Concerted Mechanism Research Articles

Using Stop Motion Animations to Activate and Analyze High School Students’ Intuitive Resources about Reaction Mechanisms

Mechanisms are part of the high school curriculum in many countries. Although research shows that university students struggle with mechanistic reasoning, very little is known about learning mechanisms in high school. Understanding the cognitive resources that high school students intuitively activate is critical to fostering meaningful learning. A readily available tool for modeling dynamic processes are stop-motion animations (SMAs). In this study, 55 high school students were asked to create SMAs of their intuitive ideas of nucleophilic substitution reactions. In a second step, the students evaluated two pre-made SMAs modeling the textbook-based stepwise (SN1) and concerted (SN2) mechanisms. Within the student-generated SMAs, SN1- and SN2-like mechanisms were equally distributed; after viewing the textbook-style animations, most students rated an SN2 mechanism as more likely. However, no group modeled both types of mechanisms or reasoned that both mechanisms were possible. Students used diverse chemical concepts as well as plausibility in their reasoning. However, simultaneous movement of atoms, conformational changes, and the idea of competing and boundary mechanisms do not seem intuitive. In conclusion, SMAs were found to be an appropriate tool for activating, analyzing, and discussing students’ resources “on the fly”, and these ideas can serve as a starting point for promoting productive mechanistic reasoning.

Development of a multiplex assay to assess activated p300/CBP in circulating prostate tumor cells.

Reduced SIRT2 deacetylation and increased p300 acetylation activity leads to a concerted mechanism of hyperacetylation at specific histone lysine sites (H3K9, H3K14, and H3K18) in castration-resistant prostate cancer (CRPC). We examined whether circulating tumor cells (CTCs) identify patients with altered p300/CBP acetylation. CTCs were isolated from 13 advanced PC patients using Exclusion-based Sample Preparation (ESP) technology. Bound cells underwent immunofluorescent staining for histone modifying enzymes (HMEs) of interest and image capture with NIS-Elements software. Using the cBioPortal PCF/SU2C dataset, the response of CRPC to androgen receptor signaling inhibitors (ARSI) was analyzed in 50 subjects. Staining optimization and specificity revealed clear expression of acetyl-p300, acetyl-H3K18, and SIRT2 on CTCs (CK positive, CD45 negative cells). Exposure to A-485, a selective p300/CBP catalytic inhibitor, reduced p300 and H3K18 acetylation. In CRPC patients, a-p300 strongly correlated with its target acetylated H3k18 (Pearson's R = 0.61), and SIRT2 expression showed robust negative correlation with a-H3k18 (R = -0.60). A subgroup of CRPC patients (6/11; 55%) demonstrated consistent upregulation of acetylation based on these markers. To examine the clinical impact of upregulation of the CBP/p300 axis, CRPC patients with reduced deacetylase SIRT2 expression demonstrate shorter response times to ARSI therapy (5.9 vs. 12 mo; p = 0.03). A subset of CRPC patients demonstrate increased p300/CBP activity based on a novel CTC biomarker assay. With further development, this biomarker suite may be used to identify candidates for CBP/p300 acetylation inhibitors in clinical development.

Regioselective and Stereospecific β‐Arabinofuranosylation by Boron‐Mediated Aglycon Delivery

AbstractRegio‐ and stereoselective formation of the 1,2‐cis‐furanosidic linkage has been in great demand for efficient synthesis of biologically active natural glycosides. In this study, we developed a regioselective and β‐stereospecific d‐/l‐arabinofuranosylation promoted by a boronic acid catalyst under mild conditions. The glycosylations proceeded smoothly for a variety of diols, triols, and unprotected sugar acceptors to give the corresponding β‐arabinofuranosides (β‐Arbf) in high yields with complete β‐stereoselectivity and high regioselectivity. The regioselectivity was completely reversed depending on the optical isomerism of the donor used and was predictable a priori using predictive models. Mechanistic studies based on DFT calculations revealed that the present glycosylation occurs through a highly dissociative concerted SNi mechanism. The usefulness of the glycosylation method was demonstrated by the chemical synthesis of trisaccharide structures of arabinogalactan fragments.

