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Acta Cryst. (2008). E64, o1054    [ doi:10.1107/S1600536808013482 ]

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

T. Klis and J. Serwatowski

Abstract top

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].

Comment top

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).

Related literature top

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

Experimental top

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

Refinement top

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.

Computing details top

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

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. The hydrogen-bonding pattern for (I). Hydrogen bonds are shown as dashed lines.
[Figure 3] 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].
tert-Butyl 2-(dihydroxyboryl)pyrrole-1-carboxylate top
Crystal data top
C9H14BNO4F000 = 896
Mr = 211.02Dx = 1.287 Mg m−3
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 mm−1
c = 17.5811 (15) ÅT = 100 (2) K
V = 2177.7 (3) Å3Prismatic, colourless
Z = 80.71 × 0.34 × 0.22 mm
Data collection top
Kuma KM4 CCD
diffractometer		2713 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 top
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 Å−3
2713 reflectionsΔρmin = −0.19 e Å−3
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
Crystal data top
C9H14BNO4V = 2177.7 (3) Å3
Mr = 211.02Z = 8
Orthorhombic, PbcaMo Kα
a = 12.9179 (12) ŵ = 0.10 mm−1
b = 9.5885 (7) ÅT = 100 (2) K
c = 17.5811 (15) Å0.71 × 0.34 × 0.22 mm
Data collection top
Kuma KM4 CCD
diffractometer		2713 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction 2005)		1911 reflections with I > 2σ(I)
Tmin = 0.95, Tmax = 0.98Rint = 0.021
19290 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.031193 parameters
wR(F2) = 0.076All H-atom parameters refined
S = 0.97Δρmax = 0.26 e Å−3
2713 reflectionsΔρmin = −0.19 e Å−3
Special details top

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) top
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
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.
Acknowledgements top

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.

references
References top

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