Formation of nucleobases in a Miller–Urey
reducing atmosphere
Martin Ferusa, Fabio Pietruccib, Antonino Marco Saittab, Antonín Kní
zeka,c, Petr Kubelíka, Ondrej Ivaneka,
a
a,1
Violetta Shestivska , and Svatopluk Civiš
a
J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic; bInstitut de Minéralogie, de Physique des
Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Muséum National d’Histoire Naturelle, Institut de Recherche
pour le Développement, UMR 7590, F-75005 Paris, France; and cDepartment of Physical and Macromolecular Chemistry, Faculty of Science, Charles
University in Prague, CZ12840 Prague 2, Czech Republic
Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 13, 2017 (received for review January 6, 2017)
The Miller–Urey experiments pioneered modern research on the
molecular origins of life, but their actual relevance in this field was
later questioned because the gas mixture used in their research is
considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the
production of only amino acids has been taken as evidence of the
limited relevance of the results. Here, we report an experimental
work, combined with state-of-the-art computational methods, in
which both electric discharge and laser-driven plasma impact
simulations were carried out in a reducing atmosphere containing
NH3 + CO. We show that RNA nucleobases are synthesized in these
experiments, strongly supporting the possibility of the emergence of
biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide
play a crucial role, in agreement with a number of recent experimental
and theoretical results.
life origins
| asteroid impact | reducing atmosphere
M
ore than 60 y ago, Stanley Lloyd Miller and Harold
Clayton Urey, in their pioneering work (1), demonstrated
the synthesis of several amino acids from a mixture of reducing
gases (CH4, NH3, H2O, and H2) treated with electric discharge.
The following explorations showed that a broad array of amino
acids could be synthesized, but there was no evidence that all of
the fundamental molecules of the RNA genetic code could be
produced alongside others in this type of experiment (2–5).
Additionally, the significant persistence of reducing atmospheres
in a geological timescale has been seriously debated (6). Finally,
many scientists have claimed that this experiment is not related
to early-Earth conditions and does not provide fundamental
building blocks (i.e., nucleobases) important for the evolution of
early life possibly based on RNA (7–13). In 2001, Saladino, Di
Mauro, and coworkers (14) proposed that the parent molecule
for the one-pot synthesis of nucleobases is formamide (15–23).
Their team, together with other authors, demonstrated the formation of (not only) fundamental nucleobases for the origin of
RNA in experiments involving the heating of formamide in
presence of manifold catalysts (17, 24–26), upon UV irradiation
(27), proton (28) and heavy-particle radiation (29), exposition to
shock waves (18), etc. Recently, Hörst et al. (30) also referred to
a positive result on qualitative detection of RNA nucleobases
and manifold amino acids from tholines created in a N2, CH4,
CO mixture. Their experiment simulated the atmosphere of Titan upon electric discharge. Such experimental results as well as
theoretical expectations (31) show that reduced, relatively reactive atmospheres are likely to be more efficient for the synthesis of biomolecules (32). However, it should be noted that
several papers report also the formation of biomolecules under
neutral (N2, CO2, H2O) conditions (33–35). In our study, we
found an interconnection between the original ideas of the pioneering Miller–Urey studies devoted to prebiotic synthesis in a
reducing atmosphere and recent results identifying the chemistry
4306–4311 | PNAS | April 25, 2017 | vol. 114 | no. 17
of formamide as a source for the synthesis of nucleobases. In
addition to traditional hydrogen cyanide (HCN)-based or reducing
atmosphere-based concepts of biomolecule formation (30, 36–38),
we show that, under the conditions demonstrated in this study, the
formamide molecule not only plays the role of parent compound
but also is an intermediate in a series of reactions leading from
very reactive and rigid small radicals to biomolecules.
During the past decade, comets (39), HCN hydrolysis (40),
chemistry in interstellar space (41), reducing atmospheres (42),
or ammonium formate dehydration (43) have been proposed as
sources of formamide. However, in most cases, the exact chemistry
of such systems has not been well explored either experimentally
or theoretically. Moreover, the plausibility and relation to a prebiotic environment is also questioned.
Using the large laser facility at the terrawatt Prague Asterix
Laser System, we comprehensively explored asteroid shock wave
impact plasma, in addition to electric discharge, in a simple reducing mixture of NH3 + CO and H2O. The formamide molecule does not directly play the role of starting substrate, but it is
rather a suspected intermediate of reactions leading from simple
model prebiotic mixtures to biomolecules.
The results are compared with similar experiments, in which
formamide is the starting compound. The chemistry is also mapped
using state-of-the-art ab initio molecular-dynamics simulations.