Slab gliding, a hidden factor that induces irreversibility and redox asymmetry of lithium-rich layered oxide cathodes

Lithium-rich layered oxides, despite their potential as high-energy-density cathode materials, are impeded by electrochemical performance deterioration upon anionic redox. Although this deterioration is believed to primarily result from structural disordering, our understanding of how it is triggered and/or occurs remains incomplete. Herein, we propose a theoretical picture that clarifies the irreversible transformation and redox asymmetry of lithium-rich layered oxides by introducing a series of global and local dynamic structural evolution processes involving slab gliding and transition-metal migration. We show that slab gliding plays a key role in trigger/initiating the structural disordering and consequent degradation of the anionic redox reaction. We further reveal that the ‘concerted disordering mechanism’ of slab gliding and transition-metal migration produces spontaneously irreversible/asymmetric lithiation and de-lithiation pathways, causing irreversible structural deterioration and the asymmetry of the anionic redox reaction. Our findings suggest slab gliding as a crucial, yet underexplored, method for achieving a reversible anionic redox reaction.

Pyrolysis mechanism of β-d-glucopyranose as a model compound of cellulose: A joint experimental and theoretical investigation

This study aims to reveal the pyrolysis reaction mechanism and product formation pathway of cellulose by combining experimental and theoretical calculation results. First, pyrolysis experiments of glucose, cellobiose, and cellulose were conducted by combined thermogravimetry-Fourier infrared spectroscopy-gas chromatography-mass spectrometry (TG-FTIR-GC-MS). The results show that glucose and cellobiose have two obvious mass loss peaks in their pyrolysis processes and cellulose has only a distinct mass loss peak. In the severe weight loss stage, cellulose forms more H2O, CO2, alkanes, and carbonyl compounds than glucose and cellobiose. Then, β-d-glucopyranose was selected as a model compound of cellulose to carry out density functional theory (DFT) calculations. The formation mechanism of furan derivatives and carbohydrate derivatives was systematically studied. And their competitive relationship was revealed. A reaction network from β-d-glucopyranose to main products was constructed. Based on the concerted reaction mechanism, β-d-glucopyranose is easier to generate furfural, followed by furan, 1,4:3,6-dianhydro-α-d-glucopyranose, and levoglucosenone, and finally 2(5H)-furanone. Based on the H radical attack mechanism, β-d-glucopyranose is easier to form 1-(2-furanyl)-ethanone, followed by 5-methyl-2-furancarboxaldehyde, and finally 2-methyl-furan. Finally, the relationship between the functional groups and the pyrolysis behavior of β-d-glucopyranose was clarified by combining the product distribution detected in experiments and DFT calculations.

Hydrocarbon Oxidation by a Porphyrin-π-Cation Radical Complex.

Heme and chlorin π-cation radical oxidants are widely implicated in biological and synthetic oxidation catalysis. Little insight into the role of π-cation radicals in proton coupled electron transfer (PCET) oxidation is available. We prepared a NiII-porphyrin-π-cation complex ([NiII(P•+)]) and found it to be capable of the oxidation of a variety of simple hydrocarbon substrates. Interestingly, some of the products were hydroxylated, with ([NiII(P•+)]) working in concert with atmospheric O2 to yield hydroxylated hydrocarbons. Kinetic data suggested that the porphyrin-π-cation radical species oxidised substrates via a concerted PCET mechanism, where the nickel porphyrin-π-cation radical accepted the electron, and the proton was transferred to a free anion. Our findings highlight the potential role of π-cation radicals as hydrocarbon activators, demonstrating that porphyrin ligand non-innocence could be a readily manipulated resource for oxidation catalyst development.

