Secondary Orbital Interactions Research Articles

Bispericyclic Ambimodal Dimerization of Pentafulvene: The Origin of Asynchronicity and Kinetic Selectivity of the Endo Transition State.

The propensity of fulvenes to undergo dimerization has long been known, although the in-depth mechanism and electronic behavior during dimerization are still elusive. Herein, we made an attempt to gain insights into the reactivity of pentafulvene for Diels-Alder (DA) and [6 + 4]-cycloadditions via conventional and ambimodal routes. The result emphasizes that pentafulvene dimerization preferentially proceeds through a unique bifurcation mechanism where two DA pathways merge together to produce two degenerate [4 + 2]-cycloadducts from a single TS. Despite the [6 + 4]-cycloadduct being thermodynamically preferred, [4 + 2]-cycloaddition reactions are kinetically driven. Singlet biradicaloid is involved in through-space 6e- delocalization as a secondary orbital interaction that originates asynchronicity and stabilizes the bispericyclic transition state (TS). The transformation of various actively participating intrinsic bonding orbitals (IBOs) unambiguously forecasts the formation of multiple products from a single TS and rationalizes the mechanism of ambimodal reactions that are rather difficult to probe with other analyses. The changes in active IBOs clearly distinguish the conventional reactions from bifurcation reactions and can be employed to characterize and confirm the ambimodal mechanism. This report gains a crucial theoretical insight into the mechanism of bifurcation, the origin of asynchronicity, and electronic behavior in ambimodal TS, which will certainly be of enormous value for future studies.

Discovery of new tetrazines for bioorthogonal reactions with strained alkenes via computational chemistry.

Tetrazines are widely employed reagents in bioorthogonal chemistry, as they react readily with strained alkenes in inverse electron demand Diels-Alder reactions, allowing for selective labeling of biomacromolecules. For optimal performance, tetrazine reagents have to react readily with strained alkenes, while remaining inert against nucleophiles like thiols. Balancing these conditions is a challenge, as reactivity towards strained alkenes and nucleophiles is governed by the same factor - the energy of unoccupied orbitals of tetrazine. Herein, we utilize computational chemistry to screen a set of tetrazine derivatives, aiming to identify structural elements responsible for a better ratio of reactivity with strained alkenes vs. stability against nucleophiles. This advantageous trait is present in sulfone- and sulfoxide-substituted tetrazines. In the end, the distortion/interaction model helped us to identify that the reason behind this enhanced reactivity profile is a secondary orbital interaction between the strained alkene and sulfone-/sulfoxide-substituted tetrazine. This insight can be used to design new tetrazines for bioorthogonal chemistry with improved reactivity/stability profiles.

Transition-State Stabilization by Secondary Orbital Interactions between Fluoroalkyl Ligands and Palladium During Reductive Elimination from Palladium(aryl)(fluoroalkyl) Complexes

Transition-State Stabilization by Secondary Orbital Interactions between Fluoroalkyl Ligands and Palladium During Reductive Elimination from Palladium(aryl)(fluoroalkyl) Complexes

Secondary Orbital Effect Involving Fluorine is Responsible for Substrate-Controlled Diastereodivergence in the Catalyzed syn-aza-Henry Reaction of α-Fluoronitroalkanes.

The fluorine atom is a powerful, yet enigmatic influence on chemical reactions. True to form, fluorine was recently discovered to effect diastereodivergence in an enantioselective aza-Henry reaction, resulting in a very rare case of syn-β-amino nitroalkane products. More bewildering was the observation of an apparent hierarchy of substituents within this substrate-controlled behavior: Ph>F>alkyl. These cases have now been examined comprehensively by computational methods, including both non-fluorinated and α-fluoro nitronate additions to aldimines catalyzed by a chiral bis(amidine) [BAM] proton complex. This study revealed the network of non-covalent interactions that dictate anti- (α-aryl) versus syn-selectivity (α-alkyl) using α-fluoronitronate nucleophiles, and an underlying secondary orbital interaction between fluorine and the activated azomethine.