We focused our effort on two environments relevant to prebiotic
chemistry: (i) transformation of an atmosphere exposed a shock
wave induced by an extraterrestrial body and the resulting impact
Significance
The study shows that Miller–Urey experiments produce RNA
nucleobases in discharges and laser-driven plasma impact
simulations carried out in a simple prototype of reducing atmosphere containing ammonia and carbon monoxide. We
carried out a self-standing description of chemistry relevant to
hypothesis of abiotic synthesis of RNA nucleobases related to
early-Earth chemical evolution under reducing conditions. The
research addresses the chemistry of simple-model reducing
atmosphere (NH3 + CO + H2O) and the role of formamide as an
intermediate of nucleobase formation in Miller–Urey experiment. The explorations combine experiments performed using
modern techniques of large, high-power shock wave plasma
generation by hall terawatt lasers, electric discharges, and
state-of-the-art ab initio free-energy calculations.
Author contributions: M.F., F.P., A.M.S., and S.C. designed research; M.F., A.K., O.I., and
S.C. performed experimental research; F.P. and A.M.S. performed computer simulations;
M.F., F.P., A.M.S., P.K., O.I., V.S., and S.C. analyzed data; and M.F., F.P., A.M.S., and S.C.
wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
1
To whom correspondence should be addressed. Email: [email protected].
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1700010114/-/DCSupplemental.
www.pnas.org/cgi/doi/10.1073/pnas.1700010114
Fig. 1. Data published in ref. 52 on the oxidation state of trace elements in
early zircons (part A, blue circles), which are compared with the timescale of
impact flux on early Earth (part B, violet curve; EHB and LHB are Early and
Late Heavy Bombardment periods), and the age of carbon inclusions
exhibiting 13C deficiency consistent with their biogenic origin (part C, red
points). Data from refs. 19, 52, 56, and 67, and references therein.
Ferus et al.
Fig. 2. Emission spectrum of a reducing atmosphere (NH3, CO, H2O) discharge plasma. Among others, carbon monoxide and the ·CN radical in a
wide range of energetic states dominate the spectra.
chemical composition (e.g., H2, CO, CH4, and NH3) (55). As
demonstrated by Miller and other authors, such conditions are
very favorable to the prebiotic synthesis of organic matter on
Earth. In Fig. 1, part C, we also compare these data with the
estimation of the age of the first biosignatures of life, which has
been recently shifted to 4.1 Gy before the present (56, 57).
Considering the direct synthesis of biomolecules on the early
Earth and regarding the expectations of a very early reducing
atmosphere together with the expectations of very ancient life on
Earth, we can assume that biomolecules were probably synthesized on Earth during transformation of the reducing atmosphere.
During a time of decreased impact activity, this atmosphere was
depleted and transformed to a CO2-rich mixture containing N2
and H2O vapor (58). In this chemistry, formamide can play a role
of reactive intermediate. However, we should note that alternative
scenario of the theory of exogenous synthesis regards impacts of
extraterrestrial bodies not only as a source of shock wave energy
and degassed reducing atmospheres but also as a direct source of
biomolecules. These assumptions are supported by recent findings
of a wide palette of organic substances (59) and biomolecules in
chondritic meteorites (60, 61).
Results and Discussion
In the following experiments, stable and unstable products were
monitored during and after the exposure of a NH3 + CO + H2O
reducing mixture to electric discharge simulating lightning and
laser shock wave simulating asteroid impact plasma. In the first
step, electric discharge in the mixture NH3 + CO + H2O was
investigated by emission time-resolved Fourier transform highresolution spectroscopy (refs. 62 and 63, and references therein).
In the emission spectra depicted in Fig. 2, several species that are
very similar to the discharge of pure formamide can be observed
(19). In all of the spectra, the most prominent bands belong to
CO, CO2, HCN, and HNC excited to high vibration–rotation
levels and the unstable but ubiquitous radical ·CN, which can
play an important role in the subsequent plasma synthesis of
nucleobases (18–20). Stable molecules, such as ammonia, carbon
monoxide, acetylene, nitrous oxide, and hydrogen cyanide, were
identified by high-resolution infrared absorption spectroscopy
during subsequent analysis of discharge products concentrated in
liquid-nitrogen trap. The absorption spectra are shown in Fig. 3.
As the most important finding, discharge treatment of NH3 +
CO + H2O led to the formation of a significant amount of
formamide and HCN. The formamide absorption band is marked
in red in Fig. 3 (details are supplied in Figs. S1 and S2). As discussed in the following section, this result fully corresponds to
theoretical predictions of the reactivity of Miller-type mixtures.
Opposite to our gas-phase discharge experiments, we also
explored the decomposition of solid samples of pyrimidine (adenine) and purine (cytosine) bases in presence of water vapor.
The samples were inserted into glass discharge tubes and treated
with nitrogen discharge plasma. Similar to the decomposition of
PNAS | April 25, 2017 | vol. 114 | no. 17 | 4307
CHEMISTRY
plasma [Early and Late Heavy Bombardment in our solar system
during evolution and stabilization of orbits (44)]; and (ii) transformation of an atmosphere by an electrical discharge (lightning
in heavy clouds of dust, vapors, and other aerosols from impact,
volcanic activity and evaporation in the early atmosphere) (45).
