Nucleophilic substitution at phosphorus (S(N)2@P): disappearance and reappearance of reaction barriers

Electrophilic C(sp2)-H Cyanation with Inorganic Cyanate (OCN-) by PIII/PV=O-Catalyzed Phase Transfer Activation

An organophosphorus -catalyzed method for the direct electrophilic cyanation of C(sp2)-H nucleophiles with sodium cyanate (NaOCN) is reported. The catalytic deoxyfunctionalization of the OCN- anion is enabled by the use of a small-ring phosphacyclic (phosphetane) catalyst in combination with a terminal hydrosilane O-atom acceptor and a malonate-derived bromenium donor. In situ spectroscopy under single-turnover conditions demonstrate that insoluble inorganic cyanate anion is activated by bromide displacement on a bromophosphonium catalytic intermediate to give a reactive N-bound isocyanatophosphonium ion, which delivers electrophilic "CN+" equivalents to nucleophilic (hetero)arenes and alkenes with loss of a phosphine oxide. These results demonstrate the feasibility of deoxyfunctionalization of insoluble inorganic salts by PIII/PV=O catalyzed phase transfer activation.

A molecular electron density theory study of the bimolecular nucleophilic substitution reactions on monosubstituted methyl compounds

The nucleophilic substitution reactions involving methyl monosubstituted compounds have been studied within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311+G(d,p) computational level in DMSO. This study aims to characterize the electronic nature of the transition state structures (TSs) involved in the so-called SN2 and SNi reactions. Both electron localization function and atom-in-molecules topological analyses indicate that the TSs involved in these nucleophilic substitutions can be described as a central methyl CH3+ carbocation, which is strongly stabilized by the presence of two neighbouring nucleophilic species through electron density transfer. This MEDT study establishes a significant electronic similarity between the so-called SN1 and SN2 reactions. Due to the weak electrophilic character of the methyl tetrahedral carbons, the departure of the leaving group should be expected with the approach of the nucleophile. However, while along the SN1 reactions, the strong stabilization of the tertiary carbocation does not demand the participation of the nucleophile, along the SN2 and SNi reactions involving primary tetrahedral carbons, the nucleophiles should participate in the reaction to stabilize the unstable methyl carbocation.

Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme

This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen-bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE-CWA complex involving Sarin (GB), Cyclosarin (GF), 2-[fluoro(methyl)phosphoryl]oxy-1,1-dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position. The AIM analysis was carried out and consistently revealed the presence of a significant interaction along the PO bond. Investigating the intrinsic nature of the PnB, the NBO and the EDA analysis unearthed the contribution of orbital factors to the overall energy of the system. Strikingly, this observation challenges the conventional σ-hole explanation commonly associated with such interactions. This finding adds a layer of complexity to understanding of PnB, encouraging further exploration into the underlying mechanisms governing these intriguing chemical phenomena.

Second Generation Catalytic Enantioselective Nucleophilic Desymmetrization at Phosphorus (V): Improved Generality, Efficiency and Modularity

A broadly improved second generation catalytic two-phase strategy for the enantioselective synthesis of stereogenic at phosphorus (V) compounds is described. This protocol, consisting of a bifunctional iminophosphorane (BIMP) catalyzed nucleophilic desymmetrization of prochiral, bench stable P(V) precursors and subsequent enantiospecific substitution allows for divergent access to a wide range of C-, N-, O- and S- substituted P(V) containing compounds from a handful of enantioenriched intermediates. A new ureidopeptide BIMP catalyst/thiaziolidinone leaving group combination allowed for a far wider substrate scope and increased reaction efficiency and practicality over previously established protocols. The resulting enantioenriched intermediates could then be transformed into an even greater range of distinct classes of P(V) compounds by displacement of the remaining leaving group as well as allowing for even further diversification downstream. Density functional theory (DFT) calculations were performed to pinpoint the origin of enantioselectivity for the BIMP-catalyzed desymmetrization, to rationalize how a superior catalyst/leaving group combination leads to increased generality in our second-generation catalytic system, as well as shed light onto observed stereochemical retention and inversion pathways when performing late-stage enantiospecific SN2@P reactions with Grignard reagents.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

