Characterizing the Dimerizations of Phenalenyl Radicals by ab Initio Calculations and Spectroscopy: σ-Bond Formation versus Resonance π-Stabilization

Radical Single-Molecule Junctions

Radicals are unique molecular systems for applications in electronic devices due to their open-shell electronic structures. Radicals can function as good electrical conductors and switches in molecular circuits while also holding great promise in the field of molecular spintronics. However, it is both challenging to create stable, persistent radicals and to understand their properties in molecular junctions. The goal of this Perspective is to address this dual challenge by providing design principles for the synthesis of stable radicals relevant to molecular junctions, as well as offering current insight into the electronic properties of radicals in single-molecule devices. By exploring both the chemical and physical properties of established radical systems, we will facilitate increased exploration and development of radical-based molecular systems.

The Story of the Little Blue Box: A Tribute to Siegfried Hünig

The tetracationic cyclophane, cyclobis(paraquat-p-phenylene), also known as the little blue box, constitutes a modular receptor that has facilitated the discovery of many host-guest complexes and mechanically interlocked molecules during the past 35 years. Its versatility in binding small π-donors in its tetracationic state, as well as forming trisradical tricationic complexes with viologen radical cations in its doubly reduced bisradical dicationic state, renders it valuable for the construction of various stimuli-responsive materials. Since the first reports in 1988, the little blue box has been featured in over 500 publications in the literature. All this research activity would not have been possible without the seminal contributions carried out by Siegfried Hünig, who not only pioneered the syntheses of viologen-containing cyclophanes, but also revealed their rich redox chemistry in addition to their ability to undergo intramolecular π-dimerization. This Review describes how his pioneering research led to the design and synthesis of the little blue box, and how this redox-active host evolved into the key component of molecular shuttles, switches, and machines.

Phenalenyl Radical: Smallest Polycyclic Odd Alternant Hydrocarbon Present in the Graphene Sheet

Phenalenyl, a zigzag-edged odd alternant hydrocarbon unit can be found in the graphene nanosheet. Hückel molecular orbital calculations indicate the presence of a nonbonding molecular orbital (NBMO), which originates from the linear combination of atomic orbitals (LCAO) arising from 13 carbon atoms of the phenalenyl molecule. Three redox states (cationic, neutral radical, and anionic) of the phenalenyl-based molecules were attributed to the presence of this NBMO. The cationic state can undergo two consecutive reductions to result in neutral radical and anionic states, stepwise, respectively. The phenalenyl-based radicals were found as crucial building blocks and attracted the attention of various research fields such as organic synthesis, material science, computation, and device physics. From 2012 onward, a strategy was devised using the cationic state of phenalenyl-based molecules and in situ generated phenalenyl radicals, which created a new domain of catalysis. The in situ generated phenalenyl radicals were utilized for the single electron transfer (SET) process resulting in redox catalysis. This emerging range of applications rejuvenates the more than six decades-old phenalenyl chemistry. This review captures such developments ranging from fundamental understanding to multidirectional applications of phenalenyl-based radicals.

Doublet Open-Shell Graphene Fragments

The recent advances on neutral delocalized radical species based on polycyclic aromatic hydrocarbons with fused hexagonal rings, herein defined as doublet open-shell graphene fragments, are summarized in this review. A few simple yet useful theoretical approaches for structural analysis and molecular design were introduced at first. Then, based on the number of fused hexagonal rings, molecular systems with different size, symmetry and edge structure were discussed with emphasis on those isolated in the crystalline form. Their unique self-association behavior, chemical reactivity and physical properties were summarized and discussed, and insights on their functions and potential applications were provided.

