Kcal Mol Research Articles

Exploration of sensing behavior B3O3 quantum dot toward methyl halides; a quantum chemical approach

In this study, B3O3 quantum dot has been used for sensing of various methyl halides for the first time. The suitable cavity of B3O3 makes it more suitable for the sensing of variety of analytes. The three, very simple and most important methyl halides (CH3F, CH3Cl and CH3Br) are selected to adsorb on B3O3 surface. Density functional theory (DFT) method with appropriate basis set was implemented. Among the considered complexes, methyl bromide complex CH3Br@B3O3) showed higher interaction energy of −16.90 kcal mol−1. The noncovalent interaction (NCI) analysis identified the existence of van der Waals interactions among all analytes and adsorbent. The density of state (DOS) and natural bond orbital (NBO) charges analyses identified the charge transfer and conductive properties of B3O3 nanosheet after interaction with alkyl halides. Frontier molecular orbital study revealed the electronic attributes of considered complexes. It is revealed that B3O3 quantum dot can be a very good choice for sensing of methyl halides and could be helpful for monitoring and reducing the environmental pollution.

Theoretical Investigation on Water-Free, Water- and Self-Assisted H-Abstraction Reactions from Dimethylamine by Hydroxy Radicals.

Accurate branching ratios of the H-abstraction reactions from dimethylamine (DMA) by OH radicals are important in understanding the atmospheric fate of DMA. In this work, the reaction kinetics of the water-free, water-assisted, and self-assisted H-abstraction reactions between DMA and OH radicals are accurately determined using the multipath canonical variational theory with the small-curvature tunneling correction, to explore the catalytic effects of the reactant (DMA) and product (water). To choose a suitable method that well describes the current reaction systems, various combinations with seven DFT methods and six basis sets are first evaluated, and the M08-HX/ma-TZVP method is identified as the most appropriate, with a mean unsigned deviation of 0.9 kcal mol-1 against the gold-standard CCSD(T)/CBS(T-Q) method. Based on the determined potential energy surfaces with the considerations of ground-state structures and specific-reaction parameters of zero-point energies, rate constants and branching ratios are calculated in a wide temperature range. The calculations show that the participation of water and DMA can lead to three-body complexes with a lower energy and influence the energy barriers, but neither of them shows the catalytic effect on the H-abstraction reactions in terms of kinetics. Additionally, the branching ratio analysis demonstrates that the product distribution is significantly altered in the presence of DMA and water.

Molecular structure, molecular docking, molecular dynamics simulation, and drug likeness evaluation of 3,7-dihydroxy-1,2-dimethoxyxanthone for its anticancer activity

A naturally occurring xanthone, named 3,7-dihydroxy-1,2-dimethoxyxanthone was experimentally and computationally investigated for its anticancer activity. Single crystal X-ray diffraction (XRD) analysis revealed that the compound crystallises in the triclinic space group P1. Vibrational frequencies, electronic properties, chemical reactivity descriptors, the molecular structure, and stability of the compound were investigated by DFT calculations using Gaussian 09 W program at the B3LYP/6–311+G(2d,p) level of theory. All calculations showed correlations to experimental data. Its thermodynamic parameters at various temperatures are presented. The title molecule was docked on the proteins of prostate, cervical, breast, and melanoma cancer cells, and the results showed comparable binding energies to the standard chemotherapeutic agent, doxorubicin with small differences in the range 0.2−0.7 kcal mol−1. Given that the compound showed significant potential on the proteins of prostate and cervical cancer cells, the dynamic properties of the bound state of title ligand with the two selected proteins were further examined through a 200 ns molecular dynamics simulation. The results showed relatively overall higher stability through the simulation time than the free target. All these findings were afterwards confirmed by the good in vitro inhibition activity of the compound against human prostate and cervical cancer cell lines with IC50 values of 9.55 and 9.19 µM, respectively in comparison to the standard drug, and additionally demonstrated innocuousness towards normal human kidney cancer cell lines. Moreover, the drug likeness properties indicated that the title compound has a high bioavailability, a good water solubility, a good gastrointestinal absorption, and can be easily synthesized.

Design, synthesis and biological activity evaluation of eco-friendly rosin-based fungicides for sustainable crop protection.