Nucleophilic Substitution at Phosphorus Centres - Old and Recent Studies and a Final Solution of Mechanistic and Related Stereochemical Problems

Among many problems of a fundamental value in the heteroatom chemistry the mechanism and stereochemistry of the nucleophilic substitution reaction at the phosphorus and other heteroatom centres have attracted great attention of phosphorus chemists already in the middle of the last century. This review, which does not have a comprehensive character, summarizes the selected original contributions aimed at solution of the mechanism of SN2-P reaction and its relationship with stereochemistry. The breakthrough in these studies was the Westheimer's concept and his rules which is presented at the beginning of this article. Next, a series of papers is presented where the stereochemistry of the substitution at phosphorus was investigated in cyclic five-, four- and six-membered ring phosphorus compound. The majority of these reactions have been found to occur with retention of the P-configuration. In the third part of this account, the selected examples of substitution reactions at phosphorus in acyclic compounds are discussed. As the results of all the investigations discussed did not allow to undoubtedly ascribe the mechanism (SN2 or A-E) to the investigated reactions, in the last part the SN-P reactions are presented, the mechanism of which has been established by combination of the stereochemical and DFT-studies.

Carboranylphosphines: B9-Substituted Derivatives with Enhanced Reactivity for the Anchoring to Dendrimers

Several ortho-carboranes bearing a phenoxy or a phenylamino group in the B9 position were prepared employing various protection and deprotection strategies. Following established protocols, dendritic compounds were synthesized from a hexachlorocyclotriphosphazene or thiophosphoryl chloride core, and possible anchoring options for the B9-substituted ortho-carboranes were investigated experimentally and theoretically (DFT). Furthermore, 1- or 1,2-phosphanyl-substituted carborane derivatives were obtained. The resulting diethyl-, diisopropyl-, di-tert-butyl-, diphenyl- or diethoxyphosphines bearing a tunable ortho-carborane moiety are intriguing ligands for future applications in homogeneous catalysis or the medicinal sector.

Formation Mechanism of the Unsubstituted Chlorophosphazene Cl3P═NH: A Theoretical Study via Quantum Mechanical Calculations

Although the synthesis of chlorophosphazene polymers has been explored for more than 100 years, the shortest yet most illusive monomer, Cl3P═NH, has never been isolated and fully characterized. Here we investigate the formation of Cl3P═NH from PCl5 and NH3 in chlorobenzene through quantum mechanical calculations. The potential energy surface was mapped using the MP2 Hamiltonian in conjunction with Dunning's correlation-consistent basis sets (aug-cc-pVXZ, where X = D and T). Along with HOMO/LUMO frontier molecular orbitals and natural bond orbital analyses, we found that instead of following the SN1 path proposed in the literature, the reaction proceeds via an addition-elimination mechanism. Our results also indicate that due to the low-lying stable intermediates (IM), most steps are exothermic such that the production of Cl3P═NH·2HCl can be completed once the energy barrier for the formation of [PCl4-NH3]+Cl- is overcome. Therefore, our theoretical work might explain the challenges in isolating any of the IMs in a typical chlorophosphazene reaction in chlorobenzene.

Phosphorus-centered ion-molecule reactions: benchmark ab initio characterization of the potential energy surfaces of the X- + PH2Y [X, Y = F, Cl, Br, I] systems

In the present work we determine the benchmark relative energies and geometries of all the relevant stationary points of the X- + PH2Y [X, Y = F, Cl, Br, I] identity and non-identity reactions using state-of-the-art electronic-structure methods. These phosphorus-centered ion-molecule reactions follow two main reaction routes: bimolecular nucleophilic substitution (SN2), leading to Y- + PH2X, and proton transfer, resulting in HX + PHY- products. The SN2 route can proceed through Walden-inversion, front-side-attack retention, and double-/multiple-inversion pathways. In addition, we also identify the following product channels: H--formation, PH2-- and PH2-formation, 1PH- and 3PH-formation, H2-formation and HY + PHX- formation. The benchmark classical relative energies are obtained by taking into account the core-correlation, scalar relativistic, and post-(T) corrections, which turn out to be necessary to reach subchemical (<1 kcal mol-1) accuracy of the results. Classical relative energies are augmented with zero-point-energy contributions to gain the benchmark adiabatic energies.