Unexpected Charge Effects Strengthen π-Stacking Pancake Bonding

Phenalenyls (PLYs) are important synthons in many functional and electronic materials, which often display favorable molecule-to-molecule overlap for electron or hole transport. They also serve as a prototype for π-stacking pancake bonding based on two-electron multicenter bonding (2e/mc). Unexpected near-doubling of the binding energy is obtained for the positively charged PLY2 + dimer with an effect similar to that seen for the positively charged olympicenyl (OPY) radical dimer. This charge effect is reversed for the perfluorinated (PF) dimers, and the negatively charged perfluorinated (PF) dimers PF-PLY2 - and PF-OPY2 - become strongly bound. Long-range interactions reflect these differences. Also surprising is that in this case the pancake bonding corresponds to single-electron (1e/mc) or a three-electron (3e/mc) multicenter bonding in contrast to the 2e/mc bonding that occurs for the neutral radical dimers. The strong preference for a large intermolecular overlap is maintained in these charged dimers. Importantly, the preference for π-bonding in the charged dimers compared to σ-bonding is strongly enhanced relative to the neutral PLY dimers.

π-Diradical Aromatic Soot Precursors in Flames

Soot emitted from incomplete combustion of hydrocarbon fuels contributes to global warming and causes human disease. The mechanism by which soot nanoparticles form within hydrocarbon flames is still an unsolved problem in combustion science. Mechanisms proposed to date involving purely chemical growth are limited by slow reaction rates, whereas mechanisms relying on solely physical interactions between molecules are limited by weak intermolecular interactions that are unstable at flame temperatures. Here, we show evidence for a reactive π-diradical aromatic soot precursor imaged using non-contact atomic force microscopy. Localization of π-electrons on non-hexagonal rings was found to allow for Kekulé aromatic soot precursors to possess a triplet diradical ground state. Barrierless chain reactions are shown between these reactive sites, which provide thermally stable aromatic rim-linked hydrocarbons under flame conditions. Quantum molecular dynamics simulations demonstrate physical condensation of aromatics that survive for tens of picoseconds. Bound internal rotors then enable the reactive sites to find each other and become chemically cross-linked before dissociation. These species provide a rapid, thermally stable chain reaction toward soot nanoparticle formation and could provide molecular targets for limiting the emission of these toxic combustion products.

Radically Enhanced Dual Recognition

Complexation between a viologen radical cation (V^.+ ) and cyclobis(paraquat-p-phenylene) diradical dication (CBPQT^2(.+) ) has been investigated and utilized extensively in the construction of mechanically interlocked molecules (MIMs) and artificial molecular machines (AMMs). The selective recognition of a pair of V^.+ using radical-pairing interactions, however, remains a formidable challenge. Herein, we report the efficient encapsulation of two methyl viologen radical cations (MV^.+ ) in a size-matched bisradical dicationic host - namely, cyclobis(paraquat-2,6-naphthalene)^2(.+) , i.e., CBPQN^2(.+) . Central to this dual recognition process was the choice of 2,6-bismethylenenaphthalene linkers for incorporation into the bisradical dicationic host. They provide the space between the two bipyridinium radical cations in CBPQN^2(.+) suitable for binding two MV^.+ with relatively short (3.05-3.25 Å) radical-pairing distances. The size-matched bisradical dicationic host was found to exhibit highly selective and cooperative association with the two MV^.+ in MeCN at room temperature. The formation of the tetrakisradical tetracationic inclusion complex - namely, [(MV)₂ ⊂CBPQN]^{4( .+)} - in MeCN was confirmed by VT ¹ H NMR, as well as by EPR spectroscopy. The solid-state superstructure of [(MV)₂ ⊂CBPQN]^{4( .+)} reveals an uneven distribution of the binding distances (3.05, 3.24, 3.05 Å) between the three different V^.+ , suggesting that localization of the radical-pairing interactions has a strong influence on the packing of the two MV^.+ inside the bisradical dicationic host. Our findings constitute a rare example of binding two radical guests with high affinity and cooperativity using host-guest radical-pairing interactions. Moreover, they open up possibilities of harnessing the tetrakisradical tetracationic inclusion complex as a new, orthogonal and redox-switchable recognition motif for the construction of MIMs and AMMs.

