Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth.

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH4 is the most efficient carbon source to produce amino acids, while CO and CO2 lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N2, NH3) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH3 in primordial oceans and to the production and liberation of molecular O2 into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.

Introduction

Since the pioneering works of Urey and Miller,[1−6] numerous studies have shown that a large variety of biologically important molecules can be synthesized using different compositions of gases and energy sources.[7−13] The chemical conditions employed ranged from highly reducing to oxidizing conditions containing CH4, CO, and CO2. Although we do not know the actual composition of early Earth’s atmosphere, the current view is that the atmosphere consisted mainly of CO2, N2, and H2O with minor amounts of CO and H2.[7]

About a decade ago, Ben-Amots and Anbar[14] hypothesized that bubble collapse during cavitation should be a highly efficient energy source for synthesis of biologically important molecules from simple primordial dissolved gases. They provided order-of-magnitude estimations demonstrating that sonochemical processes could be much more energy-efficient than lightning or meteorite impacts on Earth’s surface. It was additionally demonstrated that cavitation occurs in massive amounts in breaking sea waves, waterfalls, and rivers.[15,16] The collapse of bubbles in liquids results in an enormous concentration of energy from the conversion of the kinetic energy of the liquid motion into heating the content of the shrinking bubble. The high local temperatures (∼5000 K) and pressures (∼1000 atm), combined with extraordinarily rapid cooling rates (>1010 K s1–) due to the infinitely large cold ocean reservoir provide a unique environment for driving chemical reactions. In the cavitation of a single bubble, the conditions can be even more extreme. Cavitation is more likely to occur at the surface of microscopic mineral particulates, where the cohesive forces of water are weaker and catalytic effects of mineral surfaces can be exploited for the sonochemical synthesis of biomolecules. This means that even if the primary sonochemical carbonaceous products in water are dilute, there is a high probability of their involvement in subsequent catalytic sonochemical events. Cavitation was also shown to occur at hydrothermal vents,[17] a likely environment for the buildup of biomolecules. Recently, an experimental demonstration of sonochemical production of a wide variety of organic compounds related to the origin of life on Earth from simple gases has been demonstrated.[18] However, due to the complex nature and wide variety of several interrelated chemical reactions that occur during a bubble collapse, it is very challenging to infer mechanistic insights and decipher the underlying chemistry with molecular resolution. Moreover, the generally minute amounts of intermediates and stable species obtained limit their detection and might lead to missing links between possible important species.

In this study, we quantitatively assess the role of bubble collapse and cavitation on the synthesis of biologically significant organic molecules, using state of the art computational methods. Employing reactive molecular dynamics simulations coupled with shock-induced chemistry methodology,[19] we directly observe the chemical events occurring inside a collapsing bubble with atomistic resolution for long enough periods of time. This atomistic resolution is not accessible at present in most experimental methods or ab initio calculations. The main focus of the present study is to understand the relationship between several possible atmospheric compositions of dissolved primordial gases and sonochemical products obtained following a cavitation process. The rest of the paper is organized as follows: The Results and Discussion section starts with a detailed description of the chemical reactions that occur during a bubble collapse stage, followed by a description of the reaction products obtained following the cooling and expansion periods at the end of the cavitation process. The description of the results is concluded with the description of the mechanisms leading to the production of some simple reaction products. Following Results and Discussion, conclusions are described. The paper ends with the description of the computational method used to simulate the cavitation process.

Results and Discussion

A total of a dozen systems with different initial compositions were n class="Chemical">considered; see Table .

Table 1

Carbon and Nitrogen Sources in the Different Systems Considereda

system	carbon source	nitrogen source	HCN
1	CO	N2	no
2	CO2	N2	no
3	CH4	N2	no
4	CO	NH3	no
5	CO2	NH3	no
6	CH4	NH3	no
7	CO	N2	yes
8	CO2	N2	yes
9	CH4	N2	yes
10	CO	NH3	yes
11	CO2	NH3	yes
12	CH4	NH3	yes

The number of carbon and nitrogen source molecules is 100 for systems 1–6, while for systems 7–12 100 HCN molecules were added. The number of water molecules in all systems was set to 1000.