Alternating Stereospecificity upon Central-Atom Change: Dynamics of the F- +PH2 Cl SN 2 Reaction Compared to its C- and N-Centered Analogues

Central-atom effects on bimolecular nucleophilic substitution (SN 2) reactions are well-known in chemistry, however, the atomic-level SN 2 dynamics at phosphorous (P) centers has never been studied. We investigate the dynamics of the F- +PH2 Cl reaction with the quasi-classical trajectory method on a novel full-dimensional analytical potential energy surface fitted on high-level ab initio data. Our computations reveal intermediate dynamics compared to the F- +CH3 Cl and the F- +NH2 Cl SN 2 reactions: phosphorus as central atom leads to a more indirect SN 2 reaction with extensive complex-formation with respect to the carbon-centered one, however, the title reaction is more direct than its N-centered pair. Stereospecificity, characteristic at C-center, does not appear here either, due to the submerged front-side-attack retention path and the repeated entrance-channel inversional motion, whereas the multi-inversion mechanism discovered at nitrogen center is also undermined by the deep Walden-well. At low collision energies, 6 % of the PH2 F products form with retained configuration, mostly through complex-mediated mechanisms, while this ratio reaches 24 % at the highest energy due to the increasing dominance of the direct front-side mechanism and the smaller chance for hitting the deep Walden-inversion minimum. Our results suggest pronounced central-atom effects in SN 2 reactions, which can fundamentally change their (stereo)dynamics.

Catalytic enantioselective nucleophilic desymmetrization of phosphonate esters

Molecules that contain a stereogenic phosphorus atom are crucial to medicine, agrochemistry and catalysis. While methods are available for the selective construction of various chiral organophosphorus compounds, catalytic enantioselective approaches for their synthesis are far less common. Given the vastness of possible substituent combinations around a phosphorus atom, protocols for their preparation should also be divergent, providing facile access not only to one but to many classes of phosphorus compounds. Here we introduce a catalytic and enantioselective strategy for the preparation of an enantioenriched phosphorus(V) centre that can be diversified enantiospecifically to a wide range of biologically relevant phosphorus(V) compounds. The process, which involves an enantioselective nucleophilic substitution catalysed by a superbasic bifunctional iminophosphorane catalyst, can accommodate a wide range of carbon substituents at phosphorus. The resulting stable, yet versatile, synthetic intermediates can be combined with a multitude of medicinally relevant O-, N- and S-based nucleophiles.

Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b

Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3's catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.

Nucleophilic Substitution at Tricoordinate Sulfur-Alkaline Hydrolysis of Optically Active Dialkoxysulfonium Salts: Stereochemistry, Mechanism and Reaction Energetics

Optically active dialkoxyisopropylsulfonium salts were obtained by methylation (ethylation) of optically active alkyl isopropanesulfinates using methyl (ethyl) trifluoromethanesulfonate. Alkaline hydrolysis of a series of methoxy(alkoxy)sulfonium salts afforded the two sulfinate products methyl isopropanesulfinate and alkyl isopropanesulfinate, both formed with a slightly prevailing inversion of configuration at the sulfur atom. DFT calculations revealed that this substitution reaction proceeded stepwise according to an addition-elimination (A-E) mechanism involving the formation of high tetracoordinate SIV sulfurane intermediates. In addition, the DFT calculations showed that recombination of the hydroxy anion with the methoxy(alkoxy)sulfonium cation-leading to the parallel formation of the two most stable primary sulfuranes, with the hydroxy and alkoxy groups in apical positions and their direct decomposition-is the most energetically favorable pathway.

