Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study

Trickier than It Looks: Isomerization between Five- and Six-Coordinated Zinc in Heterometallic Li2Zn2 Molecule

This report describes the synthesis and characterization of two heterobimetallic Li-Zn coordination isomers [Li2Zn2(tbaoac)6] (tbaoac = tert-butyl acetoacetato) that have been isolated separately by the same stoichiometric reaction run in different organic solvents. The 6-coordinated zinc isomer (6-Zn) was synthesized in acetone with high yield, while the 5-coordinated one (5-Zn) was readily obtained from ethanol. The 5-Zn isomer has a low solubility in organic solvents such as alkanes and haloalkanes, while its 6-Zn counterpart exhibits a good solubility in almost all common solvents. Two isomeric molecules feature similar centrosymmetric tetranuclear cyclic assemblies, which are different in their arrangement of tbaoac ligands. While all ligands act as μ2-type in the structure of 5-Zn, the two tbaoac groups chelating Li appear as μ3-type in 6-Zn, thus providing an additional coordination for Zn ions. However, the real structural transformation between these isomers was shown to be more complex than simply making or breaking a couple of Zn-O bonds. X-ray single-crystal structure analysis, powder X-ray diffraction, multinuclear NMR, DART mass spectrometry, ICP-OES analysis, and TGA have been employed for the characterization of the isomers. The combination of powder X-ray diffraction and 1H NMR investigation revealed that 6-Zn isomer can be quantitatively transformed to 5-Zn in ethanol, while the reverse conversion instantly takes place in acetone.

Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I-PpoI

Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.

Structure-Activity Relationship Insights for Organophosphonate Hydrolysis at Ti(IV) Active Sites in Metal-Organic Frameworks

Organophosphorus nerve agents are among the most toxic chemicals known and remain threats to humans due to their continued use despite international bans. Metal-organic frameworks (MOFs) have emerged as a class of heterogeneous catalysts with tunable structures that are capable of rapidly detoxifying these chemicals via hydrolysis at Lewis acidic active sites on the metal nodes. To date, the majority of studies in this field have focused on zirconium-based MOFs (Zr-MOFs) that contain hexanuclear Zr(IV) clusters, despite the large toolbox of Lewis acidic transition metal ions that are available to construct MOFs with similar catalytic properties. In particular, very few reports have disclosed the use of a Ti-based MOF (Ti-MOF) as a catalyst for this transformation even though Ti(IV) is a stronger Lewis acid than Zr(IV). In this work, we explored five Ti-MOFs (Ti-MFU-4l, NU-1012-NDC, MIL-125, Ti-MIL-101, MIL-177(LT), and MIL-177(HT)) that each contains Ti(IV) ions in unique coordination environments, including monometallic, bimetallic, octanuclear, triangular clusters, and extended chains, as catalysts to explore how both different node structures and different linkers (e.g., azolate and carboxylate) influence the binding and subsequent hydrolysis of an organophosphorus nerve agent simulant at Ti(IV)-based active sites in basic aqueous solutions. Experimental and theoretical studies confirm that Ti-MFU-4l, which contains monometallic Ti(IV)-OH species, exhibits the best catalytic performance among this series with a half-life of roughly 2 min. This places Ti-MFU-4l as one of the best nerve agent hydrolysis catalysts of any MOF reported to date.

Experimental and computational investigation of heteroatom substitution in nucleolytic Cu(II) cyclen complexes for balancing stability and redox activity

Cu(II) complexes of cyclen-based ligands CuL¹-CuL⁶ were synthesized and characterized. The corresponding ligands L¹-L⁶ comprise different donor sets including S and O atoms. Whereas cyclen (L¹) is commercially available, L²-L⁶ were synthesized according to protocols available in the literature. Cleavage activity of the complexes towards plasmid DNA was tested in the presence and absence of ascorbate as a reducing agent (oxidative vs. hydrolytic cleavage). As previously shown, the substitution of N donor atoms with hard donor O atoms leads to efficient oxidative nucleases, but dissociation of the complex upon reduction. We thus opted for S substitution (soft donors) to stabilize the reduced Cu(I) species. Increasing the S content, however, leads to species that are difficult to reoxidize in order to ensure efficient oxidative DNA cleavage. We are showing by experimental (cyclic voltammetry) and computational means (DFT) that the rational combination of O and S atoms next to two nitrogen donors within the macrocycle (oxathiacyclen complex CuL⁶) leads to the stabilization of both redox states. The complex thus exhibits the highest oxidative DNA cleavage activity within this family of cyclen-based Cu(II) complexes - without leaching of the metal ion during reduction.

