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Renormalized chemical kinetics and benchmark quantum mechanical rates: activation energies and tunnelling transitivities for the reactions of fluorine atoms with H2 and HD 重整化化学动力学和基准量子力学速率:氟原子与H2和HD反应的活化能和隧穿传递率
IF 2 4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-12-06 DOI: 10.1007/s12210-023-01209-6
Valter H. Carvalho-Silva, Flávio O. Sanches-Neto, Guilherme M. Leão, Simonetta Cavalli, Dario De Fazio, Maria C. Nucci, Vincenzo Aquilanti

Experimental, theoretical and computational chemical kinetics contribute to progress both in molecular and materials sciences and in biochemistry, exploring the gap between elementary processes and complex systems. Stationary state quantum mechanics and statistical thermodynamics provide interpretive tools and instruments for classical molecular dynamics simulations for stable or metastable structures and near-equilibrium situations. Chemical reaction kinetics plays a key role at the mesoscales: time-dependent and evolution problems are typically tackled phenomenologically, and reactions through intermediates and transition states need be investigated and modelled. In this paper, scaling and renormalization procedures are developed beyond the Arrhenius equation and the Transition State Theory, regarding two key observables in reaction kinetics, the rate “constant” as a function of temperature (and its reciprocal, the generalised lifetime), and the apparent activation energy (and its reciprocal, the transitivity function). Coupled first-order equations—dependent on time and on temperature—are formulated in alternative coupling scheme they link experimental results to effective modelling, or vice versa molecular dynamics simulations to predictions. The passage from thermal to tunnelling regimes is uniformly treated and applied to converged quantum mechanical calculations of rate constants available for the prototypical three-atom reactions of fluorine atoms with both H2 and HD: these are exothermic processes dominated by moderate tunnel, needing formal extension to cover the low-temperature regime where aspects of universal behaviour are shown to emerge. The results that have been validated towards experimental information in the 10–350 K temperature range, document the complexity of commonly considered “elementary” chemical reactions: they are relevant for modelling atmospheric and astrophysical environments. Perspectives are indicated of advances towards other types of transitions and to a global generality of processes of interest in applied chemical kinetics in biophysics and in astrochemistry.

实验、理论和计算化学动力学有助于分子和材料科学以及生物化学的进步,探索基本过程和复杂系统之间的差距。稳态量子力学和统计热力学为稳态或亚稳态结构和近平衡状态的经典分子动力学模拟提供了解释工具和仪器。化学反应动力学在中尺度上起着关键作用:时间依赖和进化问题通常是从现象学上解决的,而通过中间体和过渡态的反应需要研究和建模。在本文中,尺度化和重整化过程超越了Arrhenius方程和过渡态理论,涉及到反应动力学中的两个关键观测值,即速率“常数”作为温度(及其倒数,广义寿命)的函数,以及表观活化能(及其倒数,传递函数)。耦合的一阶方程-依赖于时间和温度-在另一种耦合方案中制定,它们将实验结果与有效的建模联系起来,反之亦然分子动力学模拟与预测。从热隧穿机制的过渡被统一处理,并应用于氟原子与H2和HD的典型三原子反应的速率常数的收敛量子力学计算:这些是由中等隧穿主导的放热过程,需要正式扩展以涵盖低温机制,在低温机制中显示出普遍行为的各个方面。在10-350 K温度范围内的实验信息验证了结果,记录了通常被认为是“基本”化学反应的复杂性:它们与模拟大气和天体物理环境有关。展望了其他类型转变的进展,以及生物物理学和天体化学中应用化学动力学中感兴趣的全球一般过程。
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引用次数: 0
From molecular beam technologies to virtual experiments and communities 从分子束技术到虚拟实验和社区
IF 2 4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-25 DOI: 10.1007/s12210-023-01203-y
Antonio Laganà

In the last 50 years, the impressive results on chemical kinetics from crossed molecular beam experiments have been assisted by theoretical and particularly computational progress, among which are: (1) the design and implementation of the SIMBEX (SImulation of Molecular Beam EXperiments) procedure on parallel and distributed computers aimed at rationalizing the dynamical behavior of the investigated systems on the ab initio computed molecular interactions; (2) the establishing of theoretical and computational research and educational networks (like the Quantum Reactive Scattering and European Chemistry Thematic Network), the assembling of virtual research communities (like the meta- and the grid-chemistry ones within the Collaboration in Science and Technology (COST) initiatives to enhance synergic and cooperative work levering on highly productive platforms; (3) the participation in the management of both the Italian and the European grid infrastructures initiatives; (4) the development of molecular open science-enabled cloud services within the European Open Science Cloud (EOSC). Levering on the mentioned collaborative efforts, important open science initiatives have been implemented. The present paper illustrates a prototype model apparatus for the production of methane out of CO2 using renewable energy sources and a prosumer (producer–consumer) model for delivering online chemistry competence tests. Finally, a suggestion is made to establish networked local services of the academy for high school education.

