Bio‐inspired Nonheme Iron Oxidation Catalysis: Involvement of Oxoiron(V) Oxidants in Cleaving Strong C−H Bonds

Nonheme iron enzymes generate powerful and versatile oxidants that perform a wide range of oxidation reactions, including the functionalization of inert C?H bonds, which is a major challenge for chemists. The oxidative abilities of these enzymes have inspired bioinorganic chemists to design synthetic models to mimic their ability to perform some of the most difficult oxidation reactions and study the mechanisms of such transformations. Iron‐oxygen intermediates like iron(III)‐hydroperoxo and high‐valent iron‐oxo species have been trapped and identified in investigations of these bio‐inspired catalytic systems, with the latter proposed to be the active oxidant for most of these systems. In this Review, we highlight the recent spectroscopic and mechanistic advances that have shed light on the various pathways that can be accessed by bio‐inspired nonheme iron systems to form the high‐valent iron‐oxo intermediates.     

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.     

Nitrosyl iron complexes--synthesis, structure and biology

Nitrosyl complexes of iron are formed in living species in the presence of nitric oxide. They are considered a form in which NO can be stored and stabilized within a living cell. Upon entering a topic in bioinorganic chemistry the researcher faces a wide spectrum of issues concerning synthetic methods, the structure and chemical properties of the complex on the one hand, and its biological implications on the other. The aim of this review is to present the newest knowledge on nitrosyl iron complexes, summarizing the issues that are important for understanding the nature of nitrosyl iron complexes, their possible interactions, behavior in vitro and in vivo, handling of the preparations etc. in response to the growing interest in these compounds. Herein we focus mostly on the dinitrosyl iron complexes (DNICs) due to their prevailing occurrence in NO-treated biological samples. This article reviews recent knowledge on the structure, chemical properties and biological action of DNICs and some mononitrosyls of heme proteins. Synthetic methods are also briefly reviewed.     

Five-membered ring systems with one heteroatom: Synthetic routes,chemical reactivity,and biological properties of furan-carboxamide analogues

This review described the synthetic methods, chemical reactivity and biological applications of furan carboxamide compounds. Furan-carboxamides are reported to have important and variable biological properties. The aim of this review is to highlight the chemistry and biological importance of this class of bioactive compounds. The basic sections covers: structure studies, synthetic methods pathways, synthesis of different heterocycles, reactions and biological applications. The reactions mechanisms of the unexpected products are discussed. The present study covers all the published work on the furan-carboxamides until now.     

High-pressure absorption spectroscopy in polymerizing systems

Quantitative high-pressure absorption spectroscopy in the mid infrared, near infrared, and ultraviolet region enables direct and precise investigation of high-pressure ethylene polymerizations with thermal, chemical, and laser-photochemical initiation. The special advantages of kinetic studies via quantitative near infrared spectroscopy in an extended wavenumber range are outlined. Extensions of the method on copolymer systems are indicated. The spectroscopic technique is of general applicability in studies on reactions and equilibria in dense fluid states including liquids and compressed gases.     

Chemical aspects of amine oxidation by flavoprotein enzymes

The mechanism of amine oxidation by flavoprotein enzymes is critically analysed through analysis of available experimental data. The review assesses available evidence for radical and polar mechanisms, drawing on data from model reactions, kinetic and spectroscopic approaches, structural and mutagenesis studies. The review focused on studies of mammalian monoamine oxidases and the bacterial enzymes trimethylamine dehydrogenase, monomeric sarcosine oxidase and dimethylglycine oxidase.     

