1H-Pyrrolo[2,3-b]pyridine-3-acetic acid as a molecular probe for use in auxin physiology

The structural characterization of 1H-pyrrolo­[2,3-b]­pyridine-3-acetic acid (alternative name: 7-aza­indole-3-acetic acid), C₉H₈N₂O₂, reveals similar molecular geometry, i.e. with the side chain perpendicular to the 7-aza­indole ring, to that of the natural plant growth hormone indole-3-acetic acid (auxin) and its alkyl­ated and halogenated derivatives.

S1. Comment

From the discovery of (hetero)auxin as an endogenous growth factor of grass colepotiles (Went, 1927), its gradual acceptance as a universal plant hormone (Thimann, 1977) and its eventual identification as indole-3-acetic acid (IAA) (Bandurski & Schulze, 1974), a multitude of auxin-like plant growth regulators have been synthesized (Jönsson, 1961; Schneider & Wightman, 1978). In most cases, their structures deviate significantly from that of the endogenous hormone and their overall biological properties diverge accordingly. 1H-Pyrrolo[2,3-b]pyridine-3-acetic acid, (I), retains the auxin activity of IAA (Thimann, 1958), and is thus expected to bind to the proteins involved in the auxin response with about the same efficiency. The structurally similar 7-azatryptophan has been extensively used as a molecular probe in protein biochemistry, mostly exploiting the distinctive fluorescence properties contributed by the 7-azaindole ring system (Smirnov et al., 1997). These properties are shared by (I) and, in conjunction with NMR spectroscopy, should enable the monitoring of auxin-protein interactions without interference by endogenous IAA. Such studies will, however, only afford readily interpretable results if the molecular size and geometry correspond closely to that of the natural auxin. Here we show that this is indeed the case. \sch

Compound (I) has no stereogenic centre but crystallizes in the noncentrosymmetric group Pna2₁ with two conformers per asymmetric unit, molecules A and B. Their molecular structures differ slightly in the conformation of the side chain.

The overall conformation of the molecule can be described by two torsion angles. C2—C3—C8—C9 [91.5 (6) and 101.3 (6)° for molecules A and B, respectively; in Tables 1 and 2, the suffix 2 indicates molecule B] defines the relative orientation of the side chain towards the aromatic plane, whereas the orientation of the carboxylic acid group is given by the angle C3—C8—C9—O2 [−119.5 (5) and −107.0 (5)° for A and B, respectively]. The aromatic 7-azaindole nucleus is planar in both molecules, with maximum deviations of 0.010 (4) (molecule A) and 0.007 (5) Å (molecule B) for C3 from the best least-squares plane defined by C31/C4/C5/C6/N2/C71/N1/C2/C3. The molecular geometry of the 7-azaindole moiety is characterized by shortening of the C6—N2 [1.345 (6) and 1.335 (6) Å in A and B, respectively] and N2—C71 bonds [1.329 (6) and 1.334 (6) Å for A and B, respectively], and shrinkage of the C6—N2—C71 angle [114.3 (4) and 114.7 (4)° for A and B, respectively]. The same type of distortion has been observed previously in the phenyl part of the indole moiety around C7 (reference?), but with the substitution of C with N in (I) this distortion becomes more pronounced.

The crystal packing in (I) is determined by two types of hydrogen bonds, N—H···O and O—H···N. These hydrogen bonds form an eight-membered ring, graph-set notation R₂²(8) (Bernstein et al., 1995), between two neighbouring molecules of the same conformer (A···A, B···B). This pattern is a part of the infinite C(7) (N—H···O) and C(10) (O—H···N) chains running along a.

S2. Experimental

Compound (I) was synthesized from 1H-pyrrolo[2,3-b]pyridine (7-azaindole) via 3-(dimethylaminomethyl)-1-H-pyrrolo[2,3-b]pyridine (7-azagramine) and 1H-pyrrolo[2,3-b]pyridine-3-acetonitrile (7-azaindole-3-acetonitrile) (Robison & Robison, 1955, 1956). Crystals of (I) were grown by evaporation from a solution in EtOH:H₂O (1:1 v/v) over 4 d. A representative crystal was selected for the crystallographic investigation reported here.

S3. Refinement

All H atoms were calculated geometrically and refined using the SHELXL97 (Sheldrick, 1997) riding model.

