Prebiotic Chemistry of HCN Tetramerization by Automated Reaction Search

Automated Exploration of Reaction Networks and Mechanisms Based on Metadynamics Nanoreactor Simulations

We developed an automated approach to construct a complex reaction network and explore the reaction mechanisms for numerous reactant molecules by integrating several theoretical approaches. Nanoreactor-type molecular dynamics was used to generate possible chemical reactions, in which the metadynamics was used to overcome the reaction barriers, and the semiempirical GFN2-xTB method was used to reduce the computational cost. Reaction events were identified from trajectories using the hidden Markov model based on the evolution of the molecular connectivity. This provided the starting points for further transition-state searches at the electronic structure levels of density functional theory to obtain the reaction mechanism. Finally, the entire reaction network containing multiple pathways was built. The feasibility and efficiency of the automated construction of the reaction network were investigated using the HCHO and NH3 biomolecular reaction and the reaction network for a multispecies system comprising dozens of HCN and H2O molecules. The results indicated that the proposed approach provides a valuable and effective tool for the automated exploration of the reaction networks.

Impact of M Dwarfs Ultraviolet Radiation on Prebiotic Chemistry: The Case of Adenine

To date, several exoplanets have been found to orbit within the habitable zone of main sequence M stars (M dwarfs). These stars exhibit different levels of chromospheric activity that produces ultraviolet (UV) radiation. UV may be harmful to life, but it can also trigger reactions of prebiotic importance on the surface of a potentially habitable planet (PHP). We created a code to obtain the adenine yield for a known adenine synthesis route from diaminomaleonitrile (DAMN). We used computational methods to calculate the reaction coefficient rates (photolysis rate J and rate constant K) for the intermediate molecules DAMN, diaminofumaronitrile (DAFN), and 4-aminoimidazole-5-carbonitrile (AICN) of the adenine synthesis route. We used stellar UV sources and a mercury lamp to compare the theoretical results with experiments performed with lamps. The surface UV flux of planets in the habitable zone of two active M dwarfs (Proxima Centauri and AD Leonis) and the prebiotic Earth was calculated using the photochemical model ATMOS, considering a CO₂-N₂-H₂O atmosphere. We obtained UV absorption coefficients for DAMN and DAFN and thermodynamic parameters that are useful for prebiotic chemistry studies. According to our results, experiments using UV lamps may underestimate the photolysis production of molecules of prebiotic importance. Our results indicate that photolysis reactions are fast with a yield of 50% of AICN in 10 s for the young Sun and ∼1 h for Proxima Centauri b. Planets around active M dwarfs may provide the most favorable environment for UV-mediated production of compounds relevant to the origins of life. The kinetic reaction AICN + HCN  adenine is the bottleneck of the pathway with reaction rates <10^-22 L/(mol·s).

Methylenecyanamide (CH2═NCN) and (Z)- and (E)-Iminoacetonitriles (NC-CH═NH), Dimers of Hydrogen Cyanide

(Z)- and (E)-iminoacetonitriles (NCCH═NH), two hydrogen cyanide dimers, are described as key compounds in prebiotic chemistry. Among the many possible dimers of HCN with covalent bonds, even the second on the scale of thermodynamic stability, methylenecyanamide (CH₂═NCN), has been investigated little. We show that this compound can be isolated, is stable enough to give an adduct with a nucleophile or a diene, and can be easily generated under prebiotic conditions, highlighting a possible role in this medium. Comparison between isomers shows significant differences in formation and chemical reactivity.

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

For the first time, chemometrics was applied to the recently reported microwave-driven cyanide polymerization. Fast, easy, robust, low-cost, and green-solvent processes are characteristic of these types of reactions. These economic and environmental benefits, originally inspired by the constraints imposed by plausible prebiotic synthetic conditions, have taken advantage of the development of a new generation of HCN-derived multifunctional materials. HCN-derived polymers present tunable properties by temperature and reaction time. However, the apparently random behavior observed in the evolution of cyanide polymerizations, assisted by microwave radiation over time at different temperatures, leads us to study this highly complex system using multivariate analytical tools to have a proper view of the system. Two components are sufficient to explain between 84 and 98% of the total variance in the data in all principal component analyses. In addition, two components explain more than 91% of the total variance in the data in the case of principal component analysis for categorical data. These consistent statistical results indicate that microwave-driven polymerization is a more robust process than conventional thermal syntheses but also that plausible prebiotic chemistry in alkaline subaerial environments could be more complex than in the aerial part of these systems, presenting a clear example of the "messy chemistry" approach of interest in the research about the origins of life. In addition, the methodology discussed herein could be useful for the data analysis of extraterrestrial samples and for the design of soft materials, in a feedback view between prebiotic chemistry and materials science.

