Bond-forming Processes Research Articles

Deciphering the Molecular Mechanism of Intramolecular Reactions from the Perspective of Bonding Evolution Theory

The molecular mechanisms of three intramolecular rearrangements (I, the rearrangement of allyloxycycloheptatriene to yield tricyclic ketones; II, the cycloaddition of a nitrone-alkene to render two tricyclic isoxazolidines; and III, the decomposition of N-carbamoyl-L-proline in tetrahydro-1H-pyrrolo[1,2-c]imidazole-1,3(2H)-dione plus water, or tetrahydro-1H,3H-pyrrolo[1,2-c]oxazole-1,3-dione plus ammonia) have been studied by means of the bonding evolution theory (BET). The thermal rearrangement I is composed by a sigmatropic rearrangement coupled to an intramolecular Diels–Alder reaction. The sigmatropic reaction comprises four steps: (1) rupture of an O-C single chemical bond, (2) transformation of a C-O single to double bond, (3) creation of pseudo-radical centers on carbon atoms coupled with a double C-C bond evolving to single and the other C-C double bond migration, and (4) formation of the new C-C single bond. For the Diels–Alder reaction, the process can be described as an initial formation of up to four monosynaptic V(C) basins in two successive steps, coupled with the loss of the double bond character of the three initial double bonds, followed by the consecutive formation of two new C-C bonds, with the new double C-C bond formation sensed in between the formation of the first and the second C-C bonds. For reaction II, the bond forming process is described by the depopulation of N-C and C-C double bonds with the creation of a V(N) and two V(C) monosynaptic basins, followed by an O-C and C-C bond-forming processes via the creation of V(O,C) and V(C,C) disynaptic basins. Finally, for the thermal decomposition III, the reaction mechanism for the water elimination takes place in four events which can be summarized as follows: (1) the depopulation of V(N) with the formation of C-N, (2) the rupture of the C-O bond with transfer of its population to V(O), (3) the restoration of an N nitrogen lone pair via H-N bond cleavage, and (4) the formation of O-H illustrating the water molecule release. For the case of deamination, the events (1) and (2) correspond to the breaking and forming process of H-O and H-N bonds, respectively, while last events deal with the C-O bond formation and the elimination of the NH3 molecule.

Visible Light-Induced Regio- and Enantiodifferentiating [2 + 2] Photocycloaddition of 1,4-Naphthoquinones Mediated by Oppositely Coordinating 1,3,2-Oxazaborolidine Chiral Lewis Acid.

A range of asymmetric photochemical transformations using visible light have recently become considerably attractive. Among the various approaches, chiral Lewis acid association to enones for [2 + 2] and ortho photocycloadditions and oxadi-π-methane rearrangements have shown to be very promising. Naturally, chiral Lewis acid coordination protects one of the prochiral faces of the C═C double bond, which enables an effective enantiodifferentiation in the following bond-forming process(es). Here, we studied regio- and enantiodifferentiating [2 + 2] photocycloaddition reactions of naphthoquinone derivatives mediated by chiral oxazaborolidines. A stereochemical control was quite challenging for the 2-ene-1,4-dione substrate, as a double coordination of Lewis acid essentially cancels out the face selectivity, and a mono-coordination to each carbonyl group leads to an opposite stereochemical outcome. Furthermore, a stepwise coordination in the ground state of Lewis acid in a 1:1 fashion was practically inaccessible. We found that the excited-state decomplexation is a key to accomplish high regio- and enantioselectivities in the photocycloaddition of an ene-dione.

Recent Progress in Dinitrogen Activation by Gas-Phase Metal Species.

Understanding the mechanisms to activate and functionalize dinitrogen (N2) is of great importance for the rational design of nitrogen-fixation catalysts. Reactions of gas-phase species with N2 are being actively studied to understand the bond activation and formation processes at a strictly molecular level. This Perspective provides an overview of the recent progress in combined experimental and theoretical studies on the activation and functionalization of N2 by gas-phase metal species. New mechanistic insights into N2 molecular adsorption, N≡N cleavage, and N-X (X = C, B, and H) formation have been introduced, in which the new reaction channels of ejecting neutral metal fragments and the coupling reactions of N2 with other molecules are highlighted. Finally, the current challenges and outlooks of N2 activation in the gas phase are discussed as well.

