Serendipity and the Search for Short N---I Halogen Bonds

Dec 2, 2013 - the DMAP complex with 3,5-difluoro(iodoethynyl)benzene, and halogen bond distances of 2.622, 2.676, 2.700, and 2.705 Е were observed in...
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Serendipity and the Search for Short N‑-‑I Halogen Bonds Eric Bosch* Department of Chemistry, Missouri State University, Springfield, Missouri 65804, United States ABSTRACT: The X-ray structure of the complex formed between N,Ndimethylaminopyridine (DMAP) and 1,2-bis(iodoethynyl)benzene is reported. The N---I halogen bond lengths are 2.654 and 2.662 Å, approximately 75% of the sum of the van der Waals radii. On the basis of literature precedent and electrostatic potential calculations, a series of fluorosubstituted iodophenylacetylenes were prepared and individually complexed with dimethylaminopyridine in a search for shorter halogen bonds. A N---I halogen bond distance of 2.680 Å was observed in the DMAP complex with 3,5-difluoro(iodoethynyl)benzene, and halogen bond distances of 2.622, 2.676, 2.700, and 2.705 Å were observed in the complex of 4fluoro(iodoethynyl)benzene with DMAP. These N---I bond distances range from 74.3 to 76.6% of the sum of the van der Waals radii.

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A portion of these crystals were redissolved in dichloromethane and placed on a short silica column, and the 1,2-bis(iodoethynyl)benzene was eluted with a 10:1 mixture of hexanes and ethylacetate as an almost colorless oil. 1H NMR δ (300 Mz, CDCl3) 7.42 (dd, J = 3.4, 5.8 Hz, 2H), 7.26 (dd, J = 3.4, 5.8 Hz, 2H). 13C NMR δ 132.50, 128.33, 126.75, 92.35, 69.67, 11.13. Complex between N,N-Dimethylaminopyridine and 1,2-Bis(iodoethynyl)benzene, A. The complex was intentionally formed in quantitative yield when the purified bis-iodoalkyne was mixed with 2 equiv of N,N-dimethylaminopyridine in dichloromethane solution. Synthesis of 4-Fluoro-1-(iodoethynyl)benzene, 2. 4-Fluorophenylacetylene (125 mg, 1.05 mmol) was reacted with iodine (315 mg, 1.24 mmol) in the presence of N,N-dimethylamino pyridine (156 mg, 1.28 mmol) in dichloromethane (3 mL) at room temperature.5 After 16 h the reaction was treated with aqueous ammonium thiosulfate which bleached the orange/brown color. The organic layer was diluted with dichloromethane (10 mL), separated, and dried over sodium sulfate. The solution was filtered, and the solvent was removed under vacuo. The crude product was purified by flash chromatography with hexanes as eluant yielding a colorless oil (182 mg, 71 %). 1H NMR δ (300 Mz, CDCl3) 7.41 (mdd, J = 5.6, 9.2 Hz, 2H), 7.00 (mt, J = 9.2 Hz, 2H); 13 C NMR δ 162.74 (d, JFC = 249.1 Hz), 134.24 (d, JFC = 8.8 Hz), 119.44 (d, JFC = 3.6 Hz), 115.54 (d, JFC = 21.0 Hz), 92.96, 6.06 (C−I); 19 F NMR δ −109.66. Complex between N,N-Dimethylaminopyridine and 4-Fluoro-1(iodoethynyl)benzene, B. N,N-Dimethylaminopyridine and 4-fluoro1-(iodoethynyl)benzene (0.01 mmol each) were added to a small screw cap vial and dissolved with the minimum amount of dichloromethane without heating. The dichloromethane was allowed to slowly evaporate over several days to form a homogeneous mass of blocklike crystals. 1H NMR δ (300 Mz, CDCl3) 8.22 (d, J = 5.1 Hz, 2H, dmap), 7.43 (m, 2H), 7.01 (m, 2H), 6.50 (d, J = 5.1 Hz, 2H, dmap), 3.01 (s, 6H, dmap). Synthesis of 3,5-Fluoro-1-(iodoethynyl)benzene, 3. 3,5-Difluorophenylacetylene (210 mg, 1.52 mmol) was reacted with iodine (445 mg, 1.75 mmol) in the presence of N,N-dimethylamino pyridine (209 mg, 1.71 mmol) in dichloromethane (5 mL) at room temperature.5

