CO-Bound Biomimetic [Mo₃S₄M] (M = Fe, Co, Ni) Clusters: A Computational Study

令和4年度 京都大学化学研究所 スーパーコンピュータシステム 利用報告

Palladium-catalyzed regioselective and stereo-invertive ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: Experimental and computational studies

A palladium catalyzed regioselective borylative ring opening reaction of 2-arylaziridines to give β-amino-β-arylethylborates was developed. The reaction reported herein represents the first example of ring-opening borylation of non-vinylic aziridines and direct borylative C(sp3)-N bond cleavage of neutral organic substrates. NMR studies and density functional theory (DFT) calculations suggested that the active intermediate for the reaction is a PdL2 complex [L = P(t-Bu)2Me]. The multi-component artificial force-induced reaction method (MC-AFIR) located the transition states for the regioselectivity-determining aziridine ring opening that proceeds in an SN2 fashion, and explained the selectivity of the reaction. The full catalytic cycle consists of a selectivity-determining aziridine ring opening (oxidative addition), a proton transfer, phosphine ligand dissociation from the catalyst, boron-boron bond cleavage, and reductive elimination. Water is important to the drive the transmetalation step. The calculated overall mechanism and selectivity are consistent with the experimental results

Methanol formation through reaction of low energy CH3+CH_{3}^{+} ions with an amorphous solid water surface at low temperature

We have performed experimental investigations of methanol formation via the reactions of low energy $CH_{3}^{+}$ ions with an amorphous solid water (ASW) surface around 10 K. A newly developed experimental apparatus enabled irradiation of the ASW surface by several eV ions and detection of trace amounts of reaction products on the surface. It was found that methanol molecules were produced by low-energy $CH_{3}^{+}$ irradiation of the ASW surface and that hydroxy groups in produced methanol originated from water molecules in ASW, as predicted in a previous theoretical study. Little temperature dependence of observed methanol intensity is apparent in the temperature range 12 - 60 K. Ab-initio molecular dynamics simulations under constant temperature conditions of 10 K suggested that this reaction spontaneously produced a methanol molecule and an $H_{3}O^{+}$ ion, regardless of the contact point of $CH_{3}^{+}$ on the ASW surface. We have performed simulation with an astrochemical model under molecular-cloud conditions, where the reaction between $CH_{3}^{+}$ and $H_{2}O$ ice, leading to methanol formation, was included. We found that the impact of the reaction on methanol abundance was limited only at the edge of the molecular cloud (< 1 mag) because of the low abundance of $CH_{3}^{+}$ in the gas phase, whereas the reaction between the abundant molecular ion $HCO^{+}$ and $H_{2}O$ ice, which has not yet been confirmed experimentally, can considerably affect the abundance of a complex organic molecule. This work sheds light on a new type of reaction between molecular ions and ice surfaces that should be included in astrochemical models.Comment: 5 figures and Appendix, accepted to Ap

CO Binding onto Heterometals of [Mo₃S₄M] (M = Fe, Co, Ni) Cubes

We have previously shown that cyclopentadienyl (Cp[R])-supported [Mo₃S₄] platforms capture and stabilize halides of hetero-metals (M) under reducing conditions to give [Mo₃S₄M] cubes. Here we report Co and Ni variants with Cp[XL] ligands (Cp[XL] = C₅Me₄SiEt₃) and CO binding to the [Mo₃S₄M] clusters (M = Fe, Co, Ni). Properties of the isolated CO-bound [Mo₃S₄M] cubes were investigated by X-ray diffraction, IR, and electrochemical analyses. Density functional theory (DFT) calculations were performed for the isolated CO-bound clusters to evaluate M-CO interactions. These analyses constitute foundations to develop bio-mimetic molecular catalysts for the direct conversion of CO and/or CO₂ into hydrocarbons, which can contribute to the reduction of carbon emissions

Mechanistic and Computational Studies of the Atom Transfer Radical Addition of CCl4 to Styrene Catalyzed by Copper Homoscorpionate Complexes

Experimental as well as theoretical studies have been carried out with the aim of elucidating the mechanism of the Atom Transfer Radical Addition (ATRA) of styrene and carbon tetrachloride with a TpxCu(NCMe) complex as the catalyst precursor (Tpx = hydrotrispyrazolyl-borate ligand). The studies shown herein demonstrate the effect of different variables in the kinetic behavior. A mechanistic proposal consistent with theoretical and experimental data is presentedMICINN (Grants CTQ2008–00042BQU, CTQ2008-06866-CO2-02/BQU and Consolider Ingenio 2010 CSD2006-0003) and the Junta de Andalucía (Proyecto P07-FQM-02794)We thank the MICINN (Grants CTQ2008-00042BQU, CTQ2008-06866-CO2-02/BQU, and Consolider Ingenio 2010 CSD2006-0003) and the Junta de Andalucia (Proyecto P07-FQM-02794) for financial support

Sodium ion interactions with aqueous glucose: Insights from quantum mechanics, molecular dynamics, and experiment

In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a- and B-glucose

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

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