Shear-assisted contact aging of single-asperity nanojunctions

Contact aging, i.e., the strengthening of a tribological contact with time, is a phenomenon that is commonly attributed to an increase of the effective contact area between multiasperity surfaces based on contact mechanical processes. Only recently, atomic force microscopy experiments and simulations on single silica nanojunctions have also demonstrated logarithmic aging with contact time for single-asperity contacts and the effects were attributed to a gradual formation of chemical bonds in the contact, thereby suggesting an atomistic mechanism of ``contact aging.'' Generally, this atomic bond-formation process is considered as a shear-assisted thermally activated process, where both temperature and loading conditions are expected to influence the aging behavior. A direct link between aging and temperature has recently been substantiated by temperature-dependent aging experiments and complementary molecular dynamics simulations, but the potential influence of shear stress on single-asperity aging still remains largely elusive. To analyze the role of shear stress, we now apply a simple and semianalytical model for thermally activated bond formation, which explicitly considers the reduction of energy barriers by a shear-stress-related Eyring term. Based on this model, characteristic fingerprints of mechanical shear can be identified in our temperature-dependent contact aging experiments, including, for instance, the counterintuitive decrease of aging effects with increasing temperature. Our results thereby hint at a path to introduce this form of qualitative contact aging to the phenomenological rate and state friction, where the local aging effects might be closely linked to the shear-stress distribution within multiasperity contacts.

Supramolecular Template-Assisted Catalytic [2+2] Photocycloaddition in Homogeneous Solution

Supramolecular Template-Assisted Catalytic [2+2] Photocycloaddition in Homogeneous Solution

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

Regioselective Bond-Forming and Hydrolysis Reactions of Doubly Charged Vanadium Oxide Anions in the Gas Phase

The gas-phase reactivity of vanadium-containing dianions, NaV3O92− and its hydrated form H2NaV3O102−, were probed towards sulphur dioxide at room temperature by ion-molecule reaction (IMR) experiments in the collision cell of an ion trap mass spectrometer. The sequential addition of two SO2 molecules to the NaV3O92− dianion leads to the breakage of the stable V3O9 backbone, resulting in a charge separation process with the formation of new V-O and S-O bonds. On the contrary, the H2NaV3O102− hydroxide species reacts with SO2, promoting regioselective hydrolysis and bond-forming processes, the latter similar to that observed for the NaV3O92− reactant anion. Kinetic analysis shows that these reactions are fast and efficient with rate constants of the 10−9 (±30) cm3 s−1 molecule−1 order of magnitude.

Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization

We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis – i.e. at close to ambient temperatures and over a wide range of pH. The key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky particles. The simplicity of the model, its applicability in standard parallelized molecular dynamics codes, and its compatibility with the widely used MARTINI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time scales. The model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point, and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle.

A Chemo- and Regioselective Tandem [3 + 2]Heteroannulation Strategy for Carbazole Synthesis: Combining Two Mechanistically Distinct Bond-Forming Processes.

A modular approach to prepare tri- and tetracyclic carbazoles by a sequential [3 + 2]heteroannulation is described. First, optimization of Pd-catalyzed Buchwald–Hartwig amination followed by C/N-arylation in a one-pot process is established. Second, mechanistic analyses identified the origins of chemo- and regioselective sequential control of both bond-forming steps. Finally, the substrate scope is demonstrated by the preparation of a range of tri- and tetracyclic carbazoles, including expedient access to several natural products and anti-cancer agents.

Electrocatalytic Water Oxidation Activity of Molecular Copper Complexes: Effect of Redox-Active Ligands.

Two molecular copper(II) complexes, (NMe4)2[CuII(L1)] (1) and (NMe4)2[CuII(L2)] (2), ligated by a N2O2 donor set of ligands [L1 = N,N'-(1,2-phenylene)bis(2-hydroxy-2-methylpropanamide), and L2 = N,N'-(4,5-dimethyl-1,2-phenylene)bis(2-hydroxy-2-methylpropanamide)] have been synthesized and thoroughly characterized. An electrochemical study of 1 in a carbonate buffer at pH 9.2 revealed a reversible copper-centered redox couple at 0.51 V, followed by two ligand-based oxidation events at 1.02 and 1.25 V, and catalytic water oxidation at an onset potential of 1.28 V (overpotential of 580 mV). The electron-rich nature of the ligand likely supports access to high-valent copper species on the CV time scale. The results of the theoretical electronic structure investigation were quite consistent with the observed stepwise ligand-centered oxidation process. A constant potential electrolysis experiment with 1 reveals a catalytic current density of >2.4 mA cm-2 for 3 h. A one-electron-oxidized species of 1, (NMe4)[CuIII(L1)] (3), was isolated and characterized. Complex 2, on the contrary, revealed copper and ligand oxidation peaks at 0.505, 0.90, and 1.06 V, followed by an onset water oxidation (WO) at 1.26 V (overpotential of 560 mV). The findings show that the ligand-based oxidation reactions strongly depend upon the ligand's electronic substitution; however, such effects on the copper-centered redox couple and catalytic WO are minimal. The energetically favorable mechanism has been established through the theoretical calculation of stepwise reaction energies, which nicely explains the experimentally observed electron transfer events. Furthermore, as revealed by the theoretical calculations, the O-O bond formation process occurs through a water nucleophilic attack mechanism with an easily accessible reaction barrier. This study demonstrates the importance of redox-active ligands in the development of molecular late-transition-metal electrocatalysts for WO reactions.