Utilizing fungicides to protect crops from diseases is an effective method, and novel eco-friendly plant-derived fungicides with high efficiency and low toxicity are urgent requirements for sustainable crop protection. Two series of rosin-based fungicides (totally 35) were designed and synthesized. In vitro fungicidal activity revealed that Compound 6a (Co. 6a) effectively inhibited the growth of Valsa mali [median effective concentration (EC50) = 0.627 μg mL-1], and in vivo fungicidal activity suggested a significant protective efficacy of Co. 6a in protecting both apple branches (35.12% to 75.20%) and apples (75.86% to 90.82%). Quantum chemical calculations (via density functional theory) results indicated that the primary active site of Co. 6a lies in its amide structure. Mycelial morphology and physiology were investigated to elucidate the mode-of-action of Co. 6a, and suggested that Co. 6a produced significant cell membrane damage, accelerated electrolyte leakage, decreased succinate dehydrogenase (SDH) protein activity, and impaired physiological and biochemical functions, culminating in mycelial mortality. Molecular docking analysis revealed a robust binding energy (ΔE = -7.29 kcal mol-1) between Co. 6a and SDH. Subsequently, biosafety evaluations confirmed the environmentally-friendly nature of Co. 6a via the zebrafish model, yet toxicological results indicated that Co. 6a at median lethal concentration [LC50(96)] damaged the gills, liver and intestines of zebrafish. The above research offers a theoretical foundation for exploiting eco-friendly rosin-based fungicidal candidates in sustainable crop protection. © 2024 Society of Chemical Industry.

1,2,3-Triazole appended Schiff base functionalized silanes: A colorimetric sensor of Al (III) and a potent inhibitor of butyrylcholinesterase in Alzheimer’s diseases via molecular docking

The current article reports the synthesis of 1,2,3-triazole appended Schiff base functionalized silanes. The organosilane 7a used for the colorimetric detection of Al (III). The absorption studies have been performed, resulting in a limit of detection values of 1.28 × 10-7 M for the ligand7a.In order to validate the practical applicability of the synthesized probe, the real sample analysis has been performed with aluminium foil in distilled water. Further,the ligand 7a reversibility from [ligand 7a + Al (III)] complex upon EDTA addition can be utilised to build a molecular logic gate, with Al (III) and EDTA considered as inputs and the absorbance intensity at 433 nm considered as the output.The potential binding site of 7a for the Al (III) has been analysed by characterizing the metal–ligand complex using 1H NMR spectroscopy. The cytotoxicity assay of compounds 7(a-c) was performed using SAF-1 (ECACC n°00122301), rendering thenon-toxicity of synthesized compounds. The binding energy of −10.16 Kcal mol−1demonstrated that the ligand 7a is a potent inhibitor for the butyrylcholinesterase enzyme and might be employed as an anti-Alzheimer agent in the future.

Mixed Valence {Ni2+Ni1+} Clusters as Models of Acetyl Coenzyme A Synthase Intermediates.

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.

Stabilization of the Protein Structure by the Many-Body Cooperative Effect in the NH/π Hydrogen-bonding Tryptophan Triad.

The indole ring of tryptophan can form NH/π hydrogen bonds, acting both as a hydrogen donor at the NH group in the pyrrole subring and as a hydrogen acceptor at the benzene subring. In the structural core of the trimeric stable protein Pholiota squarrosa lectin (PhoSL), three indoles are symmetrically arranged and form NH/π hydrogen bonds among each other. Here, we conducted quantum chemical calculations on this indole triad by using various methods and basis sets. The analyses revealed cooperativity in triad formation, with the many-body effect contributing approximately -2 kcal mol-1, which significantly stabilizes this protein. Symmetry-adapted perturbation theory ascribed this effect to the induced polarization. The electrostatic potential and atomic charges indeed revealed a charge redistribution through the NH/π hydrogen bond, which was favorable for triad formation.

Probing σ-Aromaticity-Driven Ring Contraction of Metallabenzocyclobutadiene to Metallabenzocyclopropene.

