Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix

See allHide authors and affiliations

Science  16 Jul 2010:
Vol. 329, Issue 5989, pp. 299-302
DOI: 10.1126/science.1188002

This article has a correction. Please see:


Cyclobutadiene (CBD), the smallest cyclic hydrocarbon bearing conjugated double bonds, has long intrigued chemists on account of its strained geometry and electronic instability, but the parent compound and its unperturbed derivatives have thus far eluded crystallographic characterization. In this work, we immobilize a precursor, 4,6-dimethyl-α-pyrone, in a guanidinium-sulfonate-calixarene (G4C) crystalline network that confines the guest through a combination of CH-π and hydrogen-bond interactions. Ultraviolet irradiation of the crystals transforms the entrapped 4,6-dimethyl-α-pyrone into a 4,6-dimethyl-β-lactone Dewar intermediate that is sufficiently stable under the confined conditions at 175 kelvin to allow a conventional structure determination by x-ray diffraction. Further irradiation pushes the reaction to completion, enabling the structure determination of 1,3-dimethylcyclobutadiene Me2CBD. Our data support experimental observation of square-planar (Me2CBDS) and rectangular-bent (Me2CBDR) geometries in the G4C host matrix. The hydrogen-bonded, dissociated carbon dioxide coproduct interacts more strongly with Me2CBDS than with Me2CBDR.

Cyclobutadiene (CBD)—an unsaturated molecular ring of four carbon atoms, each capped by a single hydrogen atom—has intrigued chemists for the better part of a century (18). There is tremendous geometric strain associated with squeezing olefinic carbons down from their traditional 120° bonding angle to the 90° motif dictated by a closed square ring. In addition, the molecule is also the paradigm of Hückel anti-aromaticity (9), the electronic destabilization associated with networks of π electrons delocalized over an even number of alternating cyclic double bonds. The question of whether the molecule could be prepared at all has previously been answered, when it was observed spectroscopically in an Ar matrix at 8 K upon photolysis of α-pyrone (1) (4, 5). The sequence of transient intermediates leading to its formation was assigned, as outlined in Fig. 1. Attempts to isolate macroscopic quantities of the compound have generally furnished its dimer (6, 7), which, on heating, produces cyclooctatetraene (8). Derivatives of CBD have also been stabilized by appending electron-donating substituents (10) or by coordination of metal ions and metal complexes [for example, Ru(CO)3] (11) to the carbocycle. However, the molecule has eluded full structural characterization, which is a goal of particular interest for the clarification of the bonding impact of the compound’s anti-aromaticity.

Fig. 1

Reaction sequence of α-pyrone photolysis: electrocyclic opening of α-pyrone (1) leads to extremely unstable aldehyde-ketene (2) or Dewar β-lactone (3) transient precursors. Stepwise photofragmentation of 3 occurs via cyclobutenecarboxylate zwitterions (4, 5) that, by eliminating CO2, yield CBD. The unstable CBD dimerizes to form the transient tricyclic species (6) that rearranges to cyclooctatetraene (7). R = H (58) or CH3 (this paper). h, Planck’s constant; ν, frequency.

Attempts to isolate CBD in a confined, protective crystalline matrix could not furnish its crystal structure. In a seminal experiment, Cram et al. succeeded in isolating CBD by sequestering it in a hemicarcerand cage in solution, thereby inhibiting its dimerization (1). The solid-state hemicarcerand structure (Fig. 2A) (1214), with an estimated free internal volume of ~135 Å3, was most likely too large to immobilize the CBD molecule (volume V = 85 Å3) sufficiently for crystallographic analysis (15). Our initial experiments supported this assumption: Irradiation of β-cyclodextrin ⊂ α-pyrone (βCD ⊂ 1) inclusion crystals (with a free internal volume V = 253 Å3) led to crystal structures in which the disorder in the βCD cavity was quite complex (15).

Fig. 2

(A) Chemical and crystal structure in stick representation (1214) of Cram et al.’s hemicarcerand and of the G4C host matrix crystallized from an aqueous solution of tetra-p-sulfocalix[4]arene (C) and guanidinium chloride (G) at room temperature. Gray, carbon; red, oxygen. (B) Side (left) and top (right) views in stick representation of the G4C complex. Orange, carbon; purple, oxygen; white, hydrogen. (C) Crystal packing of the hexagonal H-bonded guanidinium-sulfonate sheets, stabilizing the C molecules in a cone conformation that affords a free hydrophobic calixarene internal cavity. Some hydrogen atoms have been omitted for clarity. Blue, nitrogen.