Effect of lubricants on the rotational transmission between solid-state gears.

Lubricants are widely used in macroscopic mechanical systems to reduce friction and wear. However, on the microscopic scale, it is not clear to what extent lubricants are beneficial. Therefore, in this study, we consider two diamond solid-state gears at the nanoscale immersed in different lubricant molecules and perform classical MD simulations to investigate the rotational transmission of motion. We find that lubricants can help to synchronize the rotational transmission between gears regardless of the molecular species and the center-of-mass distance. Moreover, the influence of the angular velocity of the driving gear is investigated and shown to be related to the bond formation process between gears.

Influence of Solvent and Oxidant in Copper-Catalyzed Synthesis of Xanthine Skeletons

An interesting approach for the synthesis of xanthine skeletons by a copper-catalyzed reaction between N,N′-dialkylated 5-bromouracil derivatives and amidines are being reported. The coupling reaction was promoted by catalytic amount of Cu(OAc)2 in the presence of molecular O2. The 1,4-dioxane was found to be a better solvent for the reaction and the reaction was believed to go through a N-arylation and subsequent C-H activation/C-N bond formation process.

Solvation in nitration of benzene and the valence electronic structure of the Wheland intermediate.

Nitration of benzene is a representative aromatic substitution reaction related to the σ-complex (arenium ion or "Wheland" intermediate) concept. This reaction is typically carried out in a mixed acid solution to generate nitronium ions, and how solvent molecules play roles in the reaction has been of great interest. Here we will shed new light on the reaction, namely the electronic structure and the microscopic insights of the solvation, which have been rarely discussed so far. We studied this process using the reference interaction site model-self consistent field with constrained spatial electron density distribution (RISM-SCF-cSED) method, considering sulfuric acid or water molecules as a solvent. In this method, the electronic structure of the solute and the solvation structure are self-consistently determined based on quantum chemistry and statistical mechanics of molecular liquids. The solvation free energy surfaces in solution and solvation structures were verified. In the bond formation process of benzene and nitronium ions, the solvation structure by sulfuric acid molecules drastically changes and the solvation effect on the free energy is quite large. We revealed largely contributing resonance structures in the π-electron system of the σ-complex in gas and solution phases by analysing the valence electronic structures.

Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams.

The interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology, radiation hardness analysis of materials, and focused ion beam etching, deposition, and lithography. Due to its vital role in the natural environment, the pyridine molecule has become the subject of both basic and applied research in recent years. Therefore, dissociation of the gas phase pyridine (C5H5N) into neutral excited atomic and molecular fragments following protons (H+) and dihydrogen cations (H2+) impact has been investigated experimentally in the 5–1000 eV energy range. The collision-induced emission spectroscopy has been exploited to detect luminescence in the wavelength range from 190 to 520 nm at the different kinetic energies of both cations. High-resolution optical fragmentation spectra reveal emission bands due to the CH(A2Δ→X2Πr; B2Σ+→X2Πr; C2Σ+→X2Πr) and CN(B2Σ+→X2Σ+) transitions as well as atomic H and C lines. Their spectral line shapes and qualitative band intensities are examined in detail. The analysis shows that the H2+ irradiation enhances pyridine ring fragmentation and creates various fragments more pronounced than H+ cations. The plausible collisional processes and fragmentation pathways leading to the identified products are discussed and compared with the latest results obtained in cation-induced fragmentation of pyridine.

BF3 -Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2-siloxy-1-propene.

The Mukaiyama aldol reaction is a powerful tool for the construction of the carbon-carbon bond and the formation of β-hydroxycarbonyl compounds. In this work, the mechanism of acetaldehyde and 2-siloxy-1-propene both in the absence and presence of the catalyst BF3 was investigated based on density functional theory. The mechanism includes two major steps: the formation of the carbon-carbon bond and the removal of SiH3 /BF2 by water. The energy barrier of the carbon-carbon bond formation process in the presence of BF3 is obviously lower, indicating that BF3 is a good catalyst for this reaction. In terms of molecular configuration, the different tensions between the five-membered-ring and six-membered-ring can be considered as the possible reason for the catalytic effect of BF3 . In terms of charge transfer, the charges of natural population analysis in the carbon atom of the carbonyl group in acetaldehyde becomes more positive, which is easier to attack by nucleophiles and promote the nucleophilic process.