Acene-Linked Zethrenes and Bisphenalenyls: A DFT Search for Organic Tetraradicals

Polycyclic aromatic hydrocarbons are of special interest due to their promising nonlinear optical and magnetic properties. A series of acene-linked zethrenes and bisphenalenyls comprising from five to nine benzene rings in the linker group have been computationally studied by the DFT UB3LYP/6-311++G(d,p) quantum-chemical modeling of their electronic structure, possible spin states, and exchange interactions. The zethrenes with octacene and nonacene linkers as well as bisphenalenyls comprising heptacene, octacene, and nonacene linker groups have been revealed to possess tetraradicaloid nature, which makes them promising building blocks for organic optoelectronic and spintronic devices. The results obtained open a way of constructing tetraradicaloid organic molecules characterized by the presence of two types of paramagnetic centers.

Unveiling the Hidden σ-Dimerization of a Kinetically Protected Olympicenyl Radical

The σ-dimer of a kinetically protected olympicenyl radical, which evaded the experimental detection, was revealed by conversion into biolympicenylidene with E-configuration in a regioselective manner. The complicated stereochemistry and energetics of the σ-dimers derived from C_2v symmetry and uneven spin distribution of the olympicenyl radical were revealed by the theoretical calculations, and the energetic preference of π-dimer over σ-dimer by a minute gap was disclosed. The E-biolympicenylidene, a polycyclic ene structure previously considered as reactive intermediate in the phenalenyl radical system, exhibited exceptional stability, which allowed for a detailed investigation on its singlet diradical character and physical properties by means of X-ray crystallography, UV-vis-NIR absorption/emission spectroscopy and cyclic voltammetry, and assisted by theoretical calculations. The E-biolympicenylidene showed high resistance towards both thermal and photochemical ring-cyclization reactions, which was attributed to high activation energies for the rate-determining electrocyclization operated on both disrotatory and conrotatory mode, as well as a small spin density at the bonding sites for the radical-radical coupling process.

Effects of structural variations on π-dimer formation: long-distance multicenter bonding of cation-radicals of tetrathiafulvalene analogues

The multicenter (pancake) bonding between cation-radicals of tetramethyltetraselenafulvalene, TMTSF⁺˙, tetramethyltetrathiafulvalene, TMTTF⁺˙, and bis(ethylenedithio)-tetrathiafulvalene, ET⁺,˙ was compared to that of tetrathiafulvalene, TTF⁺˙. To minimize counter-ion effects, the cation-radical salts with weakly coordinating anions (WCA), tetrakis(3,5-trifluoromethylphenyl)borate, dodecamethylcarborane and hexabromocarborane were prepared. Solid-state (X-ray and EPR) measurements revealed diamagnetic π-dimers in the TMTSF and ET salts and the separate monomers in the TTF salts with all WCAs, while TMTTF existed as a dimer in one and a monomer in two salts. The variable-temperature UV-Vis studies of these salts in solution showed that the thermodynamics of formation of the π-bonded dimers of TMTTF⁺˙ was close to that of TTF⁺˙, while TMTSF⁺˙ and ET⁺˙ showed a higher propensity for π-dimerization. These data indicated that the replacement of sulfur with heavier selenium or insertion of ethylenedithia-substituents into the TTF core increases the π-dimers' stability. Yet, computational analysis indicated that the weakly covalent component of π-bonding decreases in the order TTF > TMTTF > TMTSF > ET. The higher stability of the π-dimers of TMTSF⁺˙ and ET⁺˙ cation-radicals was related to a decrease of the electrostatic repulsion between cationic counter-parts and an increase of dispersion components in these associations.

Gas phase formation of phenalene via 10π-aromatic, resonantly stabilized free radical intermediates

1H-Phenalene can be synthesized via the reaction of the 1-naphthyl radical with methylacetylene and allene under high temperature conditions prevalent in carbon-rich circumstellar environments and combustion systems.

Dimerization of indenocorannulene radicals: imposing stability through increasing strain and curvature

One-electron reduction of bowl-shaped indenocorannulene affords a new stable dimeric dianion, as confirmed by single-crystal X-ray diffraction, NMR and UV-vis spectroscopy, and DFT calculations.

