Formation of Amino Acid Precursors in the Interstellar Medium. A DFT Study of Some Gas-Phase Reactions Starting with Methylenimine

Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations

Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.

Fragmentation of propionitrile (CH3CH2CN) by low energy electrons

Propionitrile (CH₃CH₂CN, PN) is a molecule relevant for interstellar chemistry. There is credible evidence that anions, molecules, and radicals that may originate from PN could also be involved in the formation of more complex organic compounds. In the present investigation, dissociative electron attachment to CH₃CH₂CN has been studied in a crossed electron-molecular beam experiment in the electron energy range of about 0-15 eV. In the experiment, seven anionic species were detected: C₃H₄N^-, C₃H₃N^-, C₃H₂N^-, C₂H₂N^-, C₂HN^-, C₂N^-, and CN^-. The anion formation is most efficient for CN^- and anions originating from the dehydrogenation of the parent molecule. A discussion of possible reaction channels for all measured negative ions is provided. The experimental results are compared with calculations of thermochemical thresholds of the detected anions.

Ketene and Ammonia Forming Acetamide in the Interstellar Medium

Background: Peptide bonds are among the fundamental building blocks of life, polymerizing amino acids to form proteins that make up the structural components of living cells and regulate biochemical processes. The detection of glycine by NASA in comet Wild 2 in 2009 suggests the possibility of the formation of biomolecules in extraterrestrial environments through the interstellar medium. Detected in the dense molecular cloud Sagittarius B2, acetamide is the largest molecule containing a peptide bond and is hypothesized to be the precursor to all amino acids; as such, viability of its formation is of important biological relevance. Methods: Under a proposed mechanism of ammonia and ketene reactants, which have also been detected in dense molecular clouds in the ISM, the reaction pathway for the formation of acetamide was modelled using quantum chemical calculations in Gaussian16, using Austin-Frisch-Petersson functional with dispersion density functional theory at a 6-31G(d) basis set level of theory to optimize geometries and determine the thermodynamic properties for the reaction. Stability of the reactants, transition states, and products were examined to establish a reasonable mechanism. Conclusion: Product formation of acetamide was found to be highly exergonic and exothermic with a low energy barrier, suggesting a mechanism that is viable in the extreme density and temperature conditions found in ISM.

Rotational spectrum simulations of asymmetric tops in an astrochemical context

Rotational spectroscopy plays a major role in the field of observational astrochemistry, enabling the detection of more than 200 species including a plethora of complex organic molecules in different space environments. Those line detections allow correctly determining the sources and physical properties, as well as exploring their morphology, evolutionary stage, and chemical evolution pathways. In this context, quantum chemistry is a powerful tool to the investigation of the molecular inventory of astrophysical environments, guiding laboratory experiments and assisting in both line assignments and extrapolation of the experimental data to unexplored frequency ranges. In the present work, we start by briefly reviewing the rotational model Hamiltonian for asymmetric tops beyond the rigid-rotor approximation, including rotational-vibrational, centrifugal, and anharmonic effects. Then, aiming at further contributing to the recording and analysis of laboratory microwave spectroscopy by means of accessible, less demanding quantum chemical methods, we performed density functional theory (DFT) calculations of the spectroscopic parameters of astrochemically relevant species, followed by their rotational spectrum simulations. Furthermore, dispersion-correction effects combined with different functionals were also investigated. Case studies are the asymmetric tops H₂CO, H₂CS, c-HCOOH, t-HCOOH, and HNCO. Spectroscopic parameter predictions were overall very close to experiment, with mean percentage errors smaller than 1% for zeroth order and [Formula: see text] for first-order constants. We discuss the implications and impacts of those constants on spectrum simulations, and compare line-frequency predictions at millimeter wavelengths. Moreover, theoretical spectroscopic parameters of c-HCOOH and HNCO are introduced for the first time in this work.

Important features of the potential energy surface of the methylamine plus O(1D) reaction

This research presents an ab initio characterization of the potential energy surface for the methylamine plus ¹D oxygen atom reaction, which may be relevant to interstellar chemistry. Geometries and harmonic vibrational frequencies were determined for all stationary points at the CCSD(T)/aug-cc-pVTZ level of theory. The focal point method along with several additive corrections was used to obtain reliable CCSDT(Q)/CBS potential energy surface features. Extensive conformational analysis and intrinsic reaction coordinate computations were performed to ensure accurate chemical connectivity of the stationary points. Five minima were determined to be possible products of this reaction and three novel transition states were found that were previously unreported or mislabeled in the literature. The pathways we present can be used to guide further searches for NH₂ containing species in the interstellar medium.

