Prediction of Nucleophilicity and Electrophilicity Based on a Machine-Learning Approach

Nucleophilicity and electrophilicity dictate the reactivity of polar organic reactions. In the past decades, Mayr et al. established a quantitative scale for nucleophilicity (N) and electrophilicity (E), which proved to be a useful tool for the rationalization of chemical reactivity. In this study, a holistic prediction model was developed through a machine-learning approach. rSPOC, an ensemble molecular representation with structural, physicochemical and solvent features, was developed for this purpose. With 1115 nucleophiles, 285 electrophiles, and 22 solvents, the dataset is currently the largest one for reactivity prediction. The rSPOC model trained with the Extra Trees algorithm showed high accuracy in predicting Mayr's N and E parameters with R² of 0.92 and 0.93, MAE of 1.45 and 1.45, respectively. Furthermore, the practical applications of the model, for instance, nucleophilicity prediction of NADH, NADPH and a series of enamines showed potential in predicting molecules with unknown reactivity within seconds. An online prediction platform (http://isyn.luoszgroup.com/) was constructed based on the current model, which is available free to the scientific community.     

用Hirshfeld 电荷定量标度亲电性和亲核性: 含氮体系

准确预测化学过程中分子内各原子提供或接受电子的能力以及化学反应可能的位点, 即定量确定亲电性、亲核性和区域选择性, 是一个十分重要却仍然亟待解决的课题. 此前, 基于我们新近提出的信息守恒原理,曾建议使用Hirshfeld 电荷和信息增益作为两个等价的描述符用于此目的. 我们的这个想法已经被成功地应用于两个系列的分子体系, 且其有效性得到了充分的验证. 然而, 先前我们只考察了碳元素的这些性质, 所以其结论的普遍性仍存在疑问. 我们尚不清楚它是否适用于其他元素, 而且对于同一元素的不同价态该结论是否适用也不清楚. 为此, 本文将考察含氮体系. 对5 个不同类别的含氮体系共计40 个分子进行了研究, 其中包括重氮苯、偶氮、重氮、一级和二级胺体系. 结果表明, 对所有五个含氮体系其Hirshfeld 电荷与实验得到的亲电性和亲核性标度之间仍然存在着较强的线性关联. 然而, 这些相关性却依赖于氮元素的化合价类型和键合环境. 该线性关系只能在同一类型中成立. 我们对其可能的原因进行了讨论.     

用Hirshfeld电荷定量标度亲电性和亲核性:含氮体系(英文)

准确预测化学过程中分子内各原子提供或接受电子的能力以及化学反应可能的位点,即定量确定亲电性、亲核性和区域选择性,是一个十分重要却仍然亟待解决的课题.此前,基于我们新近提出的信息守恒原理,曾建议使用Hirshfeld电荷和信息增益作为两个等价的描述符用于此目的.我们的这个想法已经被成功地应用于两个系列的分子体系,且其有效性得到了充分的验证.然而,先前我们只考察了碳元素的这些性质,所以其结论的普遍性仍存在疑问.我们尚不清楚它是否适用于其他元素,而且对于同一元素的不同价态该结论是否适用也不清楚.为此,本文将考察含氮体系.对5个不同类别的含氮体系共计40个分子进行了研究,其中包括重氮苯、偶氮、重氮、一级和二级胺体系.结果表明,对所有五个含氮体系其Hirshfeld电荷与实验得到的亲电性和亲核性标度之间仍然存在着较强的线性关联.然而,这些相关性却依赖于氮元素的化合价类型和键合环境.该线性关系只能在同一类型中成立.我们对其可能的原因进行了讨论.     