Formation and evolution of C-C, C-O, C[double bond, length as m-dash]O and C-N bonds in chemical reactions of prebiotic interest

A series of prebiotic chemical reactions yielding the precursor building blocks of amino acids, proteins and carbohydrates, starting solely from HCN and water is studied here. We closely follow the formation and evolution of the pivotal C-C, C-O, C[double bond, length as m-dash]O, and C-N bonds, which dictate the chemistry of the molecules of life. In many cases, formation of these bonds is set in motion by proton transfers in which individual water molecules act as catalysts so that water atoms end up in the products. Our results indicate that the prebiotic formation of carbon dioxide, formaldehyde, formic acid, formaldimine, glycolaldehyde, glycine, glycolonitrile, and oxazole derivatives, among others, are best described as highly nonsynchronous concerted single step processes. Nonetheless, for all reactions involving double proton transfer, the formation and breaking of O-H bonds around a particular O atom occur in a synchronous fashion, apparently independently from other primitive processes. For the most part, the first process to initiate seems to be the double proton transfer in the reactions where they are present, then bond breaking/formation around the reactive carbon in the carbonyl group and finally rupture of the C-N bonds in the appropriate cases, which are the most reluctant to break. Remarkably, within the limitations of our non-dynamical computational model, the wide ranges of temperature and pressure in which these reactions occur, downplay the problematic determination of the exact constraints on the early Earth.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C₁₂O₂Mg₂ system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol^-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

Aminomalononitrile inspired prebiotic chemistry as a novel multicomponent tool for the synthesis of imidazole and purine derivatives with anti-influenza A virus activity

Amino imidazole carbonitrile derivatives decorated with α-amino acid side-chains have been synthesized by a multicomponent microwave assisted reaction inspired by the prebiotic chemistry of aminomalononitrile as a tool for generating high chemical diversity. These compounds were used as annulation synthons for the preparation of 8,9-disubstituted-6,9-dihydro-1H-purin-6-ones by reaction with formic acid as a simple C-1 donor reagent. The novel heterocycles were characterized by significant activity against influenza A virus, amino imidazole carbonitrile derivatives showing the highest activity. Thus, the chemical complexity generated by prebiotic chemistry furnished a general tool for the identification of novel antiviral agents.

Amino imidazole carbonitrile derivatives decorated with α-amino acid side-chains have been synthesized by a multicomponent microwave assisted reaction inspired by the prebiotic chemistry of aminomalononitrile for generating high chemical diversity.

The Beginning of HCN Polymerization: Iminoacetonitrile Formation and Its Implications in Astrochemical Environments

Hydrogen cyanide (HCN) is known to react with complex organic materials and is a key reagent in the formation of various prebiotic building blocks, including amino acids and nucleobases. Here, we explore the possible first step in several such processes, the dimerization of HCN into iminoacetonitrile. Our study combines steered ab initio molecular dynamics and quantum chemistry to evaluate the kinetics and thermodynamics of base-catalyzed dimerization of HCN in the liquid state. Simulations predict a formation mechanism of iminoacetonitrile that is consistent with experimentally observed time scales for HCN polymerization, suggesting that HCN dimerization may be the rate-determining step in the assembly of more complex reaction products. The predicted kinetics permits for iminoacetonitrile formation in a host of astrochemical environments, including on the early Earth, on periodically heated subsurfaces of comets, and following heating events on colder bodies, such as Saturn's moon Titan.