Recently, Saitta and Saija published (42) a computer-simulated
Miller-type experiment via ab initio calculations that included external electric fields. In that study, the authors show in atomistic
computer simulations that an initial mixture of the simple Miller
molecules (CH4, NH3, H2O, CO, N2) (1, 46, 47) spontaneously
produces, on a picosecond timescale, small intermediate organic
compounds, such as formic acid and formamide, but only in strong
electric fields. Formamide, in particular, was continuously produced and fueled the formation of more complex organic molecules up to the simplest amino acid, glycine. Subsequently, a
theoretical study on formamide synthesis and dissociation chemistry pointed to the importance of HCN, NH3, CO, and H2O in its
reaction network (48).
The existence of a global reducing atmosphere on early Earth
has been debated during the almost 60 y after the famous Miller–
Urey experiment (22). So far, the most accepted theories are
inclined toward a neutral atmosphere containing an excess of
CO2 with N2 and water vapor (6, 49, 50). In contrast to previous
studies, a neutral atmosphere has also been identified as a
plausible environment for the synthesis of amino acids (33). The
existence of a neutral atmosphere was additionally supported by
the first examination of the oxidation state of igneous detrital
zircons related to magma before 3.85 Gy (51). However, recent
results (52) of further trace element analysis of igneous zircon of
crustal origin show that the Hadean continental crust was
probably more reduced than its modern counterpart and that it
oxidized 3.6 billion years ago, as shown in Fig. 1, part A (blue
circles).
It can be assumed that the low stability of reducing atmospheres was counteracted by dynamical effects, such as the exogenous transfer of reducing gases by comets (32) and chondrites
(53) or by continuous processes of endogenous synthesis (31, 54).
In particular, there is an interesting coincidence in the comparison of the timescales of reducing conditions, which were estimated using the analysis of zircons, as mentioned above (52) and
shown in Fig. 1, part A, and the timescales of Early and Late
Heavy Bombardment periods, depicted schematically in the violet curve imprinted in these data (Fig. 1, part B). We can assume that the impact-degassed atmosphere led to a reduced
Fig. 3. Absorption spectra of a reducing atmosphere (NH3, CO, H2O) discharge plasma.
formamide or the NH3 + CO + H2O mixture, we detected a
large amount of HCN, which is one of the products of formamide decomposition. As seen by comparing of Fig. 3 with Fig.
S2 B–D, we detected a similar grouping of products from nucleic
base decomposition and NH 3 + CO + H 2 O atmosphere
discharge treatment.
Finally, in the following experiments, we exposed a simple
binary reaction mixture of NH3 and CO to a plasma shock wave
without the presence of a catalyst and in the presence of montmorillonite clay and water. In our previous study, montmorillonite was identified as a plausible catalyst for nucleic base
synthesis upon laser shock wave. Fig. S2C shows the composition
of the reaction mixture after exposure to the laser shock wave
generated in the gaseous media. Comparison of both mixtures to
a blank sample is supplied in Fig. S2 A and B. As the most important result discussed in the following section, we observed
hydrogen cyanide as a main product of formamide thermal decomposition in both experiments. Additionally, we show that,
although we used a very simple mixture of Miller–Urey-type
reducing gases (and not directly formamide, similarly to previous experiments), we detected all of the RNA canonical
nucleobases—uracil, cytosine, adenine, and guanine—together
with urea and the simplest amino acid, glycine. The conclusion of
the analysis is shown in Table 1. However, we should note that
the sub-parts per million level reached in laser experiments for
pyrimidine bases is a threshold detection limit of the used
method. Nevertheless, these findings support the idea that a NH3
+ CO + H2O atmosphere can substitute for pure formamide (19)
and act as a starting environment not only for the formation of
amino acids (as shown in previous works) but also of RNA
nucleobases. Fig. S3 depicts the chromatograms of all of the canonical nucleobases using a selected mass filter for the typical m/z
ratio for each particular base. Typical mass fragments of all of the
analytes are clearly identified at the appropriate retention times,
as shown in Figs. S4–S6. We also note that we exclude any external
contamination of the samples (see SI Contamination and blank
measurements depicted in Fig. S7).