Metallaphotoredox: The Merger of Photoredox and Transition Metal Catalysis.

The merger of photoredox catalysis with transition metal catalysis, termed metallaphotoredox catalysis, has become a mainstay in synthetic methodology over the past decade. Metallaphotoredox catalysis has combined the unparalleled capacity of transition metal catalysis for bond formation with the broad utility of photoinduced electron- and energy-transfer processes. Photocatalytic substrate activation has allowed the engagement of simple starting materials in metal-mediated bond-forming processes. Moreover, electron or energy transfer directly with key organometallic intermediates has provided novel activation modes entirely complementary to traditional catalytic platforms. This Review details and contextualizes the advancements in molecule construction brought forth by metallaphotocatalysis.

N-Heterocyclic Carbene-Catalyzed 1,4-Alkylacylation of 1,3-Enynes.

The radical relay coupling reaction recently emerged as a powerful synthetic strategy for producing tetrasubstituted allenes. However, bond-forming processes involving the allenyl radical intermediate are mostly limited to those promoted by transition metals. In this report, we describe that a ketyl radical generated from single-electron oxidation of the Breslow intermediate is an excellent coupling partner of allenyl radicals. An organocatalytic 1,4-alkylacylation of 1,3-enynes occurred smoothly in the presence of an aldehyde, a radical precursor, and an N-heterocyclic carbene catalyst. This transformation showed remarkable tolerance to both aromatic and aliphatic aldehydes, enyne substitution, and diversified radical precursors.

Silyldienolates in Organocatalytic Enantioselective Vinylogous Mukaiyama-Type Reactions: A Review.

Mukaiyama aldol, Mannich, and Michael reactions are arguably amongst the most important C–C bond formation processes and enable access to highly relevant building blocks of various natural products. Their vinylogous extensions display equally high potential in the formation of important key intermediates featuring even higher functionalization possibilities through an additional conjugated C–C double bond. Hence, it is much desired to develop highly selective vinylogous methods in order to enable unconventional, more efficient asymmetric syntheses of biologically active compounds. In this regard, silyl-dienolates were discovered to display high regioselectivities due to their tendency toward γ-additions. The control of the enantio- and diastereoinduction of these processes have been for a long time dominated by transition metal catalysis, but it received serious competition by the application of organocatalytic approaches since the beginning of this century. In this review, the organocatalytic applications of silyl-dienolates in asymmetric vinylogous C–C bond formations are summarized, focusing on their scope, characteristics, and limitations.

Rate-Limiting Step of Epoxidation Reaction of the Oxoiron(IV) Porphyrin π-Cation Radical Complex: Electron Transfer Coupled Bond Formation Mechanism.

Epoxidation reactions catalyzed by high-valent metal-oxo species are key reactions in various biological and chemical processes. Because the redox potentials of alkenes are higher than those of most high-valent metal-oxo species, the electron transfer (ET) from the alkene to the high-valent metal-oxo species in the epoxidation reaction is endergonic and must be coupled with another exergonic process. To reveal the mechanism of the ET, we performed a Marcus plot analysis for the epoxidation reaction of the oxoiron(IV) porphyrin π-cation radical complex (compound I) with alkene. The Marcus plots can be simulated with a linear line with the gradient of 0.50 when the redox potential of compound I varies and 0.07 when the redox potential of alkene varies. These results indicate that the ET process is involved in the rate-limiting step and coupled with the following O-C bond formation process: ET coupled bond formation mechanism. The DFT calculations support this conclusion and disclose the details of the mechanism. As the alkene comes close to the oxo ligand, the energy of the highest occupied molecular orbital (HOMO) of the alkene increases and the energy for the ET becomes small enough to allow the ET. Finally, the ET occurs from the HOMO of the alkene to the porphyrin π-radical orbital. The shift of one electron from the HOMO of the alkene by the ET simultaneously results in the O-C half bond formation between the oxo ligand and the alkene. The ET process itself is still endergonic and reversible, but the bond formation coupled with the ET changes the overall process to exergonic and irreversible. We also discuss the similarity with the aromatic hydroxylation reaction and the relevance to the epoxidation reactions of other metal-oxo complexes and peracid.

Study of the Reactivity of CH3COOH+• and COOH+ Ions with CH3NH2: Evidence of the Formation of New Peptide-like C(O)-N Bonds.

Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH3-COOH) and methylamine (CH3-NH2) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH3COOH+• as well as COOH+ (produced from either acetic acid or formic acid) ions with neutral CH3NH2 was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.