在过去的50年里,交叉分子束实验在化学动力学方面取得了令人印象深刻的结果,这得益于理论和特别是计算方面的进步,其中包括:(1)在并行和分布式计算机上设计和实现了SIMBEX(模拟分子束实验)程序,旨在使所研究系统在从头计算分子相互作用时的动力学行为合理化;(2)建立理论和计算研究和教育网络(如量子反应散射和欧洲化学主题网络),组建虚拟研究社区(如科学与技术协作(COST)计划中的元化学和网格化学社区),利用高效的平台加强协同和合作工作;(3)参与意大利和欧洲电网基础设施倡议的管理;(4)在欧洲开放科学云(EOSC)中开发分子开放科学云服务。在上述合作努力的基础上,实施了重要的开放科学倡议。本论文说明了一个使用可再生能源从二氧化碳中生产甲烷的原型模型装置和一个提供在线化学能力测试的产消模型。最后,提出了建立网络化的高中教育学院本地服务的建议。
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引用次数: 0
The Perrey Archive: a story about collecting earthquakes and eruptions 佩里档案:一个关于收集地震和火山爆发的故事
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-13 DOI: 10.1007/s12210-023-01205-w
Corinna Guerra
The Perrey Archive, a unique historical collection of texts and manuscripts on earthquakes and volcanic eruptions of the past, is preserved in the Fondo Sismico of the library of the Società Napoletana di Storia Patria. This collection is the result of the tireless research of French scientist Alexis Perrey (1807–1882), who is regarded as one of the founders of seismology. The article illustrates what it means to “collect” earthquakes and eruptions, as well as other extreme events and how Perrey built his collection over the course of roughly 40 years, and it describes the role that the catalogs created by Perrey played for historical seismology. Finally, in addition to the value and significance of Perrey’s intellectual enterprise for the history of science, the article discusses the different aspects of archives and archiving for sciences. Photographic composition of some volumes from the Seismic Collection of the Società Napoletana di Storia Patria, photo by Claudio Novelli.
佩雷档案是一个独特的历史文献和手稿的收藏,关于过去的地震和火山爆发,保存在社会Napoletana di Storia Patria图书馆的Fondo Sismico。这是被认为是地震学创始人之一的法国科学家Alexis Perrey(1807-1882)孜孜不倦研究的成果。这篇文章阐述了“收集”地震和火山喷发以及其他极端事件的含义,以及Perrey如何在大约40年的时间里建立他的收藏,并描述了Perrey创建的目录在历史地震学中所起的作用。最后,除了论述佩里的学术事业对科学史的价值和意义外,文章还讨论了档案和科学存档的不同方面。来自社会Napoletana di Storia Patria地震收藏的部分卷的摄影组成,由Claudio Novelli拍摄。
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引用次数: 0
A comparative anatomical study on leaf and scape of Androsace taxa (Primulaceae): contribution to Androsace taxonomy 报春花科花楸属植物叶片和花葶的比较解剖学研究:对花楸分类的贡献
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-11 DOI: 10.1007/s12210-023-01208-7
Sibel Ulcay, Abdurahman Sefali, Yakup Yapar, İbrahim Demir, Betül Gıdık
In the present study, the leaf and scape anatomical features of ten Androsace taxa distributed in Türkiye were defined to contribute to plant identification. Hand sections from both the scape and leaf examined 43 anatomical characters. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were performed for the first time for Androsace. The results show that there are differences as well as similarities between Androsace species. It is noteworthy that Androsace artvinensis forms a separate main group with HCA. In addition, the fact that two of the five basic components are represented by a single variable according to the PCA results suggests that the anatomical characters examined are determinative for Androsace taxa.). In PCA, eigenvalues of PC1 (2.435), PC2 (1.749), PC3 (1.369), PC4 (1.223), and PC5 (1.006) were greater than 1.0. Cortex width, aerenchyma, arrangement of vascular bundles, and four-branched non-glandular hairs are among the important anatomical characteristics of the scape. Leaf cross-sectional shape, epidermis dimensions, glandular hair types, presence of five branched non-glandular hairs, stoma sizes, presence of crystals in the mesophyll, and types are among the qualitative and quantitative anatomical characteristics that attract attention in the leaf. This study examined almost all taxa of the genus Androsace distributed in Türkiye. The results will be important in finding new species among the examined taxa and revealing the anatomical features of the taxa for the first time. They will contribute to other studies on the genus.