Stabilization of reactive species (1618) or dynamic supramolecular self-assemblies (1921) by encapsulation within porous crystalline networks has previously enabled characterization of the solid-state structure of such species. Likewise, the chances for success in obtaining the CBD crystal structure rely on the appropriate design of a crystalline host matrix that optimally sequesters/immobilizes the precursor, intermediate, and product molecules; free motion of guest molecules within the confined space, which leads to complex disorder in the diffraction data set, would thereby be diminished or avoided. In this context, the crystalline host matrix might encompass: (i) an optimally designed confined volume in the host, dimensionally adapted to the sequestered guest molecules, (ii) specific anchoring groups to fix the guest molecules within the confined space, and finally (iii) a propensity for high-quality diffraction data. These considerations inspired us to design a distinctly appropriate crystalline framework to use as a porous host matrix for CBD synthesis.

In contrast with Cram et al.’s hemicarcerand cage (Fig. 2A), we employed slow crystallization from aqueous solution (15) to prepare a guanidinium-sulfonate-calixarene (G4C) host-matrix (Fig. 2, B and C) of restricted internal free volume (V = 45 Å3) (15, 22) optimally available to immobilize the 4,6-dimethyl-α-pyrone Me21 molecule during assembly of the crystal lattice. The cone conformation of tetra-p-sulfocalix[4]arene (C) (22) is stabilized by the guanidinium cations (G) that form hydrogen bonds with the sulfonate moieties of C (Fig. 2 and fig. S4) (23). The inclusion of Me21 within the matrix was achieved by using a fresh aqueous solution of G, C, and Me21 to form included single crystals of G4C{Me21} with completely filled host pockets (15). The use of the 4,6-dimethyl-α-pyrone, Me21, was not arbitrary: Attempts to irradiate G4C ⊂ α-pyrone (G4C ⊂ 1) inclusion crystals led once again to crystal structures in which the disorder was very complex. In contrast, the 4-methyl group of Me21 is tightly confined in a fixed position within the G4C host matrix through three CH-π interactions with neighboring aromatic units of the calixarene pocket (15). The encapsulation of Me21 also induces an unexpectedly drastic change in the orientation of the guanidinium cations (G). Here, the structural behavior of G extends beyond its role in the free porous host of stabilizing the cone conformation of C via hydrogen bonding; in the inclusion crystals, the planar compound Me21 (dimensionally fitting within the overall superstructure of the G4C host) is supplementally sandwiched between two G groups (stacking distance: dstacking = 3.5 Å), whereas the carbonyl oxygen points outward, forming anchoring H bonds (dN–O = 2.89 Å) with a third quasi-coplanar G cation (Fig. 3A). All combined host-guest interactions are vital for the encapsulation and insulation, as well as for the low mobility of the guest molecules in the G4C host cavity. As a result, the Me21 molecule is well defined in the diffraction data set, with sharp electron-density sites. The x-ray structure of Me21 is structurally similar to previously reported fully localized canonical structures of α-pyrone 1 (24).

Fig. 3

X-ray crystallographic observation of the Me2CBD formation pathway from photolysis of 4,6-dimethyl-α-pyrone (Me21) within the pores of a G4C crystalline matrix, crystallized from an aqueous solution at room temperature. Single-crystals mounted on the diffractometer were coated with protective silicone oil and held at a temperature of 175 K. Structures in stick representation and electron-density maps are shown for (A) Me21; (B) a transient intermediate Me21′ obtained after irradiation for 25 min; (C) the Dewar valence isomer Me23 (77.3%), in equilibrium with rectangular-bent Me2CBDR (22.7%) in close proximity to a noninteracting orthogonal CO2 molecule, obtained after irradiation for 25 additional minutes; and (D) square-planar 1,3-dimethylcyclobutadiene Me2CBDS (62.7%) in van der Waals contact with the CO2 molecule, and the rectangular-bent Me2CBDR (37.3%), orthogonally oriented with respect to the plane of Me2CBDS, after irradiation for 60 additional minutes.

Upon irradiation of G4C{Me21} at wavelength λ = 320 to 500 nm, we observed separate density maxima in the electronic-density map on both sides of the Me21 ring, but one was substantially more intense than the other. In the resulting G4C{Me21′} structure (Fig. 3B), the C(3) site starts to depopulate; this disorder can be modeled with 50% density on the C(3) site and 50% density on the major off-cycle site, an apparent result of the equilibrium between the initial Me21 structure and an initial irradiation product Me21′.