The number of carbon and n class="Chemical">nitrogen source molecules is 100 for systems 1–6, while for systems 7–12 100 HCN molecules were added. The number of water molecules in all systems was set to 1000.

Besides water molecules, which are the majority species in the bubble, different possibilities for carbon and nitrogen sources were examined. Various atmospheric compositions were examined because of the uncertainty in the exact composition. Moreover, the composition of the atmosphere varied during the years after Earth cooled down. Accurate ratios of primordial gases in the atmosphere are not known. Hence, the main focus in the present study is to understand how different sources of carbon and nitrogen affect the synthesis of biogenic molecules in the collapsing bubble (i.e., CO2 vs CO vs CH4 as a carbon source and likewise for nitrogen). A quantitative assessment of kinetics that would definitely be affected by initial concentrations of the reactants is beyond the scope of this study. This question will be addressed in a future study. It should be noted that similar ratios (∼1:1) of reactant carbon and nitrogen sources were used in several recent studies of Miller-like reactions.[20]

Consequently, the simulated systems span the range of possible reactant compositions, starting with a highly oxidizing atmosphere (systems 1 and 2), up to highly reducing conditions (system 6). In addition, to provide a mechanistic insight for the enhancing effect of HCN on biomolecule synthesis that was reported in several studies,[12,21] a duplicate set of systems 1–6 was created containing HCN in addition to the carbon and nitrogen sources (systems 7–12). Water molecules were chosen to be the major species in the collapsing bubble since the solubility of the other reactant gases is relatively low. In addition, it was demonstrated that vapor condensation rates are much slower than previously assumed, hence, vapors become highly supersaturated during bubble collapse.[22] The authors of ref (21) concluded that water vapor, rather than any particular gas, is the main component of collapsing bubbles.

A complex scheme of reactions occurs during bubble collapse. At this stage, elevated temperatures lead to rapid rupture of covalent bonds and to formation of new bonds with higher complexity. However, the high pressures dictate a short lifetime of many intermediates. Thus, observing such events in conventional experiments would be nearly impossible. In contrast, during the cooling regime and in ambient conditions, significantly fewer chemical transformations occur and a system reaches its final state of product synthesis. In the remainder of this section the key chemical reactions that occur during the bubble collapse stage and in the subsequent ambient conditions are identified and discussed.

Bubble Collapse and Subsequent Sonochemical Synthesis of Organic Molecules

A wide variety of organic molecules are observed during the bubble collapse. To obtain a rough estimate of the identity of the most frequently formed molecules, we counted their number of occurrences during the simulation. The results are shown in Table S2. Two of the products show an interesting behavior: hydroxylamine and isocyanic acid. These products are produced with high frequency for all systems examined but two, systems containing ammonia as nitrogen source (systems 6 and 12). Analysis of the reaction events leading to the formation of isocyanic acid reveals that mainly two reactions are operable and involve CON as a reagent:In the case of a reducing atmosphere, containing CH4 and NH3 (system 6), CON does not form at all, which might explain the reduced formation of isocyanic acid. The only source of isocyanic acid formation in this case is the decomposition of larger molecules, mainly CH2ON, but this occurs at a rather low frequency. In the case of hydroxylamine, the observed reactions that lead to its formation in oxidizing atmospheres areWhile in a reducing atmosphere (when CH4 and NH3 act as carbon and nitrogen sources), H2ON is not formed whatsoever, and •NH2 is not produced in significant amounts by NH3 decomposition. Instead, NH3 is present in the system mainly as NH3 and NH4 due to a high number of free hydrogen atoms in the system produced by water decomposition.

The inclusion of HCN as an additional nitrogen and carbon source (systems 7–12) leads to a marked increase in the quantity of many organic reaction products, in accordance with recent findings that indicated the role of HCN in the synthesis of precursors to RNA, proteins, and lipids.[46]

Mass distributions (Figure ) were calculated for every system as a quantitative measure assessing the complexity of formed products. From the top row in Figure it is evident that the largest quantity of species with a very wide chemical variety is obtained when CO2 serves as the carbon source and when pure N2 is the nitrogen source. The same trend holds when NH3 acts as nitrogen source. The addition of HCN (bottom two rows in Figure ) promotes a further increase in the number of molecular species and results in slightly wider mass distributions. The distributions obtained when CO and CO2 are carbon sources are very similar, regardless of the nature of nitrogen source. In most cases, the intensities are higher when CO and CO2 act as carbon sources than those when CH4 is used.