Electron Transfer and Charge Transfer: Twin Themes in Unifying the Mechanisms of Organic and Organometallic Reactions

The broad varieties of organic and organometallic reactions merge into a common unifying mechanism by considering all nucleophiles and electrophiles as electron donors (D) and electron acceptors (A), respectively. Comparison of outer-sphere and inner-sphere electron transfers with the aid of Marcus theory provides the thermochemical basis for the generalized free energy relationship for electron transfer (FERET) in Equation (37) and its corollaries in Equations (43) and (44) that have wide predictive applicability to electrophilic aromatic substitutions, olefin additions, organometallic cleavages, etc. The FERET is based on the conversion of the weak nucleophile–electrophile interactions extant in the ubiquitous electron donor—acceptor (EDA) precursor complex [D, A] to the radical ion pair [D^⊕, A^?], for which the free energy change can be evaluated from the charge-transfer absorption spectra according to Mulliken theory. FERET analysis thus indicates that the charge-transfer ion pairs [D^⊕, A^?] are energetically equivalent to the transition states for nucleophile/electrophile transformations. The behavior of such ion pairs can be directly observed immediately following the irradiation of the charge-transfer bands of various EDA complexes with a 25-ps laser pulse. Such studies confirm the radical ion pair [Arene^⊕, NO₂] as a viable intermediate in electrophilic aromatic nitration, as presented in the electron-transfer mechanism between arenes and the nitryl cation (NO) electrophile.     

Experimental and theoretical study on the substitution reactions of aryl 2,4-dinitrophenyl carbonates with quinuclidines

The reactions of quinuclidines with phenyl, 4-methylphenyl, and 4-chlorophenyl 2,4-dinitrophenyl carbonates are kinetically evaluated in aqueous solution. The Brønsted-type plots (log k_N vs pK_a of quinuclidinium ions) are linear. The magnitude of the slopes and validated theoretical scales of electrophilicity and nucleophilicity confirm the concerted nature of these reactions.     

Kinetics and Mechanisms of the Reactions of π‐Allylpalladium Complexes with Nucleophiles

Which nucleophiles are capable of attacking the allyl ligand of the Pd‐stabilized allyl cation 1 ? This question is answered by the electrophilicity parameter of 1 which is derived from kinetic investigations.     

ETC: A Mechanistic Concept for Inorganic and Organic Chemistry

The concept of electron transfer catalysis (ETC), or more specifically “Double Activation Induced by Single Electron Transfer” (DAISET) gives an opportunity to connect experimental facts never previously correlated. The first activation results from the transfer of an electron to (or from) a molecular species; the second activation results from the build-up of a reaction chain able to reproduce the species formed in the first step. The starting point of this review is the S_RN 1 mechanism where principle and experimental diagnostic criteria are critically discussed. The thermal and photochemical exchange and substitution reactions of Pt^IV complexes are then reviewed together with the exchange reaction [AuCl₄]^?/Cl^?, reactions with Grignard reagents and other organometallic reagents, as well as the redox behavior of electronically excited organic compounds. Photochemical applications, including solar energy conversion are discussed. New aspects are also presented for the mechanistic problem “S_N 2 reaction or SET process?” Moreover, the concept has significance for S_H2 reactions at metal centers, molecule-induced homolyses, reactions of complexes, as well as electrochemical processes.–Unless otherwise specified, only double activation (DAISET) processes will be discussed in this article.     

Oxygen Transfer from Inorganic and Organic Peroxides to Organic Substrates: A Common Mechanism?

In this progress report an attempt is made to rationalize, from a mechanistic point of view, the different ways in which oxygen is transferred from inorganic and organic peroxides to nucleophilic substrates, particularly olefins. Oxygen transfer from transition-metal peroxides, which is relevant to catalytic oxidations using O₂, H₂O₂ or ROOH, occurs via a cyclic or “pseudocyclic” peroxymetalation in which a dioxametallacycle is formed. Owing to the wide discrepancy between peroxymetalation and the conventional oxidation mechanism, i.e. nucleophilic attack of the substrate at the electrophilic “active oxygen”, we propose an alternative mechanism involving dioxiranes as the reactive species. The generation of dioxiranes appears to be a common denominator in the reactions of most organic peroxides e.g. peroxy acids, the reaction of electrophilic ketones with H₂O₂, or ozonizations. Oxygen transfer from dioxirane reagents probably involves the formation of a charge-transfer π-complex between the substrate and the carbon atom of the dioxirane, and the subsequent formation of a cyclic peroxidic intermediate.     