Hydrocarbon Oxidation by a Porphyrin‐π‐Cation Radical Complex

AbstractHeme and chlorin π‐cation radical oxidants are widely implicated in biological and synthetic oxidation catalysis. Little insight into the role of π‐cation radicals in proton coupled electron transfer (PCET) oxidation is available. We prepared a NiII‐porphyrin‐π‐cation complex ([NiII(P⋅+)]) and found it to be capable of the oxidation of a variety of simple hydrocarbon substrates. Interestingly, some of the products were hydroxylated, with ([NiII(P⋅+)]) working in concert with atmospheric O2 to yield hydroxylated hydrocarbons. Kinetic data suggested that the porphyrin‐π‐cation radical species oxidised substrates through a concerted PCET mechanism, where the porphyrin‐π‐cation radical accepted the electron, and the proton was transferred to a free anion. Our findings highlight the potential role of π‐cation radicals as hydrocarbon activators, demonstrating that porphyrin ligand non‐innocence could be a readily manipulated resource for oxidation catalyst development.

Computational Insights into the Reactivity Difference between Hypervalent Bromine(III) and Hypervalent Iodine(III) Reagent in the C−H Amination and Alkene Aziridination

AbstractWe present herein a computational exploration into the mechanism and origin of the reactivity difference between N‐triflylimino‐λ3‐iodane and N‐triflylimino‐λ3‐bromane in the C−H amination and alkene aziridination. Our calculations revealed that the preferred mechanism for C−H amination involves the generation of free nitrene intermediate, while the alkene aziridination proceeds via a concerted reaction mechanism. The superior reactivity of N‐triflylimino‐λ3‐bromane over N‐triflylimino‐λ3‐iodane could be mainly ascribed to better nucleofugality of the bromanyl moiety, which can be characterized by the strength of I−N and Br−N bond. The effect of solvent polarity on the reactivity of N‐triflylimino‐λ3‐bromane as a nitrene precursor will be discussed.

Computational Investigations of Reaction Mechanisms and Transformation Products of Olefins with Hypochlorous Acid.

Hypochlorous acid (HOCl) as the main component in chlorination and also as the innate immune factor relevant to immune defense has attracted considerable attention. Electrophilic addition reaction of olefins with HOCl, one of the most important prototype of chemical reactions, has been intensively studied for a long time; however, it has not been fully understood yet. In this study, addition reaction mechanisms and transformation products of model olefins with HOCl were systematically investigated by the density functional theory method. The results indicate that the traditionally believed stepwise mechanism with a chloronium-ion intermediate is only suitable for olefins substituted with electron-donating groups (EDGs) and weak electron-withdrawing groups (EWGs) but it is a carbon-cation intermediate that is favorable for EDGs featuring p-π or π-π conjugation with the C═C moiety. Moreover, olefins substituted with moderate or/and strong EWGs prefer the concerted and nucleophilic addition mechanisms, respectively. Epoxide and truncated aldehyde as the main transformation products can be generated from chlorohydrin through a series of reactions involving hypochlorite; however, their generation is kinetically not as feasible as the formation of chlorohydrin. The reactivity of three chlorinating agents (HOCl, Cl2O, and Cl2) and the case study of chlorination and degradation of cinnamic acid were also explored. Additionally, APT charge on the double-bond moiety in olefin and energy gap (ΔE) between the highest occupied molecular orbital (HOMO) energy of olefin and the lowest unoccupied molecular orbital (LUMO) energy of HOCl were found to be good parameters to distinguish the regioselectivity of chlorohydrin and reactivity of olefin, respectively. The findings of this work are helpful in further understanding the chlorination reactions of unsaturated compounds and identifying complicated transformation products.

Highly efficient electrocatalysis dechlorination of Dichloromethane over Single-Atom Cu/Co3O4-β spinel nanofibers