A computational investigation towards substitution effects on 8π electrocyclisation of conjugated 1,3,5,7-octatetraenes.

A computational investigation using M06-2X/6-31+G(d) method is reported for the substitution effects on 8π electrocyclisation of conjugated octatetraene. This systematic study describes the mono- and di-substitution effect across the 1,3,5,7-octatetraene skeleton. A general preference of the outward substitution over the inward, at C1 position of the monosubstituted system is observed. However, mesomerically electron donating group (-NH2 and -OH) display an opposite effect with respect to secondary orbital interaction (SOI) between the lone pair on the substituent and the orbital. A comparative evaluation on the computed activation energies for the 1-, 2-, 3-, and 4-monosubstituted system showed an insignificant impact on the rate of the reaction, in contrast to the electrocyclic ring closure of the unsubstituted compound. Computations of disubstituted system are more pronounced, where a remarkable acceleration is observed for 2-NO2-7-NO2 substituted octatetraene at 4.9 kcal mol-1, and a noticeable deceleration for 4-CH3-5-CH3 substituted octatetraene at 25.4 kcal mol-1 from the parent molecule, 17.0 kcal mol-1. A visible accelerated effects are commonly exhibited by the substitution on the terminal double bonds (C1, C2, C7, and C8), that are 1,2-, 1,7-, 1,8-, and 2,7-patterns, in regard to the greater orbital interaction for the new σ-bond formation. Despite the unfavourable steric clashes of the substituents in the 1,8-system, an apparent reduction in the energy barrier up to 7.4 kcal mol-1 is computed for 1-NH2-8-NO2 system from 17.0 kcal mol-1. This is due to the synergistic effect of the electron donor and electron acceptor, enhancing the stability of the transition structure. The electrocyclic ring closure involving vicinal substitution patterns, such as 1,2-, 2,3-, 3,4-, and 4,5-systems are critically dominated by steric crowding between the adjacent functional groups. In certain cases of the 1,2-substituted system, a noticeable accelerated effects are found for 1-NH2-2-NH2-substituted compound (9.7 kcal mol-1) due to an increased in electronic density on the substituted terminal double bond (C1-C2), hence favouring the formation of the new σ-bond.

Substituent Effects on Aluminyl Anions and Derived Systems: A High-Level Theory.

Aluminyl anions are low-valent aluminum species bearing a lone pair of electrons and a negative charge. These systems have drawn recent synthetic interest for their nucleophilic nature, allowing for the activation of σ-bonds, and have been proposed as a pathway to hydrogen energy storage. In this research, we provide high-level ab initio geometries and energies for both the simplest aluminyl anion (AlH2-) and several substituted derivatives. Geometries are reported using the gold-standard CCSD(T)/aug-cc-pV(T+d)Z level of theory. Energies were extrapolated to the complete basis set limit through the focal point approach, utilizing coupled-cluster methods through perturbative quadruples and basis sets up to five-ζ quality. Geometries were rationalized using electrostatic, steric, and orbital donation effects. The donation from substituents to Al is accompanied by back-donation effects, a property traditionally thought of in transition-metal systems. Stereoelectronic effects through the secondary orbital interaction play a fundamental role in stabilizing these low-valent aluminum compounds and would likely also affect the feasibility of their use within several industrial applications. The energetic analysis of the formation of each substituted anion is rationalized as the result of three energetic schemes. The effectiveness of these schemes for determining the relative formation energies is discussed.

Exploring Cyclization Strategies to Access Stemona Alkaloids: Subtle Effects Influencing Reactivity in Intramolecular Michael Additions.

