The carbene reactivity surface: a classification

Covalent crosslinking in gas-phase biomolecular ions. An account and perspective

Photochemical crosslinking in gas-phase ion complexes has been introduced as a method to study biomolecular structures and dynamics. Emphasis has been on carbene-based crosslinking induced by photodissociation of diazirine-tagged ions. The features that characterize gas-phase crosslinking include (1) complex formation in electrospray droplets that allows for library-type screening; (2) well defined stoichiometry of the complexes due to mass-selective isolation; (3) facile reaction monitoring and yield determination, and (4) post-crosslinking structure analysis by tandem mass spectrometry that has been combined with hydrogen-deuterium exchange, UV-vis action spectroscopy, and ion mobility measurements. In this account, examples are given of peptide-peptide, peptide-nucleotide, and peptide-ligand crosslinking that chiefly used carbene-based reactions. The pros and cons of gas-phase crosslinking are discussed. Nitrile-imine based crosslinking in gas-phase ions is introduced as a promising new approach to ion structure analysis that offers high efficiency and has the potential for wide ranging applications.

Carbene Cross-Linking in Gas-Phase Peptide Ion Scaffolds

Scaffolds consisting of a peptide, a phthalate linker, and a 4,4-azipentyl group were synthesized and used to study intramolecular peptide-carbene cross-linking in gas-phase cations. Carbene intermediates were generated by UV-laser photodissociation at 355 nm of the diazirine ring in mass-selected ions, and the cross-linked products were detected and quantified by collision-induced dissociation tandem mass spectrometry (CID-MSⁿ, n = 3-5). Peptide scaffolds containing Ala and Leu residues with a C-terminal Gly gave 21-26% yields of cross-linked products, while the presence of the Pro and His residues decreased the yields. Experiments using hydrogen-deuterium-hydrogen exchange, carboxyl group blocking, and analysis of CID-MSⁿ spectra of reference synthetic products revealed that a significant fraction of cross-links involved the Gly amide and carboxyl groups. Interpretation of the cross-linking results was aided by Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations that allowed us to establish the protonation sites and conformations of the precursor ions. Analysis of long (100 ps) BOMD trajectories was used to count close contacts between the incipient carbene and peptide atoms, and the counting statistics was correlated with the results of gas-phase cross-linking.

σ0π2 Singlet Ground State Carbenes Undergo Least-Motion Reactions with H2 and Alkenes

Ground state singlet carbenes commonly feature σ²π⁰ orbital occupations and are known for their concerted σ-bond insertion and cycloaddition reactions. Despite the facility of these transformations, orbital symmetry conservation forces them into non-least-motion π-approach reaction pathways. This situation completely changes when the singlet σ⁰π² electron configuration becomes the ground state, which we show here by means of high-level CCSD(T) geometry optimizations. Carbenes like the experimentally known 2H-imidazol-2-ylidene react with H₂ and ethylene with negligible or no barrier in a σ-fashion, which effectively corresponds to a least-motion reaction trajectory.

Tricyclo[2.1.0.02,5]pent-3-ylidene: Stereoelectronic Control of Bridge-Flapping within a Nonclassical Nucleophilic Carbene

Tricyclo[2.1.0.0^2,5]pent-3-ylidene is a carbene foreseen to rearrange to pyramidane (c-C₄H₄)C, a highly strained molecule featuring an inverted C atom. Modeling of the carbene, using the (U)MPWB1K/cc-pVTZ//(U)MPWB1K/6-311G(d) theoretical model, indicated a large singlet-triplet energy gap (ΔE_S-T = -45 kcal/mol), a high gas-phase proton affinity (PA = 258 kcal/mol), and a preference for electron-poor alkenes. These properties are consistent with those of nucleophilic carbenes. Structural differences between the C_s-symmetric singlet (ω_flap = ±44 deg) and C_2v-symmetric triplet (ω_flap = 0 deg) stem from nonclassical electron delocalization in the former and the lack thereof in the latter. Degenerate bridge-flapping of the singlet's main bridge, which comprises the reactive divalent C3 atom, is computed to be slow due to a high activation barrier of the C_2v-symmetric transition state (TS) (E_a = 17 kcal/mol). The position of the conformeric equilibrium is subject to stereoelectronic control. 1-Substituted derivatives of the carbene (R ≠ H) are sensitive to σ inductive effects. A proximal conformation is preferred when R is electron-donating and a distal one is favored when R is electron-withdrawing. Finally, carbene rearrangements via 1,2-C atom shift or enyne fragmentation were computed. The C_2v-symmetric bridge-flapping TS has the proper geometry to initiate enyne fragmentation.