Figure 1

Average mass distribution during bubble collapse. The vertical axis represents the number of species with a given mass, averaged over 10 ps starting at t = 40 ps. Masses corresponding to species associated with the amino acid backbone, NCCOO, or related to the formation of species in this family are shown explicitly. The distribution only includes species with at least one carbon/nitrogen or three oxygen atoms in order to eliminate the very high peaks of water decomposition byproducts.

Sorting the molecular species identified during bubble collapse stage shows the formation of small quantities of transient amino acids. Typical molecules are shown as insets in Figure . Their lifetime is on the order of 10–20 fs, and they rapidly transform into more stable products. We calculated the total number of reaction products with an amino acid backbone (NCCOO). The results are presented, as a function of the carbon source used, in Figure . Our data imply that when NH3 is the only nitrogen source in the system, negligible amounts of NCCOO-based species form, regardless of the carbon source. The situation is similar when CO and CO2 are the carbon sources and N2 is the nitrogen source. The amount of NCCOO-based molecules is significant only for the mixture of CH4 and N2. When HCN is added to N2, even more NCCOO backbone species are produced. On the other hand, their amount decreases as the system becomes more oxidizing. However, this behavior is reversed when HCN is added and NH3 is the nitrogen source. In this case, the smallest amount of NCCOO-based intermediates is obtained for CH4, while changing the carbon source to a more oxidizing one leads to increased amounts of NCCOO-based molecules. This behavior parallels the change in the produced amounts of cyanamide. The presence of HCN in the system generally increases the number of cyanamide occurrences by a factor of 2–9 (Table S2). These findings are supported by published studies demonstrating that the presence of cyanamide increases the synthesis yield of amino acids and peptides.[23]

Figure 2

Number of amino acid backbones (NCCOO) generated during 50 ps simulation of bubble collapse. The horizontal axis shows the carbon source used, and each line corresponds to a different nitrogen source.

Post-collapse Dynamics at Ambient Conditions

During the transition from the hot dense fluid inside the collapsing bubble into the cooled and pressure-relaxed state, most of the unstable and radical intermediates are replaced with stable molecules. Thus, the mass spectra (MS) calculated in these ambient conditions are markedly simplified. The MS of all 12 systems are presented in Figure . Inspection of these spectra reveals some interesting findings. For the case of CO2 as the carbon source, a mixture with N2 leads to synthesis of several molecules with known biological functions,[11,12,20,23] such as cyanamide, isocyanic acid, and hydroxylamine. The addition of HCN to the mixture also results in an increased production of cyanamide molecules. In these cases, mainly simple organic molecules containing a single carbon atom are produced. When the nitrogen source used is NH3 or a mixture of NH3 + HCN, the amount of these organic products decreases, however, larger molecules and clusters with multiple carbon atoms are formed. In the case of CO as the carbon source, these organic molecules are obtained only when N2 or N2 + HCN are used. In this case, the use of NH3 or its mixture with HCN as reactants leads to negligible amounts of these organic products; however, larger molecules containing several carbon atoms are synthesized.

Figure 3

Mass spectra (only masses over 30 g/mol are shown) obtained for all 12 systems examined after system cool-down.

In systems where CH4 is used as the carbon source (right column in Figure ), the spectra become much richer, indicating more efficient synthesis of different complex organic molecules. The use of CH4 as carbon source seems to enhance addition reactions during cavitation to form C (n > 3) containing molecules. This behavior is markedly enhanced when N2 is replaced by NH3 (systems 6 and 12). Here one obtains large carbon clusters (some with more than 70 atoms; see Figure S14 for example) and a relatively low yield of small molecules.

