads to hypoxanthine. Therefore, after the firststep, adenine and 2-hydroxypurine are expected to be themost favored products, although 2-aminopurine and 6-hydroxypurine, that is, hypoxanthine, are also expected toform as they are very close in energy, and there is no barrierto these reactions. Hypoxanthine and 2-hydroxypurine aremore likely to form, as H2O is 10 times more abundant inthe reaction mixture, and therefore hydroxylation has ahigher chance of occurring. Experimentally, hypoxanthinewas found to be the most abundant product followed byadenine; 2-hydroxypurine could not be tested, as a standardwas not available. Nevertheless, the most favored productsgive us a path forward for further reactions.

If the NH2 group addition is preferred over OH group,then adenine would be the energetically most-favoredproduct after the first NH2 group addition, and it would be alogical place to start for further NH2 or OH group addition.An OH group preferentially attaches with adenine at the 2position leading to isoguanine, which again is one of themain products. If we started from 2-aminopurine, thenguanine is the most favored product after OH group addi-tion. Isoguanine is lower in energy compared to guanine by3.5 kcal/mol in the condensed phase calculations and thusshould be an energetically preferred product. It can of courseadd another NH2 group to produce 2,6-diaminopurine, andit does form in the experiments. Therefore, there is no di-rect path to make guanine from adenine, but there exists apath to form isoguanine, which is why isoguanine is a majorproduct in the experiment.

If, however, OH group addition is preferred over NH2

group addition in the first step (following the horizontalpaths in Fig. 1), then we expect to see either 2-OH-purine orhypoxanthine after the first step. Since 2-hydroxypurine isthe most favored product, it can act as a starting pointfor further functionalization. An NH2 group addition to

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2-hydroxypurine would preferentially make isoguanine overthe other products as seen in Fig. 5. If, however, we startedfrom hypoxanthine, which is a less favored product after thefirst hydroxylation, then we get guanine.

Thus, starting from either adenine or 2-hydroxypurine—themajor products of the first step—we see that isoguanine is themost favored product. To produce guanine, we need to startOH or NH2 group addition to the less favored products afterthe first step. This indicates that isoguanine would probably besignificantly in higher abundance than guanine, because of thedifficulty in formation of the latter. Experimentally, Matereseet al. (2017) found that the singly substituted products hy-poxanthine, adenine, and 2-aminopurine are the mostabundant products. Doubly substituted products are anorder (or orders) of magnitude less abundant than thesingly substituted ones. Xanthine, isoguanine, guanine,and 2,6-diaminopurine are the most abundant doublysubstituted products, in order of their abundance.

4.1. Validation of cationic mechanismsfor hydroxylation and amination

Lack of detection of products in the pure NH3 samplesvalidates the cationic reaction mechanism over the othertypes of mechanisms. If other mechanisms were responsible,or dominant over the cationic mechanism, for hydroxylationand amino group substitution, then we would expect to seeproducts formed in irradiated pure NH3 ices as well. Sinceproducts are not formed in the pure NH3 ices, we canconclude that anionic purine does not lead to hydroxyl oramine substitution, at least in an efficient manner. On theother hand, positive detection of products in the 10:1H2O:NH3 and pure H2O irradiated ices, where cations ofpurine would be produced as shown by Cuylle et al. (2012),strongly indicates that the reaction proceeds through thecationic mechanism. Ions are reported to play an importantrole in hydroxyl group addition to polycyclic aromatic hy-drocarbons as well (Guennoun et al., 2011a, 2011b; Cooket al., 2015).

4.2. Astrobiological significance

Our results indicate that the nucleobases adenine andguanine can be photochemically synthesized in the con-densed phase in a mixture of purine, water, and ammoniaunder UV irradiation. The reaction proceeds via an ion-radical-type mechanism and does not require going over anybarriers and therefore could perhaps happen in cold tem-peratures, such as on the icy mantles of meteorites. Adenineand hypoxanthine are the most likely mono-substitutedproducts, whereas isoguanine, followed by guanine, are themost likely bi-substituted products. We show a sequentialnature of functional group substitution in purine. Of course,nothing in our calculations indicates that other processesleading to the formation of less energetically favorableproducts are prohibitive. Other possibilities abound, butfurther exploration is beyond the present scope.

