Synthesis of Peptides by Silver‐Promoted Coupling of Carboxylates and Thioamides: Mechanistic Insight from Computational Studies

The mechanism of the recently described N→C direction peptide synthesis through silver‐promoted coupling of N‐protected amino acids with thioacetylated amino esters was explored by using density functional theory. Calculation of the potential energy surfaces for various pathways revealed that the reaction proceeds through silver‐assisted addition of the carboxylate to the thioamide, which is followed by deprotonation and silver‐mediated extrusion of sulfur as Ag₂S. The resulting isoimide is the key intermediate, which subsequently rearranges to an imide through a concerted pericyclic [1,3]‐acyl shift (O–sp²N 1,3‐acyl migration). The proposed mechanism clearly emphasises the requirement of two equivalents of Ag^I and basic reaction conditions, which is in full agreement with the experimental findings. Alternative rearrangement pathways involving only one equivalent of Ag^I or through O–sp³N 1,3‐acyl migration can be excluded. The computations further revealed that peptide couplings involving thioformamides require significant conformational changes in the intermediate isoformimide, which slow down the rearrangement process.     

Mechanistic Insight into the Catalytic Oxidation of Cyclohexane over Carbon Nanotubes: Kinetic and In Situ Spectroscopic Evidence

As some of the most interesting metal‐free catalysts, carbon nanotubes (CNTs) and other carbon‐based nanomaterials show great promise for some important chemical reactions, such as the selective oxidation of cyclohexane (C₆H₁₂). Due to the lack of fundamental understanding of carbon catalysis in liquid‐phase reactions, we have sought to unravel the role of CNTs in the catalytic oxidation of C₆H₁₂ through a combination of kinetic analysis, in situ spectroscopy, and density functional theory. The catalytic effect of CNTs originates from a weak interaction between radicals and their graphene skeletons, which confines the radicals around their surfaces. This, in turn, enhances the electron‐transfer catalysis of peroxides to yield the corresponding alcohol and ketone.     

Mechanistic Studies on the Insertion of Carbonyl Substrates into Cu‐H: Different Rate‐Limiting Steps as a Function of Electrophilicity

We report mechanistic studies on the insertion reactions of [(NHC)Cu(μ‐H)]₂ complexes with carbonyl substrates by UV‐vis and ¹H NMR spectroscopic kinetic studies, H/D isotopic labelling, and X‐ray crystallography. The results of these comprehensive studies show that the insertion of Cu‐H with an aldehyde, ketone, activated ester/amide, and unactivated amide consist of two different rate limiting steps: the formation of Cu‐H monomer from Cu‐H dimer for more electrophilic substrates, and hydride transfer from a transient Cu‐H monomer for less electrophilic substrates. We also report spectroscopic and crystallographic characterization of rare Cu‐hemiacetalate and Cu‐hemiaminalate moieties from the insertion of an ester or amide into the Cu?H bond.     

Proton‐Coupled Electron Transfer of Unsaturated Fatty Acids and Mechanistic Insight into Lipoxygenase

A proton‐coupled electron transfer (PCET) process plays an important role in the initial step of lipoxygenases to produce lipid radicals which can be oxygenated by reaction with O₂ to yield the hydroperoxides stereoselectively. The EPR spectroscopic detection of free lipid radicals and the oxygenated radicals (peroxyl radicals) together with the analysis of the EPR spectra has revealed the origin of the stereo‐ and regiochemistry of the reaction between O₂ and linoleyl (= (2Z)‐10‐carboxy‐1‐[(1Z)‐hept‐1‐enyl]dec‐2‐enyl) radical in lipoxygenases. The direct determination of the absolute rates of H‐atom‐transfer reactions from a series of unsaturated fatty acids to the cumylperoxyl (= (1‐methyl‐1‐phenylethyl)dioxy) radical by use of time‐resolved EPR at low temperatures together with detailed kinetic investigations on both photoinduced and thermal electron‐transfer oxidation of unsaturated fatty acids provides the solid energetic basis for the postulated PCET process in lipoxygenases. A strong interaction between linoleic acid (= (9Z,12Z)‐octadeca‐9,12‐dienoic acid) and the reactive center of the lipoxygenases (Fe^III? OH) is suggested to be involved to make a PCET process to occur efficiently, when an inner‐sphere electron transfer from linoleic acid to the Fe^III state is strongly coupled with the proton transfer to the OH group.     

