Semibullvalenes and Related Molecules: Ever Closer Approaches to Neutral Homoaromaticity

Revisiting a classic carbocation - DFT, coupled-cluster, and ab initio molecular dynamics computations on barbaralyl cation formation and rearrangements

Density functional theory computations were used to model the formation and rearrangement of the barbaralyl cation (C9H+ 9). Two highly delocalized minima were located for C9H+ 9, one of C s symmetry and the other of D 3h symmetry, with the former having lower energy. Quantum chemistry-based NMR predictions affirm that the lower energy structure is the best match with experimental spectra. Partial scrambling was found to proceed through a C 2 symmetric transition structure associated with a barrier of only 2.3 kcal mol-1. The full scrambling was found to involve a C 2v symmetric transition structure associated with a 5.0 kcal mol-1 barrier. Ab initio molecular dynamics simulations initiated from the D 3h C9H+ 9 structure revealed its connection to six minima, due to the six-fold symmetry of the potential energy surface. The effects of tunneling and boron substitution on this complex reaction network were also examined.

Photoregulated fluxional fluorophores for live-cell super-resolution microscopy with no apparent photobleaching

Photoswitchable molecules have multiple applications in the physical and life sciences because their properties can be modulated with light. Fluxional molecules, which undergo rapid degenerate rearrangements in the electronic ground state, also exhibit switching behavior. The stochastic nature of fluxional switching, however, has hampered its application in the development of functional molecules and materials. Here we combine photoswitching and fluxionality to develop a fluorophore that enables very long (>30 min) time-lapse single-molecule localization microscopy in living cells with minimal phototoxicity and no apparent photobleaching. These long time-lapse experiments allow us to track intracellular organelles with unprecedented spatiotemporal resolution, revealing new information of the three-dimensional compartmentalization of synaptic vesicle trafficking in live human neurons.

Super-resolution microscopy with spontaneously blinking dyes is dependent on pH and polarity of the medium. Here the authors introduce a photoactivatable fluxional fluorophore for live cell imaging that allows control over the fraction of spontaneously blinking molecules independently of medium properties.

Synthesis of dibromo- and tetrabromo-bipyrrolines and their corresponding 2,6-diazasemibullvalene derivatives

Treatment of Δ¹-dipyrrolines with NBS afforded α,α′-dibromo-Δ¹-bipyrrolines and α,α,α′,α′-tetrabromo-Δ¹-bipyrrolines, which were efficiently transformed into 2,6-diazasemibullvalene derivatives via reduction with lithium.

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

Semibullvalene and diazasemibullvalene: recent advances in the synthesis, reaction chemistry, and synthetic applications

Semibullvalene (SBV) and its aza analogue 2,6-diazasemibullvalene (NSBV) are theoretically interesting and experimentally challenging organic molecules because of four unique features: highly strained ring systems, intramolecular skeletal rearrangement, extremely rapid degenerate (aza-)Cope rearrangement, and the predicted existence of neutral homoaromatic delocalized structures. SBV has received much attention in the past 50 years. In contrast, after NSBV was predicted in 1971 and the first in situ synthesis was realized in 1982, no progress on NSBV chemistry was made until our results in 2012. We have been interested in the reaction chemistry of 1,4-dilithio-1,3-butadienes (dilithio reagents for short), especially for their applications in the synthesis of SBV and NSBV, because (i) the cyclodimerization of dilithio reagents could provide the potential eight-carbon skeleton of SBV from four-carbon butadiene units and (ii) the insertion reaction of dilithio reagents with C≡N bonds of two nitriles could provide a 6C + 2N skeleton that might be a good precursor for the synthesis of NSBV. Therefore, we initiated a journey into the synthesis and reaction chemistry of SBV and NSBV starting from dilithio reagents that has been ongoing since 2006. In this Account, we outline mainly our recent achievements in the synthesis, structural characterization, reaction chemistry, synthetic application, and theoretical/computational analysis of NSBV. Two efficient strategies for the synthesis of NSBV from dilithio reagents and nitriles via oxidant-induced C-N bond formation are described. Structural investigations of NSBV, including X-ray crystal structure analysis, determination of the activation barrier for the aza-Cope rearrangement, and theoretical analysis, show that the localized structure of NSBV is the predominant form and that the homoaromatic delocalized structure exists as a minor component in the equilibrium. We also discuss the reaction chemistry and synthetic applications of NSBV. Several novel reaction patterns have been explored, including thermolysis, C-N bond insertion, rearrangement-cycloaddition, oxidation, and nucleophilic ring-opening reactions. Diverse and interesting N-containing polycyclic skeletons can be constructed, such as nickelaazetidine, 1,5-diazatriquinacenes, and triazabrexadienes, which are not available by other means. Our results show that NSBV not only features a rapid aza-Cope rearrangement with a low activation barrier but also acts as unique synthetic reagent that is significantly different from aziridine. The strained rigid ring systems as a whole can be involved in the reactions. Our achievements highlight two significant advances: (i) the well-established efficient synthesis and isolation of NSBV has greatly accelerated the development of NSBV chemistry, and (ii) the previously unattainable molecules have become "normal" and routine starting materials for the synthesis of otherwise unavailable but interesting structures. We expect that our pursuits will inspire and help direct future chemical and physical research on NSBV.

Quantum theory of concerted electronic and nuclear fluxes associated with adiabatic intramolecular processes

Example of concerted electronic (right) and nuclear (left) fluxes: isomerization of B₄.