Hypoxanthine (also known as d-Inosine) has been dem-onstrated to preferentially base pair with cytosine, indicat-ing its guanine surrogate capability (Budke and Kuzminov,2006). Further, a type of RNA editing in cells convertsadenosine to inosine (hypoxanthine) in order to exploit its

base-pairing abilities with cytosine (Nishikura, 2010). Thesefacts indicate that hypoxanthine, despite not being one of thebiological bases present in DNA and RNA, could haveplayed an important role in prebiotic chemistry. Our resultsshow the mechanism by which hypoxanthine, as well as thenucleobases adenine and guanine, can be synthesized easilyin the irradiated ices if purine is present.

5. Conclusions

We explored the range of possible products resulting fromhydroxyl and amino group substitutions in purine presentas a dopant in mixed 10:1 water-ammonia molecular ices.Based on quantum chemical calculations, we find that bothamino and the hydroxyl group substitutions are energeticallyfavorable processes and that the 2 and 6 positions in the six-membered cyclic ring are the most favored positions forthese functional group substitutions. The energies of aminegroup substitutions were slightly lower than the energies ofhydroxyl group substitutions, indicating that amino group–substituted products may be dominant over hydroxyl groupproducts. Nevertheless, the higher abundance of hydroxylshould produce higher yield for 2-hydroxypurine and hy-poxanthine over adenine, and xanthine over 2,6-diaminopurine.Starting from 2-hydroxypurine, an amine group substitutionshould lead to the preferential formation of isoguanine overguanine as seen from the bottom right corner of Fig. 1.Starting from adenine should also produce isoguanine fol-lowing the upper-left corner seen in Fig. 1. Starting fromhypoxanthine, an amino group substitution would lead toguanine. This was supported by the experimental observa-tion that the monoamino-substituted product adenine andthe monohydroxylated product hypoxanthine were found tobe in 1:4 ratios despite NH3 and H2O being present in a 1:10ratio. Mono-substituted products were also almost an or-der of magnitude more abundant in experimental samplescompared to the bi-substituted products. The productabundance is carried forward in the biamino and bihydroxypurine ratios as well. This is due mainly to the sequentialnature of the substitutions and further establishes our se-quential reaction mechanisms.

H2O plays multiple critical roles in the photoprocessingof purine in ices: as a reactant, as a catalyst, and as a solvent.H2O gives birth to hydroxyl radicals that take part in thehydroxylation reactions. H2O plays a central role as a cat-alyst in the substitution reactions by the cationic mechanismby abstracting a proton to make products. Further, the H2Omatrix is essential not only to capture protons that are by-products of the reaction but also to permit survival of thereactant cations. In the absence of H2O, that is, in pure NH3

ices, anions (rather than cations) are produced, which im-pedes the reactions. These crucial roles of H2O are alsoevident from the experimental observation of no products inpure ammonia ices.

The role of the water matrix in the amination and hy-droxylation is proven by the condensed phase calculations.In some cases (Figs. 2 and 3), only one H2O molecule wasenough to make the reaction proceed; but in most cases,more than one H2O molecule, that is, an H2O matrix, isnecessary. The C-PCM calculations indicated that the re-actants, intermediates, and products all become solvated, butto different extents. The products are solvated better than

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either the reactants or intermediates, which helps the reac-tions go forward. This is in agreement with the previous andcurrent gas phase calculations, which shows that the reac-tion is incomplete in the gas phase.

From our quantum chemical calculations, we predictedthat adenine and 2-hydroxypurine are the most energeticallyfavorable mono-substituted products, and isoguanine themost favored bi-substituted product. Experimentally, ade-nine and hypoxanthine (2-hydroxypurine standards were notavailable) are the most abundant products, followed by thebi-substituted products. We showed how, in the presence ofthe H2O matrix, the reaction proceeds to the products by theassistance of H2O. In a pure H2O ice, the reaction couldproceed via the cationic mechanism. However, in the pureNH3 medium, where the cations are not produced but anionsare created, no products are identified. The experimentalnondetection of the products in pure NH3 ice supports thishypothesis. Together with the catalytic and solvation ef-fects of H2O the matrix, all evidence indicates that that thecationic mechanism is operational in pure H2O and mixedmolecular ices.

