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Acta Crystallogr Sect E Struct Rep Online. 2008 June 1; 64(Pt 6): o1054.
Published online 2008 May 10. doi:  10.1107/S1600536808013482
PMCID: PMC2961599

tert-Butyl 2-(dihydroxyboryl)pyrrole-1-carboxylate

Abstract

In the title compound, C9H14BNO4, the carbonyl and boronic acid groups are essentially coplanar with the pyrrole ring and the boronic acid group has an exo-endo conformation. The exo-oriented OH is engaged in an intra­molecular O—H(...)O inter­action, while the endo-oriented one is involved in inter­molecular hydrogen bonding to form centrosymmetric dimers. A supra­molecular assembly is achieved through inter­actions involving the tert-butyl groups, forming infinite chains along the crystallographic b axis. There are, in addition, face-to-face and center-to-edge stacking inter­actions [distance between the pyrrole ring centroid and an N atom from a neighbouring mol­ecule = 3.369 (8) Å].

Related literature

For related literature, see: Dabrowski et al. (2006 [triangle]); Parry et al. (2002 [triangle]); Saygili et al. (2004 [triangle]); Seminario et al. (1998 [triangle]); Thompson et al. (2005 [triangle]); Wang et al. (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1054-scheme1.jpg

Experimental

Crystal data

  • C9H14BNO4
  • M r = 211.02
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1054-efi3.jpg
  • a = 12.9179 (12) Å
  • b = 9.5885 (7) Å
  • c = 17.5811 (15) Å
  • V = 2177.7 (3) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 100 (2) K
  • 0.71 × 0.34 × 0.22 mm

Data collection

  • Kuma KM4 CCD diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction 2005 [triangle]) T min = 0.95, T max = 0.98
  • 19290 measured reflections
  • 2713 independent reflections
  • 1911 reflections with I > 2σ(I)
  • R int = 0.021

Refinement

  • R[F 2 > 2σ(F 2)] = 0.031
  • wR(F 2) = 0.076
  • S = 0.96
  • 2713 reflections
  • 193 parameters
  • All H-atom parameters refined
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2005 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2005 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg, 1999 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536808013482/bg2173sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808013482/bg2173Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the Aldrich Chemical Company through the donation of chemicals and equipment and by the Warsaw University of Technology. The X-ray measurements were undertaken in the Crystallographic Unit of the Physical Chemistry Laboratory at the Chemistry Department of the University of Warsaw.

supplementary crystallographic information

Comment

Nitrogen-containing boronic acids are the object of interest to many chemists because of their application as potential saccharide sensors (Wang et al., 2002). However, no crystal structure of any boronic acid containing a pyrrole ring has been elucidated to date. The only crystal data concerning nitrogen-containing heterocyclic boronic acids involve some pyrydine (Parry et al., 2002), (Thompson et al., 2005), (Dabrowski et al., 2006) and pyrimidine (Saygili et al., 2004) derivatives.

The molecular structure of the title compound C9H14BO4N (I) is shown in Fig. 1. The carbonyl and boronic acid groups are essentially coplanar with the pyrrole ring [torsion angles O3—C5—N1—C1 = -1.31 (1)° and N1—C1—B1—O1 = -2.8 (2)° respectively]. The conformation between C9 from the tert-butyl- and the carbonyl groups is antiperiplanar. The boronic acid group has an exo-endo conformation. The exo-oriented OH is engaged in an intramolecular O—H···O interaction with O3. The endo- oriented one, instead, is involved into intermolecular hydrogen bonding to form centrosymmetric dimers (Fig. 2). The supramolecular assembly is achieved through interactions involving tert-butyl groups, forming infinite chains along the crystallographic b axis. Examination of the crystal packing reveals the presence of face to face, center to edge stacking (FFCE) (Seminario et al., 1998). These interactions are represented by a relatively short distance (3.369 (8) Å) between the pyrrole ring centroid and the nitrogen atom from neighbouring molecules (Fig. 3).

