Chemical reaction mechanism of decoction of traditional Chinese medicines: a review / 中国中药杂志

Complicated chemical reactions occur in the decoction of traditional Chinese medicines(TCMs) which features complex components, influencing the safety, efficacy, and quality controllability of TCMs. Therefore, it is particularly important to clarify the chemical reaction mechanism of TCMs in the decoction. This study summarized eight typical chemical reactions in the decoction of TCMs, such as substitution reaction, redox reaction, isomerization/stereoselective reaction, complexation, and supramolecular reaction. With the "toxicity attenuation and efficiency enhancement" of aconitines and other examples, this study reviewed the reactions in decoction of TCMs, which was expected to clarify the variation mechanisms of key chemical components in this process and to help guide medicine preparation and safe and rational use of medicine in clinical settings. The current main research methods for chemical reaction mechanisms of decoction of TCMs were also summed up and compared. The novel real-time analysis device of decoction system for TCMs was found to be efficient and simple without the pre-treatment of samples. This device provides a promising solution, which has great potential in quantity evaluation and control of TCMs. Moreover, it is expected to become a foundational and exemplary research tool, which can advance the research in this field.

Reaction mechanisms of flavins and flavoproteins from an electronic-structure perspective / Mecanismos de reação de flavinas e flavoproteínas por uma perspectiva de estrutura eletrônica

Proteins equipped with flavin adenine dinucleotides (FAD) or flavin mononucleotides (FMN) are named flavoproteins and constitute about 1% of all existing proteins. They catalyze redox, acid-base and photochemical reactions in a variety of biochemical phenomena that goes from energy metabolism to DNA repair and light sensing. The versatility observed in flavoproteins is ultimately a balance of flavin intrinsic properties modulated by a protein environment. This thesis aims to investigate how flavoproteins work by systematic evaluating flavin properties and reactivity. In particular, the mechanism of fumarate reduction by the flavoenzyme fumarate reductase Fcc3 was determined. Electronic-structure calculations were used for this task based on rigorous calibration with experimental data and error assessment. Flavin properties at chemical accuracy were obtained with single reference coupled-cluster CCSD(T) calculations at the complete basis set limit. Density functional theory was demonstrated an excellent alternative with lower computational costs and slightly less accuracy. Flavin protonation and tautomerism were shown to be important modulators of flavin properties and reactivity, with the possibility of various tautomers existing at neutral pH. Regarding flavin redox properties, an analysis based on multiconfigurational wave function weights was proposed for categorizing flavin redox reactions as hydride or hydrogen-atom transfers. This analysis is an upgrade over traditional partial charges methods and can be applied not only to flavin reactions but to any protoncoupled electron transfer. In the investigation of the enzymatic mechanism of fumarate reduction, the reaction was determined as a nucleophilic addition by hydride transfer with carbanion formation. Fumarate reductase employs electrostatic catalysis in contrast to previous proposals of substrate straining and general-acid catalysis. Also, hydride transfer was shown to be vibronically adiabatic with low tunneling contribution. These findings give new insights into the mechanisms of fumarate reductases and provide a framework for future computational studies of flavoproteins in general. The analyses and benchmark studies presented can be used to build better models of properties and reactivity of flavins and flavoproteins