Acknowledgments

This material is based upon work supported by the Na-tional Aeronautics and Space Administration through theNASA Astrobiology Institute under Cooperative AgreementNotice NNH13ZDA017C issued through the Science Mis-sion Directorate. This paper has greatly benefited fromconstructive discussions with Dr. Christopher Materese, Dr.Michel Nuevo, and Dr. Scott Sandford, who are simulta-neously publishing a paper in Astrobiology (Materese et al.,2017) on the experimental investigations of the photo-processing of purine in NH3:H2O ices.

References

Barone, V. and Cossi, M. (1998) Quantum calculation of mo-lecular energies and energy gradients in solution by a con-ductor solvent model. J Phys Chem A 102:1995–2001.

Becke, A.D. (1993) Density-functional thermochemistry. III.The role of exact exchange. J Chem Phys 98:5648–5652.

Bera, P.P. and Schaefer, H.F. (2005) (G–H)�–C and G–(C–H)�radicals derived from the guanine$cytosine base pair causeDNA subunit lesions. Proc Natl Acad Sci USA 102:6698–6703.

Bera, P.P., Nuevo, M., Milam, S.N., Sandford, S.A., and Lee,T.J. (2010) Mechanism for the abiotic synthesis of uracil viaUV-induced oxidation of pyrimidine in pure H2O ices underastrophysical conditions. J Chem Phys 133, doi:10.1063/1.3478524.

Bera, P.P., Nuevo, M., Materese, C.K., Lee, T.J., and Sandford,S.A. (2016) Mechanisms for the formation of thymine underastrophysical conditions and implications for the origin oflife. J Chem Phys 144, doi:10.1063/1.4945745.

Budke, B. and Kuzminov, A. (2006) Hypoxanthine incorpo-ration is nonmutagenic in Escherichia coli. J Bacteriol 188:6553–6560.

Callahan, M.P., Smith, K.E., Cleaves, H.J., II, Ruzicka, J.,Stern, J.C., Glavin, D.P., House, C.H., and Dworkin, J.P.(2011) Carbonaceous meteorites contain a wide range ofextraterrestrial nucleobases. Proc Natl Acad Sci USA 108:13995–13998.

Chai, J.-D. and Head-Gordon, M. (2009) Long-range correcteddouble-hybrid density functionals. J Chem Phys 131, doi:10.1063/1.3244209.

Charnley, S.B., Kuan, Y.-J., Huang, H.-C., Botta, O., Butner,H.M., Cox, N., Despois, D., Ehrenfreund, P., Kisiel, Z., Lee,Y.-Y., Markwick, A.J., Peeters, Z., and Rodgers, S.D. (2005)Astronomical searches for nitrogen heterocycles. Adv SpaceRes 36:137–145.

Chyba, C., Thomas, P., Brookshaw, L., and Sagan, C. (1990)Cometary delivery of organic molecules to the early Earth.Science 249:366–373.

Cook, M.A., Ricca, A., Mattioda, L.A., Bouwman, J., Roser, J.,Linnartz, H., Bregman, J., and Allamandola, J.L. (2015)Photochemistry of polycyclic aromatic hydrocarbons in cos-mic water ice: the role of PAH ionization and concentration.Astrophys J 799, doi:10.1088/0004-637X/799/1/14.

Cooper, G., Kimmich, N., Belisle, W., Sarinana, J., Brabham,K., and Garrel, L. (2001) Carbonaceous meteorites as a sourceof sugar-related organic compounds for the early Earth. Nature414:879–883.

Cronin, J.R. and Pizzarello, S. (1997) Enantiomeric excesses inmeteoritic amino acids. Science 275:951–955.

Cuylle, S.H., Tenenbaum, E.D., Bouwman, J., Linnartz, H., andAllamandola, L.J. (2012) Ly-induced charge effects ofpolycyclic aromatic hydrocarbons embedded in ammonia andammonia:water ice. Mon Not R Astron Soc 423:1825–1830.

Czako, G., Matyus, E., Simmonett, A.C., Csaszar, A.G.,Schaefer, H.F., and Allen, W.D. (2008) Anchoring the ab-solute proton affinity scale. J Chem Theory Comput 4:1220–1229.

Dartois, E. (2005) The ice survey opportunity of ISO. Space SciRev 119:293–310.

Dworkin, J.P., Deamer, D.W., Sandford, S.A., and Alla-mandola, L.J. (2001) Self-assembling amphiphilic molecules:synthesis in simulated interstellar/precometary ices. ProcNatl Acad Sci USA 98:815–819.