Benzo[cd]triangulene: A Spin 1/2 Graphene Fragment

How does edge modification affect spin distribution in open-shell graphene fragments? We investigated this effect by analyzing spin-delocalization in benzo[cd]-triangulene, a spin 1/2 graphene fragment composed of seven benzenoid rings fused in a hybrid zigzag/armchair fashion. Six rings of this system form the core of Clar's hydrocarbon triangulene, to which an additional ring is annulated in the zigzag region. The singly occupied molecular orbital (SOMO) of this hydrocarbon radical resembles both SOMOs of triangulene, but the spin density is distributed over the core in a nonuniform fashion. The uneven spin distribution is reflected in the reactivity-reaction with oxygen occurs selectively at a position with the highest spin density-and correlates nicely with relative stabilities of the corresponding Clar resonance structures. The spin distribution is different from that of a topologically similar compound composed of the same number of sp² carbon atoms but featuring six rings only, illustrating the impact of subtle structural changes on spin-density distribution. This compound was characterized by means of UV-vis and electron paramagnetic resonance spectroscopy, cyclic voltammetry, mass spectrometry, and X-ray crystallography. The experimental results are supported by density functional theory calculations.

Effect of Substitution on the Hysteretic Phase Transition in a Bistable Phenalenyl-Based Neutral Radical Molecular Conductor

The ability to tune the physical properties of bistable organic functional materials by means of chemistry can facilitate their development for molecular electronic switching components. The butylamine-containing biphenalenyl boron neutral radical, [Bu]₂ B, crystalline compound has recently attracted significant attention by displaying a hysteretic phase transition accompanied by simultaneous bistability in magnetic, electrical, and optical properties close to room temperature. In this report, substitutional doping was applied to [Bu]₂ B by crystallizing solid solutions of bistable [Bu]₂ B and its non-radical-containing counterpart [Bu]₂ Be. With increasing doping degree, the hysteretic phase transition is gradually suppressed in terms of reducing the height, but conserves the width of the hysteresis loop as observed through magnetic susceptibility and electrical conductivity measurements. At the critical doping level of about 6 %, the abrupt transformation of the crystal structure to that of the pure [Bu]₂ Be crystal packing was observed, accompanied by a complete collapse of the hysteresis loop. Further study of the structure-properties relationships of bistable neutral radical conductors based on the [Bu]₂ B host can be conducted utilizing a variety of biphenalenyl-based molecular conductors.

Distinguishing artificial and essential symmetry breaking in a single determinant: approach and application to the C60, C36, and C20 fullerenes

The existence of a generalized Hartree–Fock solution in C₆₀ has led to controversy on whether C₆₀ is polyradicaloid (or strongly correlated). We attempt to end the controversy with κ-OOMP2 which removes the illusion of this artificial symmetry breaking. We conclude that C₆₀ is not strongly correlated.

Reversible Solution π-Dimerization and Long Multicenter Bonding in a Stable Phenoxyl Radical

Reversible solution π-dimerization is observed in the stable neutral phenoxyl radical 2,6-bis-(8-quinolylamino)-4-(tert-butyl)phenoxyl baqp and is spectroscopically characterized. This behavior, not previously observed for π-extended phenoxyl radicals, is relevant to the formation of long multicenter bonding in the π-dimer at low temperature akin to previously reported phenalenyl radicals. Our experimental data are supported in a quantitative manner by results from density functional theory (DFT) and ab initio molecular orbital theory calculations. Our theoretical results indicate that the solution dimer features strong bonding interactions between the two phenoxyl rings but that the stability of the dimer is also related to dispersion interactions between the flanking nearly parallel quinolyl rings.