This report investigates the fundamental basis for rather surprising patterns of reactivity in Brønsted acid-mediated cyclizations of pyrrole substrates bearing pendant Michael acceptors that were identified during syntheses of Stemona alkaloids. Integrated experimental and theoretical studies reveal the profound influence that substituent effects have on the viability of these transformations. Additionally, we identify that electronic effects, in addition to barrier-lowering secondary orbital interactions within transition states, account for the exclusive preference for 7-endo-trig cyclizations over 6-exo-trig cyclizations.

DFT study for the Diels-Alder reactions between butadiene ethylene for evaluate the effects of electro-attractors substituents

Investigation of the effect of three electron-withdrawing atoms of the periodic table on the activation energy of the Diels-Alder reaction by substituting an ethylene hydrogen CH 2 =CH 2 by F, Cl, Br, following the decrease in electronegativity. An exception was found for the boron atom Br, which is that the activation energy decreases remarkably from 27 to 20.86. This drop-in activation energy can be explained by the secondary orbital interaction.

Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids

Isolation, characterization and semi-synthesis of natural products dimeric amide alkaloids

Rare-Earth Metal Boroxide with Formal Triple Metal–Oxygen Orbital Interaction: Synthesis from B(C 6 F 5 ) 3 ·H 2 O and Radical-Anion Ligated Rare-Earth Metal Amides

Rare-earth metal boroxides are not only rare and of great synthetic challenge but also important theoretically due to their unrevealed bonding characteristics. In this paper, we report the synthesi...

Selectivity control in inverse electron demand Diels–Alder reaction of o-Quinone methides catalyzed by chiral N,N′-Dioxide–Sc(III) complex

The reaction mechanism and origin of asymmetric induction in inverse electron demand Diels-Alder (IEDDA) reaction of ortho-quinone methide (o-QM) and fulvene mediated by chiral N,N'-dioxide–Sc(III) catalyst were rationalized using B3LYP-D3(BJ) functional with def2-TZVP basis set. The uncatalyzed IEDDA reaction was concerted but highly asynchronous with activation barriers of 29.8∼31.8 kcal mol−1. Good linear relationship between the Hammett substituent constant (σP) of o-QM and the activation barrier (ΔG≠) of DA reaction was discovered. The secondary orbital interaction (SOI) between the conjugated diene of o-QM and fulvene moiety stabilized the endo-transition state, contributing to high endo-selectivity. The catalytic asymmetric IEDDA reaction occurred via a stepwise mechanism, including the construction of Cβ−C4 bond, followed by the formation of Cα−O1 bond. The bulky substituents (i.e., adamantyl or triphenylmethyl) in amide moiety of ligand furnished sufficient steric shielding for re-face of diene, inducing the attack of fulvene from si-face in endo-pathway. The substituent at exocyclic methylene of the unsymmetrical fulvene was crucial for the adjustment of E/Z selectivity. The steric repulsion between cyclohexyl group in fulvene and aromatic ring in o-QM raised the destabilizing strain energy (ΔEstrain) at the transition state in Z-configuration, contributing to the predominant E-product.

Fluorine Effects for Tunable C–C and C–S Bond Cleavage in Fluoro-Julia–Kocienski Intermediates

Classical Julia–Kocienski fluoroolefination represents an indispensable platform for the construction of monofluoroalkenes. Nevertheless, its complex multistep mechanistic manifold along with the u...

1,5]-Sigmatropic Shifts Regulated by Built-in Frustration.