A DFT study of the polar Diels-Alder reaction between 4-aza-6-nitrobenzofuroxan and cyclopentadiene

The polar Diels-Alder reaction between 4-aza-6-nitrobenzofuroxan (ANBF) and cyclopentadiene has been studied using DFT procedures at the B3LYP/6-31G* level. Only one highly asynchronous transition state structure associated to the formation of the [4+2] adduct 13 is found. A further [3,3] sigmatropic shift on the [4+2] cycloadduct 13 allows its conversion into the thermodynamically more stable [2+4] cycloadduct 14. The analysis of the global and local electrophilicities of the reagents correctly explain the behaviour of ANBF as a strong electrophile in polar cycloadditions.     

The Mechanism of Contact Elimination,A Contribution to Understanding the Function of Polar Catalysts

The current ideas of organic chemists based on the work of Ingold and his school are applied to heterogeneous catalytic eliminations (mostly from haloalkanes and aliphatic alcohols). It is deduced from the activity of the catalysts, the reactivity of the substrates (reactants), and the primary product distribution that these eliminations proceed by a heterolytic mechanism similar to that involved in the liquid phase. The activity of the catalysts (salts and oxides) increases with increasing charge and decreasing radius of the cations and with increasing basicity of the anions. The reactivity of the substrates behaves in much the same manner as in the liquid phase. In contrast with the liquid-phase reaction, the cis-olefins are frequently favored as primary products. The stereospecificity of the reaction is determined from the relative strengths of the interactions between the catalyst cation and the leaving group X^?, and between the catalyst anion and the leaving proton. Only trans elimination has so far been found in the concerted mechanism.     

CC Bond Formation by Addition of Carbenium Ions to Alkenes: Kinetics and Mechanism

The addition of carbenium ions to CC double bonds, a key step in many syntheses in organic and macromolecular chemistry, is analyzed using the Lewis acid promoted reactions of alkyl chlorides with alkenes as an example. Stereochemical and kinetic experiments suggest that the transition state is slightly bridged and product-like. Rearrangements of the carbenium ions that result from the electrophilic attack can be minimized by adding salts with nucleophilic counter ions. The thermodynamics of the addition reactions are analyzed, and the conditions necessary in order to observe the back reaction (i.e. the Grob fragmentation) are discussed. Multiparameter equations that predict rate constants are derived from kinetic studies on the reactivities of carbenium ions and alkenes. Reactivity-selectivity relationships over a reactivity range that covers eight orders of magnitude show that the structure of the transition state is only changed by variation of substituents in the immediate vicinity of the reaction center.     

Electron Transfer Reactions in Chemistry: Theory and Experiment (Nobel Lecture)

Since the late 1940s, the field of electron transfer processes has grown enormously, both in chemistry and biology. The development of the field, experimentally and theoretically, as well as its relation to the study of other kinds of chemical reactions, presents to us an intriguing history, one in which many threads have been brought together. In this lecture, some history, recent trends, and my own involvement in this research are described.     

Reactions of Silicon Atoms with Methanol: A Combined Matrix‐Spectroscopic and Density Functional Theory Study

The reaction of silicon atoms with methanol ( 4 ) has been studied in an argon matrix at 10 K. In the initial step a triplet n‐adduct T‐5 between a silicon atom and 4 is formed. It cannot be detected directly as long as a low concentration of 4 is used. But T‐5 must be generated since upon simultaneous irradiation during cocondensation methylsilanone ( 15 ) is found. Without irradiation T‐5 undergoes immediately O,H insertion and methoxysilylene ( S‐7‐c ) is isolated, which establishes a photoequilibrium between the s,trans ( S‐7‐t ) and s,cis form ( S‐7‐c ). If a high concentration of 4 is applied the silylenes exist as complexes S‐17 . The next step needs photochemical activation. Products are dimethoxysilane ( 3 ) and (hydroxy)(methoxy)methylsilane ( 19 ). The picture becomes even more complicated when deuteromethanol ( [D]4 ) is treated with silicon atoms. In this case the primarily formed n‐adduct ( [D]T‐5 ) is stable under matrix conditions. As long as a low concentration is applied, the subsequent step has to be induced by long wavelength irradiation and leads – different from the undeuterated case – to O,CH₃ insertion, giving (hydroxy)methylsilylenes ( [D]S‐11‐c ) and ( [D]S‐11‐t ). If a high concentration is used O,D insertion is preferred instead and even without irradiation the first observable products are methanol‐solvated methoxysilylenes ( [D₂]S‐17‐c ) and ( [D₂]S‐17‐t ). Subsequent irradiation of complexes [D₂]S‐17 gives in accordance with the protonated series a mixture of [D₂]3 and [D₂]19 . Our goal, to find a way to dimethylsilanediol ( [D₂]2 ), was finally reached by preparing silylenes [D]S‐11 in a diluted matrix, its specific solvation with [D]4 and final irradiation of complexes [D₂]S‐18 . The structural elucidation of all new species is based on the comparison of the experimental observations with density functional theory calculations. Upon cocondensation of silicon atoms with pure methanol at 77 K dimethoxysilane ( 3 ) and 1,1,2‐trimethoxydisilane ( 25 ) are produced. The also present methoxysilanes 22‐24 have to be regarded as secondary products of 3 .     