Preferential N-H⋯:C[double bond splayed right] hydrogen bonding involving ditopic NH-containing systems and N-heterocyclic carbenes

Hydrogen bonding plays a critical role in maintaining order and structure in complex biological and synthetic systems. N-heterocyclic carbenes (NHCs) represent one of the most versatile tools in the synthetic chemistry toolbox, yet their potential as neutral carbon hydrogen bond acceptors remains underexplored. This report investigates this capability in a strategic manner, wherein carbene-based hydrogen bonding can be assessed by use of ditopic NH-containing molecules. N-H bonds are unique as there are three established reaction modes with carbenes: non-traditional hydrogen bonding adducts (X-H⋯:C[double bond splayed right]), salts arising from proton transfer ([H-C[double bond splayed right]]⁺[X]^-), or amines from insertion of the carbene into the N-H bond. Yet, there are no established rules to predict product distributions or the strength of these associations. Here we seek to correlate the hydrogen bond strength of symmetric and asymmetric ditopic secondary amines with 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr, a representative NHC). In symmetric and asymmetric ditopic amine adducts both the solid-state (hydrogen bond lengths, NHC interior angles) and solution-state (¹H Δδ of NH signals, ¹³C signals of carbenic carbon) can be related to the pK _a of the parent amine.

Hydrogenative Metathesis of Enynes via Piano-Stool Ruthenium Carbene Complexes Formed by Alkyne gem-Hydrogenation

The only recently discovered gem-hydrogenation of internal alkynes is a fundamentally new transformation, in which both H atoms of dihydrogen are transferred to the same C atom of a triple bond while the other position transforms into a discrete metal carbene complex. [Cp*RuCl]₄ is presently the catalyst of choice: the resulting piano-stool ruthenium carbenes can engage a tethered alkene into either cyclopropanation or metathesis, and a prototypical example of such a reactive intermediate with an olefin ligated to the ruthenium center has been isolated and characterized by X-ray diffraction. It is the substitution pattern of the olefin that determines whether metathesis or cyclopropanation takes place: a systematic survey using alkenes of largely different character in combination with a computational study of the mechanism at the local coupled cluster level of theory allowed the preparative results to be sorted and an intuitive model with predictive power to be proposed. This model links the course of the reaction to the polarization of the double bond as well as to the stability of the secondary carbene complex formed, if metathesis were to take place. The first application of “hydrogenative metathesis” to the total synthesis of sinularones E and F concurred with this interpretation and allowed the proposed structure of these marine natural products to be confirmed. During this synthesis, it was found that gem-hydrogenation also provides opportunities for C–H functionalization. Moreover, silylated alkynes are shown to participate well in hydrogenative metathesis, which opens a new entry into valuable allylsilane building blocks. Crystallographic evidence suggests that the polarized [Ru–Cl] bond of the catalyst interacts with the neighboring R₃Si group. Since attractive interligand Cl/R₃Si contacts had already previously been invoked to explain the outcome of various ruthenium-catalyzed reactions, including trans-hydrosilylation, the experimental confirmation provided herein has implications beyond the present case.