Computing details

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: HELENA (Spek, 1997a); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97; molecular graphics: PLATON97 (Spek, 1997b) and ORTEP (Johnson, 1965); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. A molecular view of (I) with the atom-numbering scheme for molecule A. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. The crystal structure of (I), with the hydrogen-bonding scheme shown as dashed lines.

7-azaindole-3-acetic acid

Crystal data

C9H8N2O2	Dx = 1.422 (1) Mg m^−3
Mr = 176.17	Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, Pna21	Cell parameters from 25 reflections
a = 14.9965 (7) Å	θ = 11–19°
b = 4.2170 (3) Å	µ = 0.86 mm^−1
c = 26.022 (1) Å	T = 293 K
V = 1645.64 (15) Å^3	Needle, colourless
Z = 8	0.15 × 0.08 × 0.06 mm
F(000) = 736

Data collection

Enraf-Nonius CAD4 diffractometer	992 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.017
Graphite monochromator	θmax = 74.2°, θmin = 3.4°
ω/2θ scans	h = −18→0
Absorption correction: ψ-scan (PLATON97; Spek, 1997b)	k = −5→0
Tmin = 0.88, Tmax = 0.95	l = 0→32
1762 measured reflections	3 standard reflections every 87 reflections
1584 independent reflections	intensity decay: 0.8%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.041	H-atom parameters constrained
wR(F^2) = 0.104	Calculated w = 1/[σ^2(Fo^2) + (0.0508P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.91	(Δ/σ)max = 0.001
1584 reflections	Δρmax = 0.15 e Å^−3
237 parameters	Δρmin = −0.20 e Å^−3
0 restraints	Absolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.0 (5)

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 (Ų)