本文对分布于台湾的10个Androsace分类群的叶片和花蕾解剖特征进行了定义,以期为植物鉴定提供依据。从茎叶和叶的手切片检查了43个解剖特征。本文首次对Androsace进行了主成分分析(PCA)和层次聚类分析(HCA)。结果表明,花楸属植物之间既有相似之处,也有差异。值得注意的是,黄花Androsace artvinensis与HCA形成了一个单独的主类群。此外,根据主成分分析结果,五个基本成分中的两个由一个变量表示,这表明所检查的解剖特征对Androsace类群是决定性的。PCA中,PC1(2.435)、PC2(1.749)、PC3(1.369)、PC4(1.223)、PC5(1.006)的特征值均大于1.0。皮层宽度、通气组织、维管束的排列和四分枝的非腺毛是鳞片的重要解剖特征。叶片的横截面形状、表皮尺寸、腺毛类型、五支非腺毛的存在、气孔大小、叶肉中晶体的存在和类型都是叶片中吸引人们注意的定性和定量解剖学特征。本文研究了分布在台湾的几乎所有Androsace属的分类群。这一结果对于在所研究的分类群中发现新种和首次揭示该分类群的解剖学特征具有重要意义。他们将对该属的其他研究作出贡献。
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引用次数: 0
Catalytic and antimicrobial activities of cucumber leaf extract-based organic@inorganic hybrid nanoflowers through Fenton-like reaction 基于Fenton-like反应的黄瓜叶提取物organic@inorganic杂交纳米花的催化抑菌活性研究
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-11 DOI: 10.1007/s12210-023-01206-9
Tuğçe Erdem, Fatih Doğan Koca
For the synthesis of organic@inorganic hybrid nanoflowers (hNFS), instead of expensive biomolecules such as DNA, enzyme, and protein, the Cucumis sativus (cucumber) leaf extract was used as an organic component in this study. In the PBS buffer with different pH (5, 7.4, and 9), hNFs were synthesized using extract with different volumes, but these parameters (concentration and pH) significantly affected the morphological characteristics of hNFs. Morphologies, elemental compositions, and organic groups that play key role in the synthesis of hNFs were detailed using FE-SEM, EDX, and FT-IR analyses, respectively. hNFs with ideal flower morphology (synthesized at pH 7.4 with 1 ml extract) showed antimicrobial activity against Staphylococcus aureus and Escherichia coli strains. Antimicrobial activity against strains and peroxidase-like activity against guaiacol of hNFs are explained by Fenton mechanisms.
