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We synthesized a new iodoargentate [Co(2,2′-bipy)3]Ag3I6 (1) (2,2′-bipy = 2,2′-bipyridine) via the reaction of AgI, KI, 2,2′-bipy and Co(NO3)2 in dimethylformamide (DMF) solvent at room temperature. The [Co(2,2′-bipy)3]3+ complex cation directs the formation of the 0 D cluster [Ag3I6]3− anion that features an irregular double-level gear wheel with a maximum diameter of 5.512 Å. The iodoargentate possesses the characteristics of semiconductors with a band gap of 2.03 eV. It exhibits excellent ion-exchange behavior for adsorbing crystal violet (CV) and methylene blue (MB), and it can function as a promising photocatalyst for degrading rhodamine B (RhB). The improved photocatalytic activity can be ascribed to the hole structure in the anions of iodoargentates. [ABSTRACT FROM AUTHOR]

CO2 hydrogenation into value-added chemicals not only offer an economically beneficial outlet but also help reduce the emission of greenhouse gases. Herein, the density functional theory (DFT) studies have been carried out on CO2 hydrogenation reaction for formamide production catalyzed by two different N–H ligand types of PNP iron catalysts. The results suggest that the whole mechanistic pathway has three parts: (i) precatalyst activation, (ii) hydrogenation of CO2 to generate formic acid (HCOOH), and (iii) amine thermal condensation to formamide with HCOOH. The lower turnover number (TON) of a bifunctional catalyst system in hydrogenating CO2 may attribute to the facile side-reaction between CO2 and bifunctional catalyst, which inhibits the generation of active species. Regarding the bifunctional catalyst system addressed in this work, we proposed a ligand participated mechanism due to the low pKa of the ligand N–H functional in the associated stage in the catalytic cycle. Remarkably, catalysts without the N–H ligand exhibit the significant transfer hydrogenation through the metal centered mechanism. Due to the excellent catalytic nature of the N–H ligand methylated catalyst, the N–H bond was not necessary for stabilizing the intermediate. Therefore, we confirmed that N–H ligand methylated catalysts allow for an efficient CO2 hydrogenation reaction compared to the bifunctional catalysts. Furthermore, the influence of Lewis acid and strong base on catalytic N-formylation were considered. Both significantly impact the catalytic performance. Moreover, the catalytic activity of PNMeP-based Mn, Fe and Ru complexes for CO2 hydrogenation to formamides was explored as well. The energetic span of Fe and Mn catalysts are much closer to the precious metal Ru, which indicates that such non-precious metal catalysts have potentially valuable applications. [ABSTRACT FROM AUTHOR]

Fluorescent base analogues are of great importance as sensitive probes to detect the dynamic structures of DNA. In this research, the structural and photophysical properties of 13-mer oligonucleotides containing 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) (4AP0, 4AP′) were characterized using both molecular dynamics simulations and quantum mechanics methods. The results indicate that the 4AP:DAP pair is well adapted to the overall B-DNA structure with higher stability and π-stacking abilities. The structural overlap of 4AP′ and 4AP0 with the neighboring adenines only lies in the 5′-direction which results in the structure distortion from native B-DNA. Furthermore, the photophysical properties of the fluorescent base monomers and the B-DNA duplex were explored in detail. A very important result is that the hydrogen bond interaction does not have more effect on the fluorescence band apart from the slight red-shifts. In particular, the identity of the neighboring bases stacked with 4AP has an important effect on the fluorescence band. How the local environment can alter the photophysical features of the nucleobases when they are incorporated into the DNA duplex is elucidated. [ABSTRACT FROM AUTHOR]