INTRODUCTION Despite the fact that halogen bonding can be traced back to 1863,1 the interaction has only become recognized as a valuable tool in crystal engineering over the past two decades.2,3 In this article we describe the crystal structure of a halogen bonded complex that we did not intend to form and then describe how this led to an exploration of other extremely short N---I halogen bonds. The specific application of iodoalkynes as halogen bond donors is best known from the elegant synthetic application to the solid-state formation of polyacetylenes based on halogen bonding ordering of dialkynes in the solid state.4 We were interested in preparing a series of bis-iodoalkynes for a crystal engineering study and used the synthetic procedure published by Meng, et al.5 We were surprised when NMR analysis of the crude crystalline product isolated on preparation of 1,2bis(iodoethynyl)benzene indicated that this product was in fact a 2:1 complex with N,N-dimethylaminopyridine. In this paper we report the molecular structure of that complex and the beautiful interlocked three-dimensional crystal packing. This will be followed by the preliminary results of the search for even stronger N---I halogen bonds using fluorinated iodoethynylbenzenes.

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EXPERIMENTAL SECTION

Synthesis. Synthesis of 1,2-Bis(iodoethynyl)benzene, 1. 1,2Bis(ethynyl)benzene (0.280 g) was reacted with iodine (1.36 g) in the presence of N,N-dimethylamino pyridine (0.564 g) in dichloromethane (8 mL) at 40 °C for 24 h.5 The dark brown reaction mixture was diluted with more dichloromethane (10 mL) and treated with aqueous ammonium thiosulfate until the color bleached. The organic layer was separated and dried over sodium sulfate. The solution was filtered and the solvent was removed under a vacuum. The crude product was diluted in 3 mL of dichloromethane and 2 equiv of N,Ndimethylamino pyridine was added. The mixture was heated to form a clear brown solution. After two days, large colorless blocklike crystals of a 1:2 complex had formed. 1H NMR δ (300 Mz) CDCl3) 8.20 (d, J = 6.6 Hz, 4 H, dmap), 7.41 (dd, J = 3.0, 5.7 Hz, 2H), 7.26 (dd, J = 3.0, 5.7 Hz, 2H), 6.49 (d, J = 6.6 Hz, 4H, dmap), 3.00 (s, 12H, dmap). © 2013 American Chemical Society

Received: August 14, 2013 Revised: November 26, 2013 Published: December 2, 2013 126

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After 16 h the organic layer was diluted with dichloromethane (10 mL) and treated with aqueous ammonium thiosulfate. The organic layer was separated and dried over sodium sulfate. The solution was filtered and the solvent was removed under vacuo. The crude product was purified by flash chromatography with hexanes as eluant yielding a pale yellow oil (233 mg, 58 %). 1H NMR δ (300 Mz, CDCl3) 6.94 (md, J = 6 Hz, 2H), 6.80 (mt, J = 9 Hz, 1H); 13C NMR δ 162.47 (dd, JFC = 247.5, 13.2 Hz), 125.84 (t, JFC = 11.7 Hz), 115.36 (dd, JFC = 19.1, 8.1 Hz), 105.21 (t, JFC = 25.6 Hz), 91.81 (t, JFC = 3.6 Hz), 10.22(C−I); 19F NMR δ −109.31. Complex between N,N-Dimethylaminopyridine and 3,5-Fluoro1-(iodoethynyl)benzene, C. N,N-Dimethylaminopyridine and 3,5fluoro-1-(iodoethynyl)benzene (0.01 mmol each) were added to a small screw cap vial and dissolved with the minimum amount of dichloromethane without heating. The dichloromethane was allowed to evaporate over several days to form homogeneous plate-like crystals. 1 H NMR δ (300 Mz, CDCl3) 8.20 (dd, J = 1.7, 5.1 Hz, 2H, dmap), 6.92 (m, 2H), 6.79 (m, 1H), 6.50 (dd, J = 1.7, 5.1 Hz, 2H, dmap), 3.00 (s, 6H, dmap). X-ray Structure Determination. For each complex a single crystal was mounted on a Kryoloop using viscous hydrocarbon oil. Data were collected using a Bruker Apex1 CCD diffractometer equipped with Mo Kα radiation with λ = 0.71073 Å. Data collection at 100 K was facilitated by use of a Kryoflex system with an accuracy of ±1 K. Initial data processing was carried out using the Apex II software suite.6 Structures were solved by direct methods using SHELXS-97 and refined against F2 using SHELXL-20137 using the program XSeed as a graphical interface.8 Hydrogen atoms were located in the difference maps but were placed in idealized positions and refined with a riding model. Crystallographic details are collected in Table 1.

