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  1. 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.

     
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  2. 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.

     
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  3. 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. 
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  4. 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. 
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  5. Glycoside hydrolase enzymes are important for hydrolyzing the β-1,4 glycosidic bond in polysaccharides for deconstruction of carbohydrates. The two-step retaining reaction mechanism of Glycoside Hydrolase Family 7 (GH7) was explored with different sized QM-cluster models built by the Residue Interaction Network ResidUe Selector (RINRUS) software using both the wild-type protein and its E217Q mutant. The first step is the glycosylation, in which the acidic residue 217 donates a proton to the glycosidic oxygen leading to bond cleavage. In the subsequent deglycosylation step, one water molecule migrates into the active site and attacks the anomeric carbon. Residue interaction-based QM-cluster models lead to reliable structural and energetic results for proposed glycoside hydrolase mechanisms. The free energies of activation for glycosylation in the largest QM-cluster models were predicted to be 19.5 and 31.4 kcal mol −1 for the wild-type protein and its E217Q mutant, which agree with experimental trends that mutation of the acidic residue Glu217 to Gln will slow down the reaction; and are higher in free energy than the deglycosylation transition states (13.8 and 25.5 kcal mol −1 for the wild-type protein and its mutant, respectively). For the mutated protein, glycosylation led to a low-energy product. This thermodynamic sink may correspond to the intermediate state which was isolated in the X-ray crystal structure. Hence, the glycosylation is validated to be the rate-limiting step in both the wild-type and mutated enzyme. 
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  6. The restricted rotation of chemical bonds may lead to the formation of stable, conformationally chiral molecules. While the asymmetry in chiral molecules is generally observed in the presence of one or more stereocenters, asymmetry exhibited by conformational chirality in compounds lacking stereocenters, called atropisomerism, depends on structural and temperature factors that are still not fully understood. This atropisomerism is observed in natural diarylether heptanoids where the length of the intramolecular tether constrains the compounds to isolable enantiomers at room temperature. In this work, we examine the impact tether length has on the activation free energies to isomerization of a diarylether cyclophane substructure with a tether ranging from 6 to 14 carbons. Racemization activation energies are observed to decay from 48 kcal/mol for a 7-carbon tether to 9.2 kcal/mol for a 14-carbon tether. Synthetic efforts to experimentally test these constraints are also presented. This work will likely guide the design and synthesis of novel asymmetric cyclophanes that will be of interest in the catalysis community given the importance of atropisomeric ligands in the field of asymmetric catalysis. 
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  7. null (Ed.)
    Heterogeneous phase astrochemistry plays an important role in the synthesis of complex organic matter (COM) as found on comets and rocky body surfaces like asteroids, planetoids, moons and planets. The proposed catalytic model is based on two assumptions: (a) siliceous rocks in both crystalline or amorphous states show surface-exposed defective centers such as siloxyl (Si-O•) radicals; (b) the second phase is represented by gas phase CO molecules, an abundant C 1 building block found in space. By means of quantum chemistry; (DFT, PW6B95/def2-TZVPP); the surface of a siliceous rock in presence of CO is modeled by a simple POSS (polyhedral silsesquioxane) where a siloxyl (Si-O•) radical is present. Four CO molecules have been consecutively added to the Si-O• radical and to the nascent polymeric CO (pCO) chain. The first CO insertion shows no activation free energy with ΔG 200 K = −21.7 kcal/mol forming the SiO-CO• radical. The second and third CO insertions show Δ G 200 K ‡ ≤ 10.5 kcal/mol. Ring closure of the SiO-CO-CO• (oxalic anhydride) moiety as well as of the SiO-CO-CO-CO• system (di-cheto form of oxetane) are thermodynamically disfavored. The last CO insertion shows no free energy of activation resulting in the stable five member pCO ring, precursor to 1,4-epoxy-1,2,3-butanone. Hydrogenation reactions of the pCO have been considered on the SiO oxygen or on the carbons and oxygens of the pCO chains. The formation of the reactive aldehyde SiO-CHO on the siliceous surface is possible. In principle, the complete hydrogenation of the (CO) 1−4 series results in the formation of methanol and polyols. Furthermore, all the SiO-pCO intermediates and the lactone 1,4-epoxy-1,2,3-butanone product in its radical form can be important building blocks in further polymerization reactions and/or open ring reactions with H (aldehydes, polyols) or CN (chetonitriles), resulting in highly reactive multi-functional compounds contributing to COM synthesis. 
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