对于organic@inorganic杂交纳米花(hNFS)的合成,本研究使用黄瓜叶提取物作为有机成分,而不是昂贵的生物分子,如DNA,酶和蛋白质。在不同pH(5、7.4和9)的PBS缓冲液中,使用不同体积的提取物合成hnf,但这些参数(浓度和pH)对hnf的形态特征有显著影响。通过FE-SEM、EDX和FT-IR分析,分别详细分析了在hNFs合成中起关键作用的形貌、元素组成和有机基团。具有理想花形态的hNFs(在pH 7.4下用1ml提取物合成)对金黄色葡萄球菌和大肠杆菌具有抗菌活性。Fenton机制解释了hnf对菌株的抗菌活性和对愈创木酚的过氧化物酶样活性。
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引用次数: 0
Intermolecular interactions and the weakly bound precursor states of elementary physicochemical processes 分子间相互作用和基本物理化学过程的弱结合前体态
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-06 DOI: 10.1007/s12210-023-01204-x
Fernando Pirani, Stefano Falcinelli, Franco Vecchiocattivi, Vincenzo Aquilanti, Annarita Laricchiuta, Gianpiero Colonna, Mario Capitelli
Abstract This study concerns the importance of the precursor (or pre-reactive) state of elementary physicochemical processes whose basic features, as structure, stability, and trapping effect of reagents, are controlled by the balance of intermolecular forces that arise at long range and operate at intermediate and short separation distances. The detailed formulation of such forces, determining formation probability and dynamical evolution of the precursor state, is of relevance in molecular science and difficult to be treated by quantum chemistry. Such a problem has been tackled by us exploiting the phenomenological approach, which employs semi-empirical and empirical formulas to represent strength, range and angular dependence of the leading interaction components involved. In addition to the study of transport phenomena, part of the attention is addressed to chemi-ionization (or Penning ionization) reactions for which neutral reagents lead to atomic and/or molecular ions plus electrons as products. Chemi-ionizations are bimolecular processes occurring in several environments of interest, where a reagent is a species, formed in excited-metastable electronic states by collisions with energetic electrons or cosmic rays. For such reactions all crucial electronic rearrangements, affecting stability and evolution of the weakly bound precursor state, here coincident with the reaction transition state, are characterized with a high detail. The results of the present study are of interest for many other processes, whose precursor states and their relevant features are difficult to characterize, often masked by several other effects. Graphical abstract
摘要本研究关注的是基本物理化学过程的前体(或反应前)状态的重要性,这些过程的基本特征,如试剂的结构、稳定性和捕获效果,是由分子间力的平衡控制的,这种力产生于远距离,作用于中短分离距离。这些力的详细公式,决定了前驱体状态的形成概率和动态演化,是分子科学的相关问题,很难用量子化学来处理。我们利用现象学方法解决了这样的问题,该方法采用半经验和经验公式来表示所涉及的主要相互作用组件的强度、范围和角度依赖性。除了对传递现象的研究外,部分注意力集中在化学电离(或潘宁电离)反应上,在这种反应中,中性试剂导致原子和/或分子离子加上电子作为产物。化学电离是发生在几种感兴趣的环境中的双分子过程,其中试剂是一种物质,通过与高能电子或宇宙射线的碰撞形成激发态亚稳态电子。对于这类反应,所有影响弱束缚前驱体状态的稳定性和演化的关键电子重排,在这里与反应过渡态一致,都具有很高的细节特征。本研究的结果对许多其他过程很有意义,这些过程的前体状态及其相关特征很难表征,通常被其他几种效应所掩盖。图形抽象
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引用次数: 0
Human secretory and excretory fluids, molecular constituents, and their biotherapeutic perspective against fungal pathogen Candida albicans 人类分泌和排泄液、分子成分及其对真菌病原体白色念珠菌的生物治疗前景
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-05 DOI: 10.1007/s12210-023-01207-8
Neha Jaiswal, Awanish Kumar
Candida albicans is a common fungal pathogen that can cause a range of infections, from superficial mucosal infections to invasive systemic infections, particularly in individuals with immunocompromised systems. The antimicrobial potential of human secretory and excretory fluids is known; however, relatively less attention has been paid to their antifungal potential. Therefore, it is important to understand the molecular constituents and antifungal properties of human secretory and excretory fluids against human fungal pathogen C. albicans to develop new strategies for combating the disease Candidiasis and enhance our understanding of the complex interplay between the host and pathogen. In this review, we discuss the potential antifungal molecules found in human saliva, vaginal fluid, cerumen, and urine. We also discussed the potential mechanisms of action of various antimicrobial peptides found in sweat, such as dermcidin and cathelicidin, and their potential as therapeutic agents against fungal infections. We have reviewed the information on anti-candidal molecules present in cerebrospinal fluid, cerumen, lacrimal fluid, sIgA, intestinal mucous, milk, saliva, seminal fluid, sweat, urine, etc. that would be very useful in a clinical context and futuristic biotherapeutic antifungal molecules.