Engel, V., Staemmler, V., Vander Wal, R.L., Crim, F.F., Sen-sion, R.J., Hudson, B., Andresen, P., Hennig, S., Weide, K.,and Schinke, R. (1992) Photodissociation of water in the firstabsorption band: a prototype for dissociation on a repulsivepotential energy surface. J Phys Chem 96:3201–3213.

Folsome, C.E., Lawless, J., Romiez, M., and Ponnamperuma, C.(1971) Heterocyclic compounds indigenous to the Murchisonmeteorite. Nature 232:108–109.

Gibb, E.L., Whittet, D.C.B., Boogert, A.C.A., and Tielens,A.G.G.M. (2004) Interstellar ice: the Infrared Space Ob-servatory legacy. Astrophys J Suppl Ser 151, doi:10.1086/381182.

Guennoun, Z., Aupetit, C., and Mascetti, J. (2011a) Photo-chemistry of coronene with water at 10 K: first tenta-tive identification by infrared spectroscopy of oxygencontaining coronene products. Phys Chem Chem Phys 13:7340–7347.

Guennoun, Z., Aupetit, C., and Mascetti, J. (2011b) Photo-chemistry of pyrene with water at low temperature: study ofatmospherical and astrochemical interest. J Phys Chem A115:1844–1852.

Hamid, A.M., Bera, P.P., Lee, T.J., Aziz, S.G., Alyoubi, A.O.,and El-Shall, M.S. (2014) Evidence for the formation ofpyrimidine cations from the sequential reactions of hydrogencyanide with the acetylene radical cation. J Phys Chem Lett5:3392–3398.

Hayatsu, R. (1964) Orgueil meteorite: organic nitrogen con-tents. Science 146:1291–1293.

MECHANISMS OF THE FORMATION OF ADENINE AND GUANINE 783D

ownl

oade

d by

Nas

a A

mes

Res

earc

h C

tr f

rom

onl

ine.

liebe

rtpu

b.co

m a

t 08/

23/1

7. F

or p

erso

nal u

se o

nly.

Hayatsu, R., Anders, E., Studier, M.H., and Moore, L.P. (1975)Purines and triazines in the Murchison meteorite. GeochimCosmochim Acta 39:471–488.

Kronik, L., Stein, T., Refaely-Abramson, S., and Baer, R.(2012) Excitation gaps of finite-sized systems from optimallytuned range-separated hybrid functionals. J Chem TheoryComput 8:1515–1531.

Kuan, Y.-J., Charnley, S.B., Huang, H.-C., Kisiel, Z., Ehren-freund, P., Tseng, W.-L., and Yan, C.-H. (2004) Searches forinterstellar molecules of potential prebiotic importance. AdvSpace Res 33:31–39.

Kvenvolden, K., Lawless, J., Pering, K., Peterson, E., Flores, J.,Ponnamperuma, C., Kaplan, I.R., and Moore, C. (1970)Evidence for extraterrestrial amino-acids and hydrocarbons inthe Murchison meteorite. Nature 228:923–926.

Lange, A.W. and Herbert, J.M. (2010a) Polarizable continuumreaction-field solvation models affording smooth potentialenergy surfaces. J Phys Chem Lett 1:556–561.

Lange, A.W. and Herbert, J.M. (2010b) A smooth, nonsingular,and faithful discretization scheme for polarizable continuummodels: the switching/Gaussian approach. J Chem Phys 133,doi:10.1063/1.3511297.

Lazcano, A. and Miller, S.L. (1996) The origin and early evo-lution of life: prebiotic chemistry, the pre-RNA world, andtime. Cell 85:793–798.

Lee, C., Yang, W., and Parr, R.G. (1988) Development of theColle-Salvetti correlation-energy formula into a functional ofthe electron density. Phys Rev B 37:785–789.

Lind, M.C., Bera, P.P., Richardson, N.A., Wheeler, S.E., andSchaefer, H.F. (2006) The deprotonated guanine-cytosinebase pair. Proc Natl Acad Sci USA 103:7554–7559.

Mardirossian, N. and Head-Gordon, M. (2016) oB97M-V: acombinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation.J Chem Phys 144, doi:10.1063/1.4952647.

Martins, Z., Botta, O., Fogel, M.L., Sephton, M.A., Glavin,D.P., Watson, J.S., Dworkin, J.P., Schwartz, A.W., and Eh-renfreund, P. (2008) Extraterrestrial nucleobases in theMurchison meteorite. Earth Planet Sci Lett 270:130–136.