Proteínas equipadas com dinucleotídeos de flavina-adenina (FAD) e mononucleotídeos de flavina (FMN) são chamadas flavoproteínas e constituem cerca de 1% de todas as proteínas existentes. Elas catalisam reações redox, ácido-base e fotoquímicas numa variedade de fenômenos bioquímicos que vão desde o metabolismo energético até reparo de DNA e captação de luz. A versatilidade observada em flavoproteínas é em última instância um balanço das propriedades intrínsecas de flavinas moduladas por um ambiente proteico. Esta tese busca investigar como flavoproteínas funcionam através de avaliações sistemáticas de propriedades e reatividade de flavinas. Em particular, o mecanismo de redução de fumarato pela flavoenzima fumarato redutase Fcc3 foi determinado. Cálculos de estrutura eletrônica foram usados para esta tarefa com base em rigorosa calibração com dados experimentais e avaliação de erros. As propriedades de flavinas foram determinadas com acurácia química com cálculos monoconfiguracionais de coupled-cluster CCSD(T) no limite de conjunto base completo. A teoria do funcional da densidade mostrou-se uma alternativa excelente com menor custo computacional e um pouco menos de acurácia. Protonação e tautomerismo de flavinas mostraram-se moduladores importantes de suas propriedades e reatividade, com a possibilidade de vários tautômeros existirem em pH neutro. Em relação às propriedades redox de flavinas, uma análise baseada nos pesos de funções de onda multiconfiguracionais foi proposta para categorizar as reações redox de flavinas como transferências de hidreto ou hidrogênio. Esta análise é uma melhoria em relação aos métodos tradicionais de cargas parciais e pode ser aplicada não apenas para reações de flavinas mas para qualquer transferência de próton acoplada a elétrons. Na investigação do mecanismo enzimático de redução de fumarato, a reação foi designada como uma adição nucleofílica por transferência de hidreto e formação de carbânion. A fumarato redutase usa catálise eletrostática diferentemente de prospostas anteriores envolvendo distorção do substrato e catálise ácida geral. Além disso, a transferência de hidreto mostrou-se vibronicamente adiabática com pouca contribuição de tunelamento. Estas descobertas abrem novas perspectivas sobre os mecanismos de fumarato redutases e fornecem uma base para estudos computacionais futuros sobre flavoproteínas em geral. As análises e estudos comparativos apresentados podem ser usados para construir melhores modelos para propriedades e reatividade de flavinas e flavoproteínas

Synthesis of Renewable Poly(limonene): A Kinetic Modeling Study to Improve the Polymerization

Abstract Despite its potential in the production of polymers from renewable sources, D-limonene faces difficulties in its polymerization, resulting in low monomer conversion and molar mass. In order to investigate the non-ideality inherent kinetics, this work explores different modeling strategies for D-limonene radical polymerization, using benzoyl peroxide as initiator. The starting model considered the classical approach for conventional radical polymerization. This model was then corrected by including reaction orders different from the unit. After an analysis and choice of the best model, computer simulations were compared with experimental results from literature, validating the chosen approach. It was found that the process is drastically influenced by chain transfer reactions, presenting a non-ideal behavior. Finally, an analysis of distinct reaction conditions provided information on monomer conversion, molar mass and polymer dispersity, which could guide future research in the synthesis optimization. Higher molar mass poly(limonene) were obtained by simultaneously reducing the monomer and initiator concentrations.

The Interaction between Gabapentin and Cations to Improve Its Stability / 中国药学杂志

OBJECTIVE: To reduce the occurrence of subsidiary reaction by studying the effects of different ions on the dehydration condensation reaction mechanism and energy barrier of gabapentin. METHODS: The molecular structure of the drug before and after adding different ions were optimized using the density functional theory (DFT) with B3LYP method at the 6-311+G (d, p) basis set level, and its structural parameters and thermodynamic parameters were calculated. RESULTS :The energy barriers of the subsidiary reaction obviously increased no matter what cations were added, and zinc ion was the best. CONCLUSION :It was proved that cations can effectively inhibit gabapentin from compensating to produce 3,3-pentamethylene-4-butyrolactam. The mechanism is using proper ion to change electrostatic interaction and the electron distribution of the active groups on the reactant so as to increase the barrier of the subsidiary reaction of gabapentin, thus inhibiting the occurrence of dehydration condensation reaction.