Synthesis, characterization and computational investigation of the phosphatase activity of a dinuclear Zinc(II) complex containing a new heptadentate asymmetric ligand

We report the synthesis of a new asymmetric heptadentate ligand based on the 1,3-diaminopropan-2-ol backbone. The ligand 3-[[3-(bis-pyridin-2-ylmethyl-amino)-2-hydroxy-propyl]-(2-carbamoyl-ethyl)-amino]-propionamide (HL1) contains two amide and two pyridine groups attached to the 1,3-diaminopropan-2-ol core. Reaction between HL1 and Zn(ClO₄)₂.6H₂O resulted in the formation of the dinuclear [Zn₂(L1)(μ-OAc)](ClO₄)₂ complex, characterized by single crystal X-ray diffraction, ¹H, ¹³C and ¹⁵N NMR, ESI-(+)-MS, CHN elemental analysis as well as infrared spectroscopy. The phosphatase activity of the complex was studied in the pH range 6-11 employing pyridinium bis(2,4-dinitrophenyl)phosphate (py(BDNPP)) as substrate. The complex exhibited activity dependent on the pH, presenting an asymmetric bell shape profile with the highest activity at pH 9; at high pH ligand exchange is rate-limiting. The hydrolysis of BDNPP^- at pH 9 displayed behavior characteristic of Michaelis-Menten kinetics, with k_cat = 5.06 × 10^-3 min^-1 and K_m = 5.7 ± 1.0 mM. DFT calculations map out plausible reaction pathways and identify a terminal, Zn(II)-bound hydroxide as likely nucleophile.

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.

Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters

Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al₂O₂(OH)₂@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.

Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis(p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK_a values of the Zn(ii)-bound water molecules or ligands in the [Zn(LⁿH)(η-H₂O)(H₂O)]²⁺ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L³ complexes were found to be more favorable for the hydrolytic cleavage of the BNPP⁻via a ligand-based nucleophilic attack pathway. This was due to the lower pK_a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L³ species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

A phenoxo-bridged dicopper(ii) complex as a model for phosphatase activity: mechanistic insights from a combined experimental and computational study

A μ-phenoxo-bis(μ₂-1,3-acetato)-bridged dicopper(ii) complex [Cu(L¹)(μ-O₂CMe)₂][NO₃] (1) has been synthesized from the perspective of modeling phosphodiesterase activity. Structural characterization was done initially with 1·3Et₂O (vapour diffusion of Et₂O into MeOH solution of 1; poor crystal quality) and finally with its perchlorate salt [Cu(L¹)(μ-O₂CMe)₂][ClO₄]·1.375MeCN·0.25H₂O, crystallized from vapour diffusion of n-pentane into a MeCN-MeOH mixture (comparatively better crystal quality). An asymmetric unit of such a crystal contains two independent molecules of compositions [Cu(L¹)(μ-O₂CMe)₂][ClO₄] and [Cu(L¹)(μ-O₂CMe)₂(MeCN)][ClO₄] (coordinated MeCN with 0.75 occupancy), and two molecules of MeCN and H₂O (each H₂O molecule with 0.25 occupancy) as the solvent of crystallization. These two cations, each having five-coordinate (μ-phenoxo)bis(μ-acetato)-bridged Cu^II ions, differ by only the coordination environment of only one Cu^II ion, which has a weakly coordinated acetonitrile molecule in its sixth position. Temperature-dependent magnetic studies on 1 reveal that the copper(ii) centres are antiferromagnetically coupled with the exchange-coupling constant J = -124(1) cm^-1. Theoretically calculated J = -126.51 cm^-1, employing a broken-symmetry DFT approach, is in excellent agreement with the experimental value. The dicopper(ii) complex has been found to be catalytically efficient in the hydrolysis of 2-hydroxypropyl-p-nitrophenylphosphate (HPNP). Detailed kinetic experiments and solution studies (potentiometry, species distribution and ESI-MS) were performed to elucidate the reaction mechanism. DFT calculations were performed to discriminate between different possible mechanistic pathways. The free-energy barrier for HPNP hydrolysis catalyzed by 1 is comparable to that obtained from the experimentally-determined value. The involvement of non-covalent (hydrogen-bonding) interaction has also been probed by DFT calculations. The activity of 1 is found to be the highest, compared to the structurally-characterized Mn, Co, Ni and Zn complexes of L¹(-) reported earlier, under identical experimental conditions, in which each metal centre is six-coordinate.