Materese, C.K., Nuevo, M., and Sandford, S.A. (2017) Theformation of nucleobases from the ultraviolet photoirradia-tion of purine in simple astrophysical ice analogues. Astro-biology 17, doi:10.1089/ast.2016.1613.

Miller, S. and Cleaves, H. (2006) Prebiotic Chemistry on thePrimitive Earth, Oxford University Press, Oxford.

Monge-Palacios, M., Corchado, J.C., and Espinosa-Garcia, J.(2013) Dynamics study of the OH + NH3 hydrogen abstrac-tion reaction using QCT calculations based on an analyticalpotential energy surface. J Chem Phys 138, doi:10.1063/1.4808109.

Mullie, F. and Reisse, J. (1987) Organic matter in carbonaceouschondrites. In Organic Geo- and Cosmochemistry, Springer,Berlin, pp 83–117.

Nakajima, A., Fuke, K., Tsukamoto, K., Yoshida, Y., and Kaya,K. (1991) Photodissociation dynamics of ammonia (NH3,NH2D, NHD2, and ND3): rovibronic absorption analysis ofthe A-*X transition. J Phys Chem 95:571–574.

Nelson, K.E., Robertson, M.P., Levy, M., and Miller, S.L.(2001) Concentration by evaporation and the prebiotic syn-thesis of cytosine. Orig Life Evol Biosph 31:221–229.

Nishikura, K. (2010) Functions and regulation of RNA editingby ADAR deaminases. Annu Rev Biochem 79:321–349.

Nuevo, M., Milam, S.N., Sandford, S.A., Elsila, J.E., andDworkin, J.P. (2009) Formation of uracil from the ultraviolet

photo-irradiation of pyrimidine in pure H2O ices. Astro-biology 9:683–695.

Nuevo, M., Milam, S.N., and Sandford, S.A. (2012) Nucleo-bases and prebiotic molecules in organic residues producedfrom the ultraviolet photo-irradiation of pyrimidine in NH3

and H2O+NH3 ices. Astrobiology 12:295–314.Nuevo, M., Materese, C.K., and Sandford, S.A. (2014) The

photochemistry of pyrimidine in realistic astrophysical icesand the production of nucleobases. Astrophys J 793:125–131.

Orgel, L.E. (2004) Prebiotic chemistry and the origin of theRNA world. Crit Rev Biochem Mol Biol 39:99–123.

Ricca, A. and Bauschlicher, C.W., Jr. (2000) The reactions ofpolycyclic aromatic hydrocarbons with OH. Chem Phys Lett328:396–402.

Roy, D., Najafian, K., and von Rague Schleyer, P. (2007)Chemical evolution: the mechanism of the formation of ad-enine under prebiotic conditions. Proc Natl Acad Sci 104:17272–17277.

Sandford, S.A., Bernstein, M.P., and Allamandola, L.J. (2004)The mid-infrared laboratory spectra of naphthalene (C10H8)in solid H2O. Astrophys J 607, doi:10.1086/383461.

Sandford, S.A., Bera, P.P., Lee, T.J., Materese, C.K., andNuevo, M. (2015) Photosynthesis and photo-stability of nu-cleic acids in prebiotic and extraterrestrial environments. TopCurr Chem 356:123–164.