Experimental

N-tert-butoxycarbonyl-pyrrole-2-boronic acid was obtained from Aldrich, crystallized from tetrahydrofurane and dried in air.

Refinement

All of hydrogen atoms were located geometrically and their positions were refined while temperature factors were not. The maximum electron-density peak in the final difference map is 0.80 Å from atom C1.

Figures

Fig. 1.
The molecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids for all non-H atoms are drawn at the 50% probability level.
Fig. 2.
The hydrogen-bonding pattern for (I). Hydrogen bonds are shown as dashed lines.
Fig. 3.
The crystal packing for (I), showing π-π interactions as dotted lines [Symmetry codes: (i) -1/2 + x, 1.5 - y, 1 - z; (ii) 0.5 - x, -1/2 + y, z].

Crystal data

C9H14BNO4F000 = 896
Mr = 211.02Dx = 1.287 Mg m3
Orthorhombic, PbcaMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 19290 reflections
a = 12.9179 (12) Åθ = 2.8–28.7º
b = 9.5885 (7) ŵ = 0.10 mm1
c = 17.5811 (15) ÅT = 100 (2) K
V = 2177.7 (3) Å3Prismatic, colourless
Z = 80.71 × 0.34 × 0.22 mm

Data collection

Kuma KM4 CCD diffractometer2713 independent reflections
Radiation source: fine-focus sealed tube1911 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.021
Detector resolution: 8.6479 pixels mm-1θmax = 28.7º
T = 100(2) Kθmin = 2.8º
ω scanh = −17→17
Absorption correction: multi-scan(CrysAlis RED; Oxford Diffraction 2005)k = −12→12
Tmin = 0.95, Tmax = 0.98l = −23→23
19290 measured reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullAll H-atom parameters refined
R[F2 > 2σ(F2)] = 0.031  w = 1/[σ2(Fo2) + (0.0461P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.076(Δ/σ)max = 0.001
S = 0.97Δρmax = 0.26 e Å3
2713 reflectionsΔρmin = −0.19 e Å3
193 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0033 (7)
Secondary atom site location: difference Fourier map