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+)

Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.

Efficient and Selective Enrichment of Ultratrace Cytokinins in Plant Samples by Magnetic Perhydroxy-Cucurbit[8]uril Microspheres

Cytokinins play a critical role in controlling plant growth and development, but it is difficult to be determined in plant samples due to the extremely low concentration level of picomole/gram. So it is important for efficient sample preparation with selective enrichment and rapid separation for accurate analysis of cytokinins. Herein, a supramolecular perhydroxy-cucurbit[8]uril (PCB[8]) was fabricated into the Fe3O4 magnetic particles via chemical bonding assembly and magnetic perhydroxy-cucurbit[8]uril (MPC) materials were obtained. The MPC had good enrichment capability to cytokinins and the enrichment factors were more than 208. The interaction of MPC and cytokinins was investigated by adsorption test and density functional theory (DFT) calculation, the results showed that the main drive forces were the host-guest interaction and hydrogen-bonding interaction between the perhydroxy-cucurbit[8]uril with analytes. Combined with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), the MPC was used as a sorbent of magnetic solid-phase extraction for the analysis of cytokinins in plant samples. A sensitive and selective UPLC-MS/MS method was developed with low detection limits of 0.14-0.32 ng/L for cytokinins analysis. Five cytokinins including zeatin riboside, meta-topolin, kinetin, kinetin riboside, and zip with 6.12-87.3 ng/kg were determined in the soybean sprout and Arabidopsis thaliana. The recoveries were in the range of 76.2-110% with relative standard deviations (n = 5) of 2.3-9.7%. On the basis of these results, magnetic perhydroxy-cucurbit[8]uril materials with selective enrichment capability have good potential on the analysis of ultratrace targets from complicated sample matrixes.

Insight into the mechanism and site-selectivity of Rh2II,II(esp)2-catalyzed intermolecular C–H amination

The mechanisms and site-selective determinants of Rh₂^II,II(esp)₂-catalyzed intermolecular C–H bond aminations of three isoamylbenzene-derived substrates, p-R–C₆H₄(CH₂)₂CH(CH₃)₂ (R = OCH₃, H, CF₃), have been investigated by the density functional theory (BPW91) method.

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

Divalent metal ions, due to their ability to stabilize high concentrations of negative charge, are important for RNA folding and catalysis. Detailed models derived from the structures and kinetics of enzymes and from computational simulations have been developed. However, in most cases the specific catalytic modes involving metal ions and their mechanistic roles and effects on transition state structures remain controversial. Valuable information about the nature of the transition state is provided by measurement of kinetic isotope effects (KIEs). However, KIEs reflect changes in all bond vibrational modes that differ between the ground state and transition state. QM calculations are therefore essential for developing structural models of the transition state and evaluating mechanistic alternatives. Herein, we present computational models for Zn2+ binding to RNA 2'O-transphosphorylation reaction models that aid in the interpretation of KIE experiments. Different Zn2+ binding modes produce distinct KIE signatures, and one binding mode involving two zinc ions is in close agreement with KIEs measured for non-enzymatic catalysis by Zn2+ aquo ions alone. Interestingly, the KIE signatures in this specific model are also very close to those in RNase A catalysis. These results allow a quantitative connection to be made between experimental KIE measurements and transition state structure and bonding, and provide insight into RNA 2'O-ransphosphorylation reactions catalyzed by metal ions and enzymes. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2'-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy relationships and kinetic isotope effects together with multi-scale computational simulations are providing tentative answers to these questions for this fundamentally important class of phosphoryl transfer reactions.