Electrochemical selective dechlorination of dichloromethane (DCM) to chloromethane is a promising and sustainable strategy of resources. However, the current lack of high-performance electrocatalysts and complicated dechlorination mechanisms pose significant challenges. In this study, we report a series of Cu single-atom catalysts (SACs) supported on Co3O4-β spinel with a tube-in-tube nanofiber structure, denoted as Cux SACs/Co3O4-β, where x represents the theoretical Cu loading (0.26 wt%, 0.30 wt% and 0.50 wt%). These catalysts effectively dechlorinate DCM, producing high-value hydrocarbons like chloromethane and methane. Notably, Cu0.30 SACs/Co3O4-β exhibited a high chloromethane production rate (2931 μmol g−1h−1) and selectivity (76%) at −2.98 V vs (Ag/AgCl/Me4NCl) due to the synergy of cobaltosic oxide (Co3O4) spinel and Cu single atom. X-ray photoelectron spectroscopy and electron paramagnetic resonance experiments confirmed the presence of additional surface oxygen vacancies in Cu0.30 SACs/Co3O4-β, which improved the electrocatalysis performance for DCM dechlorination. Furthermore, a concerted dechlorination mechanism was suggested based on the transfer coefficient α. This research paves the way for the development of novel spinel electrocatalysts and the advancement of dechlorination reactions.

Unimolecular Reactivity of [Cu(R)(CF3 )3 ]- Complexes (R=Organyl): Stepwise versus Concerted Mechanism in Copper-Mediated Trifluoromethylation.

The cuprate complexes [Cu(R)(CF3 )3 ]- (R=organyl) offer an efficient synthetic access to valuable trifluoromethylation products RCF3 . Here, electrospray-ionization mass spectrometry is used to analyze the formation of these intermediates in solution and probe their fragmentation pathways in the gas phase. Furthermore, the potential energy surfaces of these systems are explored by quantum chemical calculations. Upon collisional activation, the [Cu(R)(CF3 )3 ]- complexes (R=Me, Et, Bu, s Bu, allyl) afford the product ions [Cu(CF3 )3 ]⋅- and [Cu(CF3 )2 ]- . The former obviously results from an R⋅ loss, whereas the latter originates either from the stepwise release of R⋅ and CF3 ⋅ radicals or a concerted reductive elimination of RCF3 . The gas-phase fragmentation experiments as well as the quantum chemical calculations indicate that the preference for the stepwise reaction toward [Cu(CF3 )2 ]- increases with the stability of the formed organyl radical R⋅. This finding suggests that the recombination of R⋅ and CF3 ⋅ radicals may possibly contribute to the formation of RCF3 from [Cu(R)(CF3 )3 ]- in synthetic applications. In contrast, the [Cu(R)(CF3 )3 ]- complexes (R=aryl) only yield [Cu(CF3 )2 ]- when subjected to collision-induced dissociation. These species exclusively undergo a concerted reductive elimination because the competing stepwise pathway is disfavored by the low stability of aryl radicals.

An Asynchronous Concerted Mechanism and Its Origin in Lewis Acid-Mediated Carbonyl-Olefin [2+2] Cycloaddition.

The concerted mechanism of thermal BBr3 -mediated [2+2] carbonyl-olefin cycloaddition is intriguing considering the conflict against the Woodward-Hoffmann rule. In this work, we report a mechanistic study of the titled reaction using density functional theory calculations. The concerted [2+2] cycloaddition mechanism is operative even for the truncated model system of 2-methyl-2-butene and butanone. Intrinsic reaction coordinate analysis and potential surface mapping showed the asynchronous nature of the apparent concerted [2+2] cycloaddition, resulting from the proximity of carbocation-oxyanion in the transient zwitterionic structure. Solvent effects can change the reaction to a stepwise mechanism, highlighting the importance of zwitterion stability. Building upon this finding of the asynchronous concerted or stepwise [2+2] cycloaddition mechanism, two mechanistic classifications were elaborated based on substrates containing varied substituents and Lewis acids, with a focus on manipulating the stability of positive carbocation and negative oxyanion in the transient zwitterionic species.