Establishment and mechanisms of chemical interaction between phosphate monomer and zirconia model / 华西口腔医学杂志

<p><b>OBJECTIVE</b>To analyze chemical mechanism of bonding improvement of zirconia via 10-methacryloyloxydecyl dihydrogen phosphate (MDP) conditioning.</p><p><b>METHODS</b>Various models were created for tetragonal zirconia crystals, molecular MDP, and MDP complex, and tetragonal zirconia crystal. Thermodynamic methods were used to analyze configuration between MDP and tetragonal zirconia crystal through calculation of their Gibbs free energy values and equilibrium constants.</p><p><b>RESULTS</b>Two potential configurations (double- and single-coordinate) may occur between MDP and ZrO2 crystal clusters. Thermodynamic calculations showed that -147.761 and -158.073 kJ·mol⁻¹ Gibbs free energy were required to form single- and double-coordinate configurations; their negative signs indicate that reactions for both configurations can occur. Equilibrium constant for single-coordinate configuration was 7.72×10²⁵, which was less than that of double-coordinate configuration (4.95×10²⁷), suggesting that the latter was more stable.</p><p><b>CONCLUSIONS</b>MDP can spontaneously establish a double-coordinate configuration with zirconia.
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Proton transfer from 1,4-pentadiene to superoxide radical anion: a QTAIM analysis / Transferencia de protón desde el 1,4-pentadieno al radical anión superóxido: un análisis QTAIM / Transferência de prótons de 1,4-pentadieno o ânion radical superóxido: uma análise QTAI

We studied the bis-allylic proton transfer reaction from 1,4-pentadiene to superoxide radical anion (O2.-). Minima and transition state geometries, as well as thermochemical parameters were computed at the B3LYP/6-311+G(3df,2p) level of theory. The electronic wave functions of reactants, intermediates, and products were analyzed within the framework of the Quantum Theory of Atoms in Molecules. The results show the formation of strongly hydrogen bonded complexes between the 1,4-pentadien- 3-yl anion and the hydroperoxyl radical as the reaction products. These product complexes (PCs) are more stable than the isolated reactants and much more stable than the isolated products. This reaction occurs via pre-reactive complexes which are more stable than the PCs and the transition states. This is in agreement with the fact that the net proton transfer reaction that leads to free products is an endothermic and nonspontaneous process.

Nosotros estudiamos la reacción de transferencia de protón bis-alílico del 1,4-pentadieno al radical anión superóxido (O2.--). Las geometrías de los mínimos y de los estados de transición, así como también los parámetros termoquímicos se calcularon usando el nivel de teoría B3LYP/6-311+G(3df,2p). Las funciones de onda electrónicas de los reactantes, intermedios y productos se analizaron dentro del marco de la teoría cuántica de átomos en moléculas. Nuestros resultados muestran la formación de complejos estabilizados por enlaces de hidrógeno entre el anión 1,4pentadien-3-ilo y el radical hidroperoxilo como productos de reacción. Estos complejos producto (PCs) son más estables que los reactantes aislados y mucho más estables que los productos aislados. Esta reacción ocurre vía la formación de complejos pre-reactivos, los cuales son más estables que los PCs y los estados de transición. Estos resultados están de acuerdo con el hecho de que la reacción global de transferencia de protón que conduce a la formación de los productos libres es un proceso endotérmico y no espontáneo.

Estudou-se a reação de transferência do próton bis-alílico do 1,4-pentadieno ao radical ânion superóxido (O2.-). As geometrias dos mínimos e dos estados de transição, bem como os parâmetros termoquímicos foram calculadas utilizando o nível de teoria B3LYP/6-311+G(3df, 2p). As funçÃμes de onda eletrònica dos reagentes, intermediários e produtos foram analisadas no âmbito da teoria quântica de átomos em moléculas. Os resultados obtidos demonstram a formação de complexos estabilizados por ligaçÃμes de hidrogênio entre o ânion 1,4-pentadieno- 3-ilo e o radical hidroperoxilo como produtos de reação. Estes complexos formados como produtos (PCs) são mais estáveis do que os reagentes isolados e muito mais estáveis do que os produtos isolados. Esta reação ocorre por meio de complexos pré-reativos mais estáveis do que os PCs e os estados de transição. Estes resultados estão de acordo com o fato da reação global de transferência de próton que conduz à formação dos produtos livres, é um processo endotérmico e não espontâneo.