A dinuclear zinc(II) complex of a new unsymmetric ligand with an N(5)O(2) donor set: a structural and functional model for the active site of zinc phosphoesterases

The dinuclear complex [Zn(2)(DPCPMP)(pivalate)](ClO4), where DPCPMP is the new unsymmetrical ligand [2-(N-(3-((bis((pyridin-2-yl)methyl)amino)methyl)-2-hydroxy-5-methylbenzyl)-N-((pyridin-2-yl)methyl)amino)acetic acid], has been synthesized and characterized. The complex is a functional model for zinc phosphoesterases with dinuclear active sites. The hydrolytic efficacy of the complex has been investigated using bis-(2,4-dinitrophenyl)phosphate (BDNPP), a DNA analog, as substrate. Speciation studies using potentiometric titrations have been performed for both the ligand and the corresponding dizinc complex to elucidate the formation of the active hydrolysis catalyst; they reveals that the dinuclear zinc(II) complexes, [Zn(2)(DPCPMP)](2+) and [Zn(2)(DPCPMP)(OH)](+) predominate the solution above pH4. The relatively high pK(a) of 8.38 for water deprotonation suggests that a terminal hydroxide complex is formed. Kinetic investigations of BDNPP hydrolysis over the pH range 5.5-11.0 and with varying metal to ligand ratio (metal salt:ligand=0.5:1 to 3:1) have been performed. Variable temperature studies gave the activation parameters ΔH(‡)=95.6kJmol(-1), ΔS(‡)=-44.8Jmol(-1)K(-1), and ΔG(‡)=108.0 kJmol(-1). The cumulative results indicate the hydroxido-bridged dinuclear Zn(II) complex [Zn(2)(DPCPMP)(μ-OH)](+) as the effective catalyst. The mechanism of hydrolysis has been probed by computational modeling using density functional theory (DFT). Calculations show that the reaction goes through one concerted step (S(N)2 type) in which the bridging hydroxide in the transition state becomes terminal and performs a nucleophilic attack on the BDNPP phosphorus; the leaving group dissociates simultaneously in an overall inner sphere type activation. The calculated free energy barrier is in good agreement with the experimentally determined activation parameters.

Synergy between experimental and theoretical methods in the exploration of homogeneous transition metal catalysis

In this Perspective, we will focus on the use of both experimental and theoretical methods in the exploration of reaction mechanisms in homogeneous transition metal catalysis. The current state-of-the-art is highlighted using examples from the literature with particular focus on the synergy between experiment and theory.

Nonheme iron-mediated amination of C(sp3)-H bonds. Quinquepyridine-supported iron-imide/nitrene intermediates by experimental studies and DFT calculations

The 7-coordinate complex [Fe(qpy)(MeCN)2](ClO4)2 (1, qpy = 2,2':6',2″:6″,2''':6''',2''''-quinquepyridine) is a highly active nonheme iron catalyst for intra- and intermolecular amination of C(sp(3))-H bonds. This complex effectively catalyzes the amination of limiting amounts of not only benzylic and allylic C(sp(3))-H bonds of hydrocarbons but also the C(sp(3))-H bonds of cyclic alkanes and cycloalkane/linear alkane moieties in sulfamate esters, such as those derived from menthane and steroids cholane and androstane, using PhI═NR or "PhI(OAc)2 + H2NR" [R = Ts (p-toluenesulfonyl), Ns (p-nitrobenzenesulfonyl)] as nitrogen source, with the amination products isolated in up to 93% yield. Iron imide/nitrene intermediates [Fe(qpy)(NR)(X)](n+) (CX, X = NR, solvent, or anion) are proposed in these amination reactions on the basis of experimental studies including ESI-MS analysis, crossover experiments, Hammett plots, and correlation with C-H bond dissociation energies and with support by DFT calculations. Species consistent with the formulations of [Fe(qpy)(NTs)2](2+) (CNTs) and [Fe(qpy)(NTs)](2+) (C) were detected by high-resolution ESI-MS analysis of the reaction mixture of 1 with PhI═NTs (4 equiv). DFT calculations revealed that the reaction barriers for H-atom abstraction of cyclohexane by the ground state of 7-coordinate CNTs and ground state of C are 15.3 and 14.2 kcal/mol, respectively, in line with the observed high activity of 1 in catalyzing the C-H amination of alkanes under mild conditions.