An ETS-NOCV-based computational strategies for the characterization of concerted transition states involving CO2

Due to the presence of both a slightly acidic carbon and a slightly basic oxygen, carbon dioxide is often involved in concerted transition states (TSs) with two (or more) different molecular events interlaced in the same step. The possibility of isolating and quantitatively evaluating each molecular event would be important to characterize and understand the reaction mechanism in depth. This could be done, in principle, by measuring the relevant distances in the optimized TS, but often distances are not accurate enough, especially in the presence of many simultaneous processes. Here, we have applied the Extended Transition State-Natural Orbital for Chemical Valence-method (ETS-NOCV), also in combination with the Activation Strain Model (ASM) and Energy Decomposition Analysis (EDA), to separate and quantify these molecular events at the TS of both organometallic and organic reactions. For the former, we chose the decomposition of formic acid to CO2 by an iridium catalyst, and for the latter, a CO2 -mediated transamidation and its chemical variations (hydro- and aminolysis of an ester) as case studies. We demonstrate that the one-to-one mapping between the "molecular events" and the ETS-NOCV components is maintained along the entire lowest energy path connecting reactants and products around the TS, thus enabling a detailed picture on the relative importance of each interacting component. The methodology proposed here provides valuable insights into the effect of different chemical substituents on the reaction mechanism and promises to be generally applicable for any concerted TSs.

Nucleophilic Substitution at Heteroatoms-Identity Substitution Reactions at Phosphorus and Sulfur Centers: Do They Proceed in a Concerted (SN2) or Stepwise (A-E) Way?

The mechanisms of three selected identity substitution reactions at phosphorus and sulfur occurring with stereospecific inversion have been investigated using density functional theory (DFT). The first identity reaction between methoxyl anion and methyl ethylphenylphosphinate 1 reported in 1963 has been shown to proceed in a stepwise fashion according to the addition-elimination (A-E) mechanism involving formation of a pentacoordinate phosphorus intermediate (TBI-1). In contrast, the results of DFT studies of the identity chloride exchange reaction in (ethoxy)ethylphosphonochloridothionate 3 in acetone solution provided evidence that it proceeds synchronously according to the classical Ingold's S_N2-P mechanism. DFT calculations of the methoxyl-methoxy exchange reaction at sulfur in methyl p-toluenesulfinate 4 catalyzed by trifluoroacetic acid in methanol revealed that it proceeds stepwise (A-E mechanism), involving the formation of the high-coordinate sulfurane intermediate. In both identity transesterification reactions, 1 and 4, the transiently formed trigonal bipyramidal intermediates with the two methoxyl groups occupying apical positions (TBI-1 and TBI-4) have higher free energy barriers for the Berry-type pseudorotation than those for direct decomposition to starting phosphinate and sulfinate ensuring stereospecific inversion of configuration at the phosphinyl and sulfinyl centers. Thus, the DFT method proved its usefulness in the distinction between both mechanisms that are often indistinguishable by kinetic measurements.

Theoretical study of a derivative of chlorophosphine with aliphatic and aromatic Grignard reagents: SN2@P or the novel SN2@Cl followed by SN2@C?

The proposed SN2 reactions of a hindered organophosphorus reactant with aliphatic and aromatic nucleophiles [Ye et al., Org. Lett., 2017, 19, 5384–5387] were studied theoretically in order to explain the observed stereochemistry of the products.

The Coordinate Reaction Model: An Obstacle to Interpreting the Emergence of Chemical Complexity

The way chemical transformations are described by models based on microscopic reversibility does not take into account the irreversibility of natural processes, and therefore, in complex chemical networks working in open systems, misunderstandings may arise about the origin and causes of the stability of non-equilibrium stationary states, and general constraints on evolution in systems that are far from equilibrium. In order to be correctly simulated and understood, the chemical behavior of complex systems requires time-dependent models, otherwise the irreversibility of natural phenomena is overlooked. Micro reversible models based on the reaction-coordinate model are time invariant and are therefore unable to explain the evolution of open dissipative systems. The important points necessary for improving the modeling and simulations of complex chemical systems are: a) understanding the physical potential related to the entropy production rate, which is in general an inexact differential of a state function, and b) the interpretation and application of the so-called general evolution criterion (GEC), which is the general thermodynamic constraint for the evolution of dissipative chemical systems.

The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction

This communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.