To help interpret the reactions in the shock wave plasma (4500 K)
and electric discharge (650 K) experiments, further ab initio
molecular-dynamics simulations combined with enhanced sampling were performed (48). We remark that our simulations
proceed without introducing any information about the possible
reaction pathway. The simulations are focused on gas-phase
systems (two-body collisions) and on understanding the thermally activated reaction mechanisms (fully including anharmonic
motions and entropic contributions) pertaining to the ground
electronic state. Exploiting these ab initio simulations, we obtain
evidence that the CO + NH3 system passes through formamide
as an intermediate before transforming into HCN and water in a
second step. Starting from pairs of molecules taken from the
Table 1. The results of all of the experiments with laser and discharge plasma treatment of a reducing atmosphere
Formamide in
N2 with clay*
Chemical composition
Simple gases by
FTIR (%V)
NH3
CO
H2O
HCN
CO2
C2H2
Formamide
Biomolecules (ppmV)
Adenine
Guananine
Uracil
Cytosine
Glycine
NH3 + CO†
NH3 + CO + H2O
with clay‡
NH3 + CO + H2O§
Adenine{
Cytosine{
Discharge
Blank
LIDB
Blank
LIDB
Blank
LIDB
Blank
Discharge
Discharge
10 ppm
—
—
—
25 ppm
—
—
3
36
7
40
12
—
2
5
50
—
—
—
—
—
41
41
10
8
200 ppm
800 ppm
—
40
40
20
—
—
—
—
39
36
22
3
100 ppm
—
5 ppm
33
33
33
—
—
—
—
1
1
9
30
57
1
200 ppm
—
—
—
—
—
—
—
—
—
—
—
—
37
2
1
6
35
—
—
—
—
—
2
1
0.2
0.1
25
—
—
—
—
—
10
1
0.5
0.5
80
—
—
—
—
—
4
2
1
8
40
4,800
20
10
14
40
35
9
1
41
1
14
—
24
4
16
3,600
35
Blank and LIBD prepresent the energy source used for each experiment. The chemical composition is expressed in percent by volume
(%V) or parts per million by volume (ppmV). —, no data; LIBD, laser-induced dielectric breakdown.
*Mixture of 1 mL of liquid formamide upon 760 Torr of nitrogen.
†
Mixture of 350 Torr of NH3 and CO.
‡
Mixture of 350 Torr of NH3 and CO with 0.2 mL of water and 1 g of clay.
§
Mixture of NH3:CO:H2O, 1.5 kV and 500 mA, products trapped in liquid nitrogen.
{
Solid sample in the discharge tube in 0.3 Torr H2O and 2 Torr of N2.
4308 | www.pnas.org/cgi/doi/10.1073/pnas.1700010114
Ferus et al.
experimental Miller-like gas mixture (CO + NH3 or CO + H2O),
we simulated possible reactions in the direction of the detected
products, including formamide (traces in the mixture of NH3,
CO, and H2O in the presence of a clay) and HCN (in both experiments), at different temperatures (Fig. 4A).
The reaction between CO and NH3,
[1]
yields formamide, overcoming a free-energy barrier of 52 kcal/mol at
650 K, which increases to 116 kcal/mol at the shock wave plasma
temperature of 4500 K. When this is measured in units of
available thermal energy kBT, the free-energy barrier is reduced
from 40 to only 13, such that the calculations predict fast kinetics
at high temperature.
As mentioned above, a significantly larger amount of formamide
in the CO + NH3 discharge experiment (650 K) was observed
compared with that observed under laser shock wave plasma (4500
K) conditions. At the same time, after very fast synthesis at high
temperature, our simulations predict that formamide is significantly
destabilized with respect to CO + NH3 at 4500 K, leading to a small
observed experimental concentration. Despite the variation in
barrier height, the reaction mechanism at the two temperatures
appears basically unchanged. Destabilization of formamide leads to
its decomposition, and this molecule can then serve again as an
unstable intermediate. Following the experimental observation of
sizable amounts of H2O and HCN at both 650 K and 4500 K in
nearly a 1:1 ratio, we simulated their formation either starting from
formamide or directly from the initial Miller mixture:
HCONH2 → HCN + H2 O.
[2]
Starting from formamide, proton transfer leads first to an
intermediate OHCHNH species, which then dissociates into
water and HCN (Fig. 5A).
The two consecutive barriers are 42 and 55 kcal/mol at 650 K
and only 33 and 36 kcal/mol at 4500 K. Under the latter conditions, HCN and water are very stable compared with formamide, in contrast to the conditions at 650 K; thus, the
calculations predict observable amounts of formamide only at
the lower temperature. This in turn may explain why HCN was,
and formamide was not detected in shock wave plasma experiments (i.e., because it is a necessary, but very unstable intermediate), whereas it was found under milder conditions in
the electric discharge experiment (Table 1). Additionally, HCN
Fig. 5. Reaction mechanisms and free-energy profiles (at 650 K in blue and at 4500
K in red; values in kilocalories per mole) from metadynamics and umbrella sampling
simulations, starting from formamide (A) or from formic acid and ammonia (B).
can be decomposed to the ·CN radical, which was observed by
means of emission spectroscopy:
HCN → H · + · CN.
[3]
This radical reacts with formamide produced in this high-temperature
chemistry. This reaction channel represents an additional sink of
this molecule. As described in detail in our previous reports, such
reactions lead to the subsequent synthesis of nucleobases, also
involving the H· and ·NH2 radicals (19, 21).
