Quantum-Chemical Modeling of the First Steps of the Strecker Synthesis: From the Gas-Phase to Water Solvation

A comprehensive study of the influence of non-covalent interactions on electron density redistribution during the reaction between acetic acid and methylamine

CONTEXT

A chemical reaction can be described, from a physicochemical perspective, as a redistribution of electron density. Additionally, non-covalent interactions locally modify the electron density distribution. This study aims to characterize the modification of reactivity caused by the presence of non-covalent interactions such as hydrogen bonds, in a reaction involving the formation of two bonds and the breaking of two others: CH₃COOH + NH₂CH₃ → CH₃CONHCH₃.

METHODS

In this work, we will follow the how a reaction mechanism involving the formation of two chemical bonds and the breaking of two other chemical bonds is affected by non-covalent interaction. To this end, the reaction force will be used to define the region of the reagents, the region of the transition state, and the region of the products. We will analyze the redistributions of electron density and electron pairs in each of the regions of the reaction mechanisms, using QTAIM and ELF, topological analyses, respectively, for the reaction between methylamine and acetic acid, in the presence of 0 to 4 water molecules. DFT calculations were carried out at the LC-ωPBE/6-311 + + G(d,p) + GD3BJ level along the intrinsic reaction coordinate of the one-step reaction leading to the formation of methylacetamide.

Pyrazinyl and pyridinyl bis-azomethines formation: an experimental and computational study

Formation of bis-azomethines from hydrazine and heterocyclic aromatic carbaldehydes, namely pyridine-2-carbaldehyde and pyrazine-2-carbaldehyde, is studied using density functional theory. The theoretical investigation is correlated with experimental results obtained by means of NMR spectroscopy. The presence of bis-hemiaminal intermediates is evidenced by NMR spectra while surprisingly stable hemiaminal intermediate was isolated experimentally. Water, methanol and acetic acid were outlined to play a crucial role as active catalysts of elementary steps of the reaction mechanisms. The possible reaction sequences, i.e. addition-dehydration-addition-dehydration or addition-addition-dehydration-dehydration are investigated and discussed. Also, alternative mechanistic path via ionic mechanism was proposed for the formation of hemiaminals.

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.

Experimental identification of aminomethanol (NH2CH2OH)-the key intermediate in the Strecker Synthesis

The Strecker Synthesis of (a)chiral α-amino acids from simple organic compounds, such as ammonia (NH₃), aldehydes (RCHO), and hydrogen cyanide (HCN) has been recognized as a viable route to amino acids on primordial earth. However, preparation and isolation of the simplest hemiaminal intermediate – the aminomethanol (NH₂CH₂OH)– formed in the Strecker Synthesis to even the simplest amino acid glycine (H₂NCH₂COOH) has been elusive. Here, we report the identification of aminomethanol prepared in low-temperature methylamine (CH₃NH₂) – oxygen (O₂) ices upon exposure to energetic electrons. Isomer-selective photoionization time-of-flight mass spectrometry (PI-ReTOF-MS) facilitated the gas phase detection of aminomethanol during the temperature program desorption (TPD) phase of the reaction products. The preparation and observation of the key transient aminomethanol changes our perception of the synthetic pathways to amino acids and the unexpected kinetic stability in extreme environments.

The Strecker synthesis is considered a viable route to amino acids formation on the primordial Earth. Here the authors succeed in observing its elusive intermediate aminomethanol, formed by insertion of an electronically excited oxygen atom in methylamine and stabilized by an icy matrix, using isomer-selective photoionization time-of-flight mass spectrometry during thermal desorption of the ice mixture.

Single-ion solvation free energy: A new cluster-continuum approach based on the cluster expansion method

Accurate calculation of the solvation free energy of single ions remains an important goal, involving development in the dielectric continuum solvation models, and statistical mechanics with explicit solvent and hybrid discrete-continuum methods. In the last case, many of the research studies involve a quasi-chemical approach using the monomer cycle or the cluster cycle to calculate the solvation free energy of single ions. In this work, a different cluster-continuum approach based on the cluster expansion method was tested for solvation of 16 cations and 32 anions in aqueous solution. The SMD model was used for the dielectric continuum part and three explicit water molecules were introduced in the region of the solute with the highest interaction energy. Harmonic frequency calculations and molecular dynamics sampling of configurations are not required. An empirical γ_N parameter for cations and another for anions is introduced. The method produces a substantial improvement of the SMD model with a mean absolute deviation of 2.3 kcal mol^-1 for cations and 2.9 kcal mol^-1 for anions. The analysis of the correlation between theoretical and experimental data produces a linear regression line with a slope of 1.09 for cations and 1.01 for anions. The good results of this approximated cluster expansion approach suggest that the method could be further improved by including more solvent molecules and sampling the configurations.

