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Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison toin vivostructure and mechanism. This work introduces an MD to QM-cluster model workflow. 

In this computational study, we describe a self-consistent trajectory simulation approach to capture the effect of neutral gas pressure on ion–ion mutual neutralization (MN) reactions. The electron transfer probability estimated using Landau–Zener (LZ) transition state theory is incorporated into classical trajectory simulations to elicit predictions of MN cross sections in vacuum and rate constants at finite neutral gas pressures. Electronic structure calculations with multireference configuration interaction and large correlation consistent basis sets are used to derive inputs to the LZ theory. The key advance of our trajectory simulation approach is the inclusion of the effect of ion-neutral interactions on MN using a Langevin representation of the effect of background gas on ion transport. For H+ − H− and Li+ − H(D)−, our approach quantitatively agrees with measured speed-dependent cross sections for up to ∼105 m/s. For the ion pair Ne+ − Cl−, our predictions of the MN rate constant at ∼1 Torr are a factor of ∼2 to 3 higher than the experimentally measured value. Similarly, for Xe+ − F− in the pressure range of ∼20 000–80 000 Pa, our predictions of the MN rate constant are ∼20% lower but are in excellent qualitative agreement with experimental data. The paradigm of using trajectory simulations to self-consistently capture the effect of gas pressure on MN reactions advanced here provides avenues for the inclusion of additional nonclassical effects in future work. 

New computational and experimental studies have been carried out for the MgCCH radical in its X2Σ+ state. Coupled cluster theory with single, double, and perturbative triples, CCSD(T), was used in conjunction with post-CCSD(T) and scalar relativistic additive corrections to compute vibrational quartic force fields for this molecule. From the quartic force fields, higher-order spectroscopic properties, including rotational constants, were obtained. In tandem, the five lowest energy rotational transitions for MgCCH, N = 1→0 through N = 5→4, were measured for the first time using Fourier transform microwave/millimeter wave methods in the frequency range 9 -50 GHz. The radical was created in the Discharge Assisted Laser Ablation Source (DALAS) developed in the Ziurys group. A combined fit of these data with previous millimeter direct absorption measurements have yielded the most accurate rotational constants for MgCCH to date. The computed principle rotational constant lies within 1.51-1.65 MHz of the experimental one, validating the computational approach. High-level theory was then applied to produce accurate rovibrational spectroscopic constants for MgCCH+, including a rotational constant of B0 = 5354.5–5359.5 MHz.. These new predictions will further the experimental study of MgCCH+, and aid in the low-temperature characterization of MgCCH, detected towards the circumstellar shell of IRC+10216, a carbon-rich star. 

Abstract Human carbonic anhydrase (CA) metalloenzymes utilize a Zn 2+ -containing active site to catalyze the interconversion of carbon dioxide to bicarbonate. The Zn 2+ ion may be replaced with other divalent transition metals, though the catalytic efficiency of the enzyme will be reduced. In this work, quantum mechanical cluster models of the active site are used to map the reaction profile for the hydration mechanism of carbon dioxide. The Lipscomb proton transfer and Lindskog rotation mechanisms were examined for the native Zn 2+ -enzyme along with variants where the metal was substituted with Cd 2+ , Ni 2+ , Fe 2+ , and Fe 3+ . The findings highlight the impact the metal coordination geometry has on the reaction profile. The results also suggest Fe 2+ , which is the functional metal for a prototypical CA of an anaerobic bacterium, might also be functional for human CA if cultured within an anaerobic environment. 

By means of quantum chemistry (PBE0/def2-TZVPP; DLPNO-CCSD(T)/cc-pVTZ) and small, but reliable models of Polyhedral Oligomeric Silsesquioxanes (POSS), an array of astrochemically-relevant catalysis products, related to prebiotic and origin of life chemistry, has been theoretically explored. In this work, the heterogeneous phase hydrocyanation reaction of an unsaturated CC bond (propene) catalyzed by a Ni center complexed to a silica surface is analyzed. Of the two possible regioisomers, the branched iso-propyl-cyanide is thermodynamically and kinetically preferred over the linear n -propyl-cyanide ( T = 200 K). The formation of nitriles based on a regioselective process has profound implications on prebiotic and origin of life chemistry, as well as deep connections to terrestrial surface chemistry and geochemistry. 

ABSTRACT In this work, by means of quantum chemistry (Density Functional Theory (DFT), PW6B95/def2-TZVPP; DLPNO-CCSD(T)/CBS), HCN polymerization [(HCN)1 − 4] initiated and catalysed by a siloxyl radical (Si-O•) on a model silica surface is analysed. Linear HCN polymers (pHCN) are obtained by a radical initiated mechanism at a SiO• site and are characterized by a -(HC-N)- skeleton due to radical localization on the terminal N atom and radical attack on the C centre. NC heterocycles are formed by cyclization of the linear SiO-(HCN)3 − 4 and are always thermodynamically preferred over their linear counterparts, acting as thermodynamic sinks. Of particular interest to the astrochemistry community is the formation of the N-heterocycle 1,3,5-triazine that can be released into the gas phase at relatively low T (ΔG† = 23.3 kcal/mol). Full hydrogenation of SiO-(HCN•) follows two reaction channels with products: (a) SiO-CH3 + •NH2 or (b) amino-methanol + Si•, though characterized by slow kinetics. Nucleophilic addition of H2O to the electron-rich SiO-(HCN•) shows an unfavourable thermodynamics as well as a high-activation energy. The cleavage of the linear (HCN)1−4 from the SiO• site also shows a high thermodynamic energy penalty (ΔG≥82.0 kcal/mol). As a consequence, the silicate surface will be passivated by a chemically active ‘pHCN brush’ modifying the surface physico-chemical properties. The prospect of surface-catalysed HCN polymers exhibiting a high degree of chemical reactivity and proposed avenues for the formation of 1,3,5-triazine and amino-methanol opens exciting new chemical pathways to Complex Organic Matter formation in astrochemistry. 

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.