Shao, Y., Gan, Z., Epifanovsky, E., Gilbert, A.T.B., Wormit,M., Kussmann, J., Lange, A.W., Behn, A., Deng, J., Feng, X.,Ghosh, D., Goldey, M., Horn, P.R., Jacobson, L.D., Kaliman,I., Khaliullin, R.Z., Kus, T., Landau, A., Liu, J., Proynov,E.I., Rhee, Y.M., Richard, R.M., Rohrdanz, M.A., Steele,R.P., Sundstrom, E.J., Woodcock, H.L., III, Zimmerman,P.M., Zuev, D., Albrecht, B., Alguire, E., Austin, B., Beran,G.J.O., Bernard, Y.A., Berquist, E., Brandhorst, K., Bravaya,K.B., Brown, S.T., Casanova, D., Chang, C.-M., Chen, Y.,Chien, S.H., Closser, K.D., Crittenden, D.L., Diedenhofen,M., DiStasio, R.A., Jr., Do, H., Dutoi, A.D., Edgar,R.G., Fatehi, S., Fusti-Molnar, L., Ghysels, A., Golubeva-Zadorozhnaya, A., Gomes, J., Hanson-Heine, M.W.D., Har-bach, P.H.P., Hauser, A.W., Hohenstein, E.G., Holden, Z.C.,Jagau, T.C., Ji, H., Kaduk, B., Khistyaev, K., Kim, J., Kim, J.,King, R.A., Klunzinger, P., Kosenkov, D., Kowalczyk, T.,Krauter, C.M., Lao K.U., Laurent, A.D., Lawler, K.V., Lev-chenko, S.V., Lin, C.Y., Liu, F., Livshits, E., Lochan, R.C.,Luenser, A., Manohar, P., Manzer, S.F., Mao, S.-P., Mar-dirossian, N., Marenich, A.V., Maurer, S.A., Mayhall, N.J.,Neuscamman, E., Oana, C.M., Olivares-Amaya, R., O’Neill,D.P., Parkhill, J.A., Perrine, T.M., Peverati, R., Prociuk, A.,Rehn, D.R., Rosta, E., Russ, N.J., Sharada, S.M., Sharma, S.,Small, D.W., Sodt, A., Stein, T., Stuck, D., Su, Y.-C., Thom,A.J.W., Tsuchimochi, T., Vanovschi, V., Vogt, L., Vydrov,O., Wang, T., Watson, M.A., Wenzel, J., White, A., Wil-liams, C.F., Yang, J., Yeganeh, S., Yost, S.R., You, Z.-Q.,Zhang, I.Y., Zhang, X., Zhao, Y., Brooks, B.R., Chan,G.K.L., Chipman, D.M., Cramer, C.J., Goddard, W.A., III,Gordon, M.S., Hehre, W.J., Klamt, A., Schaefer, H.F., III,Schmidt, M.W., Sherrill, C.D., Truhlar, D.G., Warshel, A.,Xu, X., Aspuru-Guzik, A., Baer, R., Bell, A.T., Besley, N.A.,Chai, J.-D., Dreuw, A., Dunietz, B.D., Furlani, T.R., Gwalt-ney, S.R., Hsu, C.-P., Jung, Y., Kong, J., Lambrecht, D.S.,Liang, W.Z., Ochsenfeld, C., Rassolov, V.A., Slipchenko,L.V., Subotnik, J.E., Van Voorhis, T., Herbert, J.M., Krylov,A.I., Gill, P.M.W., and Head-Gordon, M. (2015) Advances inmolecular quantum chemistry contained in the Q-Chem 4program package. Mol Phys 113:184–215.

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Shapiro, R. (1999) Prebiotic cytosine synthesis: a criticalanalysis and implications for the origin of life. Proc NatlAcad Sci USA 96:4396–4401.

Simon, M.N. and Simon, M. (1973) Search for interstellaracrylonitrile, pyrimidine, and pyridine. Astrophys J 184:757–762.

Stoks, P.G. and Schwartz, A.W. (1979) Uracil in carbonaceousmeteorites. Nature 282:709–710.

Stuhl, F. (1973) Absolute rate constant for the reactionOH+NH3/NH2+H2O. J Chem Phys 59:635–637.

Suto, M. and Lee, L.C. (1983) Photodissociation of NH3 at 106–200 nm. J Chem Phys 78:4515–4522.

Tomasi, J., Mennucci, B., and Cammi, R. (2005) Quantummechanical continuum solvation models. Chem Rev 105:2999–3094.

Weast, R.C. (1989) CRC Handbook of Chemistry and Physics,Chemical Rubber Company, Boca Raton, FL.

Address correspondence to:Partha P. Bera

NASA Ames Research CenterMS245-6 Moffett Field

Mountain View, CA 94035

E-mail: Partha.P.Bera@nasa.gov

Submitted 28 October 2016Accepted 27 February 2017

Abbreviation Used

PCM¼ polarizable continuum model

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This article has been cited by:

1. Materese Christopher K., Nuevo Michel, Sandford Scott A.. 2017. The Formation of Nucleobases from the UltravioletPhotoirradiation of Purine in Simple Astrophysical Ice Analogues. Astrobiology 17:8, 761-770. [Abstract] [Full Text HTML][Full Text PDF] [Full Text PDF with Links] [Supplemental Material]

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