How a Quantum Chemical Topology Analysis Enables Prediction of Electron Density Transfers in Chemical Reactions. The Degenerated Cope Rearrangement of Semibullvalene

Recent works on the reaction mechanism for the degenerated Cope rearrangement (DCR) of semibullvalene (SBV) in the ground state prompted us to investigate this complex rearrangement in order to assign experimentally observed contrast features in the simulated electron distribution. We present a joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) as a powerful tool to analyze the electron density transfers along the DCR. The progress of the reaction is monitored by the structural stability domains of the topology of ELF, while the change between them is controlled by turning points derived from CT. The ELF topological analysis shows that the DCR of SBV corresponds to asynchronous electron density rearrangement taking place in three consecutive stages. We show how the pictures anticipated by drawing Lewis structures of the rearrangement correlate with the experimental data and time-dependent quantum description of the process.

Calculations predict that carbon tunneling allows the degenerate cope rearrangement of semibullvalene to occur rapidly at cryogenic temperatures

Calculations on the role of tunneling in the degenerate Cope rearrangements of semibullvalene (1) and barbaralane (3) predict that, at temperatures below 40 K, tunneling from the lowest vibrational level should make the temperature-independent rate constants k = 1.43 x 10(-3) s(-1) and k = 7.28 x 10(-9) s(-1), respectively. An experiment, using semibullvalene-2(4)-d(1), is proposed to test the prediction of rapid tunneling by 1 at cryogenic temperatures.

Hetero-Cope Rearrangements of Nitrosobutenes. DFT Studies of Thermal and Acid-Catalyzed Reactions

[Structure: see text] Density functional theory studies of the hetero-Cope reactions of 4-nitroso-1-butenes and nitrosobicyclo[2.2.2]hexenes are reported. The reactions proceed via concerted mechanisms. The electron-withdrawing methoxycarbonyl group alpha- to the nitroso group decreases the activation barrier. Lewis acids such as SbF5 and TiCl4 accelerate the reactions, as has been found experimentally by Zakarian and Lu.

Localized and delocalized perfluorosemibullvalenes

On the basis of the experimental Gibbs free-energy barrier of the degenerate Cope arrangement in semibullvalene, B3P86 shows the best agreement, while B3LYP and MP2 underestimate and CCSD(T) overestimates the barrier. The substituent effect proposal by Hoffmann has been verified. In contrast to semibullvalenes with either localized energy-minimum structures or delocalized transition-state structures, perfluorosemibullvalene has both localized and delocalized energy-minimum structures that are very close in energy.

Experimental and Theoretical Study of Stabilization of Delocalized Forms of Semibullvalenes and Barbaralanes by Dipolar and Polarizable Solvents. Observation of a Delocalized Structure that Is Lower in Free Energy than the Localized Form

[reaction: see text] UV/vis spectra of thermochromic semibullvalenes 1 and barbaralanes 2, which undergo rapid degenerate Cope rearrangements, display temperature-dependent shoulders (1b, 1d, 1e) or absorption maxima (1c, 2c, 2f) at the low-energy side of their strong UV bands. These long-wavelength absorptions are ascribed to Franck-Condon transitions from delocalized structures 1(deloc) and 2(deloc). Gibbs free energy differences, DeltaG*, between delocalized and localized forms were calculated from the temperature dependence of the long-wavelength absorptions. Dipolar and polarizable solvents strongly affect and even may reverse the relative stabilities of the localized and delocalized forms of 1c, 2c, and 2f. For example, DeltaG*(2c) = 8 kJ mol(-)(1) in cyclohexane, 2 kJ mol(-)(1) in dimethylformamide, and -3 kJ mol(-)(1) in N,N'-dimethylpropylene urea (DMPU), so that (2c(deloc))(DMPU) becomes the global minimum. In contrast to the case for 2c, the intensities of the long-wavelength shoulders of the yellow semibullvalenes 1b, 1d, and 1e are only moderately influenced by solvents, and the rates of Cope rearrangements of the nonthermochromic, colorless barbaralanes 2a and 2b, determined by NMR methods, are almost solvent-invariant. In search of the solute properties that are decisive in determining the influence of solvent upon DeltaG*, electrical dipole and quadrupole moments and molecular polarizabilities have been calculated using the B3LYP/6-31G* method and solvation energies have been computed with the conductorlike polarized continuum model (CPCM). The results of these calculations indicate that the solvent effects are due to the greater polarity and polarizability of the delocalized structures relative to the localized structures.

How Important Is Bishomoaromatic Stabilization in Determining the Relative Barrier Heights for the Degenerate Cope Rearrangements of Semibullvalene, Barbaralane, Bullvalene, and Dihydrobullvalene?

[structure: see text] B3LYP/6-31G* calculations have been used to investigate the origins of the relative barrier heights for the degenerate Cope rearrangements of semibullvalene (1), barbaralane (2), bullvalene (3), and dihydrobullvalene (4). We conclude from our calculations that, of the four transition structures (TSs), that for rearrangement of 1 has the smallest amount of interallylic bonding. Nevertheless, relief of strain in the reactant confers on 1 the lowest barrier to Cope rearrangement. Conjugation between the cyclopropane ring and the pi bond of the etheno bridge in 3 makes the barrier for its Cope rearrangement higher than that for 4 and also contributes to making the barrier for 3 higher than that for 2. However, the relatively low barrier to the Cope rearrangement of 2 is largely due to the TS for this reaction having the largest amount of interallylic bonding of all four TSs.

Palladium-catalyzed, stereoselective rearrangement of a tetracyclic allyl cyclopropane under arylation

The first example of a pi,sigma domino-Heck reaction under concomitant rearrangement of the tetracyclic allylcyclopropane endo,exo-bishomobarrelene (5) is reported; the stereoselective reaction proceeds via an intramolecular insertion of a primarily-formed carbopalladation intermediate into a strained cyclopropane C-C sigma-bond, giving 9.