formula weight crystal dim. (mm3) crystal system space group a (Ǻ ) b (Ǻ ) c (Ǻ ) α (deg) β (deg) γ (deg) Z V (Ǻ 3) ρcalcd (mg m−3) T (K) μ (mm−1) reflections/ unique data/restraints/ parameters goodness of fit R1/wR2 R1/wR2 (all data)

A, 1·(N,N-dmap)2

B, 2·(N,N-dmap)

C, 3·(N,N-dmap)

C10H4I2· 2(C7H10N2) 311.14 0.45 × 0.25 × 0.15

C8H4FI·C7H10N2

triclinic P1̅ 9.8722(5) 10.1925(5) 13.8977(6) 110.3020(10) 90.0060(10) 112.9040(10) 4 1193.27(10) 1.732 100 2.653 14321/5293

368.18 0.31 × 0.20 × 0.20 monoclinic C2/c 25.481(8) 19.4100(8) 24.5312(10) 90 121.2270(1) 90 28 10365.7(7) 1.651 100 2.161 66248/11538

C8H3F2I· C7H10N2 386.17 0.40 × 0.20 × 0.05 orthorhombic Pbca 7.5059(5) 12.9763(9) 30.407(2) 90 90 90 8 2961.6(3) 1.732 100 2.175 34394/3289

5293/0/275

11538/0/611

3289/0/183

1.065 0.0258/0.0579 0.0334/0.0615

1.084 0.0260/0.0486 0.0331/0.0508

1.060 0.0302/0.0516 0.0458/0.0564

RESULTS AND DISCUSSION

This project began when we prepared a few bis-iodoalkynes as part of an, as yet unpublished, crystal engineering study. We were surprised to find that 1,2-bis(iodoethynyl)benzene cocrystallized with dimethylaminopyridine from the crude reaction product as established by 1H NMR analysis. A similar reaction of 1,4-diethynylbenzene yielded uncomplexed 1,4bis(iodoethynyl)benzene. Naturally, we decided to investigate the structure of the cocrystals we isolated. Complex between 1,2-Bis(iodoethynyl)benzene and N,N-Dimethylaminopyridine, A. The single crystal X-ray structure of the 1:2 complex is shown in Figure 1A with the asymmetric unit labeled. The two halogen bonds are almost linear with C1−I−N1 and C10−I2−N3 bond angles of 174.92 and 174.17°, respectively. The nitrogen−iodine distance of 2.654 and 2.662 Å for I1−N1 and I2−N3 respectively are 75.2 and 75.4% of the sum of the van der Waals radii. The iodine atoms are above the plane of the N,N-dimethylaminopyridine rings to which they are bound with angles I1−N1−C13 and I2−N3−C20 of 160.87 and 163.84° respectively. The N,N-dimethylaminopyridine molecules in the complex are almost parallel to each other with a tweezer-like orientation and a centroid−centroid distance of 7.099 Å. This distance between the two N,N-dimethylaminopyridine rings accommodates a N,N-dimethylaminopyridine molecule from another 2:1 complex with a reversed orientation for a good electronic interaction. This amino pyridine ring is slightly asymmetrically π-stacked. Thus the closest interaction between the entrapped N,N-dimethylaminopyridine molecule and one of the two other N,N-dimethylaminopyridine rings is about 3.45 Å, whereas the distance to the other pyridine is about 3.69 Å. This interaction results in a series of interlocked complexes where the pyridines are all π-stacked. This is illustrated in the space filling model shown in Figure 1B. These interlocked complexes then form two-dimensional sheets with the benzene rings fitting together like a zipper as shown in Figure 2A. There are no exceptionally close interactions between adjacent benzene rings. The two-dimensional sheets fit neatly on top of each other as shown in Figure 2B. There is a weak C−H---benzene interaction between the N,N-dimethylaminopyridine rings and the benzene ring with one H of each pyridine positioned above the centroid of the benzene ring with H18-benzene centroid and H12-benzene centroid distances of 2.661 and 2.752 Å respectively. Rather than intermolecular forces controlling the three-dimensional structure, it is the close packing of appropriately sized one-dimensional strands of the interlocked molecular complexes in both of the other two dimensions that controls the three-dimensional structure. On examination of N---I halogen bonds reported in the Cambridge Crystallographic Database,9 we were surprised to discover that the halogen bond distance of 2.622 Å is in fact shorter that any N---I halogen bond reported to date. A short N---I interaction of 2.633 was evident in the structure of trimethylsilylamino triphenylphosphonium iodocyanide.10 Two of the next three shortest N---I bond distances in the database were reported for complexes between the halogen bond acceptor N,N-dimethylaminopyridine. The N---I distance for the complex with 1,4-diiodotetrafluorobenzene is 2.667 Å11 and that with iodopentafluorobenzene is 2.693 Å.12 The N---I bond distance in the complex between (S)-(−)-(1-(dimethylamino)ethyl)ferrocene and 1,4-diiodoperfluorobutane is 2.689 Å.13 Interestingly three of the 11 shortest N---I bond distances