Nucleophilic Substitution at Tetracoordinate Phosphorus. Stereochemical Course and Mechanisms of Nucleophilic Displacement Reactions at Phosphorus in Diastereomeric cis- and trans-2-Halogeno-4-methyl-1,3,2-dioxaphosphorinan-2-thiones: Experimental and DFT Studies

Geometrical cis- and trans- isomers of 2-chloro-, 2-bromo- and 2-fluoro-4-methyl-1,3,2-dioxaphosphorinan-2-thiones were obtained in a diastereoselective way by (a) sulfurization of corresponding cyclic P^III-halogenides, (b) reaction of cyclic phosphorothioic acids with phosphorus pentachloride and (c) halogen–halogen exchange at P^IV-halogenide. Their conformation and configuration at the C₄-ring carbon and phosphorus stereocentres were studied by NMR (¹H, ³¹P) methods, X-ray analysis and density functional (DFT) calculations. The stereochemistry of displacement reactions (alkaline hydrolysis, methanolysis, aminolysis) at phosphorus and its mechanism were shown to depend on the nature of halogen. Cyclic cis- and trans-isomers of chlorides and bromides react with nucleophiles (HO⁻, CH₃O⁻, Me₂NH) with inversion of configuration at phosphorus. DFT calculations provided evidence that alkaline hydrolysis of cyclic thiophosphoryl chlorides proceeds according to the S_N2-P mechanism with a single transition state according to the potential energy surface (PES) observed. The alkaline hydrolysis reaction of cis- and trans-fluorides afforded the same mixture of the corresponding cyclic thiophosphoric acids with the thermodynamically more stable major product. Similar DFT calculations revealed that substitution at phosphorus in fluorides proceeds stepwise according to the A–E mechanism with formation of a pentacoordinate intermediate since a PES with two transition states was observed.

Origins of Lewis acid acceleration in nickel-catalysed C–H, C–C and C–O bond cleavage

The effects of charge transfer, Pauli repulsion and electrostatics/polarization are identified as dominant factors for Lewis acid accelerations in Ni-catalyzed C–X (X = H, C and O) bond cleavages.

How Lewis Acids Catalyze Diels-Alder Reactions

The Lewis acid(LA)-catalyzed Diels-Alder reaction between isoprene and methyl acrylate was investigated quantum chemically using a combined density functional theory and coupled-cluster theory approach. Computed activation energies systematically decrease as the strength of the LA increases along the series I2 Collapse

Key Words

• Activation strain model
• Diels-Alder reactions
• Lewis acid catalysis
• Pauli repulsion
• density functional calculations

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MESH Headings Collapse

Grants

• NWO Nederlandse Organisatie voor Wetenschappelijk Onderzoek
• CTQ2016-78205-P and CTQ2016-81797-REDC MINECO
• Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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Affiliation(s)

Pascal Vermeeren Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
Trevor A. Hamlin Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
Israel Fernández Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Facultad de Ciencias QuímicasUniversidad Complutense de Madrid28040MadridSpain
F. Matthias Bickelhaupt Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands Institute for Molecules and Materials (IMM)Radboud UniversityHeyendaalseweg 1356525AJNijmegenThe Netherlands

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Multiscale modeling of reaction rates: application to archetypal SN2 nucleophilic substitutions

We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers' theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al., J. Comput. Chem. 2019, 40, 679-705]. This, in turn, allows to keep into account barrier recrossing, i.e. the transmission coefficient that is employed in correcting transition state theory evaluations. To test the capabilities and the flaws of the approach we use as case studies two archetypal SN2 reactions. First, we consider to the standard substitution of chloride ion to bromomethane. The rate constant at 295.15 K is evaluated to k/c⊖ = 2.7 × 10-6 s-1 (with c⊖ = 1 M), which compares well to the experimental value of 3.3 × 10-6 s-1 [R. H. Bathgate and E. A. Melwyn-Hughes, J. Chem. Soc 1959, 2642-2648]. Then, the method is applied to the SN2 reaction of methylthiolate to dimethyl disulfide in water. In biology, such an interconversion of thiols and disulfides is an important metabolic topic still not entirely rationalized. The predicted rate constant is k/c⊖ = 7.7 × 103 s-1. No experimental data is available for such a reaction, but it is in accord with the fact that the alkyl thiolates to dialkyl disulfides substitutions in water have been found to be fast reactions [S. M. Bachrach, J. M. Hayes, T. Dao and J. L. Mynar, Theor. Chem. Acc. 2002, 107, 266-271].