	x	y	z	Uiso*/Ueq
C31	0.4789 (3)	0.3875 (10)	0.21329 (16)	0.0393 (10)
C4	0.4889 (3)	0.2704 (12)	0.1642 (2)	0.0530 (12)
H4	0.5378	0.1463	0.1554	0.064*
C5	0.4242 (4)	0.3427 (13)	0.1286 (2)	0.0572 (13)
H5	0.4290	0.2653	0.0952	0.069*
C6	0.3523 (4)	0.5297 (13)	0.1421 (2)	0.0543 (12)
H6	0.3105	0.5774	0.1168	0.065*
N2	0.3391 (2)	0.6469 (9)	0.18957 (15)	0.0455 (10)
C71	0.4026 (3)	0.5737 (11)	0.22313 (17)	0.0411 (11)
N1	0.4037 (2)	0.6671 (9)	0.27306 (15)	0.0457 (10)
H1	0.3643	0.7826	0.2880	0.055*
C2	0.4794 (3)	0.5436 (11)	0.29547 (19)	0.0465 (12)
H2	0.4959	0.5751	0.3295	0.056*
C3	0.5266 (3)	0.3688 (11)	0.26079 (17)	0.0416 (11)
C8	0.6128 (3)	0.2005 (11)	0.2706 (2)	0.0506 (12)
H8A	0.6145	0.0094	0.2499	0.061*
H8B	0.6149	0.1370	0.3064	0.061*
C9	0.6942 (3)	0.3968 (11)	0.2588 (2)	0.0452 (11)
O1	0.6991 (2)	0.4892 (9)	0.21113 (13)	0.0564 (8)
H1A	0.7454	0.5890	0.2068	0.085*
O2	0.7487 (2)	0.4621 (10)	0.29103 (15)	0.0698 (11)
C312	0.2850 (3)	0.5514 (9)	0.48132 (17)	0.0392 (11)
C42	0.2689 (3)	0.6192 (12)	0.53230 (19)	0.0509 (12)
H42	0.2196	0.7395	0.5418	0.061*
C52	0.3270 (4)	0.5062 (14)	0.56906 (19)	0.0604 (13)
H52	0.3167	0.5465	0.6037	0.072*
C62	0.4005 (3)	0.3331 (13)	0.55409 (19)	0.0583 (14)
H62	0.4391	0.2620	0.5796	0.070*
N22	0.4198 (2)	0.2607 (9)	0.50541 (16)	0.0465 (10)
C712	0.3619 (3)	0.3718 (10)	0.47085 (17)	0.0418 (11)
N12	0.3675 (2)	0.3284 (9)	0.41905 (14)	0.0453 (10)
H12	0.4085	0.2252	0.4031	0.054*
C22	0.2964 (3)	0.4773 (12)	0.39685 (19)	0.0459 (11)
H22	0.2851	0.4811	0.3617	0.055*
C32	0.2444 (3)	0.6189 (11)	0.43277 (18)	0.0419 (11)
C82	0.1614 (3)	0.8106 (11)	0.4237 (2)	0.0531 (14)
H82A	0.1606	0.8830	0.3883	0.064*
H82B	0.1624	0.9962	0.4457	0.064*
C92	0.0772 (3)	0.6229 (11)	0.4343 (2)	0.0475 (12)
O12	0.0647 (2)	0.5692 (9)	0.48320 (13)	0.0657 (11)
H12A	0.0190	0.4648	0.4871	0.099*
O22	0.0288 (2)	0.5275 (9)	0.40090 (14)	0.0687 (11)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C31	0.039 (2)	0.034 (2)	0.045 (3)	−0.0079 (18)	0.001 (2)	−0.003 (2)
C4	0.045 (3)	0.053 (3)	0.061 (3)	−0.001 (2)	0.005 (3)	−0.014 (2)
C5	0.059 (3)	0.067 (4)	0.045 (3)	0.000 (3)	0.001 (3)	−0.016 (2)
C6	0.048 (3)	0.070 (3)	0.045 (3)	−0.005 (2)	−0.007 (2)	−0.006 (2)
N2	0.039 (2)	0.054 (2)	0.044 (2)	−0.0074 (17)	0.000 (2)	−0.0017 (18)
C71	0.030 (2)	0.053 (3)	0.040 (3)	−0.0080 (18)	0.003 (2)	0.003 (2)
N1	0.037 (2)	0.056 (2)	0.043 (2)	0.0008 (17)	0.0074 (18)	−0.0082 (18)
C2	0.038 (3)	0.054 (3)	0.047 (3)	−0.010 (2)	0.000 (2)	−0.003 (2)
C3	0.035 (2)	0.043 (2)	0.046 (3)	−0.0046 (19)	−0.003 (2)	0.000 (2)
C8	0.050 (3)	0.047 (3)	0.055 (3)	−0.004 (2)	−0.007 (3)	0.011 (2)
C9	0.037 (2)	0.048 (3)	0.051 (3)	0.005 (2)	0.000 (2)	0.007 (2)
O1	0.047 (2)	0.075 (2)	0.0473 (19)	−0.0084 (18)	−0.0003 (17)	0.0083 (18)
O2	0.0544 (19)	0.093 (3)	0.062 (3)	−0.020 (2)	−0.008 (2)	0.021 (2)
C312	0.034 (2)	0.040 (2)	0.043 (2)	−0.0109 (18)	0.004 (2)	−0.003 (2)
C42	0.049 (3)	0.057 (3)	0.046 (3)	−0.002 (2)	0.009 (3)	−0.007 (2)
C52	0.061 (3)	0.082 (4)	0.037 (3)	−0.008 (3)	0.005 (3)	−0.008 (3)
C62	0.055 (3)	0.074 (4)	0.045 (3)	−0.006 (3)	−0.006 (3)	0.004 (2)
N22	0.039 (2)	0.053 (2)	0.048 (2)	−0.0030 (18)	−0.002 (2)	0.0031 (19)
C712	0.035 (3)	0.047 (2)	0.043 (3)	−0.007 (2)	0.006 (2)	0.000 (2)
N12	0.0333 (19)	0.061 (3)	0.041 (2)	0.0004 (17)	0.0042 (19)	−0.0053 (18)
C22	0.044 (3)	0.056 (3)	0.037 (2)	−0.007 (2)	0.003 (2)	0.000 (2)
C32	0.040 (2)	0.039 (2)	0.047 (3)	−0.0101 (19)	0.002 (2)	0.003 (2)
C82	0.046 (3)	0.042 (3)	0.072 (4)	0.001 (2)	−0.004 (3)	0.008 (2)
C92	0.040 (3)	0.043 (2)	0.060 (4)	0.009 (2)	0.002 (3)	0.007 (2)
O12	0.048 (2)	0.093 (3)	0.056 (2)	−0.0171 (19)	0.0004 (19)	−0.007 (2)
O22	0.056 (2)	0.096 (3)	0.054 (2)	−0.019 (2)	−0.008 (2)	0.013 (2)

Geometric parameters (Å, º)