Mechanistic Insight into Binding of Huperzine A with Human Serum Albumin: Computational and Spectroscopic Approaches

Human serum albumin (HSA) is the most abundant protein in plasma synthesized by the liver and the main modulator of fluid distribution between body compartments. It has an amazing capacity to bind with multiple ligands, offering a store and transporter for various endogenous and exogenous compounds. Huperzine A (HpzA) is a natural sesquiterpene alkaloid found in Huperzia serrata and used in various neurological conditions, including Alzheimer’s disease (AD). This study elucidated the binding of HpzA with HSA using advanced computational approaches such as molecular docking and molecular dynamic (MD) simulation followed by fluorescence-based binding assays. The molecular docking result showed plausible interaction between HpzA and HSA. The MD simulation and principal component analysis (PCA) results supported the stable interactions of the protein–ligand complex. The fluorescence assay further validated the in silico study, revealing significant binding affinity between HpzA and HSA. This study advocated that HpzA acts as a latent HSA binding partner, which may be investigated further in AD therapy in experimental settings.     

Combining Experimental and Computational Studies to Understand and Predict Reactivities of Relevance to Homogeneous Catalysis

This article showcases three major uses of computational chemistry in reactivity studies: the application after, in combination with, and before experiment. Following a brief introduction of suitable computational tools, challenges and opportunities in the implementation of computational chemistry in reactivity studies are discussed, exemplified with selected case studies from our and other laboratories.     

Mechanistic analysis and thermochemical kinetic simulation of the pathways for volatile product formation from pyrolysis of polystyrene, especially for the dimer

Simulations of the initial distribution of volatiles from pyrolysis of polystyrene were based on propagation rate constants estimated by thermochemical kinetic procedures. The voluminous database exhibits a disturbing lack of consistency with respect to effects of conversion level, temperature, and reactor type. It therefore remains difficult to assign the true primary distribution of the major products, styrene, 2,4-diphenyl-1-butene (“dimer”), 2,4,6-triphenyl-1-hexene (“trimer”), 1,3-diphenylpropane, and toluene, and its dependence on conditions. Probable perturbations by secondary reactions and selective evaporation are considered. The rate constant for 1,3-hydrogen shift appears much too small to accommodate the commonly proposed “back-biting” mechanism for dimer formation. Dimer more likely arises by addition of benzyl radical to olefinic chain-ends, followed by β-scission, although ambiguities remain in assigning rate constants for the addition and β-scission steps. With this modification, the major products can be successfully associated with decay of the sec-benzylic chain-end radical. In contrast, the minimal formation of allylbenzene, 2,4-diphenyl-1-pentene, and 2,4,6-triphenyl-1-heptene suggests a minimal chain-propagating role for the prim chain-end radical. Compared with polyethylene, the much enhanced “unzipping” to form monomer from polystyrene and the more limited depth of “back-biting” into the chain arise from an enthalpy-driven acceleration of β-scission coupled with a kinetically driven deceleration of intramolecular hydrogen transfer. In contrast, the greater “unzipping” of poly(isobutylene) compared with polyethylene is proposed to result from relief of steric strain.     

Mechanistic Insight into Formation of Oxo‐Iron(IV) Porphyrin π‐Cation Radicals from Enzyme Mimics of Cytochrome P450 in Organic Solvents

Two new models for cytochrome P450 in which the thiolate axial ligand is replaced by an RSO₃^? group, form oxo‐iron(IV) porphyrin π‐cation radicals as sole oxidation products in “peroxo shunt” reactions (see scheme) independent of the nature of the employed solvent (polar or non‐polar) and electronic nature of the porphyrin rings.

     

Experimental and Computational Studies on the CH Amination Mechanism of Tetrahydrocarbazoles via Hydroperoxides

The acid‐catalyzed reactions of photochemically generated tetrahydrocarbazole peroxides with anilines have been studied experimentally and computationally to identify the underlying reaction mechanism. The kinetic data indicate a reaction order of one in the hydroperoxide and zero in the aniline. Computational investigations using density functional theory support the experimental findings and predict an initial tautomerization between an imine and enamine substructure of the primarily generated tetrahydrocarbazole peroxide to be the rate controlling step. The enamine tautomer then loses hydrogen peroxide upon protonation, generating a stabilized allylic carbocation that is reversibly trapped by solvent or aniline to form the isolated products.     