Study of the Reactivity of CH3COOH+• and COOH+ Ions with CH3NH2: Evidence of the Formation of New Peptide-like C(O)-N Bonds

Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH₃-COOH) and methylamine (CH₃-NH₂) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH₃COOH^+• as well as COOH⁺ (produced from either acetic acid or formic acid) ions with neutral CH₃NH₂ was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.

Computational studies on the gas phase reaction of methylenimine (CH2NH) with water molecules

In this work, we used quantum chemical methods and chemical kinetic models to answer the question of whether or not formaldehyde (CH2O) and ammonia (NH3) can be produced from gas phase hydration of methylenimine (CH2NH). The potential energy surfaces (PESs) of CH2NH + H2O → CH2O + NH3 and CH2NH + 2H2O → CH2O + NH3 + H2O reactions were computed using CCSD(T)/6-311++G(3d,3pd)//M06-2X/6-311++G(3d,3pd) level. The temperature-and pressure-dependent rate constants were calculated using variational transition state theory (VTST), microcanonical variational transition state theory [Formula: see text] and Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) simulations. The PES along the reaction path forming a weakly bound complex (CH2NH⋯H2O) was located using VTST and [Formula: see text]VTST, however, the PES along the tight transition state was characterized by VTST with small curvature tunneling (SCT) approach. The results show that the formation of CH2NH + H2O → CH2NH⋯H2O is pressure -and temperature-dependent. The calculated atmospheric lifetimes of CH2NH⋯H2O (~ 8 min) are too short to undergo secondary bimolecular reactions with other atmospheric species. Our results suggest that the formation of CH2O and NH3 likely to occur in the combustion of biomass burning but the rate of formation CH2O and NH3 is predicted to be negligible under atmospheric conditions. When a second water molecule is added to the reaction, the results suggest that the rates of formation of CH2O and NH3 remain negligible.

The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space

Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H₂O, CH₃OH, CO, and NH₃ yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C₇N₄H₁₄O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH₂OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (T_d) symmetry, whereas HMT-methanol has C₁ symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.

Theoretical study on the gas phase reaction of CH2O + NH3: the formation of CH2ONH3, NH2CH2OH, or CH2NH + H2O

The gas phase reaction between CH₂O and NH₃ is an important reaction in cold interstellar clouds, combustion chemistry and organic chemistry. In this study, the stationary point on the potential energy surfaces (PESs) for the CH₂O + NH₃ reaction was computed at the CCSD(T)/6-311++G(3df,3pd)//M06-2X/6-311++G(3df,3pd) level. The temperature- and pressure-dependent rate constants were computed using advanced kinetic models, including microcanonical variational transition state theory and Rice-Ramsperger-Kassel-Marcus (RRKM)/master equation (ME) techniques. Our result predicts that the CH₂O + NH₃ reaction forms a collisionally thermalized CH₂ONH₃ complex with respect to thermal unimolecular dissociation and the other products, i.e., NH₂CH₂OH and CH₂NH + H₂O, are negligible under atmospheric conditions. The calculated atmospheric lifetime of the CH₂ONH₃ complex is ∼17 min, which suggests that the CH₂ONH₃ complex can react with other atmospheric species. The results also suggest that the formation of CH₂NH and H₂O from the Strecker's process is negligibly small under all the conditions studied here. The decay rate of CH₂O + NH₃ (5.1 × 10^-4 s^-1 at 1500 K) suggests that aminomethanol (NH₂CH₂OH) is likely to occur in the high-temperature combustion of biomass burning, but the rate of formation of NH₂CH₂OH is negligible under atmospheric conditions. The predicted atmospheric lifetime (∼4 days) of NH₂CH₂OH in the presence of the OH radical suggests that further reactions with other atmospheric species are possible. The formation of the NH₂CHOH radical from the reaction OH + NH₂CH₂OH can lead to carcinogenic products, such as nitrosamines, acetamide, hydrocycnic acid, NH₂ and CO₂.