Alkali Cation Effects on Redox-Active Formazanate Ligands in Iron Chemistry

Noncovalent interactions of organic moieties with Lewis acidic alkali cations can greatly affect structure and reactivity. Herein, we describe the effects of interactions with alkali-metal cations within a series of reduced iron complexes bearing a redox-active formazanate ligand, in terms of structures, magnetism, spectroscopy, and reaction rates. In the absence of a crown ether to sequester the alkali cation, dimeric complexes are isolated wherein the formazanate has rearranged to form a five-membered metallacycle. The dissociation of these dimers is dependent on the binding mode and size of the alkali cation. In the dimers, the formazanate ligands are radical dianions, as shown by X-ray absorption spectroscopy, Mössbauer spectroscopy, and analysis of metrical parameters. These experimental measures are complemented by density functional theory calculations that show the spin density on the bridging ligands.

Hydrogen-adduction to open-shell graphene fragments: spectroscopy, thermochemistry and astrochemistry

We apply a combination of state-of-the-art experimental and quantum-chemical methods to elucidate the electronic and chemical energetics of hydrogen adduction to a model open-shell graphene fragment. The lowest-energy adduct, 1H-phenalene, is determined to have a bond dissociation energy of 258.1 kJ mol-1, while other isomers exhibit reduced or in some cases negative bond dissociation energies, the metastable species being bound by the emergence of a conical intersection along the high-symmetry dissociation coordinate. The gas-phase excitation spectrum of 1H-phenalene and its radical cation are recorded using laser spectroscopy coupled to mass-spectrometry. Several electronically excited states of both species are observed, allowing the determination of the excited-state bond dissociation energy. The ionization energy of 1H-phenalene is determined to be 7.449(17) eV, consistent with high-level W1X-2 calculations.

The nature of the multicenter bonding in π-[TCNE]22− dimer: 4c/2e, 12c/2e, or 20c/2e?

Composition of the 20c–2e bonding orbital in the π-[TCNE]₂²⁻ dimer, and the partial occupancy numbers C1, C2 and N in the 20c–2e bond.

Electronic Characterization of Reaction Intermediates: The Fluorenylium, Phenalenylium, and Benz[f]indenylium Cations and Their Radicals

Three vibrationally resolved absorption systems commencing at 538, 518, and 392 nm were detected in a 6 K neon matrix after mass-selected deposition of C13 H9 (+) ions (m/z=165) produced from fluorene in a hot-cathode discharge ion source. The benz[f]indenylium (BfI(+) : 538 nm), fluorenylium (FL9(+) : 518 nm), and phenalenylium (PHL(+) : 392 nm) cations are the absorbing molecules. Two electronic systems corresponding to neutral species are apparent at 490 and 546 nm after irradiation of the matrix with λ<260 nm photons and were assigned to the FL9 and BfI radicals, respectively. The strongest peak at 518 nm is the origin of the 2 (1) B2 ←X̃ (1) A1 absorption of FL9(+) , and the 490 nm band is the 2 (2) A2 ←X̃ (2) B1 origin of FL9. The electronic systems commencing at 538 nm and 546 nm were assigned to the 1 (1) A1 ←X̃ (1) A1 and 1 (2) A2 ←X̃ (2) A2 transitions of BfI(+) and BfI. The 392 nm band is the 1 (1) E'←X̃ (1) A1 ' transition of PHL(+). The electronic spectra of C13 H9 (+) /C13 H9 were assigned on the basis of the vertical excitation energies calculated with SAC-CI and MS-CASPT2 methods.

A Study of π-π Stacking Interactions and Aromaticity in Polycyclic Aromatic Hydrocarbon/Nucleobase Complexes

We analysed the interactions and aromaticity electron-density delocalisation observed in π-π complexes between the phenalenyl radical and acenaphthylene, and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine and uracil). Interaction energies are obtained at the M06-2X/6-311++G(2df,p) computational level for gas phase and PCM-water conditions. For both the phenalenyl radical and acenaphthylene, the complexes formed with guanine are the most stable ones. Atoms in molecules and natural bond orbital results reveal weak π-π interactions between both interacting moieties, characterized by bond critical points between C⋅⋅⋅C and C⋅⋅⋅N atoms. Nucleus independent chemical shifts (NICS) indicate the retention of the aromatic character of the monomers in the outer region of the complex. The fluctuation indexes reveal a loss of electron delocalisation upon complexation for all cases except guanine complexes. Nevertheless, the interface region shows large negative NICS values, which is not associated with an increase of the aromaticity or electron-density delocalisation, but with magnetic couplings of both molecules, leading to an unrealistic description of the aromatic behaviour in that region.