Mechanistic Insight into the CO2 Capture by Amidophosphoranes: Interplay of the Ring Strain and the trans Influence Determines the Reactivity of the Frustrated Lewis Pairs

CO₂ capture has attracted increasing attention owing to its contribution to global warming and climate change as a greenhouse gas. As an alternative strategy to transition‐metal‐based chemistry and catalysis, frustrated Lewis pairs have been developed to sequester CO₂ efficiently under mild conditions. However, the mechanism of CO₂ sequestration with amidophosphoranes remains unclear. Herein, we present a thorough density functional theory study on a series of amidophosphoranes. Our results reveal that the interplay of the ring strain and the trans influence determines the reactivities, thus opening a new avenue to the design of frustrated Lewis pairs for CO₂ capture.     

Halogen-Bonded Assemblies of Arylene Imides and Diimides: Insight from Electronic,Structural, and Computational Studies

Halogen-bonding interactions in electron-deficient π scaffolds have largely been underexplored. Herein, the halogen-bonding properties of arylene imide/diimide-based electron-deficient scaffolds were studied. The influence of scaffold size, from small (phthalimide) to moderately sized (pyromellitic diimide or naphthalenediimides) to large (perylenediimide), axial-group modification, and number of halo substituents on the halogen bonding and its self-assembly was probed in a set of nine compounds. The structural modification leads to tunable optical and redox properties. The first reduction potential ranges between −1.09 and −0.17 V (vs. SCE). Two of the compounds, that is, 6 and 9 , have deep-lying LUMOs with values reaching −4.2 eV. Single crystals of all nine systems were obtained, which showed Br ⋅⋅⋅ O, Br ⋅⋅⋅ Br, or Br ⋅⋅⋅ π halogen-bonding interactions, and a few systems are capable of forming all three types. These interactions lead to halogen-bonded rings (up to 12-membered), which propagate to form stacked 1D, 2D, or corrugated sheets. A few outliers were also identified, for example, molecules that prefer C−H ⋅⋅⋅ O hydrogen bonding over halogen bonding, or noncentrosymmetric rather than centrosymmetric organization. Computational studies based on Atoms in Molecules and Natural Bond Orbital analysis provided further insight into the halogen-bonding interactions. This study can lead to a predictive design tool-box to further explore related systems on surfaces reinforced by these weak directional forces.     

CNN Pincer Ruthenium Catalysts for Hydrogenation and Transfer Hydrogenation of Ketones: Experimental and Computational Studies

Reaction of [RuCl(CNN)(dppb)] ( 1‐Cl ) (HCNN=2‐aminomethyl‐6‐(4‐methylphenyl)pyridine; dppb=Ph₂P(CH₂)₄PPh₂) with NaOCH₂CF₃ leads to the amine‐alkoxide [Ru(CNN)(OCH₂CF₃)(dppb)] ( 1‐OCH₂CF₃ ), whose neutron diffraction study reveals a short RuO ??? HN bond length. Treatment of 1‐Cl with NaOEt and EtOH affords the alkoxide [Ru(CNN)(OEt)(dppb)] ? (EtOH)_n ( 1‐OEt?n EtOH ), which equilibrates with the hydride [RuH(CNN)(dppb)] ( 1‐H ) and acetaldehyde. Compound 1‐OEt?n EtOH reacts reversibly with H₂ leading to 1‐H and EtOH through dihydrogen splitting. NMR spectroscopic studies on 1‐OEt?n EtOH and 1‐H reveal hydrogen bond interactions and exchange processes. The chloride 1‐Cl catalyzes the hydrogenation (5 atm of H₂) of ketones to alcohols (turnover frequency (TOF) up to 6.5×10⁴ h^?1, 40 °C). DFT calculations were performed on the reaction of [RuH(CNN′)(dmpb)] ( 2‐H ) (HCNN′=2‐aminomethyl‐6‐(phenyl)pyridine; dmpb=Me₂P(CH₂)₄PMe₂) with acetone and with one molecule of 2‐propanol, in alcohol, with the alkoxide complex being the most stable species. In the first step, the Ru‐hydride transfers one hydrogen atom to the carbon of the ketone, whereas the second hydrogen transfer from NH₂ is mediated by the alcohol and leads to the key “amide” intermediate. Regeneration of the hydride complex may occur by reaction with 2‐propanol or with H₂; both pathways have low barriers and are alcohol assisted.     