The results presented in Figure suggest that the use of N2 leads mostly to synthesis of simple organic reaction products containing C, N, and O. At the high temperatures reached during bubble collapse, water molecules decompose to yield •H and •OH radicals. The •H radicals are observed to react with N2 molecules sequentially to yield N2H with n = 1–6. In each case where the •H radicals are unevenly distributed between the two N atoms, the atom with the least amount of H atoms is expected to be highly reactive and can easily form C–N or N–O bonds. Hence, during cavitation, the low concentration of carbon source molecules and the high concentration of •H, N2 serves as a more efficient reactive nitrogen source than NH3, resulting in synthesis of small biologically important organic molecules with higher yield.

Let us examine now the formation of NH3 and O2 as sonochemical products. The variation in the produced amounts of these species is presented in Figure as the difference between the final and initial amounts. Note that in all cases the initial amount of each one of the nitrogen containing molecules (NH3, N2, and HCN) was 100 molecules.

Figure 4

Production of NH3 and O2 at the end of the simulations: (a) NH3 and (b) O2. In all cases the initial amounts of each one of the nitrogen containing molecules (NH3, N2, and HCN) was 100 molecules. Note that O2 is normalized by dividing by the total number of oxygen atoms, which varies between 1000 and 1200 for the different systems, whereas NH3 is normalized by the total number of nitrogen atoms, which varies between 100−300 for the different systems.

From Figure a it is inferred that a more reduced carbon source leads to larger production of NH3. In addition, N2 leads to a significant production of NH3 via nitrogen fixation. This process is markedly enhanced by the presence of HCN. This large NH3 production from N2 was also observed in a recent study of sonolysis of aqueous mixtures in nitrogen atmosphere.[18] The present simulations suggest that H• radicals and water molecules independently react with molecular N2 to produce various N2H (n = 1–5) species (reactions and 7) that dissociate into dinitrogen hydrides (reactions ), finally producing two NH3 molecules (reaction ). The overall mechanism observed isHCN enhances the production of NH3 mainly due to supply of an additional nitrogen source that facilitates a hydrogenation of the HCN species and further disintegration similarly to the reaction network shown above.

Inspection of the results in Figure b shows that the cavitation process is also the driving force to the generation of molecular oxygen in oxidizing atmospheres containing the carbon oxides, CO and CO2. In the case of CO2 and CO, all nitrogen sources considered here lead to O2 release. Mixtures with N2 and N2 + HCN give rise to larger amount of O2 than those obtained by NH3 and NH3 + HCN, by a factor ∼2–3. When CH4 is used as carbon source, only negligible amounts of O2 are obtained, meaning that H2O does not contribute to O2 production. In this case, the only source for oxygen is water and the reactions leading to O2 formation have a low probability of occurrence. Analysis of the bond rupture and formation during the simulations reveals the following mechanism for oxygen production:

Effects of Sequential Cavitation Events

As presented previously,[14] cavitation is an inherently autocatalytic process. To illustrate the effect of subsequent cavitation events on the production of more complex molecules, an additional simulation was performed on the system that produced the largest variety of reaction products (system 9, see Figure ). The major products of system 9 after its cooling and expansion period were added to the original initial composition of this system. This resulted in a reactant composition of 100 CH4, 260 NH3, 131 CO, 35 CHON, 100 N2, 100 HCN, 1000 H2O, 5 HNCNH, and 20 H2NCN molecules. This system was then subjected to the shock-induced decomposition methodology, to simulate a successive cavitation event on the previously obtained products. The mass spectra obtained after the first and second cavitation events are presented in Figure . It is inferred that the subsequent cavitation results in a marked increase in the chemical variety together with an increase in the amounts of reaction products. This clearly demonstrates that consecutive cavitation processes could lead to increasingly complex reaction products starting from simple molecules.

Figure 5

Mass spectra at (a) end of the simulation of system 9 and (b) end of successive cavitation event on system 9 main products and atmospheric gases.