Ring contraction of metallacyclobutadiene to metallacyclopropene is rare because of the increasing strain from a four-membered ring to a three-membered one. Here we demonstrate a new series of reactions of metallabenzocyclobutadiene to metallabenzocyclopropene via density functional theory calculations. The results suggest that these reactions are thermodynamically favorable ranging from -17.4 to -29.4 kcal mol-1, and a low reaction barrier (10.3 kcal mol-1) is achieved when the metal center is Ru and the ligands are one cyanide and one chloride. Further analysis suggests that a strengthened binding energy helps stabilize the transition state in the protonation process. The aromaticity during the reaction was investigated using the electron density of delocalized bonds (EDDB), isomerization stabilization energy, and isodesmic reactions. The EDDB shows that the π-conjugation is disrupted in the intermediate, and then σ-aromaticity is generated and dominant in the products. Our findings could be helpful for experimentalists in developing novel ring contraction reactions driven by aromaticity.

Theoretical Investigations of Hydrolysis Mechanisms of N(SiMe3)3.

Tris(trimethylsilyl)amine (N(SiMe3)3) is one of the most important intermediate products in the indirect synthesis of ammonia (NH3) from nitrogen (N2), which could be hydrolyzed to NH3 under mild conditions. Herein, the hydrolysis mechanism of N(SiMe3)3 has been systematically investigated using density functional theory (DFT) with explicit combined implicit water models. Under neutral conditions, the active barrier of the hydrolysis of N(SiMe3)3 is 17.6 kcal mol-1 in water solvent. The attacking of proton to N center and OH group to the Si atom from water is decoupled for the stabilization of OH group by solvent water molecules, which lower the hydrolysis energy barriers. Furthermore, under acid conditions, N(SiMe3)3 is easily coordinated with proton to form [NH(SiMe3)3]+, and the energy barrier of the hydrolysis reaction could be reduced to 11.5 kcal mol-1 of the first stage, making it being promoted according to the chemical equilibrium. Thus, the results provide an explanation for the possible mechanism of the quantitative conversion of N(SiMe3)3 to NH3 under mild conditions. The decoupled hydrolysis mechanism may play important role in other hydrolysis processes.

Insight from Electrochemical Analysis in the Radical Cation State of a Monopyrrolotetrathiafulvalene-Based [2]Rotaxane.

Mechanically interlocked molecules are a class of compounds used for controlling directional movement when barriers can be raised and lowered using external stimuli. Applied voltages can turn on redox states to alter electrostatic barriers but their use for directing motion requires knowledge of their impact on the kinetics. Herein, we make the first measurements on the movement of cyclobis(paraquat-p-phenylene) (CBPQT4+) across the radical-cation state of monopyrrolotetrathiafulvalene (MPTTF) in a [2]rotaxane using variable scan-rate electrochemistry. The [2]rotaxane is designed in a way that directs CBPQT4+ to a high-energy co-conformation upon oxidation of MPTTF to either the radical cation (MPTTF⋅+) or the dication (MPTTF2+). 1HNMR spectroscopic investigations carried out in acetonitrile at 298 K showed direct interconversion to the thermodynamically more stable ground-state co-conformation with CBPQT4+ moving across the oxidized MPTTF2+ electrostatic barrier. The electrochemical studies revealed that interconversion takes place by movement of CBPQT4+ across both the MPTTF•+ (19.3 kcal mol-1) and MPTTF2+ (18.7 kcal mol-1) barriers. The outcome of our studies shows that MPTTF has three accessible redox states that can be used to kinetically control the movement of the ring component in mechanically interlocked molecules.

Demystifying group-4 polyolefin hydrogenolysis catalysis: Gaseous propane hydrogenolysis mechanism over the same catalysts