Six Low-Lying Isomers of C11H8 Are Unidentified in the Laboratory-A Theoretical Study

Isomers of C₁₁H₈ have been theoretically examined using density functional theory and coupled-cluster methods. The current investigation reveals that 2aH-cyclopenta[cd]indene (2), 7-ethynyl-1H-indene (6), 4-ethynyl-1H-indene (7), 6-ethynyl-1H-indene (8), 5-ethynyl-1H-indene (9), and 7bH-cyclopenta[cd]indene (10) remain elusive till date in the laboratory. The puckered low-lying isomer 2 lies at 9 kJ mol^-1 below the experimentally known molecule, cyclobuta[de]naphthalene (3), at the fc-CCSD(T)/cc-pVTZ//fc-CCSD(T)/cc-pVDZ level of theory. 2 lies at 36 kJ mol^-1 above the thermodynamically most stable and experimentally known isomer, 1H-cyclopenta[cd]indene (1), at the same level. It is identified that 1,2-H transfer from 1 yields 2H-cyclopenta[cd]indene (14) and subsequent 1,2-H shift from 14 yields 2. Appropriate transition states have been identified, and intrinsic reaction coordinate calculations have been carried out at the B3LYP/6-311+G(d,p) level of theory. Recently, 1-ethynyl-1H-indene (11) has been detected using synchrotron-based vacuum ultraviolet ionization mass spectrometry. 2-Ethynyl-1H-indene (4) and 3-ethynyl-1H-indene (5) have been synthetically characterized in the past. While the derivatives of 7bH-cyclopenta[cd]indene (10) have been isolated elsewhere, the parent compound remains unidentified till date in the laboratory. Although C₁₁H₈ is a key elemental composition of astronomical interest for the formation of polycyclic aromatic hydrocarbons in the interstellar medium, none of its low-lying isomers have been characterized by rotational spectroscopy though they are having a permanent dipole moment (μ ≠ 0). Therefore, energetic and spectroscopic properties have been computed, and the present investigation necessitates new synthetic studies on C₁₁H₈, in particular 2, 6-10, and also rotational spectroscopic studies on all low-lying isomers.

A Comprehensive Review of HCN-Derived Polymers

HCN-derived polymers are a heterogeneous group of complex substances synthesized from pure HCN; from its salts; from its oligomers, specifically its trimer and tetramer, amino-nalono-nitrile (AMN) and diamino-maleo-nitrile (DAMN), respectively; or from its hydrolysis products, such as formamide, under a wide range of experimental conditions. The characteristics and properties of HCN-derived polymers depend directly on the synthetic conditions used for their production and, by extension, their potential applications. These puzzling systems have been known mainly in the fields of prebiotic chemistry and in studies on the origins of life and astrobiology since the first prebiotic production of adenine by Oró in the early years of the 1960s. However, the first reference regarding their possible role in prebiotic chemistry was mentioned in the 19th century by Pflüger. Currently, HCN-derived polymers are considered keys in the formation of the first and primeval protometabolic and informational systems, and they may be among the most readily formed organic macromolecules in the solar system. In addition, HCN-derived polymers have attracted a growing interest in materials science due to their potential biomedical applications as coatings and adhesives; they have also been proposed as valuable models for multifunctional materials with emergent properties such as semi-conductivity, ferroelectricity, catalysis and photocatalysis, and heterogeneous organo-synthesis. However, the real structures and the formation pathways of these fascinating substances have not yet been fully elucidated; several models based on either computational approaches or spectroscopic and analytical techniques have endeavored to shed light on their complete nature. In this review, a comprehensive perspective of HCN-derived polymers is presented, taking into account all the aspects indicated above.

A dual perspective on the microwave-assisted synthesis of HCN polymers towards the chemical evolution and design of functional materials

In this paper, the first study on NH4CN polymerization induced by microwave radiation is described, where a singular kinetic behaviour, especially when this reaction is conducted in the absence of air, is found. As a result, a complex conjugated N-heterocyclic polymer system is obtained, whose properties are very different, and even improved according to morphological features, characterized by their X-ray diffraction patterns and scanning electron microscopy analysis, with respect to those produced under conventional thermal treatment. In addition, a wide variety of relevant bioorganics have been identified, such as amino acids, nucleobases, co-factors, etc., from the synthetized NH4CN polymers. These particular families of polymers are of high interest in the fields of astrobiology and prebiotic chemistry and, more recently, in the development of smart multifunctional materials. From an astrobiological perspective, microwave-driven syntheses may simulate hydrothermal environments, which are considered ideal niches for increasing organic molecular complexity, and eventually as scenarios for an origin of life. From an industrial point of view and for potential applications, a microwave irradiation process leads to a notable decrease in the reaction times, and tune the properties of these new series macromolecular systems. The characteristics found for these materials encourage the development of further systematic research on this alternative HCN polymerization.

