Study of proton-coupled electron transfer (PCET) with four explicit diabatic states at the ab initio level

Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer

We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.

pH Effect and Chemical Mechanisms of Antioxidant Higenamine

In this article, we determine the pH effect and chemical mechanism of antioxidant higenamine by using four spectrophotometric assays: (1) 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide radical (PTIO•)-scavenging assay (at pH 4.5, 6.0, and 7.4); (2) Fe³⁺-reducing power assay; (3) Cu²⁺-reducing power assay; and (4) 1,1-diphenyl-2-picryl-hydrazyl (DPPH•)-scavenging assay. The DPPH•-scavenging reaction product is further analyzed by ultra-performance liquid chromatography, coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) technology. In the four spectrophotometric assays, higenamine showed good dose-response curves; however, its IC₅₀ values were always lower than those of Trolox. In UPLC-ESI-Q-TOF-MS/MS analysis, the higenamine reaction product with DPPH• displayed three chromatographic peaks (retention time = 0.969, 1.078, and 1.319 min). The first gave m/z 541.2324 and 542.2372 MS peaks; while the last two generated two similar MS peaks (m/z 663.1580 and 664.1885), and two MS/MS peaks (m/z 195.9997 and 225.9971). In the PTIO•-scavenging assays, higenamine greatly decreased its IC₅₀ values with increasing pH. In conclusion, higenamine is a powerful antioxidant—it yields at least two types of final products (i.e., higenamine-radical adduct and higenamine-higenamine dimer). In aqueous media, higenamine may exert its antioxidant action via electron-transfer and proton-transfer pathways. However, its antioxidant action is markedly affected by pH. This is possibly because lower pH value weakens its proton-transfer pathway via ionization suppression by solution H⁺, and its electron-transfer pathway by withdrawing the inductive effect (-I) from protonated N-atom. These findings will aid the correct use of alkaloid antioxidants.

E-Configuration Improves Antioxidant and Cytoprotective Capacities of Resveratrols

The antioxidant and cytoprotective capacities of E-resveratrol and Z-resveratrol were compared using chemical and cellular assays. Chemical assays revealed that the two isomers were dose-dependently active in •O₂^--scavenging, ferric reducing antioxidant power (FRAP), Cu²⁺-reducing antioxidant capacity (CUPRAC), 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO•)-scavenging (pH 7.4 and pH 4.5), and 1,1-diphenyl-2-picryl-hydrazyl (DPPH•)-scavenging assays. The cellular assay indicated that the two isomers could also increase cell viabilities. However, quantitative analyses suggested that E-resveratrol exhibited stronger effects than Z-resveratrol in all chemical and cellular assays. Finally, the conformations of E-resveratrol and Z-resveratrol were analyzed. It can be concluded that both E-resveratrol and Z-resveratrol can promote redox-related pathways to exhibit antioxidant action and consequently protect bone marrow-derived mesenchymal stem cells (bmMSCs) from oxidative damage. These pathways include electron transfer (ET) and H⁺-transfer, and likely include hydrogen atom transfer (HAT). The E-configuration, however, improves antioxidant and cytoprotective capacities of resveratrols. The detrimental effect of the Z-configuration may be attributed to the non-planar preferential conformation, where two dihedral angles block the extension of the conjugative system.

2-Phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide Radical (PTIO•) Trapping Activity and Mechanisms of 16 Phenolic Xanthones

This study used the 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO•) trapping model to study the antioxidant activities of 16 natural xanthones in aqueous solution, including garcinone C, γ-mangostin, subelliptenone G, mangiferin, 1,6,7-trihydroxy-xanthone, 1,2,5-trihydroxyxanthone, 1,5,6-trihydroxyxanthone, norathyriol, 1,3,5,6-tetrahydroxy-xanthone, isojacareubin, 1,3,5,8-tetrahydroxyxanthone, isomangiferin, 2-hydroxyxanthone, 7-O-methylmangiferin, neomangiferin, and lancerin. It was observed that most of the 16 xanthones could scavenge the PTIO• radical in a dose-dependent manner at pH 4.5 and 7.4. Among them, 12 xanthones of the para-di-OHs (or ortho-di-OHs) type always exhibited lower half maximal inhibitory concentration (IC₅₀) values than those not of the para-di-OHs (or ortho-di-OHs) type. Ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) analysis revealed that most of these xanthones gave xanthone-xanthone dimers after incubation with PTIO•, except for neomangiferin. Based on these data, we concluded that the antioxidant activity of phenolic xanthone may be mediated by electron-transfer (ET) plus H⁺-transfer mechanisms. Through these mechanisms, some xanthones can further dimerize unless they bear huge substituents with steric hindrance. Four substituent types (i.e., para-di-OHs, 5,6-di-OHs, 6,7-di-OHs, and 7,8-di-OHs) dominate the antioxidant activity of phenolic xanthones, while other substituents (including isoprenyl and 3-hydroxy-3-methylbutyl substituents) play a minor role as long as they do not break the above four types.