Stemming from the strong similarity between the experimental
products obtained when starting from the Miller mixture (passing through the formation of formamide) and the experimental
products obtained when starting from formamide (formation of
the Miller mixture, i.e., NH3 + CO together with HCN), with the
creation of nucleobases in both cases (Table 1), we hypothesized
that formamide is indeed an obligate intermediate of reactions
leading to HCN and further reactions toward nitrogenous bases.
It was very interesting that, in a separate benchmark simulation
starting from CO + NH3, which was aimed at producing HCN
without introducing any information about the possible reaction
pathway (SI Methods) in our simulations, we found that the system
passes through formamide as an intermediate before transforming
into HCN and water in a second step. This unbiased result thus
supports our hypothesis of formamide as an obligate intermediate.
We also addressed the formation of formic acid in the solution
phase and its role as a possible intermediate toward other molecules, including formamide (Fig. 4B). Starting from CO + H2O,
according to the following equation:
CO + H2 O → HCOOH,
[4]
the formation barrier increases from 57 kcal/mol at 650 K to
96 kcal/mol at 4500 K. At both temperatures, the barriers are thus
comparable with those for the formation of formamide, a situation
already observed in aqueous solution (48). Once formed, the collision
of HCOOH with ammonia yields formamide and water (Fig. 5B):
HCOOH + NH3 → HCONH2 + H2 O,
[5]
with barriers of 54 kcal/mol at 650 K and 48 kcal/mol at 4500 K.
Interestingly, in this latter case, the mixture of CO + NH3 + H2O
is formed as an intermediate, that is, HCOOH breaks down into
CO + NH3 before the formation of formamide:
Fig. 4. Reaction mechanisms and free-energy profiles (at 650 K in blue and
at 4500 K in red; values in kilocalories per mole) from metadynamics and
umbrella sampling simulations, for binary reactions between simple Millerlike molecules, leading to formamide (A) and formic acid (B).
Ferus et al.
HCOOH + NH3 → CO + H2 O + NH3 .
[6]
We did not actually detect HCOOH in any of our experiments
with the reducing mixture.
PNAS | April 25, 2017 | vol. 114 | no. 17 | 4309
CHEMISTRY
CO + NH3 → HCONH2 ,
Fig. 6. Summary of the chemistry in our model reducing atmosphere (NH3,
CO). A reducing atmosphere is generated by impact delivery and degassing
as proposed in ref. 52. Upon exposure to shock waves and discharges,
formamide is synthesized as a reactive intermediate (A). In subsequent
chemistry described in our previous work (19, 66), reactive molecules are
produced by formamide decomposition (B), and nucleobases are synthesized
(C) in subsequent steps from 2,3-diaminofumaronitrile (DAFN) and 4-amino5-cyanoimidazole (AlCN).
The reactions investigated here have been previously studied
using static quantum chemistry calculations, for instance, in ref.
64 (formamide and HCN formation) and in ref. 65 (HCOOH
formation). The transition states and barrier heights in the latter
works are quite similar to our results at T = 650 K, considering
the different treatment of temperature (approximations based
on harmonic vibrations in the literature versus moleculardynamics in our case) and the different quantum-mechanical
approximations [B3LYP, G2M, MP2, and CCSD(T) in the literature versus density functional theory–Perdew–Burke–Ernzerhof
(DFT-PBE) in our case]. We carefully verified that each reaction
pathway was reproduced at least three times in the metadynamics,
either in independent or in the same simulations (due to multiple
forward and backward transitions). This fact, together with the
similarity between pathways found at 650 K and in the aforementioned literature, makes us confident in the robustness of
our results.
to the synthesis of formamide and the subsequent formation of
all RNA nucleobases driven by impact plasma or electric discharge. In comparison with previous works, in our investigation,
formamide is not only a parent molecule or starting substrate but
an intermediate that quickly enters subsequent reaction chains
leading to the synthesis of reactive species, such as HCN, ·CN,
H·, etc. Further reactions with formamide (48) occur in plasma
chemistry, producing many intermediates, as described in previous
works (19, 66), such as 2-amino-2-hydroxy-malononitrile (AHMN),
2-amino-2-hydroxy-acetonitrile (AHAN), 2,3-diaminomaleonitrile
(DAMN), and 4-amino-5-cyanoimidazole (AlCN). More importantly, the outcome of these reactions is the observation of all
of the canonical RNA nucleobases. It should be noted that this
result does not contradict other scenarios, such as formamide
exogenous delivery or its formation in HCN hydrolysis (see, e.g.,
ref. 3 and citations therein). Overall, our calculations predict that
formamide can be formed either directly from CO + NH3 or
through a pathway starting from CO + H2O and passing through
formic acid as an intermediate. The pertinent range of kinetic
rates can be estimated very roughly from transition state theory,
keeping in mind that the simulated concentration of molecules in
reacting collisions is an upper bound to the actual conditions.