High-pressure rate rules for alkyl + O2 reactions. 2. The isomerization, cyclic ether formation, and β-scission reactions of hydroperoxy alkyl radicals

The unimolecular reactions of hydroperoxy alkyl radicals (QOOH) play a central role in the low-temperature oxidation of hydrocarbons as they compete with the addition of a second O(2) molecule, which is known to provide chain-branching. In this work we present high-pressure rate estimation rules for the most important unimolecular reactions of the β-, γ-, and δ-QOOH radicals: isomerization to RO(2), cyclic ether formation, and selected β-scission reactions. These rate rules are derived from high-pressure rate constants for a series of reactions of a given reaction class. The individual rate expressions are determined from CBS-QB3 electronic structure calculations combined with canonical transition state theory calculations. Next we use the rate rules, along with previously published rate estimation rules for the reactions of alkyl peroxy radicals (RO(2)), to investigate the potential impact of falloff effects in combustion/ignition kinetic modeling. Pressure effects are examined for the reaction of n-butyl radical with O(2) by comparison of concentration versus time profiles that were obtained using two mechanisms at 10 atm: one that contains pressure-dependent rate constants that are obtained from a QRRK/MSC analysis and another that only contains high-pressure rate expressions. These simulations reveal that under most conditions relevant to combustion/ignition problems, the high-pressure rate rules can be used directly to describe the reactions of RO(2) and QOOH. For the same conditions, we also address whether the various isomers equilibrate during reaction. These results indicate that equilibrium is established between the alkyl, RO(2), and γ- and δ-QOOH radicals.     

Thermal reactions of selected solids including reactants that melt during chemical change

Selected kinetic and mechanistic studies of thermal reactions of initially solid substances are reviewed with emphasis on the evidence that some of these chemical changes proceed with the essential participation of melting. The reactions considered are classified on the extent and the role of such melting and the various types of behaviour observed are discussed with reference to solid state rate processes in crystals. It is stressed that melting is an important feature in theoretical considerations of crystal reactivity because chemical changes often proceed more rapidly in a melt than in the solid state. However, literature reports concerned with reactions of solids do not always explicitly mention the possibility of melting during discussions of reactions mechanisms. The present paper comments on methods capable of detecting liquefaction during reaction, a feature of behaviour that is not always easily identified experimentally. Also considered here is the recognition of reaction intermediates, which provide important evidence concerning the course of the chemical changes through which the reactant is transformed into product. This short review draws attention to the considerable value of chemical evidence in elucidating mechanisms of reactions of solids including the necessity for identifying intermediates and the role of any melt or liquid participating.     

检测生理内源性一氧化氮分子探针的研究及应用进展

本文介绍和评述了荧光光度法、化学发光法、分光度度法、电化学和电子自旋共振光谱法中的分子探针及在检测生理内源性一氧化氮的应用及研究进展。引用文献42篇。     

Metal complex-assisted activation of small molecules. From NO to superoxide and peroxides

Transition metal centres are one of the primary targets for nitric oxide (NO), superoxide (O2(-)) and hydrogen peroxide (H2O2), which are small molecules present in a biological milieu, and of industrial and environmental interest. Coordination to a metal centre modulates their redox behaviour in such a way that they become activated for an inner-sphere oxidation or reduction, depending on the electronic and redox properties of a particular transition metal ion. Since the related redox reactions play multiple roles in physiological and pathophysiological processes, as well as in chemical catalysis in terms of synthetic applications and exhaust gas purification, the elucidation of the mechanisms of the elementary reaction steps behind these complex processes is of fundamental importance. This review concentrates on our work in this area, where by applying low temperature and high pressure kinetic and thermodynamic techniques we shed more light on the mechanisms of the particular reaction steps involved in the activation of NO, O2(-) and various peroxides. The studies include work on solvent exchange reactions that control the binding of small molecules to the metal centre and subsequent electron-transfer processes. We paid special attention to different iron and manganese complexes with heme and non-heme ligand systems.     

二氧化铈催化剂的氧化还原和酸碱性质的原位光谱表征

二氧化铈作为催化剂、催化剂载体和助剂被广泛应用于各类氧化还原的催化反应中,是多相催化领域中至关重要的金属氧化物.氧化铈因具有丰富的缺陷结构、较强的氧化还原能力以及异常的酸碱功能等独特性质,在催化领域中非常重要.在分子层面上理解氧化铈的储氧能力、氧化还原效应和酸碱性质对建立催化构效关系尤为重要,是有效合理地改善和设计铈基催化材料的关键.在诸多的表征手段中,光谱在氧化铈结构和表面性质的研究中显示出无可争议的优势,可以提供原子和分子层面的化学信息.本文总结了各种光谱方法(包括光学、X射线、中子、电子和核磁谱学)对氧化铈表面性质表征的研究进展.分析了直接光谱表征及其与探针分子耦合两种方法在氧化铈表征中的应用;归纳了预处理条件、氧化铈纳米粒子的形貌和尺寸对其表面位点的性质、强度和密度的影响.最后展望了如何利用反应条件下的原位光谱来更好地理解和揭示铈基材料的催化作用机制的可能性.     