Theoretical Investigations on the Possibility of Prebiotic HCN Formation via O-Addition Reactions

Until now, reactions between methane photolysis products (CH₃^•, CH₂) and active N atom or reactive NO radical are proposed as routes of HCN formation in the prebiotic Earth. Scientists think that the reducing atmosphere of primitive Earth was made of H₂, He, N₂, NO, CH₄, H₂O, CO₂, etc., and there was no molecular oxygen. However, it has been evident from experiments that the vacuum ultraviolet (VUV) photolysis of CO₂ can produce atomic oxygen. Therefore, it can be presumed that atomic oxygen was likely present in early Earth's atmosphere. Was there any impact of atomic oxygen in production of early atmospheric HCN for the emergence of life? To hunt for the answer, we have employed computational methods to study the mechanism and kinetics of CH₃NO + O(¹D) and CH₂NO^• + O(³P) addition reactions. Current study suggests that the addition of O(¹D) into nitrosomethane (CH₃NO) and the addition of O(³P) into nitrosomethylene radical (CH₂NO^•) can efficiently produce HCN through an effectively barrierless pathway. At STP, Bartis-Widom phenomenological loss rate coefficients of O(¹D) and O(³P) are obtained as 2.47 × 10^-12 and 4.67 × 10^-11 cm³ molecule^-1 s^-1, respectively. We propose that addition reactions of atomic oxygen with CH₃NO and CH₂NO^• might act as a potential source for early atmospheric HCN.

Si2C5H2 isomers - search algorithms versus chemical intuition

The pros and cons of using search algorithms alone in identifying new geometries have been discussed by using the Si₂C₅H₂ elemental composition as an example. Within 30 kcal mol^-1 at the CCSD(T)/def2-TZVP//PBE0/def2-TZVP level of theory, the coalescence kick and cuckoo methods postulate merely four isomers (1, 3, 6, and 7) for Si₂C₅H₂ (O. Yañez et. al., Chem. Commun., 2017, 53, 12112). On the contrary, chemical intuition yields fourteen (2, 4, 5, and 8-18) new isomers within the same energy range at the B3LYP/6-311++G(2d,2p) level of theory. Based on the relative energies of the first eleven isomers of Si₂C₅H₂ (1, C_2v, 0.00; 2, C_s, 21.39; 3, C_s, 21.95; 4, C_s, 22.76; 5, C_s, 24.74; 6, C_s, 25.34; 7, C_s, 25.64; 8, C_s, 25.79; 9, C_s, 27.20; 10, C_2v, 28.59; and 11, C_2v, 29.16 kcal mol^-1) calculated at the CCSD(T)/cc-pVTZ level of theory, it is evident that the search algorithms had missed at least seven isomers in the same energy range. The relative energy gaps of isomers 12-18 fall in the range of 30-40 kcal mol^-1 at the latter level of theory. Consequentially, this scenario triggers a speculation going forward with search algorithms alone in the search of all new isomers. While one cannot underestimate the power of these algorithms, the role of chemical intuition may not be completely neglected. Retrospectively, the fourteen new isomers found by chemical intuition may help in writing better search algorithms. All eighteen isomers - including the most stable isomer with a planar tetracoordinate carbon atom 1- remain elusive in the laboratory to date. Thus, structural and spectroscopic parameters have been presented here, which may possibly aid the future experimental studies.

CH3NO as a potential intermediate for early atmospheric HCN: a quantum chemical insight

Hydrogen cyanide (HCN) has played a central role in the production of several biological molecules under prebiotic conditions on primitive Earth. Previously, K. J. Zahnle (J. Geophys. Res.: Atmos., 1986, 91, 2819) and Tian et al. (Earth Planet. Sci. Lett., 2011, 308, 417) emphasized that HCN production in the early Earth's CH₄-rich atmosphere could have been possible through the reaction between active nitrogen atoms (N) and methane photolysis products. Here, we have proposed alternative pathways for the formation of early atmospheric HCN via the decomposition of CH₃NO as an intermediate. In the early Earth's O₂-free atmosphere, CH₃˙ could preferentially attach to NO, which was generated via early atmospheric volcanism or lightning and photochemical processes. We have quantum chemically explored both unimolecular and bimolecular decomposition pathways of CH₃NO via the assistance of another CH₃NO molecule and via H₂O, NH₃, HCl, HCOOH, HNO₃ and H₂SO₄ catalysis. Both energetic and kinetic analyses reveal that H₂SO₄ is more efficient in this regard than other atmospheric species. Overall, it has been suggested that the proposed bimolecular decomposition pathways might have been alternative pathways for the formation of HCN under certain conditions on prebiotic Earth, while the unimolecular decomposition of CH₃NO could lead to the formation of HCN in the high temperature volcanic environment on early Earth.