The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems

Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as “name reactions”. This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical‐mediated, and rearrangements, which are subdivided by name reactions.     

Displacement Reactions of Phosphorus(V) Compounds and Their Pentacoordinate Intermediates

Reactions of phosphorus(v) compounds involving the mutual interconversion of tetra- and pentacoordinate species are discussed in a critical review emphasizing stereochemical implications of the reaction mechanism. This discussion includes the formation and decomposition of the stable oxyphosphoranes, the Michaelis-Arbusov, Perkov, and Wittig reactions, interconversions of phosphines and their oxides, and the nucleophilic displacements on phosphonium compounds. Reactions of phosphate esters and related compounds receive particular attention. All chemical arguments are derived by considering the effect of factors determining the relative stabilities of phosphorane derivatives, their rates of formation, decomposition and rearrangement by bond deformation or rupture and recombination processes, considerations which are uniformly applied on the basis of concepts developed in a preceding communication^[2]. It is shown that a comprehensive mechanistic interpretation of the foregoing reactions requires substantial addition to available conceptual foundations such that, in many cases, present concepts and mechanisms must be revised.     

Spectroscopy of Fluid Phases—The Study of Chemical Reactions and Equilibria up to High Pressures

The properties of fluid phases can be altered considerably by the external conditions. Phase equilibria and chemical equilibria can be greatly affected, and it is possible to carry out chemical reactions by exploiting the special properties of compressed fluid phases. The use of high pressure in chemical reactions is of considerable diagnostic and preparative value. Applied research is directed towards elucidating the details of existing technical high pressure processes and to the development of novel fluid phase reactions where the application of high pressure is able to induce selectivity. In order to pursue these lines of research, and to study structure and dynamics throughout the entire range from gaseous to liquidlike states, it is important to have spectroscopic methods for characterizing systems at high pressures and temperatures. This article is concerned with quantitative absorption spectroscopy in the infrared to the ultraviolet spectral region at pressures up to about 7 kbar and temperatures up to 900 K.     

Enantioselective Addition of Organometallic Reagents to Carbonyl Compounds: Chirality Transfer,Multiplication, and Amplification

Nucleophilic addition of organometallic reagents to carbonyl substrates constitutes one of the most fundamental operations in organic synthesis. Modification of the organometallic compounds by chiral, nonracemic auxiliaries offers a general opportunity to create optically active alcohols, and the catalytic version in particular provides maximum synthetic efficiency. The use of organozinc chemistry, unlike conventional organolithium or -magnesium chemistry, has realized an ideal catalytic enantioselective alkylation of aldehydes leading to a diverse array of secondary alcohols of high optical purity. A combination of dialkylzinc compounds and certain sterically constrained β-dialkylamino alcohols, such as (–)-3-exo-dimethylaminoiso- borneol [(–)-DAIB], as chiral inducers affords the best result (up to 99% ee). The alkyl transfer reaction occurs via a dinuclear Zn complex containing a chiral amino alkoxide, an aldehyde ligand, and three alkyl groups. The chiral multiplication method exhibits enormous chiral amplification: a high level of enantioselection (up to 98%) is attainable by use of DAIB in 14% ee. This unusual nonlinear effect is a result of a marked difference in chemical properties of the diastereomeric (homochiral and heterochiral) dinuclear complexes formed from the dialkylzinc and the DAIB auxiliary. This phenomenon may be the beginning of a new generation of enantioselective organic reactions.