Table 1. Crystallographic Data for Complexes A−C formula

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XPRD Determination. The bulk product was ground in a glass mortar and pestle and packed in a clear plexiglass holder. The data were collected using a Bruker D8 Discover X-ray diffractometer at room temperature with a 2θ range from 10 deg to 40 deg using 0.05 deg increments. Simulated XPRD spectra were obtained using Mercury software from CCDC. 127

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Figure 1. (A) Oblique view of the 1:2 complex, A, formed between 1,2-bis(iodoethynyl)benzene and N,N-dimethylaminopyridine with thermal ellipsoids drawn at the 50% probability level. (B) Space-filling side view of the interaction between two of the 1:2 halogen bonded complexes formed between 1,2-bis(iodoethynyl)benzene and N,N-dimethylaminopyridine.

Figure 2. (A) View of a portion of the two-dimensional sheet of interlocked 1:2 complexes formed between 1,2-bis(iodoethynyl)threedimensionalbenzene and N,N-dimethylaminopyridine. (B) View along (0 1 1) showing packing between the two-dimensional layers of the 1:2 complex formed between 1,2-bis(iodoethynyl)three-dimensionalbenzene and N,N-dimethylaminopyridine.

correspond to N-iodoalkyne halogen bonds.14−16 There are currently a total of 17 iodoalkyne structures in the Cambridge Database.15,17,18 Clearly, the effect of the sp-C on the halogen bond donor properties of the attached iodine is great, and we wondered if we could increase that halogen bond donor ability by adding electron-withdrawing fluoro substitutents to the phenyl ring. This idea was based on several elegant halogen bonding studies. For example, Bruce et al. studied the halogen bonding between a series of differentially fluorinated iodobenzenes and N,Ndimethylaminopyridine.12 In this study, Bruce clearly demonstrated that progressive addition of fluorine substituents onto the iodobenzene ring resulted in a uniform decrease in the N---I bond distance. A similar effect was reported in the studies of Pennington et al., who reported and compared the structures of 1,4-diiodobenzene and tetrafluoro-1,4-diiodobenzene with a variety of N-acceptors.19 In all cases, the N---I bond distances were much shorter for the perfluorinated diiodoarene. Accordingly, we first evaluated the extent of the positive hole on the iodine atom in a series of readily available fluorinated iodophenylacetylenes using the Spartan Molecular Modeling program.20 The ground state equilibrium geometry and electrostatic potential was calculated using the Hartree−Fock method with the 3-21G basis set assuming vacuum. The results are compared to pentafluoroiodobenzene and perfluoro-1,4diiodobutane in Scheme 1. On the basis of these calculations, we expected the mono and difluorinated iodophenylacetylenes 2 and 3 to be stronger halogen bond donors than 1,2bisiodoethynylbenzene and comparable pentafluoroiodobenzene and 1,4-diiodoperfluorobutane possibly resulting in shorter halogen bond distances with N,N-dimethylaminopyridine than we observed in complex A.

Scheme 1. Electrostatic Potential of Various Halogen Bonding Donors20

Accordingly we prepared representative iodoalkynes 2 and 3 to evaluate the possibility that, on complexation with N,Ndimethylaminopyridine, these would yield even shorter halogen bond distances than previously observed. On mixing 4-fluoro-1(2′-iodoethynyl)benzene, 2, and N,N-dimethylaminopyridine in dichloromethane at room temperature and allowing the solvent to slowly evaporate a homogeneous mass of crystals formed. X-ray analysis of a single crystal revealed a complex arrangement with four independent iodoalkyne-dimethylaminopyridine complexes as shown in Figure 3. One of the complexes lies on a C2 axis. Repeated attempts to grow crystals from different solvents and under different conditions did not yield crystal suitable for X-ray analysis. The N---I bond distances are 2.700, 2.676, 2.705, and 2.622 Å for I1−N1, I2−N3, I3−N5, and I4−N7 respectively with C− I−N bond angles of 176.37, 174.86, 174.29, and 180°. Similar, mixing 3,5-difluoro-1-(2′-iodoethynyl)benzene, 4, and N,Ndimethylaminopyridine in dichloromethane at room temper128