Symmetry-Adapted Perturbation Theory Decomposition of the Reaction Force: Insights into Substituent Effects Involved in Hemiacetal Formation Mechanisms

The decomposition of the reaction force based on symmetry-adapted perturbation theory (SAPT) has been proposed. This approach was used to investigate the substituent effects along the reaction coordinate pathway for the hemiacetal formation mechanism between methanol and substituted aldehydes of the form CX₃CHO (X = H, F, Cl, and Br), providing a quantitative evaluation of the reaction-driving and reaction-retarding force components. Our results highlight the importance of more favorable electrostatic and induction effects in the reactions involving halogenated aldehydes that leads to lower activation energy barriers. These substituent effects are further elucidated by applying the functional-group partition of symmetry-adapted perturbation theory (F-SAPT). The results show that the reaction is largely driven by favorable direct noncovalent interactions between the CX₃ group on the aldehyde and the OH group on methanol.

Homo- and heterodehydrocoupling of phosphines mediated by alkali metal catalysts

Catalytic chemistry that involves the activation and transformation of main group substrates is relatively undeveloped and current examples are generally mediated by expensive transition metal species. Herein, we describe the use of inexpensive and readily available tBuOK as a catalyst for P-P and P-E (E = O, S, or N) bond formation. Catalytic quantities of tBuOK in the presence of imine, azobenzene hydrogen acceptors, or a stoichiometric amount of tBuOK with hydrazobenzene, allow efficient homodehydrocoupling of phosphines under mild conditions (e.g. 25 °C and < 5 min). Further studies demonstrate that the hydrogen acceptors play an intimate mechanistic role. We also show that our tBuOK catalysed methodology is general for the heterodehydrocoupling of phosphines with alcohols, thiols and amines to generate a range of potentially useful products containing P-O, P-S, or P-N bonds.

How Dihalogens Catalyze Michael Addition Reactions

We have quantum chemically analyzed the catalytic effect of dihalogen molecules (X2 =F2 , Cl2 , Br2 , and I2 ) on the aza-Michael addition of pyrrolidine and methyl acrylate using relativistic density functional theory and coupled-cluster theory. Our state-of-the-art computations reveal that activation barriers systematically decrease as one goes to heavier dihalogens, from 9.4 kcal mol-1 for F2 to 5.7 kcal mol-1 for I2 . Activation strain and bonding analyses identify an unexpected physical factor that controls the computed reactivity trends, namely, Pauli repulsion between the nucleophile and Michael acceptor. Thus, dihalogens do not accelerate Michael additions by the commonly accepted mechanism of an enhanced donor-acceptor [HOMO(nucleophile)-LUMO(Michael acceptor)] interaction, but instead through a diminished Pauli repulsion between the lone-pair of the nucleophile and the Michael acceptor's π-electron system.

Influence of the charge on the reactivity of azafullerenes

The influence of the charge on the Diels-Alder reactivity of azafullerenes (C59N+ and C59N-) has been computationally explored by means of density functional theory calculations. In addition, the regioselectivity of the process has been investigated and compared to the analogous cycloaddition reaction involving the parent neutral azahydro[60]fullerene C59NH. It is found that the [4+2]-cycloaddition reaction between C59N+ and cyclopentadiene, which occurs concertedly through a synchronous transition state, proceeds with a lower activation barrier and is more exothermic than the analogous process involving C59NH. In contrast, the anionic C59N- counterpart is clearly less reactive. This reactivity trend is quantitatively analyzed in detail by means of the activation strain model of reactivity in combination with the energy decomposition analysis method. It is found that the frontier molecular orbital interactions are not responsible for the observed reactivity trend but the Pauli repulsion between closed-shells mainly governs the transformation.

Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent

The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.