A kinetic/mechanistic investigation of gaseous propane hydrogenolysis over the single-site heterogeneous polyolefin depolymerization catalysts AlS/ZrNp2 and AlS/HfNp2 (AlS = sulfated alumina, Np = neopentyl), is use to probe intrinsic catalyst properties without the complexities introduced by time- and viscosity-dependent polymer medium effects. In a polymer-free automated plug-flow catalytic reactor, propane hydrogenolysis turnover frequencies approach 3,000 h-1 at 150 °C. Both catalysts exhibit approximately linear relationships between rate and [H2] at substoichiometric [H2] with rate law orders of 0.66 ± 0.09 and 0.48 ± 0.07 for Hf and Zr, respectively; at higher [H2], the rates approach zero-order in [H2]. Reaction orders in [C3H8] and [catalyst] are essentially zero-order under all conditions, with the former implying rapid, irreversible alkane binding/activation. This rate law, activation parameter, and DFT energy span analysis support a scenario in which [H2] is pivotal in one of two plausible and competing rate-determining transition states-bimolecular metal-alkyl bond hydrogenolysis vs. unimolecular β-alkyl elimination. The Zr and Hf catalyst activation parameters, ΔH‡ = 16.8 ± 0.2 kcal mol-1 and 18.2 ± 0.6 kcal mol-1, respectively, track the relative turnover frequencies, while ΔS‡ = -19.1 ± 0.8 and -16.7 ± 1.4 cal mol-1 K-1, respectively, imply highly organized transition states. These catalysts maintain activity up to 200 °C, while time-on-stream data indicate multiday activities with an extrapolated turnover number ~92,000 at 150 °C for the Zr catalyst. This methodology is attractive for depolymerization catalyst discovery and process optimization.

Accurate abinitio based potential energy surface and kinetics of the Cl + NH3 → HCl + NH2 reaction.

The gas-phase reaction Cl + NH3 → HCl + NH2 is a prototypical hydrogen abstraction reaction, whose minimum energy path involves several intermediate complexes. In this work, a full-dimensional, spin-orbit corrected potential energy surface (SOC PES) is constructed for the ground electronic state of the Cl + NH3 reaction. About 52 000 energy points are sampled and calculated at the UCCSD(T)-F12a/aug-cc-pVTZ level, in which the data points located in the entrance channel are spin-orbit corrected. The spin-orbit corrections are predicted by a fitted three-dimensional energy surface from about 7520 energy points in the entrance channel at the level of CASSCF (15e, 11o)/aug-cc-pVTZ. The fundamental-invariant neural network method is utilized to fit the SOC PES, resulting in a total root mean square error of 0.12kcal mol-1. The calculated thermal rate constants of the Cl + NH3 → HCl + NH2 reaction on the SOC PES with the soft-zero-point energy constraint agree reasonably well with the available experimental values.

Ultrasensitive and selective colorimetric and smartphone-based detection of arsenic ions in aqueous solution using alliin-chitosan-AgNPs.

In this study, we developed a highly selective and sensitive colorimetric sensor for arsenic [As(iii)] detection using alliin-chitosan-stabilized silver nanoparticles (AC-AgNPs). The AC-AgNPs were synthesized using a complex prepared by mixing aqueous garlic extract containing alliin and chitosan extracted from shrimp. The synthesis of AC-AgNPs was confirmed by UV-vis spectroscopy, which showed a surface plasmon resonance (SPR) band at 403 nm, and TEM analysis revealing spherical nanoparticles with a mean diameter of 7.57 ± 3.52 nm. Upon the addition of As3+ ions, the brownish-coloured solution of AC-AgNPs became colourless. Moreover, the computational study revealed that among all the metal ions, only As3+ was able to form a stable complex with AC-AgNPs, with a binding energy of 8.7 kcal mol-1. The sensor exhibited a linear response to As(iii) concentrations ranging from 0.02 to 1.4 fM, with a detection limit of 0.023 fM. The highest activity was observed at pH 7 and temperature 25 °C. Interference studies demonstrated high selectivity against common metal ions. The study also demonstrated that the concentration of As3+ ions can be estimated by the decrease in red intensity and increase in green intensity in smartphone optical transduction signals. These results indicate the potential of the AC-AgNP-based sensor for reliable and efficient arsenic detection in environmental monitoring.

Formation, Structure and Reactivity of a Beryllium(0) Complex with Mgδ+-Beδ- Bond Polarization.