Studies on the Toxic Oil Syndrome: proposal of a mechanism for the thermal conversion of 3-N-phenylamino-1,2-propanediol esters into anilides under deodorisation conditions

A study on the reaction mechanism for the conversion of title esters, the species recognised as toxic biomarkers of the oil batches responsible for the Toxic Oil Syndrome, into the corresponding anilides under the thermal conditions of an oil deodorisation process was performed using experimental and computational techniques. The results obtained suggest a reaction course that includes two basic steps: an intramolecular process involving the reaction of the amine group of the diester derivative with the secondary ester of the same compound, followed by the attack of an aniline molecule to form the (E)-isomer of an imidic acid, which would finally tautomerise to give the final anilide.     

Computational Insight into Nickel‐Catalyzed Carbon–Carbon versus Carbon–Boron Coupling Reactions of Primary,Secondary, and Tertiary Alkyl Bromides

The nickel‐catalyzed alkyl–alkyl cross‐coupling (C?C bond formation) and borylation (C?B bond formation) of unactivated alkyl halides reported in the literature show completely opposite reactivity orders in the reactions of primary, secondary, and tertiary alkyl bromides. The proposed Ni^I/Ni^III catalytic cycles for these two types of bond‐formation reactions were studied computationally by means of DFT calculations at the B3LYP level. These calculations indicate that the rate‐determining step for alkyl–alkyl cross‐coupling is the reductive elimination step, whereas for borylation the rate is determined mainly by the atom‐transfer step. In borylation reactions, the boryl ligand involved has an empty p orbital, which strongly facilitates the reductive elimination step. The inability of unactivated tertiary alkyl halides to undergo alkyl–alkyl cross‐coupling is mainly due to the moderately high reductive elimination barrier.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Combined Experimental and Computational Investigations of Rhodium‐Catalysed CH Functionalisation of Pyrazoles with Alkenes

Detailed experimental and computational studies have been carried out on the oxidative coupling of the alkenes C₂H₃Y (Y=CO₂Me ( a ), Ph ( b ), C(O)Me ( c )) with 3‐aryl‐5‐R‐pyrazoles (R=Me ( 1 a ), Ph ( 1 b ), CF₃ ( 1 c )) using a [Rh(MeCN)₃Cp*][PF₆]₂/Cu(OAc)₂ ? H₂O catalyst system. In the reaction of methyl acrylate with 1 a , up to five products ( 2 aa – 6 aa ) were formed, including the trans monovinyl product, either complexed within a novel Cu^I dimer ( 2 aa ) or as the free species ( 3 aa ), and a divinyl species ( 6 aa ); both 3 aa and 6 aa underwent cyclisation by an aza‐Michael reaction to give fused heterocycles 4 aa and 5 aa , respectively. With styrene, only trans mono‐ and divinylation products were observed, whereas with methyl vinyl ketone, a stronger Michael acceptor, only cyclised oxidative coupling products were formed. Density functional theory calculations were performed to characterise the different migratory insertion and β‐H transfer steps implicated in the reactions of 1 a with methyl acrylate and styrene. The calculations showed a clear kinetic preference for 2,1‐insertion and the formation of trans vinyl products, consistent with the experimental results.     

Comparative Computational Studies of Gaseous Alkali Metal Amidoboranes MNH2BH3 and their Carbon Analogs MC2H5 (M = Li – Cs): Formation and Unimolecular Hydrogen Evolution

Comparative computational studies of reaction mechanisms of formation and unimolecular hydrogen evolution from alkali metal amidoboranes MNH₂BH₃ and their carbon analogs MC₂H₅ (M = Li – Cs) were performed at the B3LYP/def2‐TZVPPD level of theory. Transition states (TS) for the consecutive dehydrogenation reactions were optimized. In contrast to endergonic dehydrogenation of carbon analogs, dehydrogenation reactions of alkali metal amidoboranes are exergonic at room temperature. The nature of the alkali metal does not significantly affect the thermodynamic characteristics and activation energies of unimolecular gas phase dehydrogenation reactions. The influence of the alkali metal is qualitatively similar for amidoboranes and their carbon analogs.     