白色念珠菌是一种常见的真菌病原体,可引起一系列感染,从浅表粘膜感染到侵袭性全身感染,特别是在免疫系统受损的个体中。人类分泌物和排泄物的抗菌潜力是已知的;然而,对其抗真菌潜力的关注相对较少。因此,了解人类分泌和排泄液对人类真菌病原菌白色念珠菌的分子组成和抗真菌特性,对制定新的防治念珠菌病的策略以及加深我们对宿主与病原菌之间复杂相互作用的认识具有重要意义。在这篇综述中,我们讨论了在人类唾液、阴道液、耵聍和尿液中发现的潜在抗真菌分子。我们还讨论了汗液中发现的各种抗菌肽的潜在作用机制,如皮杀素和抗菌肽,以及它们作为真菌感染治疗药物的潜力。我们回顾了脑脊液、耵聍、泪液、sIgA、肠粘膜、牛奶、唾液、精液、汗液、尿液等中存在的抗念珠菌分子的信息,这些信息将在临床环境和未来的生物治疗抗真菌分子中非常有用。
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引用次数: 0
Comparing geographic information systems-based fuzzy-analytic hierarchical process approach and artificial neural network to characterize soil erosion risk indexes 基于地理信息系统的模糊层次分析法与人工神经网络表征土壤侵蚀风险指标的比较
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-02 DOI: 10.1007/s12210-023-01201-0
Nursaç Serda Kaya, Sena Pacci, Inci Demirağ Turan, Mehmet Serhat Odabas, Orhan Dengiz
The pressure on the lands has increased with the dramatic increase in the world population in the last century. Erosion which is a natural process has become a serious artificial concern with this growing pressure. Especially, most of the farmlands in Turkey are particularly affected by erosion. In the current study, it is aimed to determine erosion risk index classes and generate their maps using F-AHP and ANN approaches applied for the estimate of soil erosion risk index (ERI). In addition, these approaches were associated with GIS and geostatistical techniques based on seven soil erosion indicators in Sinop Province including humid and sub-humid coastal environmental ecosystems in the central Black Sea Region of Turkey. In this research, vegetation cover, land use, soil depth, erosivity (precipitation), erodibility (USLE-K), slope (%), and parent material/geology were used as input data by taking into consideration of several literature reviews. According to study results, index values of ERIF-AHP and ERIANN classes were determined quite close to each other. The soil erosion risk index for Sinop province in Turkey indicates that less than 35% of the study area has a low and very low erosion risk area (34.3%), 32.4% is of moderate soil erosion risk area and about 33.2% of the area has high and very high erosion risk when based on F-AHP method. In addition, as for ERIANN, high and very high erosion risk classes made up 30.9% of the total area, while low- and very-low-risk classes made up 37.3%.