Bent Singlet Cyclobutylcarbene: Computed Geometry, Properties, and Product Selectivity of a Nonclassical Carbene

Ab initio computations of cyclobutylcarbene (c-C₄H₇CH) were performed using the UMP4(fc)/6-311++G(2df,2p)//UMP2(full)/6-311++G(d,p) theoretical model. The carbene's most striking feature is its :CH-group. It is markedly bent toward the elongated C1'-C2' bond in the singlet ground-state but not in the triplet state, which is at least 1.1 kcal/mol higher in energy. Nonclassical 3C2E bonding among the C1, C1', and C2' atoms is prominent in the HOMO{-1}. The electron-donating ability of the nonbonding HOMO is thereby enhanced. The intensified nucleophilicity of the singlet carbene is manifested in quantifiable ways. For example, its hard and soft acid and base (HSAB) hardness, HSAB absolute electronegativity, and gas-phase proton affinity rival those of ylide-stabilized N-heterocyclic carbenes. It is computed to act as a nucleophile toward alkenes with higher HSAB hardness values. Transition states from singlet cyclobutylcarbene to bicyclo[2.1.0]pentane, cyclopentene, and methylenecyclobutane were computed and confirmed by intrinsic reaction coordinate calculations. Activation energies depend on the singlet's conformation with regard to c-C₄H₇ ring-puckering, :CH-group rotation, and :CH-group bending. The singlet's bent :CH-group favors bicyclo[2.1.0]pentane and cyclopentene formation.

Three Ways Isolable Carbenes Can Modulate Emission of NH-Containing Fluorophores

Fluorescent molecules and materials that exhibit emission changes in response to analytes are of great interest across multiple disciplines. Herein, we investigate the response of NH-containing fluorophores carbazole and 2-phenylbenzimidazole (Ph-BIM) with two representative isolable singlet carbenes. Specifically, N-heterocyclic carbene 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) and cyclic (alkyl)(amino)carbene (2,6-diisopropylphenyl)-4,4-diethyl-2,2-dimethyl-pyrrolidin-5-ylidene (^EtCAAC) were discovered to afford three different types of reaction products with carbazole and Ph-BIM. Depending on the reaction pair, hydrogen bonding (1), NH-insertion (2,3), or proton transfer (4) products can be isolated, each displaying variable photophysical responses. These products have been structurally authenticated by single crystal X-ray diffraction and NMR spectrometric methods. Studies of the solution state behavior of 1-4 reveals that these adducts are labile and can reversibly dissociate to free carbenes and fluorophores to varying extents. These equilibria produce concentration dependent solution state behavior as identified and quantified via UV-visible absorption, emission, ¹H DOSY, and NMR spectroscopic measurements.

Electronic and ligating properties of carbocyclic carbenes: A theoretical investigation

Carbocyclic carbenes (CCCs) are a class of nucleophilic carbenes which are very similar to N-heterocyclic carbenes (NHCs) in terms of their reactivity, but they do not contain a stabilizing heteroatom in their cyclic ring system. In this study, 17 representative known CCCs and 34 newly designed CCCs are evaluated using quantum chemical methods, and the results are compared in terms of their stability, nucleophilicity, and proton affinity (PA) parameters. The results are divided on the basis of ring size of the known and reported CCCs. The stability, nucleophilicity, PA, complexation energy, and bond strength-related parameters were estimated using M06/6-311++G(d,p) method. The results indicated that the CCCs known in the literature are strong σ-electron donating species and have considerable π-accepting properties. This study led to the design and identification of a few new CCCs with dimethylamine and diaminomethynyl substituents which can be singlet stable and are substantially nucleophilic. © 2018 Wiley Periodicals, Inc.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