Band Structure Engineering by Substitutional Doping in Solid-State Solutions of [5-Me-PLY(O,O)]2B(1-x)Be(x) Radical Crystals

We report the substitutional doping of solid-state spiro-bis(5-methyl-1,9-oxido-phenalenyl)boron radical ([2]2B) by co-crystallization of this radical with the corresponding spiro-bis(5-methyl-1,9-oxido-phenalenyl)beryllium compound ([2]2Be). The pure compounds crystallize in different space groups ([2]2B, P1̅, Z = 2; [2]2Be, P2₁/c, Z = 4) with distinct packing arrangements, yet we are able to isolate crystals of composition [2]2B(1-x)Be(x), where x = 0-0.59. The phase transition from the P1̅ to the P2₁/c space group occurs at x = 0.1, but the conductivities of the solid solutions are enhanced and the activation energies reduced for values of x = 0-0.25. The molecular packing is driven by the relative concentration of the spin-bearing ([2]2B) and spin-free ([2]2Be) molecules in the crystals, and the extended Hückel theory band structures show that the progressive incorporation of spin-free [2]2Be in the lattice of the [2]2B radical (overall bandwidth, W = 1.4 eV, in the pure compound) leads to very strong narrowing of the bandwidth, which reaches a minimum at [2]2Be (W = 0.3 eV). The results provide a graphic picture of the structural transformations undergone by the lattice, and at certain compositions we are able to identify distinct structures for the [2]2B and [2]2Be molecules in a single crystalline phase.

Concave or convex π-dimers: the role of the pancake bond in substituted phenalenyl radical dimers

π-stacking phenalenyl radical dimers are overwhelmingly convex (a) and not concave (b) due to electron sharing at the SOMO centers.

Reversible sigma C-C bond formation between phenanthroline ligands activated by (C5Me5)2Yb

The electronic structure and associated magnetic properties of the 1,10-phenanthroline adducts of Cp*2Yb are dramatically different from those of the 2,2'-bipyridine adducts. The monomeric phenanthroline adducts are ground state triplets that are based upon trivalent Yb(III), f(13), and (phen(•-) ) that are only weakly exchange coupled, which is in contrast to the bipyridine adducts whose ground states are multiconfigurational, open-shell singlets in which ytterbium is intermediate valent ( J. Am. Chem. Soc 2009 , 131 , 6480 ; J. Am. Chem. Soc 2010 , 132 , 17537 ). The origin of these different physical properties is traced to the number and symmetry of the LUMO and LUMO+1 of the heterocyclic diimine ligands. The bipy(•-) has only one π*1 orbital of b1 symmetry of accessible energy, but phen(•-) has two π* orbitals of b1 and a2 symmetry that are energetically accessible. The carbon pπ-orbitals have different nodal properties and coefficients and their energies, and therefore their populations change depending on the position and number of methyl substitutions on the ring. A chemical ramification of the change in electronic structure is that Cp*2Yb(phen) is a dimer when crystallized from toluene solution, but a monomer when sublimed at 180-190 °C. When 3,8-Me2phenanthroline is used, the adduct Cp*2Yb(3,8-Me2phen) exists in the solution in a dimer-monomer equilibrium in which ΔG is near zero. The adducts with 3-Me, 4-Me, 5-Me, 3,8-Me2, and 5,6-Me2-phenanthroline are isolated and characterized by solid state X-ray crystallography, magnetic susceptibility and LIII-edge XANES spectroscopy as a function of temperature and variable-temperature (1)H NMR spectroscopy.