在上个世纪,随着世界人口的急剧增加,对土地的压力也增加了。随着这种日益增长的压力,本来是自然过程的侵蚀已成为一个严重的人为问题。特别是,土耳其的大部分农田特别受到侵蚀的影响。本研究的目的是利用F-AHP和ANN方法确定土壤侵蚀风险指数类别,并生成它们的地图。此外,这些方法还与基于Sinop省七个土壤侵蚀指标的GIS和地质统计技术相关联,包括土耳其黑海中部地区湿润和半湿润沿海环境生态系统。本研究以植被覆盖、土地利用、土壤深度、侵蚀力(降水)、可蚀性(USLE-K)、坡度(%)和母质/地质为输入数据,并参考了几篇文献综述。研究结果表明,ERIF-AHP和ERIANN分类的指数值非常接近。基于F-AHP方法的土耳其Sinop省土壤侵蚀风险指数表明,低于35%的研究区为低和极低侵蚀风险区(34.3%),32.4%的研究区为中等侵蚀风险区,33.2%的研究区为高和极高侵蚀风险区。此外,ERIANN高、极高侵蚀风险等级占总面积的30.9%,低、极低侵蚀风险等级占总面积的37.3%。
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引用次数: 0
Protective effects of vitamin E on spinosad-induced small intestine damage in rats 维生素E对脊髓糖诱导的大鼠小肠损伤的保护作用
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-11-02 DOI: 10.1007/s12210-023-01202-z
Sevim İpek Acar-Cömert, Mehmet Özcan, Hakan Eskizengin, Nursel Gül
This study investigated vitamin E’s protective effects against spinosad-induced damage in adult male Wistar albino rats. Rats were administered vitamin E (200 mg/kg) and different spinosad doses (9 mg/kg and 37.38 mg/kg) orally. Intestinal tissues were collected for analysis on the first, third, and seventh days after administration. Lipid peroxidation (malondialdehyde [MDA]) and total glutathione (GSH) levels were quantified, and the structures of columnar epithelial cells in small intestine tissue were observed. Light, fluorescent, and electron microscope showed cell damage, such as deterioration in chromatin distribution and nuclear morphology, cell separation, large numbers of goblet cells, and impaired villus structure, in tissues collected from rats treated with spinosad compared to control rats. However, vitamin E ameliorated intestinal columnar cell damage. While GSH levels were lower in the 37.38 mg/kg spinosad group on all assay days, there was no significant difference in the 9 mg/kg spinosad group. The administration of vitamin E decreased in the 37.38 mg/kg spinosad group after the first day. The GSH levels in the 37.38 mg/kg spinosad with vitamin E group were lower than in the control group on the third and seventh days. However, while MDA levels were higher in the 37.38 mg/kg spinosad group on all assay days, there was no significant difference in the 9 mg/kg spinosad group. Nevertheless, MDA levels were higher in the 37.38 mg/kg Spinosad with vitamin E group compared to the control group on the third and seventh days. This study’s findings highlight the need for further studies on spinosad and the protective role of antioxidants.
本研究探讨了维生素E对成年雄性Wistar白化大鼠脊髓损伤的保护作用。大鼠口服维生素E (200 mg/kg)和不同剂量的spinosad (9 mg/kg和37.38 mg/kg)。分别于给药后第1、3、7天采集肠道组织进行分析。定量测定脂质过氧化(丙二醛[MDA])和总谷胱甘肽(GSH)水平,观察小肠组织柱状上皮细胞的结构。光镜、荧光显微镜和电镜显示,与对照大鼠相比,经spinosad处理的大鼠组织出现细胞损伤,如染色质分布和细胞核形态恶化、细胞分离、大量杯状细胞和绒毛结构受损。然而,维生素E可改善肠柱状细胞损伤。37.38 mg/kg spinosad组的GSH水平在所有试验日均较低,而9 mg/kg spinosad组的GSH水平无显著差异。37.38 mg/kg人参皂苷组维生素E给药量在第1天后减少。37.38 mg/kg人参皂苷加维生素E组第3天和第7天GSH水平低于对照组。然而,尽管37.38 mg/kg spinosad组的MDA水平在所有试验日均较高,但9 mg/kg spinosad组的MDA水平无显著差异。然而,37.38 mg/kg维生素E组在第3天和第7天的MDA水平高于对照组。这项研究的发现强调了对spinosad和抗氧化剂的保护作用进行进一步研究的必要性。
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引用次数: 0
Quantum chemistry and metadynamics study of kinetic routes to alanine formation by CO or CO2 insertions in E- or Z-ethanimine isomers E-或z -乙胺异构体中CO或CO2插入生成丙氨酸的动力学途径的量子化学和元动力学研究
4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-10-30 DOI: 10.1007/s12210-023-01199-5
Matheus A. R. Nogueira-da-Silva, Nayara D. Coutinho, Wender A. da Silva, Valter H. Carvalho-Silva
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引用次数: 0
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