检测活性氧物种的氧杂蒽类光学探针的研究进展

活性氧物种在维持生物体的生理功能方面发挥着重要的作用.高于正常水平的活性氧物种会损伤蛋白质、DNA等生物分子,进而导致疾病.因此,活性氧物种的高选择性、高灵敏度检测研究对疾病的预防、诊断和治疗均具有重要意义.荧光探针因具有分析灵敏度高、样品时空分辨能力强等特点,已在该方面获得了广泛的应用.其中,具有发射波长长,光稳定性好,荧光量子产率高等优点的氧杂蒽类荧光探针已成为检测活性氧物种的研究热点.本论文主要总结了近五年来应用于活性氧物种检测的氧杂蒽类荧光探针的研究进展与成像分析,归纳了不同活性氧物种的识别单元,并展望了此类探针的发展趋势与应用前景.     

Recent developments in the detection of singlet oxygen with molecular spectroscopic methods

Singlet oxygen is a unique reactive oxygen species, as its chemical reactivity derives from its characteristic electronically-excited state. The involvement of singlet oxygen in many important atmospheric, physical, chemical, biological, and therapeutic processes has attracted intense research interest in recent years. The detection and the quantification of singlet oxygen are very important for understanding its mechanism of action in various processes.Due to its highly reactive nature, singlet oxygen has very few direct methods of determination. Only molecular phosphorescence at 1270 nm has been utilized. Indirect methods using spectrophotometric, fluorescent or chemiluminescent probes have therefore been extensively studied.This review reflects recent developments in singlet-oxygen detection with molecular spectroscopic methods. We begin with a brief introduction of the basic properties, the production and the applications of singlet oxygen. With this background information, we review the four molecular spectroscopic methods (i.e., emission, spectrophotometry, fluorescence and chemiluminescence). We pay special attention to attractive chemical probes with high selectivity and sensitivity in quantifying singlet oxygen.     

Mechanistic studies of nitrite reactions with metalloproteins and models relevant to mammalian physiology

This review provides a summary of reaction mechanisms involving the interactions of nitrite ion with metal centers relevant to physiology. The majority of the systems that have been investigated are heme proteins and models, where nitrite reacts with the central metal ions to generate important iron-NO_x intermediates and subsequent NO_x products. We also discuss reactions with other potentially relevant systems. Nitrite is formed as a product of NO autoxidation in aqueous media and can be formed by the bacterial reduction of ingested nitrate as well. It is now generally accepted that under certain conditions nitrite, which is present in mammalian fluids and tissue at micromolar concentrations, can serve as a biological reserve of the bioregulatory agent nitric oxide. However, it is possible that nitrite serves other functions as well. The goal of this review is to evaluate the present state of understanding regarding these pathways and the delicate interplay between nitrite and the various NO_x species of biological relevance.     

Probing the Interactions of Porphyrins with Macromolecules Using NMR Spectroscopy Techniques

Porphyrinic compounds are widespread in nature and play key roles in biological processes such as oxygen transport in blood, enzymatic redox reactions or photosynthesis. In addition, both naturally derived as well as synthetic porphyrinic compounds are extensively explored for biomedical and technical applications such as photodynamic therapy (PDT) or photovoltaic systems, respectively. Their unique electronic structures and photophysical properties make this class of compounds so interesting for the multiple functions encountered. It is therefore not surprising that optical methods are typically the prevalent analytical tool applied in characterization and processes involving porphyrinic compounds. However, a wealth of complementary information can be obtained from NMR spectroscopic techniques. Based on the advantage of providing structural and dynamic information with atomic resolution simultaneously, NMR spectroscopy is a powerful method for studying molecular interactions between porphyrinic compounds and macromolecules. Such interactions are of special interest in medical applications of porphyrinic photosensitizers that are mostly combined with macromolecular carrier systems. The macromolecular surrounding typically stabilizes the encapsulated drug and may also modify its physical properties. Moreover, the interaction with macromolecular physiological components needs to be explored to understand and control mechanisms of action and therapeutic efficacy. This review focuses on such non-covalent interactions of porphyrinic drugs with synthetic polymers as well as with biomolecules such as phospholipids or proteins. A brief introduction into various NMR spectroscopic techniques is given including chemical shift perturbation methods, NOE enhancement spectroscopy, relaxation time measurements and diffusion-ordered spectroscopy. How these NMR tools are used to address porphyrin–macromolecule interactions with respect to their function in biomedical applications is the central point of the current review.     