Antioxidant and Cytoprotective Effects of Kukoamines A and B: Comparison and Positional Isomeric Effect

In this study, two natural phenolic polyamines, kukoamine A and B, were comparatively investigated for their antioxidant and cytoprotective effects in Fenton-damaged bone marrow-derived mesenchymal stem cells (bmMSCs). When compared with kukoamine B, kukoamine A consistently demonstrated higher IC50 values in PTIO•-scavenging (pH 7.4), Cu2+-reducing, DPPH•-scavenging, •O₂−-scavenging, and •OH-scavenging assays. However, in the PTIO•-scavenging assay, the IC50 values of each kukoamine varied with pH value. In the Fe2+-chelating assay, kukoamine B presented greater UV-Vis absorption and darker color than kukoamine A. In the HPLC⁻ESI⁻MS/MS analysis, kukoamine A with DPPH• produced radical-adduct-formation (RAF) peaks (m/z 922 and 713). The 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl (MTT) assay suggested that both kukoamines concentration-dependently increased the viabilities of Fenton-damaged bmMSCs at 56.5⁻188.4 μM. However, kukoamine A showed lower viability percentages than kukoamine B. In conclusion, the two isomers kukoamine A and B can protect bmMSCs from Fenton-induced damage, possibly through direct or indirect antioxidant pathways, including electron-transfer, proton-transfer, hydrogen atom transfer, RAF, and Fe2+-chelating. Since kukoamine B possesses higher potentials than kukoamine A in these pathways, kukoamine B is thus superior to kukoamine A in terms of cytoprotection. These differences can ultimately be attributed to positional isomeric effects.

Antioxidation and Cytoprotection of Acteoside and Its Derivatives: Comparison and Mechanistic Chemistry

The study tried to explore the role of sugar-residues and mechanisms of phenolic phenylpropanoid antioxidants. Acteoside, along with its apioside forsythoside B and rhamnoside poliumoside, were comparatively investigated using various antioxidant assays. In three electron-transfer (ET)-based assays (FRAP, CUPRAC, PTIO•-scavenging at pH 4.5), the relative antioxidant levels roughly ruled as: acteoside >forsythoside B > poliumoside. Such order was also observed in H⁺-transfer-involved PTIO•-scavenging assay at pH 7.4, and in three multiple-pathway-involved radical-scavenging assays, i.e., ABTS⁺•-scavenging, DPPH•-scavenging, and •O₂^--scavenging. In UV-vis spectra, each of them displayed a red-shift at 335→364 nm and two weak peaks (480 and 719 nm), when mixed with Fe²⁺; however, acteoside gave the weakest absorption. In Ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) analysis, no radical-adduct-formation (RAF) peak was found. MTT assay revealed that poliumoside exhibited the highest viability of oxidative-stressed bone marrow-derived mesenchymal stem cells. In conclusion, acteoside, forsythoside B, and poliumoside may be involved in multiple-pathways to exert the antioxidant action, including ET, H⁺-transfer, or Fe²⁺-chelating, but not RAF. The ET and H⁺-transfer may be hindered by rhamnosyl and apiosyl moieties; however, the Fe²⁺-chelating potential can be enhanced by two sugar-residues (especially rhamnosyl moiety). The general effect of rhamnosyl and apiosyl moieties is to improve the antioxidant or cytoprotective effects.

Electronic spectrum and characterization of diabatic potential energy surfaces for thiophenol

We present an accurate simulation of the UV spectrum and a diabatization of three singlet potential surfaces along four coordinates.