Intermolecular Reactions of a Foiled Carbene with Carbonyl Compounds: The Effects of Trishomocyclopropyl Stabilization

endo-Tricyclo[3.2.1.0(2,4)]oct-8-ylidene is a foiled carbene reaction intermediate. It was generated by thermolyzing Δ(3)-1,3,4-oxadiazoline precursors dissolved in benzaldehyde and acetophenone. The products appear to stem from direct insertion of the carbene's divalent C atom into the α-bonds of the carbonyl compounds; however, this is only superficial. The strict stereochemistry observed is due to the topologies of the reaction intermediates of the proposed two-step mechanism. Bimolecular nucleophilic addition generates bent 1,3-zwitterions. The neutral reaction intermediates undergo pinacolic rearrangements to form the observed adducts. Product ratios reflect the migratory aptitudes of the carbonyl compounds' α-substituents. The carbene reaction was modeled using DFT. The singlet carbene's bicoordinate C atom bends 31° toward the endo-fused cyclopropane bond, elongating it to r = 1.69 Å. The resulting trishomocyclopropyl HOMO{-1} is a three-center two-electron bond responsible for the electron-deficient carbene's nucleophilicity. Its calculated properties are consistent with this assertion: (1) singlet-triplet (ΔE(S-T)) energy gap of -25 kcal/mol, (2) gas-phase proton affinity (PA) value of 272 kcal/mol, (3) hard and soft acid and base (HSAB) ΔN value of -0.2 in its initial reaction with the carbonyl compounds, and (4) negative frontier orbital interaction values ΔΔE(PhC(O)H) = -4.38 eV and ΔΔE(PhC(O)Me) = -3.97 eV.

Nucleophilic intermolecular chemistry and reactivity of dimethylcarbene

Experimental and computational studies find that dimethylcarbene (DMC), the parent dialkylcarbene, is both predicted to be and functions as a very reactive nucleophilic carbene in addition reactions with five simple alkenes. Activation energies and enthalpies for DMC additions to 2-ethyl-1-butene and methyl acrylate are computed and observed to be negative.

2-Adamantylidene and its heavier analogues: hyperconjugation versus lone pair stability and electrophilicity versus nucleophilicity

Too heavy to bend: The Cieplak-type hyperconjugative interaction mainly contributes to the stability of 2C and 2Si whereas the inertness of lone pairs is the major factor for 2Ge and 2Sn. These molecules (2X; X = C–Sn) can be classified as a class of ambiphilic compounds.

The nucleophilicity of a dialkylcarbene: unusual activation parameters for additions of adamantanylidene to simple alkenes

Computational and experimental results demonstrate that adamantanylidene (1) behaves as a highly reactive nucleophile toward common alkenes. It is the only known saturated nucleophilic carbene that lacks direct or vinylogous heteroatomic substitution. The activation energy and enthalpy for addition of 1 to methyl acrylate are the most negative values yet encountered in any carbene-alkene addition.

α-Bromodiazoacetamides - a new class of diazo compounds for catalyst-free, ambient temperature intramolecular C-H insertion reactions

In this work, we introduce a new class of halodiazocarbonyl compounds, α-halodiazoacetamides, which through a metal-free, ambient-temperature thermolysis perform intramolecular C-H insertions to produce α-halo-β-lactams. When carried out with α-bromodiazoacetamides bearing cyclic side chains, the thermolysis reaction affords bicyclic α-halo-β-lactams, in some cases in excellent yields, depending on the ring size and substitution pattern of the cyclic amide side chains.

Theory of divalent main group H2 activation: electronics and quasiclassical trajectories