Exogenous donors of nitric oxide (a chemical aspect)

The review considers problems related to the formation, in the living organism, of nitric oxide, a versatile and vitally important regulator of cell metabolism. The pathways of formation of endogenous nitric oxide from L-arginine are discussed and the main approaches to increasing the NO concentration by introducing various types of exogenous nitric oxide donors into the organism and chemical and biological characteristics of these donors are considered. Primary attention is devoted to the known drugs that were shown to release NO under hydrolytic, oxidative, or reductive conditions. The solution of problems related to the elucidation of the mechanisms of drug action requires that the formation of nitric oxide be taken into account.     

Nicotinamide adenine dinucleotide: beyond a redox coenzyme

ADP-ribosylation using nicotinamide adenine dinucleotide (NAD+) is an important type of enzymatic reaction that affects many biological processes. A brief introductory review is given here to various ADP-ribosyltransferases, including poly(ADP-ribose) polymerase (PARPs), mono(ADP-ribosyl)-transferases (ARTs), NAD(+)-dependent deacetylases (sirtuins), tRNA 2'-phosphotransferases, and ADP-ribosyl cyclases (CD38 and CD157). Focus is given to the enzymatic reactions, mechanisms, structures, and biological functions.     

Thermal decomposition of decalin: an ab initio study

Density functional theory calculations (B3LYP and BH&HLYP functionals) of the potential energy surface have been performed to investigate the mechanisms of decalin breakdown, and the Rice-Ramsperger-Kassel-Marcus and transition state theory methods have been used to compute the high-pressure limit thermal rate constants for the new reaction pathways. The new pathways connect decalin to five primary monoaromatic species: benzene, toluene, styrene, ethylbenzene, and xylene. The reactions used for the new routes are carbon-carbon bond cleavage reaction, dissociation reaction, and hydrogen abstraction and addition reactions. A kinetic analysis was performed for pyrolytic conditions, and benzene, toluene, and xylene were identified as major products.     

Investigating the structure and function of cupredoxins

Copper is widely used in nature to promote electron transfer in a variety of processes. The metal is usually found as a mononuclear type 1 copper site protected by a protein envelope, which has become known as a cupredoxin fold. In the past few years, the use of protein engineering combined with various spectroscopic and kinetic approaches has provided detailed information about cupredoxins and cupredoxin domains. This review will describe some of the recent advances that have been made, highlighting that there is still a long way to go before we fully appreciate the complexity of biological electron transfer proteins.     

Equivalency of Kinetic Schemes: Causes and an Analysis of Some Model Fitting Algorithms

The same experimental data can often be equally well described by multiple mathematically equivalent kinetic schemes. In the present work, we investigate several model‐fitting algorithms and their ability to distinguish between mechanisms and derive the correct kinetic parameters for several different reaction classes involving consecutive reactions. We have conducted numerical experiments using synthetic experimental data for six classes of consecutive reactions involving different combinations of first‐ and second‐order processes. The synthetic data mimic time‐dependent absorption data as would be obtained from spectroscopic investigations of chemical kinetic processes. The connections between mathematically equivalent solutions are investigated, and analytical expressions describing these connections are derived. Ten optimization algorithms based on nonlinear least squares methods are compared in terms of their computational cost and frequency of convergence to global solutions. Performance is discussed, and a preferred method is recommended. A response surface visualization technique of projecting five‐dimensional data onto the three‐dimensional search space of the minimal function values is developed.