Conceptually, many organic reactions involve a flow of electron density from electron-rich to electron-poor regions. When the direct flow of electron density is blocked, the innate "frustration" can provide a driving force for a reaction that removes the blockade. Herein, we show how this idea can be used for the design of molecular rearrangements promoted by remotely placed donor-acceptor pair of substituents. We evaluate effects of such "frustration" on the rates of competing [1,5]-hydrogen and [1,5]-halogen shifts in boron-substituted 1,3-pentadienes. As the sp3 hybridized carbon (C1) in these dienes interrupts the conjugation path between the donor to the acceptor, the system conceptually resembles a frustrated Lewis pair (FLP). Frustration is weakened when the formation of a new chemical bond in the TS opens communication between electron-rich and -poor regions and is removed completely when the resonance interaction between donor and acceptor develops fully in the rearranged product. Such relief of chemical frustration is directly translated into more favorable thermodynamic driving force and decreased intrinsic activation energies. Marcus theory separates thermodynamic contribution to the activation barriers and suggests that the electronic communication between electron rich and poor regions lowers the activation barrier via the formation of stabilizing 3-center contacts in the TS. Dramatic TS stabilization illustrates that the migrating groups function as an electronic relay between migration origin and terminus with properties fine-tuned by the boronyl acceptor. The combined effects of the C-X bond strength (X = migrating group), Lewis acidities of the acceptors, thermodynamic driving forces, and secondary orbital interactions control the observed barrier trends and selectivity of migration.

Transition-State-like Planar Structures for Amine Inversion with Ultralong C-C Bonds in Diamino-o-carborane and Diamino-o-dodecahedron.

Umbrella-like inversion of pyramidalized amines proceed through a planar transition state (TS). Stabilization of the TS through N(lone-pair) → σ*(C-C) "negative hyperconjugation" in diamino-o-carborane (1) causes rapid inversion in the amine, which results in the observation of a planarized -NH2 from the X-ray crystal structure. This proceeds through quantum mechanical tunneling across the small and narrow barrier (low pyramidalization). Tuning this secondary orbital (donor-acceptor) interaction for various derivatives of 1 and diamino-o-dodecahedron (2) provides a rational approach toward increasing dC-C to as large as 2.001, 2.011, and 1.807 Å for 1b (amino oxide-o-carborane), 1i (di-N,N-dimethylamino-o-carborane), and 2g (di-N,N-diisopropylamino-o-dodecahedron), respectively.

Orbital-Weighted Dual Descriptor for the Study of Local Reactivity of Systems with (Quasi-) Degenerate States.

An alternative response function, based on the dual descriptor in terms of Koopmans' approximation, is hereby proposed for the description of chemical reactivity in systems with (quasi-) degenerate frontier molecular orbitals. This descriptor is constructed from Fukui functions that include contributions from different orbitals, i.e., orbital-weighted Fukui functions. The methodology is applied to three case studies: the first case consists of a series of benchmark organic and inorganic molecules from which the dual descriptor, based only on frontier orbitals, is not appropriate to describe their reactivity. The second case deals with the proper description of chemical reactivity in Diels-Alder reactions between fullerene C60 and cyclopentadiene (CP), revealing the importance of considering secondary orbital interactions for an adequate regioselectivity description. The third, and last case, consists of a series of polycyclic aromatic hydrocarbons (PAHs) possessing molecular orbital degeneracy. By means of analyzing of this descriptor, an alternative approach to the description of aromaticity is proposed. In all cases, the proposed index called "orbital-weighted dual descriptor" has proven to accurately describe the chemical reactivity and aromaticity of the studied systems.

Influence of Non-Covalent Interactions in the Exo- and Regioselectivity of Aza-Diels-Alder Reactions: Experimental and DFT Calculations.

A systematic experimental and theoretical study of the intermolecular Aza-Diels-Alder reaction using 5-aminopyrrole as a building block shows that the commonly accepted endo selectivity, ruled by controversial secondary orbital interactions, are overcome by non-covalent interactions affording to the unusual exo adduct. Additionally, the regioselectivity is also influenced for such interactions. The starting materials are easily prepared, and the use of water as the solvent is a great achievement for the development of cleaner synthetic methodologies.