A Global Optimizer for Nanoclusters

We have developed an algorithm to automatically build the global minimum and other low-energy minima of nanoclusters. This method is implemented in PyAR (https://github.com/anooplab/pyar) program. The global optimization in PyAR involves two parts, generation of several trial geometries and gradient-based local optimization of the trial geometries. While generating the trial geometries, a Tabu list is used for storing the information of the already used trial geometries to avoid using the similar trial geometries. In this recursive algorithm, an n-sized cluster is built from the geometries of n−1 clusters. The overall procedure automatically generates many unique minimum energy geometries of clusters with size from 2 up to n using this evolutionary growth strategy. We have used our strategy on some of the well-studied clusters such as Pd, Pt, Au, and Al homometallic clusters, Ru-Pt and Au-Pt binary clusters, and Ag-Au-Pt ternary cluster. We have analyzed some of the popular parameters to characterize the clusters, such as relative energy, singlet-triplet energy difference, binding energy, second-order energy difference, and mixing energy, and compared with the reported properties.

A Comparative Study on HCN Polymers Synthesized by Polymerization of NH4 CN or Diaminomaleonitrile in Aqueous Media: New Perspectives for Prebiotic Chemistry and Materials Science

HCN polymers are a group of complex and heterogeneous substances that are widely known in the fields of astrobiology and prebiotic chemistry. In addition, they have recently received considerable attention as potential functional material coatings. However, the real nature and pathways of formation of HCN polymers remain open questions. It is well established that the tuning of macromolecular structures determines the properties and practical applications of a polymeric material. Herein, different synthetic conditions were explored for the production of HCN polymers from NH₄ CN or diaminomaleonitrile in aqueous media with different concentrations of the starting reactants and several reaction times. By using a systematic methodology, both series of polymers were shown to exhibit similar, but not identical, spectroscopic and thermal fingerprints, which resulted in a clear differentiation of their morphological and electrochemical properties. New macrostructures are proposed for HCN polymers, and promising insights are discussed for prebiotic chemistry and materials science on the basis of the experimental results.

Fundamental Vibrational Analyses of the HCN Monomer, Dimer and Associated Isotopologues

In this work we provide high level ab initio treatments of the structures, vibrational frequencies, and electronic energies of the HCN monomer and dimer systems along with several isotopologues. The plethora of information related to this system within the literature is summarized and serves as a basis for comparison with the results of this paper. The geometry of the dimer and monomer are reported at the all electroncoupled-cluster singles, doubles, and perturbative triples level of theory [AE-CCSD(T)] with the correlation consistent quadruple-zeta quality basis sets with extra core functions (cc-pCVQZ) from Dunning. The theoretical geometries and electronic structures are further analyzed through the use of the Natural Bond Orbital (NBO) method and Natural Resonance Theory (NRT). At the AE-CCSD(T)/cc-pCVQZ level of theory, the full cubic with semi-diagonal quartic force field for nine dimer and four monomer isotopologues (the parent isotopologue along with 15 N, 13 C, and D derivatives) were obtained to treat the anharmonicity of the vibrations via second order vibrational perturbation theory (VPT2). Lastly, the enthalpy change associated with the formation of the dimer from two monomer units was determined using the focal point analysis. Computations including coupled-cluster through perturbative quadruples as well as basis sets up to six-zeta quality, including core functions (cc-pCVXZ, X=D,T,Q,5,6) were used to extrapolate to the AE-CCSDT(Q)/CBS energy associated with this hydrogen-bond forming process. After appending anharmonic zero-point vibrational, relativistic, and diagonal Born-Oppenheimer corrections, we report a value of -3.93 kcal mol-1 for the enthalpy of formation. To our knowledge, each set of results (geometries, vibrational frequencies, and energetics) reported in this study represents the highest-level and most reliable theoretical predictions reported for this system.