Mechanistic origin of cross-coupling selectivity in Ni-catalysed Tishchenko reactions

Mechanistic studies have been performed for the recently developed, Ni-catalysed selective cross-coupling reaction between aryl and alkyl aldehydes. A mono-carbonyl activation (MCA) mechanism (in which one of the carbonyl groups is activated by oxidative addition) was found to be the most favourable pathway, and the rate-determining step is oxidative addition. Analysing the origin of the observed cross-coupling selectivity, we found the most favourable carbonyl activation step requires both coordination of the aryl aldehyde and oxidative addition of the alkyl aldehyde. Therefore, the stronger π-accepting ability of the aryl aldehyde (relative to alkyl aldehyde) and the ease of oxidative addition of the alkyl aldehyde (relative to aryl aldehyde) are responsible for the cross-coupling selectivity.

Dynamic cyclen-metal complexes for molecular sensing and chirality signaling

Structural dynamism plays important roles in artificial and biological systems, because it controls structures and functions of various molecules and assemblies. In this review, molecular recognition and self-assembling behavior of dynamic armed cyclen-metal complexes are discussed at the molecular and supramolecular levels. These metal complexes provide useful platforms for molecular receptors, supramolecules, and molecular assemblies that can respond rapidly to guest molecules and environments. Since armed cyclens have many structural and geometrical variations, they form a wide variety of metal complexes having specific sensing and signaling functions. The Lewis acidity of the metal cations plays an essential role in anion binding and in hydrolytic catalysis of phosphate esters. Characteristic luminescence and magnetic properties of lanthanides also enable techniques for effective bio-imaging. They also serve as chiral building blocks for self-assembled architectures, which offer chirality integration effective for chirality sensing and signaling at the supramolecular level.

Theoretical study on the mechanism of Ni-catalyzed alkyl-alkyl Suzuki cross-coupling

Ni-catalyzed cross-coupling of unactivated secondary alkyl halides with alkylboranes provides an efficient way to construct alkyl-alkyl bonds. The mechanism of this reaction with the Ni/L1 (L1=trans-N,N'-dimethyl-1,2-cyclohexanediamine) system was examined for the first time by using theoretical calculations. The feasible mechanism was found to involve a Ni(I)-Ni(III) catalytic cycle with three main steps: transmetalation of [Ni(I)(L1)X] (X=Cl, Br) with 9-borabicyclo[3.3.1]nonane (9-BBN)R(1) to produce [Ni(I)(L1)(R(1))], oxidative addition of R(2) X with [Ni(I)(L1)(R(1))] to produce [Ni(III)(L1)(R(1))(R(2))X] through a radical pathway, and C-C reductive elimination to generate the product and [Ni(I)(L1)X]. The transmetalation step is rate-determining for both primary and secondary alkyl bromides. KOiBu decreases the activation barrier of the transmetalation step by forming a potassium alkyl boronate salt with alkyl borane. Tertiary alkyl halides are not reactive because the activation barrier of reductive elimination is too high (+34.7 kcal mol(-1)). On the other hand, the cross-coupling of alkyl chlorides can be catalyzed by Ni/L2 (L2=trans-N,N'-dimethyl-1,2-diphenylethane-1,2-diamine) because the activation barrier of transmetalation with L2 is lower than that with L1. Importantly, the Ni(0)-Ni(II) catalytic cycle is not favored in the present systems because reductive elimination from both singlet and triplet [Ni(II)(L1)(R(1))(R(2))] is very difficult.