Summary and Conclusions

The suggestion that cavitation had a significant role in the development of life on earth was raised over 60 years ago.[14,15] However, very little research effort was aimed at revealing the importance of this suggestion mainly because of the limitations of the experimental equipment available to measure chemical species with high resolutions for ultrashort time scales. The present study used computer simulations with a reactive molecular dynamics approach to elucidate the potential role of cavitation in the synthesis of organic molecules of biological importance. According to the results, cavitational processes have had significant contributions to the synthesis of biologically important molecules. Figure summarizes the main findings obtained in the present study. The top part shows the various atmospheric compositions considered. The next section in Figure presents the richness of transient reaction products formed during the bubble collapse. Among these reaction intermediates are several examples of biologically significant molecules identified in the various conditions. The lower half of Figure presents the stable reaction products identified at the end of the cooling period. All the molecules presented are precursors in the synthesis of biologically required end-products as shown by the links. Thus, one can regard the collapsing bubble as a microbioreactor that generates complex reaction products from simple inorganic reactants due to the extreme conditions that develop for a very short time within the collapsing bubble. The frequent and enormous amounts of cavitation processes are expected to increase the concentration of many reaction products. Consequently, reaction products formed in previous cavitation processes become reactants in later events and lead to the synthesis of more complex molecules.

Figure 6

Stable and short-lived products of cavitation-induced synthesis for a wide variety of atmospheric compositions.

The use of CH4 as a n class="Chemical">carbon source is highly efficient in producing molecules with the backbone required to obtain amino acids. However, if carbon oxides serve as the sole carbon source, one obtains products with NCCOO backbone mainly when NH3 with HCN are both present.

Experimental studies related to the chemistry of aqueous solutions in an ultrasonic field report results that are related to various aspects of the present study. For example, it was shown that CO2 led mainly to production of CO as product,[24−26] together with organic reaction products including formic acid and formaldehyde. These findings are in good agreement with our results. It was also shown that O2[25] is a possible cavitation product with continuous production as was discussed above. Several studies by Sokolskaya[27,28] have demonstrated that different mixtures of reacting gases such as CO, H2, and N2 result in synthesis of NH3, small amounts of HCN, and formaldehyde. The formaldehyde is also produced when starting CO is replaced by CH4. Similar results were obtained in our simulations that included these reactants. An additional experimental study[29] confirmed the formation of glycine, alanine, and glutamic acid as sonolysis products of solutions containing hydroxylamine and formaldehyde. Henglein et al.[26] demonstrated that sonolysis of solutions in the presence of CH4 yields different carbon containing organic products including ethane, ethylene, formaldehyde, and several C (n = 3, 4) containing products, as well as large amounts of H2. The production of hydrogen was also confirmed to be a result of laser- and spark-induced cavitation bubbles.[30] These types of organic compounds were also found in our simulations starting with methane as the carbon source. A study that started with formamide in water[31] in an N2 atmosphere as reactants resulted in the production of glycine, alanine, and aspartic acid. It was found that longer sonication times increased the concentration of amino acids but the concentration of formamide remained nearly constant, suggesting that it is also formed during the sonication. Formamide was found to be an intermediate in simulations that started with N2 as nitrogen source, in good agreement with the experimental findings. Several studies related to sonolysis in the presence of N2 have been carried out. Supeno et al.[32] reports that unless oxygen is present as an initial reactant, no NO is generated. Others[18,27] report NH3 as a major product when the nitrogen source is N2. All this experimental data is consistent with our findings. Dharmarathne et al.[18] suggest a mechanism of N–N bond rupture that led to disappearance of molecular N2, based on the reaction O + N2 → NO + N. Our results indicate that the dissociation of molecular N2 takes place by reduction derived by water-originating hydrogen atoms, as described above. Furthermore, they report on the formation of several amino acids, including glycine and alanine, as products when starting with either acetic acid, CH4 and CO2. This on par with our results.

The results reported in this study suggest that cavitation processes contributed to the synthesis of organic compounds in primordial Earth. At present, it is believed that the composition of the primordial atmosphere was neutral, containing mainly CO2 and N2.[7,10,33−37] For these reactants, cavitation is a very efficient process for converting N2 into NH3. Hence, the cavitation process might have contributed in converting the atmospheric composition into a more reducing one. In addition, the high solubility of ammonia in water could increase markedly the participation of NH3 in more complex reactions as well as increase the pH of oceans. Moreover, when CO2 is the main carbon source in the atmosphere, cavitation leads to an increase in the O2 content. The very limited solubility of oxygen in water suggests that most of the O2 was released into the atmosphere.