Under extreme shock wave plasma conditions, we predict the
facile formation of HCN and water, passing through formamide
as an intermediate with a rate of the order of 108 s−1. Such an intermediate should be difficult to observe due to its low relative
population, which is in agreement with our experiments. On the
other hand, at the milder temperatures (650 K) observed in electric
discharge experiments, our simulations predict again the formation
of HCN, passing through formamide as an intermediate, and its
relatively large thermal population is in this case compatible with
facile observation, which is also in agreement with our experiments.
However, the height of the barriers suggests very slow kinetics of
the order of 10−5 s−1, which cannot account for the observed reactions on the millisecond timescale. Therefore, we expect a driving
force that is different from thermal activation to be responsible for
these latter experiments, possibly intense electric fields near the
electrode surface or plasma chemistry driven by excited states or
radical species. Finally, we also demonstrate that any nucleic acid
base can be decomposed to reducing gases by electric discharge in
the presence of water, and these gases can react again to produce
all RNA nucleobases, according to chemistry described above.
Conclusions
The results of this study, summarized in Fig. 6, give an overview
of the rich prebiotic chemistry occurring in CO + NH3 + H2O
reducing atmosphere. Starting from this gaseous mixture, we
have experimentally and theoretically demonstrated a pathway
ACKNOWLEDGMENTS. We thank Dr. J. Skála, Dr. L. Juha, P. Prchal, and
J. Mareš. This work was funded by Czech Science Foundation Grants
14-12010S and 17-05076S; Ministry of Education, Youth, and Sports Grants
7AMB16FR035, LG15013, and LM2015083; Institut du Développement et des
Ressources en Informatique Scientifique; and Centre Informatique National
de l’Enseignement Supérieur French national supercomputing facilities for
central processing unit time (Grant 2016-091387).
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Supporting Information
Ferus et al. 10.1073/pnas.1700010114
SI Methods
To explore the viability of the nucleobase synthesis from simple
prototype of Miller–Urey atmosphere in shock wave plasma (at a
temperature of 4500 K, simulating an extraterrestrial body impact into the early planetary atmosphere) and in an electric field
(with a temperature of 650 K, simulating lightning discharges),
we treated a mixture of NH3 + CO + H2O, representing a reducing atmosphere, with a laser spark and glow discharge. The
reactive intermediates were monitored using time-resolved
emission spectroscopy, simple molecular gases by means of infrared absorption spectroscopy, and biomolecules by the GC-MS
(derivatization) technique.
Laser Shock Wave Plasma Experiments. Laser shock wave plasma
experiments have been carried out using the high-energy laser
Prague Asterix Laser System. Treatment of simple mixtures of
NH3 + CO, NH3 + CO + H2O, and NH3 + CO + H2O in the
presence of montmorillonite has been explored using 1 L cells
filled with the reactants ammonia and carbon monoxide in the
gas phase (600 torr), which were purchased from Linde Gas, at
300 torr of NH3 and 300 torr of CO, and also in the presence
of 10 mL of liquid water (CHROMASOLV HPLC grade) and
subsequently with 1 g of montmorillonite (Sigma-Aldrich;
K-10 type). In all of the experiments, laser radiation was focused
in the center of the cell using a CaF2 lens with a diameter of 40 cm
and focal length of 50 cm. Using this optical setup, a total of 25 laser
pulses were applied with a concentrated energy of 3,750 J, with
peak power of 4.3 × 1010 W.
After the irradiation, gas phase was transferred using vacuum
line and analyzed using high-resolution Fourier transform spectrometer (Bruker IFS 125 HR) in the multipass cell with 50-m
optical path. The pressure in the cell reached 1.5 torr. Four
hundred scans have been accumulated in the range of 600–
4,000 cm−1 using MCT semiconductor detector at resolution of
0.05 cm−1.
Discharge Experiments. Discharge experiments have been conducted in a glow–discharge emission cell for spectroscopic
monitoring of unstable products using time-resolved spectroscopy. The principles of the method have been discussed in our
previous papers (62, 63). Briefly, a mixture of the reduced gases
(NH3 + CO + H2O at pressure of 10 torr) was led in a positive
column discharge tube equipped with CaF2 windows. In the
second type of the experiment, precursor molecule of 1 g of
adenine (free base Sigma grade ≥99%; Sigma-Aldrich) or cytosine (free base Sigma grade ≥99%; Sigma-Aldrich) was directly
placed in the discharge tube in nitrogen buffer gas and water
vapor (10 torr). Again, glow discharge was maintained in the
cell for 1 h.
