Towards an understanding of the CO2-philicity in glycine: Deepening into the CO2:Aminoacid interactions

Maximal occupation by bases of π-hole bands surrounding linear molecules

Linear molecules such as CO₂ contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO₂ , where T = C, Si, Ge, Sn; bases are NCH and NH₃ . CO₂ engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH₃ . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH₃ . But like GeO₂ , SiO₂ can sustain only two bases in its equatorial ring. The π-hole ring of SnO₂ can engage in up to four tetrel bonds with either NCH or NH₃ , even though these bonds are weaker than those with GeO₂ or SiO₂ . As all of these complexes cast TO₂ in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.

Anatomy of π-hole bonds: Linear systems

The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.

Origins and properties of the tetrel bond

The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.

Glycine formation in CO2:CH4:NH3 ices induced by 0-70 eV electrons

Glycine (Gly), the simplest amino-acid building-block of proteins, has been identified on icy dust grains in the interstellar medium, icy comets, and ice covered meteorites. These astrophysical ices contain simple molecules (e.g., CO₂, H₂O, CH₄, HCN, and NH₃) and are exposed to complex radiation fields, e.g., UV, γ, or X-rays, stellar/solar wind particles, or cosmic rays. While much current effort is focused on understanding the radiochemistry induced in these ices by high energy radiation, the effects of the abundant secondary low energy electrons (LEEs) it produces have been mostly assumed rather than studied. Here we present the results for the exposure of multilayer CO₂:CH₄:NH₃ ice mixtures to 0-70 eV electrons under simulated astrophysical conditions. Mass selected temperature programmed desorption (TPD) of our electron irradiated films reveals multiple products, most notably intact glycine, which is supported by control measurements of both irradiated or un-irradiated binary mixture films, and un-irradiated CO₂:CH₄:NH₃ ices spiked with Gly. The threshold of Gly formation by LEEs is near 9 eV, while the TPD analysis of Gly film growth allows us to determine the "quantum" yield for 70 eV electrons to be about 0.004 Gly per incident electron. Our results show that simple amino acids can be formed directly from simple molecular ingredients, none of which possess preformed C-C or C-N bonds, by the copious secondary LEEs that are generated by ionizing radiation in astrophysical ices.