Abstract B051: Alterations in SIRT2-H3K18Ac identify increased P300 activity in circulating tumor cells from patients with CRPC

Abstract Background: Histone modifying enzymes (HMEs) hold significant promise as targets for drug discovery in cancer. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) dictate the presence of acetyl marks, which regulate the openness of chromatin and transcriptional activation. We previously developed a novel histone array on a chip to measure HME dysregulation with the development of castration resistance (ACS Chem Biol 2017). This approach identified decreased SIRT2 expression and increased p300 activity leads to a concerted mechanism of hyperacetylation at specific histone lysine sites (H3K9, H3K14, and H3K18) in CRPC. This alteration was subsequently identified in a subset of castration-resistant tumors (BMC Cancer 2017). The goal of the current study was to determine if the isolation of circulating tumor cells (CTCs) could be used as a biomarker to identify patients with altered p300 acetylation activity. Methods: Peripheral blood was collected from 13 patients (15 samples) with advanced PC after informed written consent under the University of Wisconsin IRB-approved protocol. Peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-paque PLUS, and lymphocytes were depleted using pre-conjugated, anti-CD45 magnetic beads. CTCs were then captured with EpCAM labeled Sera-Mag streptavidin-coated magnetic beads (SM). Cells bound to SMs were isolated with ESP technology using an automated magnetic PipetMax pipetting robot. SM-bound cells were moved through staining and washing wells prior to imaging at 20x with a Nikon Eclipse Ti fluorescent microscope and NIS-Elements AR 4.10 software, and finally images were analyzed with NIS Elements software. Results: We first optimized the staining of acetyl-p300, total p300, H3K18ac, and SIRT2 in prostate cancer cell lines. Employing a selective inhibitor of p300 acetylation (A-485) reduced levels of p300 and H3K18 acetylation. We then confirmed that CTCs from patient samples were successfully captured by the EpCAM antibody and show clear expression of acetyl-p300, acetyl-H3K18, SIRT2, and CK (cytokeratin). No expression of CD45+ cells (lymphocyte exclusion) is noted. Increased acetylation of p300 and H3K18 and decreased SIRT2 is found in 6/10 CRPC samples compared to HSPC patients. Paired samples collected from one patient show a marked increase in p300 activity, H3K18 hyperacetylation, and a decrease in SIRT2 expression in the later developed CRPC sample compared to the HSPC sample. Another CRPC subject, decreased acetyl p300 and histone acetyl-H3k18, and increased SIRT2 staining is noted several months after beginning enzalutamide administrated. Analysis in CTCs indicates a positive correlation between acetyl-p300 and H3K18ac (R=0.61) and between SIRT2 and H3K18ac (R=-0.59). Conclusions: This study suggests that acetyl-p300, H3K18ac, and SIRT2 are epigenetic biomarkers that increase in a subset of CTC from CRPC. These biomarkers could potentially be used for monitoring outcomes and predicting tumor responses to developing p300 acetylation inhibitors. Citation Format: Mikolaj Filon, Bing Yang, Jennifer Schehr, Anupama Singh, Marcelo Bigarella, John Denu, Joshua Lang, David Jarrard. Alterations in SIRT2-H3K18Ac identify increased P300 activity in circulating tumor cells from patients with CRPC [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B051.

Development and initial clinical testing of a multiplex assay evaluating histone modifier p300 acetylation in prostate cancer circulating tumor cells.