The emission spectra from the discharge plasma were measured using the time-resolved Fourier transform high-resolution
Bruker IFS 120 HR interferometer (Bruker). The AC discharge
was maintained by a high-voltage transistor switch HTS 81
(Behlke Electronic) and applied between the stainless-steel anode and the grounded cathode. The plasma was cooled by liquid
water in the outer jacket of the cell. The voltage drop across the
discharge was 1,000 V, with a pulse width of 22 μs and 0.6-A peakto-peak current. The scanner velocity of Fourier transform
spectroscopy was set to produce a 10-kHz HeNe laser fringe
frequency, which was used to trigger the discharge pulse. The
recorded spectral range was 1,800–4,000 cm–1 with an optical filter, at an unapodized resolution of 0.02 cm–1. A total of 50 scans
Ferus et al. www.pnas.org/cgi/content/short/1700010114
was averaged to obtain a reasonable signal-to-noise ratio. The
initial pressure was changed from 1 to 10.0 torr.
All of the products have been concentrated in liquid-nitrogen
trap for further analysis. After the experiment, frozen samples
were analyzed using high-resolution Fourier transform spectrometer (Bruker IFS 125 HR; Bruker) after evaporation to the
multipass cell with 50-m optical path. Four hundred scans have
been accumulated in the range of 600–4,000 cm−1 using MCT
semiconductor detector at resolution of 0.05 cm−1.
Detection of Nucleic Bases by Means of GC-MS. In our experiments,
we usually observed parts per million level of biomolecules.
Therefore, we apply the technique of GC-MS with volatilization
of biomolecules using silylation agent in the derivatization process. According to our calibration with several standards of
biomolecules detection using classical TLC approach or LC-MS
chromatography, GC-MS derivatization technique is very sensitive and selective, and allows detection of these concentrations
of biomolecules with high reliability and reproducibility. The
vessel was open and the liquid sample was filtered and dried
under vacuum. Subsequently, 200 μL of methanol extract from
the solid residue was sampled and transferred to a 1.5-mL vial
and dried again under vacuum to remove the liquid phase and
other volatile fractions. The solid residue was derivatized
for 120 min at 110 °C in 240 μL of pyridine aprotic reaction
solvent (99.9%; Sigma Aldrich) and N-(tert-butyldimethylsilyl)N-methyl-trifluoroacetamide (99% MTBSTFA) (CAS 77377-52-7;
Sigma-Aldrich) at a ratio of 3:1. After the derivatization process,
1 μL of derivative was injected into the nonpolar column TG5MS of a Trace 1300 Series Gas Chromatograph equipped with a
mass detector MS 1100 Ion Trap and analyzed using temperature gradient 10 °C·min−1 in the range of 180–280 °C. Chromatograms and mass spectra have been compared with standards
of uracil (U), thymine (T), cytosine (C), adenine (A), guanine
(G), and urea and glycine (GL).
Theoretical Calculations. We exploited Born–Oppenheimer moleculardynamics (MD) simulations based on the PBE exchange correlation
function (68) including the dispersion correction method (69, 70) as
implemented in the code Quantum Espresso (71). We simulated
periodically repeated cubic supercells (with a side of 12 Å) at a
temperature of either 650 or 4500 K. All simulation details are given
in ref. 48. We performed metadynamics simulations (72) using a
modified version of the plugin Plumed 1.3 (73).
As a convenient space of collective variables to track the reactions, we followed the definition of where we introduced two
path coordinates (s and z) based on a metric comparing the
patterns of coordination numbers (48). This class of variables
was demonstrated to be capable, in both the gas phase and
formamide solution chemistry, of discovering reaction mechanisms, achieving reversible (forward and backward) reactive
trajectories and providing free-energy landscapes. To obtain an
unbiased prediction of the reaction mechanisms, here we define
the collective variables starting only from the reactant and
product as reference frames, without making any guess or assumptions about possible intermediates and transition states.
The key advantages of this approach are the full inclusion of
thermal effects (without harmonic approximation, considering
all entropic contributions without approximate decompositions)
and the lack of a priori assumptions about the mechanisms and
pathways at the atomic scale.
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To accelerate the transition of free-energy barriers and enhance the sampling of the configuration space, a two-step strategy
was adopted: First, we used metadynamics to explore the reaction
pathways in a relatively short simulation time (∼10–20 ps).
Second, we reconstructed precise free-energy profiles along the
reaction pathways exploiting robust umbrella sampling simulations (74). The latter consisted of a set of independent equilibrium MD simulations, each one limited to a narrow range of the
s coordinate by means of a (fixed) parabolic potential. For each
investigated reaction, we used between 16 and 30 windows, with
a simulation time of at least 3 ps per window. All trajectories are
combined in a single free-energy profile using standard weighted
histogram analysis (75). Umbrella sampling allows the systematic
reducing of statistical uncertainty in free-energy differences
simply by accumulating longer trajectories, but it requires good
starting configurations in each window, here provided by the
preliminary metadynamics simulations. Based on tests reducing
the data by 30% and from independent simulations, we estimate
an error bar of ±1.5 kBT on the umbrella-sampling free-energy
profiles (namely ± 2 kcal/mol at 650 K and ±13 kcal/mol at 4500 K).