Attempts to create a novel Mg-Be bond by reaction of [(DIPePBDI*)MgNa]2 with Be[N(SiMe3)2]2 failed; DIPePBDI*=HC[(tBu)C=N(DIPeP)]2, DIPeP=2,6-Et2C-phenyl. Even at elevated temperatures, no conversion was observed. This is likely caused by strong steric shielding of the Be center. A similar reaction with the more open Cp*BeCl gave in quantitative yield (DIPePBDI*)MgBeCp* (1). The crystal structure shows a Mg-Be bond of 2.469(4) Å. Homolytic cleavage of the Mg-Be bond requires ΔH=69.6 kcal mol-1 (cf. CpBe-BeCp 69.0 kcal mol-1 and (DIPPBDI)Mg-Mg(DIPPBDI) 55.8 kcal mol-1). Natural-Population-Analysis (NPA) shows fragment charges: (DIPePBDI*)Mg +0.27/BeCp* -0.27. The very low NPA charge on Be (+0.62) compared to Mg (+1.21) and the strongly upfield 9Be NMR signal at -23.7 ppm are in line with considerable electron density on Be and the formal oxidation state assignment of MgII-Be0. Despite this Mgδ+-Beδ- polarity, 1 is extremely thermally stable and unreactive towards H2, CO, N2, cyclohexene and carbodiimide. It reacted with benzophenone, azobenzene, phenyl acetylene, CO2 and CS2. Reaction with 1-adamantyl azide led to reductive coupling and formation of an N6-chain. The azide reagent also inserted in the Cp*-Be bond. The inertness of 1 is likely due to bulky ligands protecting the Mg-Be unit.

Weak-cooperative binding of a long single-stranded DNA chain on a surface.

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.

Modulating Hydrogen Shuttling in Ammonia by Neutral and Cationic Boron‐Containing Frustrated Lewis Pairs (FLPs)

AbstractXanthene‐backbone FLPs featuring secondary borane functions −B(ArX)H (where ArX=C6F5 (ArF) or C6Cl5 (ArCl)) have been targeted through reactions of the dihydroboranes Me2S ⋅ BArXH2 with [4,5‐xanth(PR2)Li]2 (R=Ph, iPr), and investigated in the synthesis of related cationic systems via hydride abstraction. The reactivity of these systems (both cationic and charge neutral) with ammonia have been probed, with a view to probing the potential for proton shuttling via N−H bond ‘activation.’ We find that in the case of four‐coordinate boron systems (cationic or change neutral), the N−H linkage remains intact, supported by a NH⋅⋅⋅P hydrogen bond which is worth up to 17 kcal mol−1 thermodynamically, and enabled by planarization of the flexible xanthene scaffold. For cationic three coordinate systems, N‐to‐P proton transfer is viable, driven by the ability of the boron centre to stabilise the [NH2]− conjugate base through N‐to‐B π bonding. This proton transfer can be shown to be reversible in the presence of excess ammonia, depending on the nature of the B‐bound ArX group. It is viable in the case of C6F5 substituents, but is prevented by the more sterically encumbering and secondary donor‐stabilising capabilities of the C6Cl5 substituent.

Stereochemical Control of Redox CoII/CoIII-Cages with Switchable Cotton Effects Based on Labile-Static States.

The structural dynamics of artificial assemblies, in aspects such as molecular recognition and structural transformation, provide us with a blueprint to achieve bioinspired applications. Here, we describe the assembly of redox-switchable chiral metal-organic cages Λ8/Δ8-[Pd6(CoIIL3)8]28+ and Λ8/Δ8-[Pd6(CoIIIL3)8]36+. These isomeric cages demonstrate an on-off chirality logic gate controlled by their chemical and stereostructural dynamics tunable through redox transitions between the labile CoII-state and static CoIII-state with a distinct Cotton effect. The transition between different states is enabled by a reversible redox process and chiral recognition originating in the tris-chelate Co-centers. All cages in two states are thoroughly characterized by NMR, ESI-MS, CV, CD, and X-ray crystallographic analysis, which clarify their redox-switching behaviors upon chemical reduction/oxidation. The stereochemical lability of the CoII-center endows the Λ8/Δ8-CoII-cages with efficient chiral-induction by enantiomeric guests, leading to enantiomeric isomerization to switch between Λ8/Δ8-CoII-cages, which can be stabilized by oxidation to their chemically inert forms of Λ8/Δ8-CoIII-cages. Kinetic studies reveal that the isomerization rate of the Δ8-CoIII-cage is at least an order of magnitude slower than that of the Δ8-CoII-cage even at an elevated temperature, while its activation energy is 16 kcal mol-1 higher than that of the CoII-cage.

Probing the Effects of Size and Charge on the Monohydration and Dihydration of SiF5- and SiF62- via Comparisons with BF4- and PF6.