e17020 Background: Histone modifying enzymes (HMEs) hold promise as targets for drug discovery in cancer. Histone acetyltransferases and histone deacetylases dictate the presence of acetyl marks, which regulate chromatin and transcriptional activation. We previously developed a novel ‘histone array on a chip’ to measure HME dysregulation associated with the development of castration resistant prostate cancer (CRPC) (ACS Chem Biol 2017). This approach identified decreased SIRT2 expression and increased p300 activity leads to a concerted mechanism of hyperacetylation at specific histone lysine sites (H3K9, H3K14, and H3K18) in CRPC xenografts. These alterations were subsequently validated in castration-resistant tissues (BMC Cancer 2017). The goal of the current study was to determine if circulating tumor cells (CTCs) could be used as a therapeutic biomarker to identify patients with altered p300 acetylation activity. Methods: Blood was collected from 11 CRPC and 3 hormone-sensitive patients with advanced PC under an IRB-approved protocol. PBMCs were isolated with Ficoll-paque PLUS, and lymphocytes were depleted using anti-CD45 magnetic beads. CTCs were then captured with EpCAM labeled coated magnetic beads. Bound cells were isolated with Exclusion-based Sample Preparation (ESP) technology. Bound cells were moved through staining and washing wells prior to imaging at 20x on a fluorescent microscope. Images were analyzed with NIS Elements software. Results: We initially optimized the staining of acetyl-p300, total p300, H3K18ac, and SIRT2 in single cell prostate cancer cell cultures. Exposure to A-485, a selective p300/CBP catalytic inhibitor, reduced levels of p300 and H3K18 acetylation confirming assay specificity. CTCs from patient samples were then captured by EpCAM antibody binding and target staining revealed clear expression of acetyl-p300, acetyl-H3K18, SIRT2, and CK (cytokeratin). No expression of CD45+ cells (lymphocyte exclusion) is noted. Acetyl-p300 displayed a strong positive correlation with its target acetylated H3k18 (Pearson’s r = 0.61), and SIRT2 expression showed robust negative correlation with H3k18 (r = -0.60). A distinct group of 6/11 (55%) of CRPC patients demonstrated altered expression. In one subject with an untreated CSPC sample and subsequent CRPC sample ( > 12mo) a loss of SIRT2 expression, increased p300 activity, and histone H3 hyperacetylation are associated with the transition from hormone-sensitive to CRPC. Conclusions: Acetyl-p300, H3K18ac, and SIRT2 increase in a subset of CTC from patients with CRPC. These biomarkers are associated with increased CBP/p300 activity. This biomarker suite could potentially be used for noninvasive monitoring of outcomes and predicting tumor responses to CBP/p300 acetylation inhibitors in clinical development.

吸着を伴う電子移動の分子機構

Herein, we describe our recent studies on the molecular mechanism of adsorption-coupled electron transfer (ACET). ACET is ubiquitous and crucial in many important electrode reactions to generate irreversibly adsorbed products in electrodeposition and electrointercalation and reversibly adsorbed intermediates in electrocatalysis and photoelectrocatalysis. ACET reactions, however, are highly complex owing to the coexistence of concerted and non-concerted mechanisms. We established the theoretical framework of voltammetry to discriminate between the two mechanisms, which was demonstrated experimentally for the first time by using not cyclic voltammetry but transient voltammetry based on scanning electrochemical microscopy (SECM). The novel ACET mode of SECM will enable us to quantitatively understand the coupling between electron transfer and specific adsorption.

Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine-Cytosine Base Pair.

In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine-cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

Three-body fragmentation dynamics of BrCNq+ (q=3–6) induced by 1-keV electron impact

The three-body fragmentation dynamics of $\mathrm{BrC}{\mathrm{N}}^{q+} (q=3--6)$ produced by 1-keV electron impact has been investigated using the ion momentum imaging technique. Up to 11 three-body Coulomb explosion channels were identified and analyzed. The corresponding kinetic energy release (KER) distributions were obtained and compared with the predictions of the Coulomb explosion model. By means of the Dalitz plot, Newton diagram, and native frame method, we have studied the concerted and sequential fragmentation mechanisms for channels leading to ${\mathrm{Br}}^{l+}+{\mathrm{C}}^{+}+{\mathrm{N}}^{+} (l=1--3)$. The KER for the intermediate dications $\mathrm{Br}{\mathrm{C}}^{2+}$ and $\mathrm{C}{\mathrm{N}}^{2+}$ from the sequential mechanism were determined and the electronic states of the intermediate molecular ion $\mathrm{C}{\mathrm{N}}^{2+}$ were discussed. For the channels leading to higher charge states of the carbon and nitrogen ions, only the concerted fragmentation mechanism was observed.

Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method.

l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one.