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Figure 3. Asymmetric unit of the complex B formed between 4-fluoro1-(2′-iodoethynyl)benzene, 4, and N,N-dimethylaminopyridine with thermal ellipsoids drawn at the 50% probability level.

ature and allowing the solvent to slowly evaporate yielded a homogeneous batch of plate-like crystals. X-ray analysis of a single crystal revealed the iodoalkyne-dimethylaminopyridine complex shown in Figure 4.

Figure 5. (A) Simulated XPRD pattern experimental XPRD pattern of complex A (1·2(C7H10N2), compared to the experimental XPRD shown in (B).

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AUTHOR INFORMATION

Corresponding Author

*Phone: 417-836-4277. FAX: 417-836-5507. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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Figure 4. Asymmetric unit of the complex, C, formed between 3,5difluoro-1-(2′-iodoethynyl)benzene, 4, and N,N-dimethylaminopyridine with thermal ellipsoids drawn at the 50% probability level.

ACKNOWLEDGMENTS The Missouri State University Provost Incentive Fund funded the purchase of the X-ray diffractometer. I thank Jerrod R. McCleod for his initial work on the synthesis of bis(iodoethynyl)benzenes.

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Despite the significantly more positive σ-hole on the iodine atom in the difluoro derivative (Scheme 1), the halogen bond defined by a distance, N1---I1, of 2.684 Å and angles C1−N1− I1 and C11−N1−I1 of 175.11 and 167.02° respectively was similar to the others reported in this manuscript. The identity between the single crystal structures and the bulk material obtained for complex A, 1·2(C7H10N2), was confirmed by comparison of the predicted XPRD pattern21 simulated from the single crystal X-ray analysis with the experimental XPRD pattern obtained from the bulk material as shown in Figure 5. Similar analysis of compounds B and C was unsuccessful and gave variable results primarily due to decomposition during sample preparation.

REFERENCES

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CONCLUSIONS The N---I halogen bond distances reported in this manuscript for a series of halogen bonded complexes between iodoalkynes and N,N-dimethylaminopyridine are marginally shorter than previously reported halogen bonded complexes. We did not, however, observe the expected reduction in N---I bond distances on addition of electron withdrawing fluorine substituents to the iodoethynyl compounds. It is clear that the hybridization of the carbon atom to which the iodine atom is attached has a profound effect on the extent of the σ-hole on iodine and the halogen bond donor strength. This is a consequence of the higher s-character of the orbitals and the higher electronegativity of sp-C’s.22 129

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(17) (a) Goroff, N. S.; Curtis, S. M.; Webb, J. A.; Fowler, F. W.; Lauher, J. W. Org. Lett. 2005, 7, 1891. (b) Wilhelm, C.; Boyd, S. A.; Chawda, S.; Fowler, F. W.; Goroff, N. S.; Halada, G. P.; Grey, C. P. J. Am. Chem. Soc. 2008, 130, 4415. (18) Sun, A.; Lauher, J. W.; Goroff, N. S. Science 2006, 312, 1030. (19) Walsh, R. B.; Padgett, C. W.; Metrangolo, P.; Resnati, G.; Hanks, T. W.; Pennington, W. T. Cryst. Growth Des. 2001, 1, 165. (20) Spartan ’10 running on a Windows platform, as provided by Wavefunction, Inc., 18401 Von Karman Ave., Suite 370, Irvine, CA 92612 (www.wavefun.com). (21) Macrae, C. F.; Bruno, I. J.; Chisholm, J. A.; Edgington, P. R.; McCabe, P.; Pidcock, E.; Rodriguez-Monge, L.; Taylor, R.; van de Streek, J.; Wood, P. A. J. Appl. Crystallogr. 2008, 41, 466−470. (22) (a) Huheey, J. E. J. Phys. Chem. 1966, 70, 2086. (b) Advanced Organic Chemistry, Part A: Structure and Mechanism, 4th ed.; Carey, F. A.; Sundberg, R. J.; Kluwer Academic/Plenum Publishers: New York, 2000.

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