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O10.54350 (6)0.63771 (7)0.45212 (4)0.02586 (19)
O20.40336 (6)0.64180 (8)0.53731 (4)0.02619 (19)
O30.60617 (5)0.83554 (7)0.36263 (4)0.02260 (18)
O40.56150 (5)1.04637 (7)0.31656 (4)0.02186 (18)
N10.46192 (6)0.95162 (8)0.40642 (4)0.01800 (19)
C10.42176 (8)0.85423 (10)0.45945 (5)0.0187 (2)
C20.33504 (8)0.91604 (11)0.48868 (6)0.0223 (2)
C30.32126 (8)1.05007 (11)0.45569 (6)0.0242 (2)
C40.39900 (8)1.06957 (10)0.40571 (6)0.0218 (2)
C50.54985 (8)0.93691 (9)0.36119 (5)0.0186 (2)
C60.64575 (8)1.04984 (10)0.25803 (5)0.0225 (2)
C70.63032 (10)0.93008 (12)0.20274 (6)0.0285 (3)
C80.75028 (9)1.04896 (12)0.29709 (6)0.0269 (2)
C90.62477 (10)1.18889 (12)0.22011 (7)0.0304 (3)
B10.46066 (9)0.70564 (12)0.48297 (6)0.0204 (2)
H1O0.5763 (11)0.6964 (15)0.4187 (8)0.056 (4)*
H2O0.4234 (12)0.5504 (17)0.5442 (8)0.060 (5)*
H20.2915 (8)0.8741 (11)0.5269 (5)0.018 (2)*
H30.2680 (9)1.1122 (12)0.4668 (6)0.028 (3)*
H40.4168 (8)1.1463 (11)0.3729 (6)0.020 (3)*
H7A0.5580 (11)0.9321 (12)0.1830 (7)0.038 (3)*
H7B0.6429 (9)0.8387 (12)0.2253 (6)0.029 (3)*
H7C0.6788 (9)0.9424 (11)0.1603 (6)0.029 (3)*
H8A0.7576 (9)1.1342 (13)0.3317 (7)0.038 (3)*
H8B0.7629 (9)0.9613 (12)0.3252 (6)0.031 (3)*
H8C0.8046 (10)1.0547 (12)0.2579 (7)0.036 (3)*
H9A0.6288 (8)1.2649 (12)0.2567 (7)0.034 (3)*
H9B0.5551 (10)1.1878 (13)0.1981 (6)0.040 (3)*
H9C0.6768 (9)1.2037 (12)0.1802 (7)0.039 (3)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0238 (4)0.0218 (4)0.0320 (4)0.0014 (3)0.0056 (3)0.0085 (3)
O20.0255 (4)0.0253 (4)0.0278 (4)−0.0001 (3)0.0051 (3)0.0059 (3)
O30.0227 (4)0.0186 (4)0.0265 (4)0.0021 (3)0.0044 (3)0.0032 (3)
O40.0240 (4)0.0180 (4)0.0235 (4)0.0007 (3)0.0031 (3)0.0038 (3)
N10.0172 (4)0.0178 (4)0.0190 (4)0.0001 (3)−0.0011 (3)−0.0005 (3)
C10.0181 (5)0.0220 (5)0.0159 (4)−0.0040 (4)−0.0023 (4)−0.0013 (4)
C20.0188 (5)0.0286 (6)0.0194 (5)−0.0018 (4)−0.0009 (4)−0.0039 (4)
C30.0195 (5)0.0264 (6)0.0267 (5)0.0049 (5)−0.0040 (4)−0.0071 (4)
C40.0220 (5)0.0194 (5)0.0239 (5)0.0029 (4)−0.0061 (4)−0.0022 (4)
C50.0203 (5)0.0170 (5)0.0186 (5)−0.0027 (4)−0.0026 (4)−0.0011 (4)
C60.0245 (6)0.0228 (5)0.0203 (5)−0.0023 (4)0.0036 (4)0.0031 (4)
C70.0341 (7)0.0281 (6)0.0233 (6)−0.0037 (5)0.0027 (5)−0.0002 (4)
C80.0258 (6)0.0270 (6)0.0278 (6)−0.0045 (5)0.0011 (5)0.0047 (5)
C90.0339 (7)0.0270 (6)0.0304 (6)−0.0027 (5)0.0012 (5)0.0087 (5)
B10.0193 (6)0.0230 (6)0.0190 (5)−0.0038 (5)−0.0027 (5)−0.0013 (5)

Geometric parameters (Å, °)

