The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations.

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints.

The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.

Evaluating Computational Chemistry Methods for Isotopic Fractionation between CO2(g) and H2O(g).

Quantum mechanical calculations can be useful in predicting equilibrium isotopic fractionations of geochemical reactions. However, these computational chemistry methods vary widely in their effectiveness in the prediction of various physical observables. Most studies employing the approach known as density functional theory (DFT) to model these observable quantities focus on predictive accuracy for energetics and geometries. In this study, several density functionals are evaluated against experimental bond lengths, harmonic vibrational frequencies, frequency shifts upon isotopic substitution, and 18O/16O isotopic fractionation between CO2(g) and H2O(g). Successful prediction of harmonic vibrational frequencies strongly correlates with successful prediction of isotopic fractionation, despite the possible introduction of errors by the harmonic approximation. Harmonic experimental frequencies, not anharmonic ones, must be used when comparing spectra and when predicting isotope fractionation. The B3LYP and X3LYP functionals perform more accurately in the evaluation of both harmonic vibrational frequencies and isotopic fractionation factors using the 6-311+G(d,p) and 6-311++G(2d,p) basis sets, achieving fractionation factor errors of 0.2-0.6‰ at 25 °C out of a total fractionation of 51‰. Error cancellation between vibrational frequencies and the harmonic approximation is crucial to their success. The above combination of exchange-correlation functionals and basis sets also well predicts the vibrational properties of interacting CO2 and H2O molecules, suggesting that they may be applicable to more complex geochemical reactions involving C and O isotopic fractionations.