C31—C4	1.378 (6)	C312—C42	1.378 (6)
C31—C71	1.410 (6)	C312—C712	1.407 (6)
C31—C3	1.431 (6)	C312—C32	1.431 (6)
C4—C5	1.375 (7)	C42—C52	1.378 (7)
C5—C6	1.382 (7)	C52—C62	1.378 (7)
C6—N2	1.345 (6)	C62—N22	1.335 (6)
N2—C71	1.329 (6)	N22—C712	1.334 (6)
C71—N1	1.358 (6)	C712—N12	1.363 (6)
N1—C2	1.377 (5)	N12—C22	1.366 (6)
C2—C3	1.364 (6)	C22—C32	1.355 (6)
C3—C8	1.497 (6)	C32—C82	1.503 (6)
C8—C9	1.505 (6)	C82—C92	1.515 (7)
C9—O2	1.204 (5)	C92—O22	1.202 (6)
C9—O1	1.301 (6)	C92—O12	1.306 (6)
O1···C31	3.329 (5)	C5···H62^v	2.9345
O1···N2^i	2.662 (5)	C6···H1A^iv	2.8265
O2···C22^ii	3.395 (5)	C6···H42^x	3.0786
O2···N1^i	2.840 (5)	C9···H1^i	2.9852
O12···N22^iii	2.644 (5)	C9···H8A^vi	2.8557
O12···C312	3.305 (5)	C32···H82B^viii	2.9190
O12···C42	3.325 (5)	C52···H6^xi	3.0114
O22···N12^iii	2.886 (5)	C62···H12A^vii	2.7890
O22···C2^iv	3.369 (5)	C71···H1A^iv	2.7865
O1···H52^v	2.8097	C92···H12^iii	3.0353
O1···H8A^vi	2.7263	C92···H82B^viii	2.9506
O2···H22^vii	2.6785	C312···O12	3.305 (5)
O2···H1^i	2.0419	C712···H12A^vii	2.7830
O12···H42	2.8698	H1···C9^iv	2.9852
O22···H8B^iii	2.8633	H1···O2^iv	2.0419
O22···H2^iv	2.5496	H1···H22	2.5894
O22···H12^iii	2.0961	H1A···C6^i	2.8265
N1···O2^iv	2.840 (5)	H1A···N2^i	1.8484
N2···C9^iv	3.416 (6)	H1A···C71^i	2.7865
N2···O1^iv	2.662 (5)	H2···O22^i	2.5496
N12···O22^vii	2.886 (5)	H6···C52^xii	3.0114
N22···O12^vii	2.644 (5)	H6···H42^x	2.4601
N22···C92^vii	3.408 (6)	H8A···C2^viii	3.0628
N2···H1A^iv	1.8484	H8A···C3^viii	3.0196
N22···H12A^vii	1.8292	H8A···C9^viii	2.8557
C2···O22^i	3.369 (5)	H8A···O1^viii	2.7263
C2···C8^vi	3.479 (6)	H8B···O22^vii	2.8633
C4···C71^viii	3.558 (7)	H12···O22^vii	2.0961
C5···C62^v	3.541 (7)	H12···C92^vii	3.0353
C8···C2^viii	3.479 (6)	H12A···N22^iii	1.8292
C9···N2^i	3.416 (6)	H12A···C62^iii	2.7890
C22···C82^viii	3.534 (7)	H12A···C712^iii	2.7830
C22···O2^iii	3.395 (5)	H22···O2^iii	2.6785
C31···O1	3.329 (5)	H22···H1	2.5894
C42···O12	3.325 (5)	H42···O12	2.8698
C62···C5^ix	3.541 (7)	H42···C6^ii	3.0786
C71···C4^vi	3.558 (7)	H42···H6^ii	2.4601
C82···C22^vi	3.534 (7)	H52···O1^ix	2.8097
C92···N22^iii	3.408 (6)	H62···C5^ix	2.9345
C2···H8A^vi	3.0628	H82B···C32^vi	2.9190
C3···H8A^vi	3.0196	H82B···C92^vi	2.9506
C4—C31—C71	117.2 (4)	C42—C312—C712	116.2 (4)
C4—C31—C3	136.6 (4)	C42—C312—C32	137.3 (4)
C71—C31—C3	106.2 (4)	C712—C312—C32	106.6 (4)
C5—C4—C31	117.9 (5)	C52—C42—C312	119.1 (5)