Experimental and Computational Studies on the 1:1 Complex of Anthranilic Acid with P-Toluenesulfonic Acid

Abstract

The proton-transfer compound (3) was synthesized in good yields by the reaction of anthranilic acid with p-toluenesulfonic acid. It was characterized by elemental analysis, infrared spectroscopy, and X-ray single-crystal determination. The crystal structure analysis of 2-carboxyanilinium p-toulenesulfonate (3) has revealed a one-dimensional hydrogen-bonded network structure, involving the tosylate anion, the carboxyl group, and the ammonium group. The H(N)···O distances range from 1.97 to 2.23 Å. The molecular geometry and vibrational frequencies of 3 were calculated using the ab-initio method (HF) with the 6–31G(d) and 6–31+G(d,p) basis sets. The computed results indicate that the optimized geometry reproduces the crystal structure well, and the assignments of fundamental vibrations also agree well with the theoretical frequencies. The intermolecular proton transfer process between the ionic (3) and nonionic (4) structures was also investigated with the theoretical computations. The nonionic form (4) is energetically more stable than the ionic form (3) and TS(3→4) by 9.76 and 7.01 kcal/mol, respectively, including the zero-point vibrational energy correction at the HF/6–31+G(d,p) level. In addition, the atomic charges, the molecular electrostatic potentials, the nucleus-independent chemical shifts, and the frontier molecular orbitals of 3 were carried out at the HF/6–31+G(d,p) level of theory.

Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional figures and tables     

Mechanistic Insight into Energy-Transfer Dynamics and Color Tunability of Na4CaSi3O9:Tb3+,Eu3+ for Warm White LEDs

In this work, a latent energy-transfer process in traditional Eu³⁺,Tb³⁺-doped phosphors is proposed and a new class of Eu³⁺,Tb³⁺-doped Na₄CaSi₃O₉ (NCSO) phosphors is presented which is enabled by luminescence decay dynamics that optimize the electron-transfer energy process. Relative to other Eu³⁺,Tb³⁺-doped phosphors, the as-synthesized Eu³⁺,Tb³⁺-doped NCSO phosphors show improved large-scale tunable emission color from green to red upon UV excitation, controlled by the Tb³⁺/Eu³⁺ doping ratio. Detailed spectroscopic measurements in the vacuum ultraviolet (VUV)/UV/Vis region were used to determine the Eu³⁺–O²⁻ charge-transfer energy, 4f–5d transition energies, and the energies of 4f excited multiplets of Eu³⁺ and Tb³⁺ with different 4f^N electronic configurations. The Tb³⁺→Eu³⁺ energy-transfer pathway in the co-doped sample was systematically investigated, by employing luminescence decay dynamics analysis to elucidate the relevant energy-transfer mechanism in combination with the appropriate model simulation. To demonstrate their application potential, a prototype white-light-emitting diode (WLED) device was successfully fabricated by using the yellow luminescence NCSO:0.03Tb³⁺, 0.05Eu³⁺ phosphor with high thermal stability and a BaMgAl₁₀O₁₇:Eu²⁺ phosphor in combination with a near-UV chip. These findings open up a new avenue to realize and develop multifunctional high-performance phosphors by manipulating the energy-transfer process for practical applications.     

Oxidative N‐Heterocyclic Carbene‐Catalyzed γ‐Carbon Addition of Enals to Imines: Mechanistic Studies and Access to Antimicrobial Compounds

The reaction mechanism of the γ‐carbon addition of enal to imine under oxidative N‐heterocyclic carbene catalysis is studied experimentally. The oxidation, γ‐carbon deprotonation, and nucleophilic addition of γ‐carbon to imine were found to be facile steps. The results of our study also provide highly enantioselective access to tricyclic sulfonyl amides that exhibit interesting antimicrobial activities against X. oryzae, a bacterium that causes bacterial disease in rice growing.