The results presented here can be used to estimate the amount of reaction products expected in a single bubble collapse event. Ben-Amots and Anbar[14] estimated that the number of reaction products formed in a single cavitation event are on the order of 109. Assuming that the size of an average bubble is 50 μm in diameter (consistent with 10,000 bubbles in a cm3 as assumed in ref (14)), the number of reaction products obtained for each one of the systems multiplied by the volume ratio between an average bubble and the simulation volume will yield the number of reaction products in a single bubble collapse. The calculated number of organic molecules formed during the bubble collapse based on the results presented here is in the range 0.7–6.0 × 1013, and this value can increase in consecutive cavitation events to 1.14 × 1014 or more. These values are 4–5 orders of magnitude larger than the value used by Ben-Amots and Anbar.[14] Our estimation can be viewed as an upper bound.

In conclusion, the present study demonstrated, using computer simulations, that naturally occurring cavitation in primordial oceans can yield biologically important organic molecules under a wide range of atmospheric compositions. Cavitation certainly was not the only active synthesis mechanism, but it had a significant contribution.

Computational Method

ReaxFF-RMD[38−42] simulations were employed to reveal the chemical transformations taking place under a simulated cavitation event in primordial gases dissolved in a water bubble. The simulations employ a recently developed reactive force field (ReaxFF) designed to reproduce density functional theory calculations of conformations and dynamics in amino acids, short peptides, proteins, and pharmaceutical molecules in gas phase and aqueous solutions.[43] The force field is an evolution of previous force fields describing glycine[44] and hydrocarbon oxidation[45] in extreme conditions. Both ambient and high-energy bonding environments including the rupture and formation of chemical bonds were included in the training sets to properly account for dynamics in extreme conditions of temperature and pressure, such as occur during the collapse of a cavitation bubble. Our method is limited to describing the dynamics on the ground electronic state. While this might lead to unacceptable errors for temperatures above >104 K (>1 eV), where significant ionization and excitations are present, for temperatures below ∼6000 K (0.5 eV), one can safely neglect excited state dynamics, as was recently justified in ground state dynamics of a detonating liquid explosive.[38] The calculations were carried out in a sequence of steps during which the extreme conditions that develop due to collapse are followed by a cooling and volume-expansion period resulting in ambient temperature and pressure conditions.

The general protocol for the calculations is the following:

Twelve systems were prepared with different chemical gaseous compositions, representing highly reducing to highly oxidizing atmospheres, see Table . The initial density of all systems was ∼1.0 g/cm3 so that relatively smaller initial simulation cells could be used with a sufficient number of molecules in the system while still obtaining reliable statistics. Each system was independently subjected to a converging shock wave, during which chemical bonding between the various atoms was monitored.

Atomistic scale description of cavitation was modeled using two converging planar shock waves resembling a single uniaxial collapsing bubble. A similar method was recently used to study shock-induced chemistry of high-energy-containing nanobubbles.[19] A schematic description of this approach is presented in Figure . The high pressure and temperature conditions achieved were maintained for 50 ps to reach a steady state.

Figure 7

Illustration of the computational system used to simulate a collapsing water bubble with dissolved primordial gases. The inertial collapse process is approximated by moving the system boundaries in a constant velocity, vp, generating two uniaxially converging planar shock fronts with velocity vs. The shock fronts drive the system into a hot, compressed state until the time the two symmetric shock fronts meet at the middle of the cell. At this precise moment, the system stops compressing and dynamics continues in the standard microcanonical ensemble in a fully shocked system.

After 50 ps, the compressed volume was allowed to expand to preshock density (1 g/cm3). The system cooled down by about 400 K during the volume expansion, and its cooling rate was further maintained for approximately 30 ps until room temperature was reached.

The simulation ended following an additional equilibration period for 10 ps at T = 300 K.

A detailed description of the computational methods used in the present study is given in the Supporting Information.