C4—C5—C6	120.4 (5)	C42—C52—C62	119.5 (5)
N2—C6—C5	123.9 (5)	N22—C62—C52	124.3 (5)
C71—N2—C6	114.3 (4)	C712—N22—C62	114.7 (4)
N2—C71—N1	124.8 (4)	N22—C712—N12	125.4 (4)
N2—C71—C31	126.3 (4)	N22—C712—C312	126.3 (4)
N1—C71—C31	109.0 (4)	N12—C712—C312	108.3 (4)
C71—N1—C2	107.8 (4)	C712—N12—C22	108.0 (4)
C3—C2—N1	110.6 (4)	C32—C22—N12	111.1 (4)
C2—C3—C31	106.4 (4)	C22—C32—C312	106.1 (4)
C2—C3—C8	126.3 (4)	C22—C32—C82	127.2 (5)
C31—C3—C8	127.3 (4)	C312—C32—C82	126.7 (4)
C3—C8—C9	113.9 (4)	C32—C82—C92	112.4 (4)
O2—C9—O1	123.9 (4)	O22—C92—O12	124.0 (5)
O2—C9—C8	122.2 (5)	O22—C92—C82	123.1 (5)
O1—C9—C8	113.9 (4)	O12—C92—C82	112.8 (5)
C2—C3—C8—C9	−91.5 (6)	C31—C3—C8—C9	86.4 (6)
C3—C8—C9—O2	119.5 (5)	C31—C4—C5—C6	0.6 (8)
C22—C32—C82—C92	101.3 (6)	C5—C4—C31—C3	178.7 (5)
C32—C82—C92—O22	−107.0 (5)	C5—C4—C31—C71	0.1 (7)
C71—N1—C2—C3	−0.6 (5)	C4—C5—C6—N2	−1.3 (9)
C2—N1—C71—C31	0.1 (5)	C3—C8—C9—O1	−59.9 (5)
C2—N1—C71—N2	179.6 (4)	C4—C31—C71—N1	−179.8 (4)
C6—N2—C71—N1	179.6 (4)	C3—C31—C71—N1	0.8 (5)
C71—N2—C6—C5	1.3 (7)	C4—C31—C71—N2	−0.1 (7)
C6—N2—C71—C31	−0.8 (7)	C3—C31—C71—N2	−178.9 (4)
C712—N12—C22—C32	0.3 (6)	N12—C22—C32—C82	178.8 (4)
C22—N12—C712—C312	0.3 (4)	N12—C22—C32—C312	−0.7 (5)
C22—N12—C712—N22	−179.9 (4)	C22—C32—C312—C712	0.9 (5)
C712—N22—C62—C52	0.4 (8)	C312—C32—C82—C92	−79.3 (6)
C62—N22—C712—N12	−180.0 (4)	C82—C32—C312—C42	0.2 (9)
C62—N22—C712—C312	−0.2 (7)	C82—C32—C312—C712	−178.6 (4)
N1—C2—C3—C8	179.3 (4)	C22—C32—C312—C42	179.7 (5)
N1—C2—C3—C31	1.1 (5)	C312—C42—C52—C62	1.1 (8)
C2—C3—C31—C4	179.9 (8)	C52—C42—C312—C32	−179.5 (5)
C8—C3—C31—C71	−179.3 (4)	C52—C42—C312—C712	−0.8 (7)
C8—C3—C31—C4	1.8 (9)	C42—C52—C62—N22	−0.9 (9)
C2—C3—C31—C71	−1.1 (5)	C32—C82—C92—O12	71.2 (5)

Symmetry codes: (i) x+1/2, −y+3/2, z; (ii) −x+1/2, y+1/2, z+1/2; (iii) x−1/2, −y+1/2, z; (iv) x−1/2, −y+3/2, z; (v) −x+1, −y+1, z−1/2; (vi) x, y+1, z; (vii) x+1/2, −y+1/2, z; (viii) x, y−1, z; (ix) −x+1, −y+1, z+1/2; (x) −x+1/2, y−1/2, z−1/2; (xi) −x, −y, z+1/2; (xii) −x, −y, z−1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^iv	0.86	2.04	2.840 (5)	154
O1—H1A···N2^i	0.82	1.85	2.662 (5)	171
N12—H12···O22^vii	0.86	2.10	2.886 (5)	152
O12—H12A···N22^iii	0.82	1.83	2.644 (5)	172
C2—H2···O22^i	0.93	2.55	3.369 (5)	147

Symmetry codes: (i) x+1/2, −y+3/2, z; (iii) x−1/2, −y+1/2, z; (iv) x−1/2, −y+3/2, z; (vii) x+1/2, −y+1/2, z.