This study systematically examines the interactions of the trigonal bipyramidal silicon pentafluoride and octahedral silicon hexafluoride anions with either one or two water molecules, (SiF5-(H2O)n and SiF62-(H2O)n, respectively, where n = 1, 2). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using the CCSD(T) ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for Si, O, and F; denoted as haTZ). Two monohydrate and six dihydrate minima have been identified for the SiF5-(H2O)n systems, whereas one monohydrate and five dihydrate minima have been identified for the SiF62-(H2O)n systems. Both monohydrated anions have a minimum in which the water molecule adopts a symmetric double ionic hydrogen bond (DIHB) motif with C2v symmetry. However, a second unique monohydrate minimum has been identified for SiF5- in which the water molecule adopts an asymmetric DIHB motif along the edge of the trigonal bipyramidal anion between one axial and one equatorial F atom. This Cs structure is more than 2 kcal mol-1 lower in energy than the C2v local minimum at the CCSD(T)/haTZ level of theory. While the interactions between the solvent and ionic solute are quite strong for the monohydrated anions (electronic dissociation energies of ≈12 and ≈24 kcal mol-1 for the SiF5-(H2O)1 and SiF62-(H2O)1 global minima, respectively), these values are nearly perfectly doubled for the dihydrates, with the lowest-energy SiF5-(H2O)2 and SiF62-(H2O)2 minima exhibiting dissociation energies of ≈24 and ≈47 kcal mol-1, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -100 cm-1 for the SiF5-(H2O)2 minimum and -300 cm-1 for the SiF62-(H2O)2 minimum relative to an isolated H2O molecule at the CCSD(T)/haTZ level of theory. This work also corrects the OH stretching frequency shifts for two dihydrate minima of PF6- that were previously erroneously reported ( J. Phys. Chem. A 2020, 124, 8744-8752, DOI: 10.1021/acs.jpca.0c06466).

High-Temperature Pyrolysis Study of 2-Methyl-2-butanol behind Reflected Shock Wave: Shock Tube and Computational Study.

Pyrolysis of a branched alcohol, 2-methyl-2-butanol (2M2BOH), was carried out behind the reflected shock wave in the temperature range of 1011-1303 K and under pressures varying from 9.3 to 14.6 atm. Qualitative and quantitative analysis of the postshock mixture was performed using gas chromatography-mass spectrometry and gas chromatography with a flame ionization detector, respectively. The rate coefficients for the C-C and C-O bond cleavage reaction pathways were calculated using the variational transition-state theory. The Rice-Ramsperger-Kessel-Marcus/Master equation was employed to calculate the rate coefficients for the H2O-elimination reactions, unimolecular dissociation, and isomerization reaction pathways. The overall decomposition rate coefficient for the 2-methyl 2-butanol (2M2BOH) was estimated to be , where activation energy is given in kcal mol-1. The reaction path analysis was performed, which gives information regarding the contribution of individual intermediate species toward the decomposition of 2M2BOH. A set of reactions was proposed and used to simulate the combustion chemistry of 2M2BOH, which consists of 48 reactions and 39 species. The experimentally measured and simulated mole fractions for the reactant and products showed reasonably good agreement. This work additionally investigates the effect of branching on the decomposition kinetics of long-chain alcohols.

Tackling SARS‐CoV‐2: Deep Purpose Virtual Screening Identified Compounds to Target the Glycosylated Full‐Length GRP78

AbstractThe glucose‐regulated protein 78 (GRP78) is pivotal in endoplasmic reticulum protein homeostasis and the unfolded protein response during cellular stress. Experimental validation has shown its role in SARS‐CoV‐2 attachment and entry. Here, the full GRP78 sequence, adding carbohydrate sugars to nucleotide‐binding domain sites, and conduct molecular dynamics simulations is modeled. Utilizing DeepPurpose virtual screening on the COCONUT database, followed by blind structure‐based screening with AutoDock Vina, top interacting binders is identified. Molecular dynamic simulations with MM/GBSA reveal stable binding of CNP0339053 and CNP0400762 to GRP78 (free energies of −43.5 ±6.7 and −34.8 ±3.9 kcal mol−1, respectively). These compounds hold promise as safe antiviral treatments for COVID‐19.