Further irradiation induced conversion of G4C{Me21′} into G4C{Me23 and Me2CBDR} (here, Me2CBDR indicates the rectangular-bent conformation) (Fig. 3C). An increase in the off-plane maximum density site supported conversion of Me21 into its Dewar-β-lactone valence isomer, 1,5-dimethyl-2-oxa-3-oxobicyclo[2,2,0]hex-5-ene, Me23 (77.3%), previously predicted by theory (25) and experimentally observed (4, 5). Supplementary separate density maxima on the electronic-density map were detected on both sides of Me23, corresponding to 22.7% conversion of Me23 to Me2CBDR and CO2. The butterfly type geometry of Me23, kinetically stabilized at 175 K, exhibits bond lengths similar to those predicted by theory, with the exception of the bridging bond (dC3-C6 = 1.70 versus 1.55 Å in theory) and its direct neighbors (dC2-C3 = dC3-C4 = 1.37 versus 1.53 Å in theory), inducing a ±10% variation of the angle values (25). The –C=O…..HN– hydrogen bond (dNO = 2.89 Å) anchoring the confined Me23 to the crystal matrix and the position of the methyl group interacting inside the calixarene pocket remain constant. The free motion of Me23 within these confined conditions is highly restricted; thus, we were able to determine its crystallographic structure unequivocally by x-ray analysis. The present results suggest that under confinement in the calixarene cavity, the mechanistic pathway for the transformation of Me21 into Me23 favors the ππ* photochemical channel over the nπ* channel (26), producing the Dewar valence isomer Me23 rather than ketene 2; no α-bond cleavage intermediate was observed at any stage of the irradiation (Fig. 1). The Me2CBDR molecule presents a rectangular-bent geometry oriented at 90° relative to the C3C4C5C6 ring of Me23 in the G4C host matrix. The CO2 is orthogonally oriented with respect to the Me2CBDR ring (Fig. 4B). The C6–O1 (1.58 Å) and C2–C3 (1.57 Å) bonds point more to a non-interactive contact than to covalent bonding, as is possible in zwitterionic structure 5 (Fig. 1).

Fig. 4

Mechanistic considerations. (A) Automerization reaction of CBD including an equilibrium between two rectangular mmm ground states, proceeding through the square-shaped triplet state 4/mmm. (B) Side- (top) and top-view (bottom) stick representation of the confined square-planar Me2CBDS molecule (62.7%) in equilibrium with distorted rectangular Me2CBDR (37.3%).

Further irradiation led to the quantitative transformation of Me23 into 1,3-dimethylcyclobutadiene (Me2CBD) and CO2. Based on the diffraction data, we assigned two different geometries—square-planar (Me2CBDS, 62.7%) and rectangular-bent (Me2CBDR, 37.3%)—in the crystalline structure of G4C{Me2CBDS and Me2CBDR} under confined conditions (Fig. 3D and fig. S7). They are disposed in an orthogonal relative orientation along the axes lining the opposite alternative sulfonate moieties of C (fig. S2). The bridging bond in Me23 (dC3-C6 = 1.70 Å) is substantially longer than the edge bond C3–C6 (1.48 Å) observed in Me2CBDS, though the C6–O1 (1.48 Å) and C2–C3 (1.35 Å) bonds expand by ~0.15 to 1.61 and 1.50 Å, respectively, between Me2CBDS and CO2. These data are more indicative of a strong van der Waals contact than of covalent bonding between the confined CO2 and Me2CBDS molecules in the calixarene cavity.

The presence of CO2, sequestered via hydrogen bonding within the G4C host matrix, is clearly an important influence on the observed structures; its interaction is stronger with Me2CBDS than with the Me2CBDR isomer in the G4C host matrix environment. Through this interaction, the CO2 may stabilize Me2CBDS in the G4C host matrix (Fig. 4B), helping to account for its abundance that is a factor of 2 greater than that of the rectangular isomer Me2CBDR. The hydrogen-bonded CO2 molecule generates an asymmetry in the G4C host matrix cavity: Whereas the Me2CBDS molecule, interacting with the CO2, presents a square-planar geometry, the Me2CBDR ring shows a relaxed rectangular-bent geometry that is asymmetrically distorted, its plane slightly flipped with the methyl groups lying out of the plane (Fig. 4B and fig. S2).

The automerization reaction of CBD (Fig. 4A), previously predicted by modeling (27), is experimentally supported by the crystal structure of G4C{Me2CBDS and Me2CBDR} determined here. We observed both distinct geometries: (i) the thermodynamic square planar Me2CBDS/CO2 complex and (ii) the kinetic rectangular-bent Me2CBDR molecule, stabilized under confinement by the G4C host matrix in different orientations.

Supporting Online Material

Materials and Methods

Scheme S1

Figs. S1 to S7

Table S1


References and Notes

  1. Materials and methods are available as supporting material on Science Online.
  2. This work—conducted as part of the award “Dynamic adaptive materials for separation and sensing Microsystems” (M.B.) made under the European Heads of Research Councils and European Science Foundation European Young Investigator (EURYI) Awards scheme in 2004—was supported by funds from the Participating Organizations of EURYI and the European Comission Sixth Framework Program (see The x-ray crystallographic coordinates for structures reported in this paper have been deposited at the Cambridge Crystallographic Data Centre (CCDC) under deposition numbers CCDC 764864 to 764868. These data can be obtained free of charge from the CCDC (
View Abstract

Navigate This Article