Keto‐Enol Tautomerization Controls the Acid‐Catalyzed Robinson Annulation ‐ A DFT Study

AbstractThree Robinson annulation reactions (A), (B) and (C) were investigated by DFT calculations. (A) is a base catalyzed one, where cyclohexanone, methyl vinyl ketone (MVK) and OH−(H2O)7 were employed as reactants. Eight elementary steps were obtained. The second transition state, TS2(A), is of the Michael addition prompted by the secondary orbital interaction, and TS5(A) is of the aldol condensation. The second TS of E1cB, TS8(A), has an appreciable activation energy, which would make the diketone A‐4 and ketol A‐7 detectable species. (B) is an acid catalyzed reaction, where 2‐methylcyclohexanone, MVK and H3O+(H2O)7 were adopted as reactants. Seven elementary steps were obtained. All the intermediates in B‐2 to B‐7 are neutral species (not protonated). The keto‐enol tautomerization assisted by the proton transfer is involved in all TSs. (C) is a neutral reaction, where 2‐methylcyclopentane‐1,3‐dione, 1‐chloro‐3‐pentanone and (H2O)8 were reactants. The first C−C bond formation is brought about by the nucleophilic substitution (SN2) where the leaving group is the chloride ion. The concomitantly generated H3O+ works as the acid catalyst to promote the subsequent processes. Again, the keto‐enol tautomerization is involved in all TSs.

Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopyrylium Ylides: The Significance of Molecular Orbital Isosymmetry.

By drawing analogies from the dimerization of cyclopentadiene, a novel reaction pathway bifurcation is uncovered in the cycloaddition of oxidopyrylium ylides and butadiene. Analysis of the potential energy surface (at the M06-2X/6-311+G(d,p) level of theory) in combination with Born-Oppenheimer molecular dynamics simulations (M06-2X/6-31+G(d)) demonstrate that both the (4 + 3)- and (5 + 2)-cycloaddition products are accessed from the same transition state. Key indicators of a pathway bifurcation (asynchronous bond formation, and a second transition state for the interconversion of the products) are also observed. The absence of a post-transition state bifurcation in the related oxidopyridinium systems of Krenske and Harmata is rationalized. Finally, the isosymmetry of the oxidopyrylium and cyclopentadiene molecular orbitals as well as the presence of "secondary orbital interactions" are emphasized as the common source of nonstatistical behavior. Application of these principles will allow for the rapid identification of new reaction pathway bifurcations.

Secondary Orbital Interactions Enhance the Reactivity of Alkynes in Diels-Alder Cycloadditions.

We have investigated the inverse electron-demand Diels–Alder reactions of trans-cyclooctene (TCO) and endo-bicyclo[6.1.0]nonyne (BCN) with a 1,2,4,5-tetrazine, a cyclopentadienone, and an ortho-benzoquinone. Tetrazines react significantly faster with TCO compared to BCN because the highest occupied molecular orbital (HOMO) of TCO is significantly higher in energy than the HOMO of BCN and there is less distortion of the tetrazine. Despite the different HOMO energies, TCO and BCN have similar reactivities toward cyclopentadienones, while BCN is significantly more reactive than TCO in the cycloaddition with ortho-benzoquinone. We find that the higher reactivity of BCN compared to TCO with ortho-benzoquinone is due to secondary orbital interactions of the BCN HOMO-1 with the diene LUMO.

Regioselective Three Component Domino Synthesis of Polyhydrospiro[indoline-3,3'-pyrrolizine]-2-one via [3+2] Cycloaddition Reaction

In present work, we have reported the synthesis and characterisation of novel hexahydrospiro[indoline-3,3′-pyrrolizine]-2-one derivatives in good to excellent yields via [3+2] cycloaddtion reaction in regioselective manner. These compounds were synthesized via multicomponent reaction of substituted 3-cinnamoyl-4-hydroxy-6-methyl-2H-pyran-2-one, isatin, L-proline at room temperature. All the synthesized hexahydrospiro molecules were characterized by 1H and 13C NMR, IR spectra, mass spectra and elemental analysis. Regioselectivity in synthesized molecules were also explained on the basis of secondary orbital interactions. A simple and facile methodology is developed which has great importance in synthetic chemistry.