Nucleophilic Substitution in Solution: Activation Strain Analysis of Weak and Strong Solvent Effects

We have quantum chemically studied the effect of various polar and apolar solvents on the shape of the potential energy surface (PES) of a diverse collection of archetypal nucleophilic substitution reactions at carbon, silicon, phosphorus, and arsenic by using density functional theory at the OLYP/TZ2P level. In the gas phase, all our model SN 2 reactions have single-well PESs, except for the nucleophilic substitution reaction at carbon (SN 2@C), which has a double-well energy profile. The presence of the solvent can have a significant effect on the shape of the PES and, thus, on the nature of the SN 2 process. Solvation energies, charges on the nucleophile or leaving group, and structural features are compared for the various SN 2 reactions in a spectrum of solvents. We demonstrate how solvation can change the shape of the PES, depending not only on the polarity of the solvent, but also on how the charge is distributed over the interacting molecular moieties during different stages of the reaction. In the case of a nucleophilic substitution at three-coordinate phosphorus, the reaction can be made to proceed through a single-well [no transition state (TS)], bimodal barrier (two TSs), and then through a unimodal transition state (one TS) simply by increasing the polarity of the solvent.

How Mg2+ ions lower the SN2@P barrier in enzymatic triphosphate hydrolysis

Our quantum chemical activation strain analyses demonstrate how Mg2+ lowers the barrier of the enzymatic triphosphate hydrolysis through two distinct mechanisms: (a) weakening of the leaving-group bond, thereby decreasing activation strain; and (b) transition state (TS) stabilization through enhanced electrophilicity of the triphosphate PPP substrate, thereby strengthening the interaction with the nucleophile.

An interacting quantum atom study of model SN 2 reactions (X- ···CH3 X, X = F, Cl, Br, and I)

The quantum chemical topology method has been used to analyze the energetic profiles in the X-  + CH3 X → XCH3  + X- SN 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the reaction coordinate has been analysed. The interacting quantum atoms (IQA) method has been used to evaluate the intra-atomic and interatomic energy variations along the reaction path. The different energetic terms have been examined by the relative energy gradient method and the ANANKE program, which enables automatic and unbiased IQA analysis. Four of the six most important IQA energy contributions were needed to reproduce the reaction barrier common to all reactions. The four reactions considered share many common characteristics but when X = F a number of particularities occur. © 2017 Wiley Periodicals, Inc.

Reactivity of hydropersulfides toward the hydroxyl radical unraveled: disulfide bond cleavage, hydrogen atom transfer, and proton-coupled electron transfer

Hydropersulfides (RSSH) are highly reactive as nucleophiles and hydrogen atom transfer reagents. These chemical properties are believed to be key for them to act as antioxidants in cells. The reaction involving the radical species and the disulfide bond (S-S) in RSSH, a known redox-active group, however, has been scarcely studied, resulting in an incomplete understanding of the chemical nature of RSSH. We have performed a high-level theoretical investigation on the reactions of the hydroxyl radical (˙OH) toward a set of RSSH (R = -H, -CH₃, -NH₂, -C(O)OH, -CN, and -NO₂). The results show that S-S cleavage and H-atom abstraction are the two competing channels. The electron inductive effect of R induces selective ˙OH substitution at one sulfur atom upon S-S cleavage, forming RSOH and ˙SH for the electron donating groups (EDGs), whereas producing HSOH and ˙SR for the electron withdrawing groups (EWGs). The H-Atom abstraction by ˙OH follows a classical hydrogen atom transfer (hat) mechanism, producing RSS˙ and H₂O. Surprisingly, a proton-coupled electron transfer (pcet) process also occurs for R being an EDG. Although for RSSH having EWGs hat is the leading channel, S-S cleavage can be competitive or even dominant for the EDGs. The overall reactivity of RSSH toward ˙OH attack is greatly enhanced with the presence of an EDG, with CH₃SSH being the most reactive species found in this study (overall rate constant: 4.55 × 10¹² M^-1 s^-1). Our results highlight the complexity in RSSH reaction chemistry, the extent of which is closely modulated by the inductive effect of the substituents in the case of the oxidation by hydroxyl radicals.