Ferroptosis is a recently discovered iron-dependent form of non-apoptotic cell death caused by the accumulation of membrane lipid peroxidation products, which is involved in various pathological conditions of the brain, kidney, liver and heart. A potent spiroquinoxalinamine derivative named liproxstatin-1 is discovered by high-throughput screening, which is able to suppress ferroptosis via lipid peroxide scavenging in vivo. Thus, molecular simulations, density functional theory (DFT) and variational transition-state theory with a small-curvature tunneling (SCT) coefficient are utilized to elucidate the detailed mechanisms of inactivation of a lipid peroxide radical by liproxstatin-1. H-atom abstracted from liproxstatin-1 by a CH3OOṖ radical occurs preferentially at the aromatic amine site (1′-NH) under thermodynamic and frontier molecular orbital analysis. The value of a calculated rate constant at 300 K is up to 6.38 × 103 M−1 S−1, indicating that the quantum tunneling effect is responsible for making a free radical trapping reaction more efficient by liproxstatin-1. The production of a liproxstatin-1 radical is easily regenerated to the active reduced form by ubiquinol in the body to avoid secondary damage by free radicals. A benzene ring and the higher HOMO energy are beneficial to enhance the lipid radical scavenging activity based on the structure–activity relationship study. Overall, the present results provide theoretical insights into the exploration of novel ferroptosis inhibitors. [ABSTRACT FROM AUTHOR]

The detailed formation mechanisms of C-ribonucleoside and N-ribonucleoside via the reaction of 2,4,6-triaminopyrimidine (TAP) with (d)-ribose in aqueous solution were explored using density functional theory (DFT). The calculations indicate that five isomers (α,β-furanose, α,β-pyranose and open-chain aldehyde) of (d)-ribose can exist in equilibrium in aqueous solution. In contrast to cyclic isomers, an open-chain aldehyde is most feasible to react with TAP. In general, the formation pathways of C-nucleoside and N-nucleoside proceed in three steps including nucleophilic addition, dehydration and cyclization. The calculated apparent activation energies are 28.8 kcal mol−1 and 29.2 kcal mol−1, respectively. It suggests that both C- and N-nucleoside can be formed in aqueous solution, which is in good agreement with the experimental results. The water molecule plays an important “H-bridge” role by the hydrogen atom relay. Finally, a model structure of nucleobase, which will be beneficial for the C–C glycosidic bond formation, is proposed. [ABSTRACT FROM AUTHOR]

Computational studies have been applied to gain insight into the mechanism of Pd(ii) catalyzed α-C–H functionalization of N-methoxy cinnamamide. The results show that the whole catalytic cycle proceeds via sequential six steps, including (i) catalyst Pd(t-BuNC)2 oxidation with O2, (ii) O–H deprotonation, (iii) t-BuNC migratory insertion to the Pd–C bond, (iv) acyl migration, (v) C–H activation and (vi) reductive elimination. The regioselectivity for different C–H activation sites depends on the coordination structures of α-C or β-C to the palladium(ii) center. The coordination of α-C to the palladium(ii) center shows a regular planar quadrilateral structure, which is stable. However, the β-C coordinating to the palladium(ii) center mainly exhibits a distorted quadrilateral structure, which is relatively unstable. Thus, the barrier of α-C–H activation is much lower than that of β-C–H activation. The present results provide a deep understanding of the site-selectivity of C–H activation. [ABSTRACT FROM AUTHOR]

The addition of the unnatural P:Z base pair to the four naturally occurring DNA bases expands the genetic alphabet and yields an artificially expanded genetic information system (AEGIS). Herein, the structural feature of oligonucleotides containing a novel unnatural P:Z base pair is characterized using both molecular dynamics and quantum chemistry. The results show that the incorporation of the novel artificial base pair (P:Z) preserves the global conformational feature of duplex DNA except for some local structures. The Z-nitro group imparts new properties to the groove width, which widens the major groove. The unnatural oligonucleotides containing mismatched base pairs exhibit low stability. This ensures efficient and high-fidelity replication. In general, the incorporation of the P:Z pair strengthens the stability of the corresponding DNA duplex. The calculated results also show that the thermostability originates from both hydrogen interaction and stacking interaction. The Z-nitro group plays an important role in enhancing the stability of the H-bonds and stacking strength of the P:Z pair. Overall, the present results provide theoretical insights in the exploration of artificially expanded genetic information systems. [ABSTRACT FROM AUTHOR]