Quasielastic neutron scattering probing H− dynamics in the H− conductors LaH3−2xOx

Using an incoherent quasielastic neutron scattering (QENS) technique, we investigate ${\mathrm{H}}^{\ensuremath{-}}$ dynamics in a series of oxyhydrides $\mathrm{La}{\mathrm{H}}_{3\ensuremath{-}2x}{\mathrm{O}}_{x}$ that exhibit characteristic high ${\mathrm{H}}^{\ensuremath{-}}$ conductivity. In the end member $\mathrm{La}{\mathrm{H}}_{3}$ ($x$ = 0), two kinds of ${\mathrm{H}}^{\ensuremath{-}}$ dynamics are identified: the jump diffusion and the localized motion. The jump length in the jump diffusion mode increases with increasing $T$. The localized motion is identified as a jump between the two inequivalent sites. These dynamics are corroborated by our molecular dynamical simulations. Our QENS data suggest that similar ${\mathrm{H}}^{\ensuremath{-}}$ dynamics occurs also in oxyhydrides $\mathrm{La}{\mathrm{H}}_{3\ensuremath{-}2x}{\mathrm{O}}_{x}$ ($x\ensuremath{\ne}$ 0), whose ${\mathrm{H}}^{\ensuremath{-}}$ concentration dependence is consistent with the previous measurement of ionic conductivity. We also discuss the possibility that $\mathrm{La}{\mathrm{H}}_{3\ensuremath{-}2x}{\mathrm{O}}_{x}$ is an example of ${\mathrm{H}}^{\ensuremath{-}}$ ion conductors governed by the concerted migration mechanism. The identified ${\mathrm{H}}^{\ensuremath{-}}$ dynamics is key to understanding the anomalous hydrogen concentration dependence of the diffusion coefficient in lanthanum hydrides, which has been a longstanding mystery in this compound.

Theoretical insight into the unexpected initial (3 + 2) cycloaddition reaction of mesitonitrile oxide with 1, 4-diazepine derivatives: A computational study

1,4-Diazepine as an active drug component underlies the potency of most psychotic, anticancer, anticonvulsant, and antibacterial drugs in the market and is, therefore crucial in chemotherapeutic treatment in biomedicine. Proper functionalization of this moiety can afford even more potent drugs. As a result of their therapeutic significance, this study aims at precisely giving a comprehensive computational insight into the unexpected initial reactivity of 1,4-diazepine derivatives and mesitonitrile oxide. The initial reaction between mesitonitrile oxide and 1,4-diazepine derivatives proceeds via a (3 + 2) cycloaddition reaction which leads to the formation of a cycloadduct where the mesitonitrile oxide unexpectedly adds across the imine functionality at the expense of the potential olefinic carbon-carbon double bond. Calculations at the density functional theory (DFT) M06/6-311G (d, p) level of theory indicate that the initial (3 + 2) cycloaddition reaction of mesitonitrile oxide (1,3-dipole) and 1,4-diazepine derivatives (dipolarophile) in all cases proceeds to form the cycloadduct where the 1,3-dipole adds preferentially to the imine functionality at the expense of the potential olefinic carbon-carbon double bond. In light of the parent reaction, the most kinetically favored cycloadductP3A had a rate constant of 5.1 × 106 M−1s−1, which is about 12 manifolds faster than the next competing stereoisomer P1A with a rate constant of 4.1 × 105 M−1s−1 and about 1024 faster than the most favored cycloadduct P3B with a rate constant of 7.2 × 10−19 M−1s−1 in the unfavored pathway (Path B). Irrespective of the electronic and steric nature of the electron-donating (EDG) and electron-withdrawing (EWG) substituents placed on the dipolarophile, the selectivities of the reaction were maintained. Rationalization of the potential energy surface depicts that the 1,3-dipole adds across the dipolarophile via an asynchronous concerted mechanism. Rationalization of the HOMO-LUMO energies of the mesitonitrile oxide (1,3-dipole) and the 1,4-diazepine derivatives (dipolarophile) depict that the EDG-substituted dipolarophile react as nucleophiles, whereas the dipole reacts as an electrophile. Conversely, the HOMO-LUMO interaction between the EWG-substituted dipolarophile indicates that the EWG-substituted dipolarophile react as electrophiles, whereas the dipole reacts as a nucleophile. The electrophilic parr function at various reactive sites of the dipolarophile shows that the 1,3-dipole preferentially adds across the local centers with the largest electrophilic NBO or Mulliken spin densities which is consistent with the energetic trend observed. The reactivity of the 1,4-diazepine derivatives and the mesitonitrile oxide showed poor stereoselectivity.