Using collocation and a hierarchical basis to solve the vibrational Schrödinger equation

We show that it is possible to compute vibrational energy levels of polyatomic molecules with a collocation method and a basis of products of one-dimensional harmonic oscillator functions pruned so that it does not include functions for which the indices of many of the one-dimensional functions are nonzero. Functions with many nonzero indices are coupled only by terms that depend simultaneously on many coordinates, and they are typically small. The collocation equation is derived without invoking differences of interpolation operators, which simplifies implementation of the method. This, however, requires inverting a matrix whose elements are values of the pruned basis functions at the collocation points. The collocation points are the points on a Smolyak grid whose size is equal to the size of the pruned basis set. The Smolyak grid is built from symmetrized Leja points. Because both the basis and the grid are not tensor products, the inverse is not straightforward. It can be done by using so-called hierarchical 1-D basis functions. They are defined so that the matrix whose elements are the 1-D hierarchical basis functions evaluated at points is lower triangular. We test the method by applying it to compute 100 energy levels of CH₂NH with an iterative eigensolver.

A theoretical study of imine hydrocyanation catalyzed by halogen-bonding

A detailed theoretical study of the mechanism and energetics of an organocatalysis based on C=N activation by halogen-bonding is presented for the hydrocyanation of N-benzylidenemethylamine. The calculations at the level of scalar-relativistic gradient-corrected density functional theory give an insight in this catalytic concept and provide information on the characteristics of four different monodentate catalyst candidates acting as halogen-bond donors during the reaction.

High-pressure phases of hydrogen cyanide: formation of hydrogenated carbon nitride polymers and layers and their electronic properties

We have performed a set of first-principles simulations to consider the possible phase transitions in molecular crystals of HCN under high pressure. Our calculations reveal several transition paths from the orthorhombic phase to tetragonal and then to triclinic phases. The transitions from the orthorhombic to the tetragonal phases are of the second order, whereas those from the tetragonal to the triclinic phases turn out to be of the first-order type and characterized by an abrupt decrease in volume. Our calculations show that, by adjustment of the temperature and pressure of the HCN molecular crystal, novel layered and polymeric crystals with insulating, semiconducting or metallic properties can be found. Based on our simulation results, two different crystal formation mechanisms are deduced. The stabilities of the predicted structures at ambient pressure are further assessed by performing phonon or MD simulations. In addition, the electron transport properties of the predicted polymers are obtained using the non-equilibrium Green's function technique combined with density functional theory. The results show that the polymers have metallic-like I-V characteristics.

Formation of nitriles and imines in the atmosphere of Titan: combined crossed-beam and theoretical studies on the reaction dynamics of excited nitrogen atoms N(2D) with ethane

The dynamics of the H-displacement channels in the reaction N(2D) + C2H6 have been investigated by the crossed molecular beam technique with mass spectrometric detection and time-of-flight analysis at two different collision energies (18.0 and 31.4 kJ mol(-1)). From the derived center-of-mass product angular and translational energy distributions the reaction micromechanisms and the product energy partitioning have been obtained. The interpretation of the scattering results is assisted by new ab initio electronic structure calculations of stationary points and product energetics for the C2H6N ground state doublet potential energy surface. C-C bond breaking and NH production channels have been theoretically characterized and the statistical branching ratio derived at the temperatures relevant for the atmosphere of Titan. Methanimine plus CH3 and ethanimine plus H are the main reaction channels. Implications for the atmospheric chemistry of Titan are discussed.

Radical formation of amino acid precursors in interstellar regions? Ser, Cys and Asp

It is proposed that the glycine precursor NH(2)CH(2)CN may be synthesised in interstellar dust clouds by the radical combination reactions NH(2)˙ + ˙CH(2)CN → NH(2)CH(2)CN (ΔG = -302 kJ mol(-1)) and/or NH(2)CH(2)˙ + ˙CN → NH(2)CH(2)CN (ΔG = -414 kJ mol(-1)). All calculations at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31+G(d) level of theory. This paper extends that concept to radical/radical coupling reactions to form Ser, Cys and Asp precursor nitriles. The hydrogen abstraction process NH(2)CH(2)CN + HO˙→ NH(2)˙CHCN + H(2)O (ΔG = -130 kJ mol(-1)) is suggested to precede the radical coupling reactions NH(2)˙CHCN + R˙→ NH(2)CHRCN (R˙ = ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN) to form nitrile precursors of the amino acids Ser, Cys and Asp. These three reactions are all favourable (ΔG = -240, -227 and -223 kJ mol(-1)). The radical species ˙CH(2)NH(2), ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN are shown to be stable for the microsecond timeframe by a combination of theoretical calculations and the experimental mass spectrometric neutralization/reionization procedure.