O1—B11.3652 (13)C3—H30.931 (12)
O1—H1O0.917 (15)C4—H40.963 (10)
O2—B11.3547 (13)C6—C81.5149 (15)
O2—H2O0.922 (16)C6—C91.5151 (14)
O3—C51.2143 (11)C6—C71.5176 (14)
O4—C51.3191 (11)C7—H7A0.996 (13)
O4—C61.4981 (12)C7—H7B0.976 (11)
N1—C41.3928 (12)C7—H7C0.981 (12)
N1—C51.3937 (12)C8—H8A1.023 (13)
N1—C11.4178 (12)C8—H8B0.989 (12)
C1—C21.3676 (14)C8—H8C0.985 (13)
C1—B11.5665 (15)C9—H9A0.973 (12)
C2—C31.4211 (15)C9—H9B0.980 (13)
C2—H20.964 (10)C9—H9C0.983 (12)
C3—C41.3474 (15)
B1—O1—H1O108.9 (9)O4—C6—C7109.13 (8)
B1—O2—H2O111.6 (9)C8—C6—C7113.78 (9)
C5—O4—C6120.61 (7)C9—C6—C7111.13 (9)
C4—N1—C5123.55 (8)C6—C7—H7A109.4 (7)
C4—N1—C1109.10 (8)C6—C7—H7B113.4 (6)
C5—N1—C1127.35 (8)H7A—C7—H7B108.4 (10)
C2—C1—N1105.15 (8)C6—C7—H7C108.2 (6)
C2—C1—B1123.90 (9)H7A—C7—H7C109.3 (9)
N1—C1—B1130.94 (9)H7B—C7—H7C108.1 (9)
C1—C2—C3109.95 (9)C6—C8—H8A110.3 (7)
C1—C2—H2124.0 (6)C6—C8—H8B112.2 (7)
C3—C2—H2126.0 (6)H8A—C8—H8B111.5 (9)
C4—C3—C2107.35 (9)C6—C8—H8C108.5 (7)
C4—C3—H3126.8 (7)H8A—C8—H8C107.8 (9)
C2—C3—H3125.9 (7)H8B—C8—H8C106.2 (9)
C3—C4—N1108.44 (9)C6—C9—H9A111.0 (7)
C3—C4—H4132.4 (6)C6—C9—H9B109.2 (7)
N1—C4—H4119.1 (6)H9A—C9—H9B108.6 (10)
O3—C5—O4125.51 (9)C6—C9—H9C108.6 (7)
O3—C5—N1123.88 (8)H9A—C9—H9C109.1 (10)
O4—C5—N1110.60 (8)H9B—C9—H9C110.4 (9)
O4—C6—C8109.64 (8)O2—B1—O1119.54 (10)
O4—C6—C9101.06 (8)O2—B1—C1114.96 (9)
C8—C6—C9111.34 (9)O1—B1—C1125.49 (9)
C4—N1—C1—C20.54 (10)C4—N1—C5—O3178.49 (9)
C5—N1—C1—C2−179.63 (8)C1—N1—C5—O3−1.32 (14)
C4—N1—C1—B1179.79 (9)C4—N1—C5—O4−2.55 (12)
C5—N1—C1—B1−0.38 (15)C1—N1—C5—O4177.64 (8)
N1—C1—C2—C3−0.70 (10)C5—O4—C6—C8−64.93 (11)
B1—C1—C2—C3179.99 (9)C5—O4—C6—C9177.47 (8)
C1—C2—C3—C40.62 (11)C5—O4—C6—C760.31 (11)
C2—C3—C4—N1−0.26 (11)C2—C1—B1—O2−1.97 (14)
C5—N1—C4—C3179.99 (8)N1—C1—B1—O2178.91 (9)
C1—N1—C4—C3−0.17 (10)C2—C1—B1—O1176.28 (10)
C6—O4—C5—O33.95 (14)N1—C1—B1—O1−2.85 (16)
C6—O4—C5—N1−174.99 (7)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O···O30.917 (15)1.704 (15)2.5941 (10)162.9 (13)
O2—H2O···O1i0.922 (16)1.855 (17)2.7728 (11)173.7 (13)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BG2173).

References

  • Brandenburg, K. (1999). DIAMOND Crystal Impact GbR, Bonn, Germany.
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  • Oxford Diffraction (2005). CrysAlis CCD andCrysAlis RED Oxford Diffraction Ltd., Abingdon, Oxfordshire, England.
  • Parry, P. R., Changsheng, W., Batsanov, A. S., Bryce, M. R. & Tarbit, B. (2002). J. Org. Chem.67, 7541–7543. [PubMed]
  • Saygili, N., Batsanov, A. S. & Bryce, M. R. (2004). Org. Biomol. Chem.2, 852–853. [PubMed]
  • Seminario, J. M., Zacarias, A. G. & Tour, J. M. (1998). J. Am. Chem. Soc 120, 3970–3974.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
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  • Wang, W., Gao, X. & Wang, B. (2002). Curr. Org. Chem.6, 1285–1317.

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