Density functional theory (DFT), absolutely localized molecular orbital (ALMO) analysis, and quasiclassical trajectories (QCTs) were used to study the structure, barrier heights, thermodynamics, electronic properties, and dynamics of dihydrogen (H2) activation by singlet divalent main group compounds (ER2; E = C, Si, Ge). ALMO energy and charge decomposition calculations reveal that in the transition state CR2 acts as an ambiphile toward H2 because of equal forward-bonding and back-bonding orbital stabilization while SiR2 and GeR2 act as nucleophiles with dominant orbital energy stabilization arising from ER2 to H2 donation. Frontier molecular orbital (FMO) energy gaps do not provide a reasonable estimate of energy stabilization gained between the ER2 and H2 in the transition state or an accurate description of the nucleophilic versus electrophilic character because of electron repulsion and orbital overlap influences that are neglected. In CR2 transition states, forward-bonding and back-bonding are maximized in the nonleast motion geometry. In contrast, SiR2/GeR2 transition states have side-on geometries to avoid electron-electron repulsion. Electron repulsion, rather than orbital interactions, also determines the relative barrier heights of CR2 versus SiR2/GeR2 reactions. Examination of barrier heights and reaction energies shows a clear kinetic-thermodynamic relationship for ER2 activation of H2. A computational survey of R groups on ER2 divalent atom centers was performed to explore the possibility for H2 activation to occur with a low barrier and thermodynamically reversible. QCTs show that dihydrogen approach and reaction with CR2 may involve geometries significantly different than the static transition-state structure. In contrast, trajectories for dihydrogen addition to SiR2 involve geometries close to the side-on approach suggested by the static transition-state structure. QCTs also demonstrate that addition of H2 to CR2 and SiR2 is dynamically concerted with the average time gap of bond formation between E-H bonds of approximately 11 and 21 fs, respectively.

Putative irreversible inhibitors of the human sodium-dependent bile acid transporter (hASBT; SLC10A2) support the role of transmembrane domain 7 in substrate binding/translocation

PURPOSE

To explore the involvement of transmembrane domain (TM) 7 of the human apical sodium-dependent bile acid transporter (hASBT) on bile acid (BA) binding/translocation, using two electrophilic BA derivatives as molecular probes.

METHODS

Two electrophilic derivatives of chenodeoxycholic acid (CDCA) were designed, synthesized and evaluated for their ability to inactivate hASBT, and the human organic cation/carnitine transporter (hOCTN2) as a control (i.e. a non-BA transporting model). The ability of electrophilic derivatives to interact with hASBT was evaluated by 2-aminoethyl-methanethiosulfonate (MTSEA)-biotin labeling of thiol groups in TM7 cysteine mutants.

RESULTS

Unlike native BAs, the electrophilic CDCA derivatives specifically inactivated hASBT, but not hOCTN2, and inhibited hASBT in a time- and concentration-dependent fashion. Preincubation of hASBT Cys-mutants in the exofacial half of TM7 with reactive electrophilic probes blocked transporter biotinylation by MTSEA-biotin, similar to 2-(trimethylammonium)ethyl-methanethiosulfonate (MTSET) blocking. This blocking pattern differed from that produced by native BAs, which exposed exofacial TM7 residues, thereby increasing staining.

CONCLUSION

Kinetic and biochemical data indicate these novel electrophilic BAs are potent and specific irreversible inhibitors of hASBT and offer new evidence about the role of TM7 in binding/translocation of bile acids.

Intermolecular reactions of foiled carbenes with N-H bonds: evidence for an ylidic pathway

The chemistry of endo-tricyclo[6.2.1.0 (2.7)]undec-9-en-11-ylidene (10), an archetypal foiled carbene, has been investigated. The intermolecular reactions of 10 are most conveniently performed with oxadiazoline 6 because the corresponding diazirine can be obtained only in very low yield. Furthermore, the aziridinyl imine is difficult to decompose and the tosylhydrazone sodium salt poorly soluble in common organic solvents. Photolysis of 6 in diethylamine leads merely to a reduction of the diazo group and regeneration of acetyl hydrazone 5, whereas thermolysis cleanly affords tertiary amine 12(anti) in 77% yield. Calculations show that even stabilized-nucleophilic carbenes react with amines through an ylidic pathway and not by a concerted insertion into the N-H bond. Nevertheless, in the gas phase, norbornen-7-ylidene (13) is predicted to be stabilized by one molecule of NH3 more efficiently through a hydrogen bond than by ylide formation.