RuBisCO-Inspired CO2 Activation and Transformation by an Iridium(I) Complex

The synthesis of a new iridium(I) complex containing an enamido phosphine anion (dbuP^- ) and its unique reactivity with CO₂ is reported. The complex binds two equivalents of CO₂ and initiates a highly selective reaction cascade. The reaction leads to the reversible cleavage of CO₂ and the enamido ligand as well. Computational analysis points to the existence of a relatively stable Ir-CO₂ complex as a reaction intermediate prior to CO₂ cleavage, which was confirmed experimentally. The observed transformation resembles several aspects of enzymatic CO₂ fixation by RuBisCO.

First principles computational study on hydrolysis of hazardous chemicals phosphorus trichloride and oxychloride (PCl3 and POCl3) catalyzed by molecular water clusters

Using first principles calculations we unveil fundamental mechanism of hydrolysis reactions of two hazardous chemicals PCl₃ and POCl₃ with explicit molecular water clusters nearby. It is found that the water molecules play a key role as a catalyst significantly lowing activation barrier of the hydrolysis via transferring its protons to reaction intermediates. Interestingly, torsional angle of the molecular complex at transition state is identified as a vital descriptor on the reaction rate. Analysis of charge distribution over the complex further reinforces the finding with atomic level correlation between the torsional angle and variation of the orbital hybridization state of phosphorus (P) in the complex. Electronic charge separation (or polarization) enhances thermodynamic stability of the activated complex and reduces the activation energy through hydrogen bonding network with water molecules nearby. Calculated potential energy surfaces (PES) for the hydrolysis of PCl₃ and POCl₃ depict their two contrastingly different profiles of double- and triple-depth wells, respectively. It is ascribed to the unique double-bonding O=P in the POCl₃. Our results on the activation free energy show well agreements with previous experimental data within 7kcalmol^-1 deviation.

Tandem dihetero-Diels–Alder and Huisgen cycloaddition reactions. Synthesis, crystal structure and hydrolysis of the novel cage phosphoranes

The reaction of 2-(1-phenylvinyloxy)benzo-1,3,2-dioxaphosphole with activated carbonyl compounds leads to the stereoselective formation of cage phosphoranes.

ETS-NOCV decomposition of the reaction force for double-proton transfer in formamide-derived systems

The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide–thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of the reaction force, considering the intra-fragments strain and the inter-fragments interaction terms, and further—the electrostatic, Pauli-repulsion and orbital interaction components, with the latter being decomposed into the NOCV components. Two methods of the system partitioning into the fragments were considered (‘reactant perspective’/bond-formation, ‘product perspective’ / bond-breaking). In agreement with previous studies, the results indicate that the major changes in the electronic structure occur in the transition state region; the bond-breaking processes are, however, initiated already in the reactant region, prior to entering the TS region. The electrostatic contributions were identified as the main factor responsible for the increase in the activation barrier in the order R1 < R2 < R3.

A multifunctional catalyst that stereoselectively assembles prodrugs

The catalytic stereoselective synthesis of compounds with chiral phosphorus centers remains an unsolved problem. State-of-the-art methods rely on resolution or stoichiometric chiral auxiliaries. Phosphoramidate prodrugs are a critical component of pronucleotide (ProTide) therapies used in the treatment of viral disease and cancer. Here we describe the development of a catalytic stereoselective method for the installation of phosphorus-stereogenic phosphoramidates to nucleosides through a dynamic stereoselective process. Detailed mechanistic studies and computational modeling led to the rational design of a multifunctional catalyst that enables stereoselectivity as high as 99:1.

Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.

Racemization and transesterification of alkyl hydrogeno-phenylphosphinates

In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These intermediates are shown to subsequently competitively undergo alcohol eliminations and/or Berry pseudorotations. This offers several possible routes for racemizations and/or alcohol exchange reactions. Transition standard Gibbs free energies predicted from DFT calculations for the overall alcohol exchange mechanism are shown to be compatible with those experimentally measured in case ethanol reacts with ethyl hydrogeno-phenylphosphinate (134.5∼136.0 kJ mol^-1 at 78 °C). Graphical abstract ᅟ.