The formation of the stable radicals ˙CH2CN, CH3˙CHCN and ˙CH2CH2CN from the anions−CH2CN, CH3−CHCN and−CH2CH2CN in the gas phase. A joint experimental and theoretical study

Franck-Condon one-electron oxidation of the stable anions -CH2CN, CH3-CHCN and -CH2CH2CN (in the collision cell of a reverse-sector mass spectrometer) produce the radicals .CH2CN, CH3.CHCN and .CH2CH2CN, which neither rearrange nor decompose during the microsecond duration of the neutralisation-reionisation experiment. Acetonitrile (CH3CN) and propionitrile (CH3CH2CN) are known interstellar molecules and radical abstraction of these could produce energised .CH2CN and CH3.CHCN, which might react with NH2. (a known interstellar radical) on interstellar dust or ice surfaces to form NH2CH2CN and NH2CH(CH3)CN, precursors of the amino acids glycine and alanine.

Protonation thermochemistry of aminoacetonitrile

The gas-phase basicity (GB) of aminoacetonitrile (NH2CH2CN, 1) has been determined from measurement of proton transfer equilibrium constants in an ion cyclotron resonance mass spectrometer (GB(1) = 789.3 +/- 1.0 kJ x mol(-1)). Molecular orbital calculations up to the G2 level demonstrate that protonation occurs preferentially on the nitrogen atom of the NH2 group, and provide a theoretical proton affinity (PA(1)) of 824.0 kJ x mol(-1). Exact calculation of the entropy associated with hindered rotations and consideration of Boltzman distribution of conformers allow a theoretical estimate of the molar protonation entropy S degrees (1H+) - S degrees (1) = 8.6 J x mol(-1) x K(-1). Combining this value with experimental GB(1) leads to an 'experimental' proton affinity of 819.2 kJ x mol(-1), in close agreement with the G2 expectation.

Quantum studies of hydrogen bonding in formic acid and water ice surface

The structure and spectroscopy (electronic and vibrational) of formic acid (HCOOH) dimers and trimers are investigated by means of the hybrid (B3LYP) density-functional theory. Adsorption of single and dimer HCOOH on amorphous water ice surface is modeled using two different water clusters. Particular attention has been given to spectroscopic consequences. Several hypotheses on formic acid film growing on ice and incorporation of a single water molecule in the formic acid film are proposed.

Global Mapping of Equilibrium and Transition Structures on Potential Energy Surfaces by the Scaled Hypersphere Search Method: Applications to ab Initio Surfaces of Formaldehyde and Propyne Molecules

Technical details of a new global mapping technique for finding equilibrium (EQ) and transition structures (TS) on potential energy surfaces (PES), the scaled hypersphere search (SHS) method (Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277), are presented. On the basis of a simple principle that reaction pathways are found as anharmonic downward distortions of PES around an EQ point, the reaction pathways can be obtained as energy minima on the scaled hypersphere surface, which would have a constant energy when the potentials are harmonic. Connections of SHS paths between each EQ are very similar to corresponding intrinsic reaction coordinate (IRC) connections. The energy maximum along the SHS path reaches a region in close proximity to the TS of the reaction pathway, and the subsequent geometry optimization from the SHS maximum structure easily converges to the TS. The SHS method, using the one-after-another algorithm connecting EQ and TS, considerably reduces the multidimensional space to be searched to certain limited regions around the pathways connecting each EQ with the neighboring TS. Applications of the SHS method have been made to ab initio surfaces of formaldehyde and propyne molecules to obtain systematically five EQ and nine TS for formaldehyde and seven EQ and 32 TS for propyne.

Density functional study on the mechanism of bicyclic guanidine-catalyzed Strecker reaction

As a direct and viable synthesis of amino acids, the small organic molecule catalyzed asymmetric Strecker reactions have been explored successfully in recent years. For these catalysts, the active sites may be a guanidine group or similarly a urea group. In an effort to elucidate the reaction mechanism, we have investigated the bicyclic guanidine-catalyzed Strecker reaction of HCN and methanimine using density functional theory with the B3LYP method. Assisted by guanidine, two competitive pathways to aminoacetonitrile were rationalized. The aminoisoacetonitrile may not form due to the instability of the product.