We synthesized a new iodoargentate [Co(2,2'-bipy) 3 ]Ag 3 I 6 (1) (2,2'-bipy = 2,2'-bipyridine) via the reaction of AgI, KI, 2,2'-bipy and Co(NO 3 ) 2 in dimethylformamide (DMF) solvent at room temperature. The [Co(2,2'-bipy) 3 ] 3+ complex cation directs the formation of the 0 D cluster [Ag 3 I 6 ] 3- anion that features an irregular double-level gear wheel with a maximum diameter of 5.512 Å. The iodoargentate possesses the characteristics of semiconductors with a band gap of 2.03 eV. It exhibits excellent ion-exchange behavior for adsorbing crystal violet (CV) and methylene blue (MB), and it can function as a promising photocatalyst for degrading rhodamine B (RhB). The improved photocatalytic activity can be ascribed to the hole structure in the anions of iodoargentates.

CO2 hydrogenation into value-added chemicals not only offer an economically beneficial outlet but also help reduce the emission of greenhouse gases. Herein, the density functional theory (DFT) studies have been carried out on CO2 hydrogenation reaction for formamide production catalyzed by two different N-H ligand types of PNP iron catalysts. The results suggest that the whole mechanistic pathway has three parts: (i) precatalyst activation, (ii) hydrogenation of CO2 to generate formic acid (HCOOH), and (iii) amine thermal condensation to formamide with HCOOH. The lower turnover number (TON) of a bifunctional catalyst system in hydrogenating CO2 may attribute to the facile side-reaction between CO2 and bifunctional catalyst, which inhibits the generation of active species. Regarding the bifunctional catalyst system addressed in this work, we proposed a ligand participated mechanism due to the low pKa of the ligand N-H functional in the associated stage in the catalytic cycle. Remarkably, catalysts without the N-H ligand exhibit the significant transfer hydrogenation through the metal centered mechanism. Due to the excellent catalytic nature of the N-H ligand methylated catalyst, the N-H bond was not necessary for stabilizing the intermediate. Therefore, we confirmed that N-H ligand methylated catalysts allow for an efficient CO2 hydrogenation reaction compared to the bifunctional catalysts. Furthermore, the influence of Lewis acid and strong base on catalytic N-formylation were considered. Both significantly impact the catalytic performance. Moreover, the catalytic activity of PNMeP-based Mn, Fe and Ru complexes for CO2 hydrogenation to formamides was explored as well. The energetic span of Fe and Mn catalysts are much closer to the precious metal Ru, which indicates that such non-precious metal catalysts have potentially valuable applications.

Computational studies have been applied to gain insight into the mechanism of Pd(ii) catalyzed α-C-H functionalization of N-methoxy cinnamamide. The results show that the whole catalytic cycle proceeds via sequential six steps, including (i) catalyst Pd(t-BuNC) 2 oxidation with O 2 , (ii) O-H deprotonation, (iii) t-BuNC migratory insertion to the Pd-C bond, (iv) acyl migration, (v) C-H activation and (vi) reductive elimination. The regioselectivity for different C-H activation sites depends on the coordination structures of α-C or β-C to the palladium(ii) center. The coordination of α-C to the palladium(ii) center shows a regular planar quadrilateral structure, which is stable. However, the β-C coordinating to the palladium(ii) center mainly exhibits a distorted quadrilateral structure, which is relatively unstable. Thus, the barrier of α-C-H activation is much lower than that of β-C-H activation. The present results provide a deep understanding of the site-selectivity of C-H activation.

Density functional theory calculations have been performed to investigate the detailed mechanism of the carbonyl hydrogenation catalyzed by the first well-defined bifunctional iron catalyst. The catalytic reaction proceeds by hydrogen transfer and dihydrogen activation. The hydrogen transfer reaction occurs via the bifunctional mechanism in which the two hydrogen atoms attached on the Fe and O of the catalyst are transferred to the oxygen and carbon atom of the carbonyl compound concertedly. Both the alcohol-mediated and nonalcohol-mediated dihydrogen activation processes are explored.