We remark that the free-energy differences reported below, due to
the size of the simulation box, refer to a gas-phase concentration of
about one molecular species per cubic nanometer, so that in reactions where the number of molecules is different between reactants
and products, their relative stability depends on the actual concentration in the gas.
SI Contamination
To be sure that we have avoided any contamination of our experiments, all of the cells and materials have been washed by
deionized water and methanol, and heated for 12 h in a furnace up
to 600 °C. We have also performed reference measurements
using the same procedures as used for biomolecules detection.
Particularly, we have tested washing of the discharge and laser
irradiation cells by deionized water (Fig. S7 B and C), washing of
the cell touched for several times with fingers without gloves
(Fig. S7D), and washing of montmorillonite catalyst by water
(Fig. S7E). Similarly with a procedure applied for nucleobase
analyses, all of the samples have been dried under vacuum,
and then the vessel was extracted by methanol, and subsequently,
200 μL of methanol extract was sampled and, again, dried under
vacuum in a vial vessel. Derivatization agent has been added in
pyridine solvent and GC-MS analysis was performed. We have
again observed miscellaneous derivatization products (as result
of mutual reactions in derivatization agent), but we have not
observed any specific masses of particular nucleobases in corresponding or nearby retention times. The corresponding chromatographic records together with the chromatogram of the
discharge products are supplied in Fig. S7.
Fig. S1. A portion of absorption spectrum in the region of a carbonyl vibration shows the absorption v4 band of formamide covered with very strong series of
water lines. The formamide reference spectrum is shown in red.
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Fig. S2. Absorption spectra of ammonia and carbon monoxide with treatment by an LIDB plasma shock wave. A shows the blank before the irradiation, B supplies the spectra recorded after 15 pulses of the laser without
catalytic material, C depicts the spectra after 15 laser pulses in presence of montmorillonite, and D shows spectra of products of nucleobase treatment in discharge plasma.
Ferus et al. www.pnas.org/cgi/content/short/1700010114
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Fig. S3. GC-MS detection of nucleic bases in all of the experiments. All samples were analyzed after derivatization by with MTBSTFA. A shows the chromatogram of a blank of the canonical nucleic bases, B shows the chromatogram of the experiment with irradiation of the mixture of NH3 + CO, C depicts
chromatogram of the experiment with NH3 + CO + H2O in presence of clay, and D shows the discharge decomposition of NH3 + CO + H2O. E and F depict,
respectively, chromatograms of adenine and cytosine glow discharge decomposition upon nitrogen atmosphere in presence of water vapor.
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Fig. S4. The typical mass spectra received using GC-MS for nucleic bases and glycine after derivatization. All the mass spectra are observed exlusively in typical retention time of each particular molecule as shown in Fig. S3 [for
nucleobases; Fig. S3A for standards and Fig. S3 B–F for experimental samples) and in the Fig. S5 (for glycine; Fig. S5A for standard and Fig. S5 B–F for experimental samples). A depicts mass spectrum of uracil standard with the
typical fragment m/z = 283 compared with uracil mass spectra discovered in the experimental sample; B shows comparison of experimental spectra with adenine-1 standard with the typical fragment m/z = 192; C carries out
the similar comparison for cytosine with the typical fragment m/z = 282; D depicts this comparison for the adenine-2 mass spectrum with typical m/z = 306; E depicts this comparison for guanine with typical fragment m/z =
322; and F shows glycine with fragments m/z = 147, 226, and 246. The corresponding structures of typical mass fragments are depicted in Fig. S6.
Fig. S5. GC-MS detection of the simplest amino acid glycine in all of the experiments. All samples were analyzed after derivatization by with MTBSTFA.
A shows the chromatogram of a blank of the glycine standard, B shows the chromatogram of the experiment with irradiation of the mixture of NH3 + CO,
C depicts chromatogram of the experiment with NH3 + CO + H2O in presence of clay, and D shows the discharge decomposition of NH3 + CO + H2O. E and
F depict, respectively, chromatograms of adenine and cytosine glow discharge decomposition upon nitrogen atmosphere in presence of water vapor.
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Fig. S6. Structure and typical masses of main fragments of the canonical nucleic bases and glycine after derivatization. Corresponding chromatograms and
mass spectra are presented in the Figs. S3–S5.
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Fig. S7. Chromatograms of blank measurements, all of them with a silylation agent, together with a chromatogram of NH3 + CO + H2O discharge products for
comparison depicted in A. Nucleobases are observed on the parts per million level in this experiment. B and C show a chromatographic record of a cell for laser
shock wave experiment not exposed to plasma and discharge cell, respectively, both washed after 1 d with water; D shows chromatogram of a cell touched
with finger without gloves; and E shows a record of water after washing of montmorillonite catalyst. Numbers 1–9 mark manifold products of mutual reactions
in derivatization agent.
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