Indole–picric acid (1/1)

Saminathan, K.; Sivakumar, K.

doi:10.1107/S1600536806052512

Indole–picric acid (1/1)

In the title molecular complex, C₈H₇N·C₆H₃N₃O₇, the picric acid molecule is disordered, corresponding to a rotation about one H—C

C—N axis and resulting in two sites for the hydroxyl group. In the crystal structure, the indole and picric acid molecules are stacked in columns parallel to the b axis with significant π–π interactions. In addition, intermolecular hydrogen bonds link molecules in a zigzag fashion along the a axis, giving ring patterns with graph-set motifs R₂²(8) and R₂²(7).

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806052512/lh2191sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536806052512/lh2191Isup2.hkl Contains datablock I

CCDC reference: 633906

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.009 Å
Disorder in main residue
R factor = 0.069
wR factor = 0.271
Data-to-parameter ratio = 11.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT026_ALERT_3_B Ratio Observed / Unique Reflections too Low ....         32 Perc.
PLAT242_ALERT_2_B Check Low       Ueq as Compared to Neighbors for         N2

Alert level C
RFACR01_ALERT_3_C  The value of the weighted R factor is > 0.25
            Weighted R factor given   0.271
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.97
PLAT084_ALERT_2_C High R2 Value ..................................       0.27
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N1
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N3
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C4
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C6
PLAT243_ALERT_4_C High  'Solvent' Ueq as Compared to Neighbors for        C10
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for        C14
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.46
PLAT301_ALERT_3_C Main Residue  Disorder .........................       6.00 Perc.
PLAT313_ALERT_2_C Oxygen with three covalent bonds (rare) ........         O1
PLAT313_ALERT_2_C Oxygen with three covalent bonds (rare) ........        O1'
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          9
PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond  C1     -   C2     ...       1.36 Ang.
PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond  C1     -   C6     ...       1.35 Ang.
PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond  C4     -   C5     ...       1.38 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H7     ..  O2      ..       2.69 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H8     ..  O3      ..       2.70 Ang.

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K

   0 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
  20 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  12 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   5 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97.

Indole–picric acid (1/1) top

Crystal data top

C₈H₇N·C₆H₃N₃O₇	F(000) = 712
M_r = 346.26	D_x = 1.579 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 13.4586 (19) Å	θ = 15–20°
b = 6.723 (3) Å	µ = 0.13 mm⁻¹
c = 16.158 (4) Å	T = 293 K
β = 94.912 (19)°	Needle, red
V = 1456.7 (8) Å³	0.4 × 0.2 × 0.2 mm
Z = 4

Data collection top

Enraf–Nonius CAD-4 diffractometer	816 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.015
Graphite monochromator	θ_max = 25.0°, θ_min = 2.5°
ω–2θ scans	h = 0→15
Absorption correction: ψ scan (North et al., 1968)	k = 0→7
T_min = 0.989, T_max = 1.000	l = −19→19
2659 measured reflections	2 standard reflections every 100 reflections
2546 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.069	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.271	H-atom parameters constrained
S = 0.91	w = 1/[σ²(F_o²) + (0.1531P)²] where P = (F_o² + 2F_c²)/3
2546 reflections	(Δ/σ)_max < 0.001
231 parameters	Δρ_max = 0.40 e Å⁻³
1 restraint	Δρ_min = −0.24 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

	x	y	z	U_iso*/U_eq	Occ. (<1)
O2	0.9954 (3)	0.6384 (8)	0.3538 (3)	0.132 (2)
O3	0.9088 (3)	0.5860 (8)	0.2402 (3)	0.1146 (17)
O4	0.5585 (4)	0.5859 (12)	0.2248 (4)	0.187 (3)
O5	0.4805 (4)	0.6338 (11)	0.3266 (4)	0.180 (3)
O6	0.6683 (7)	0.6280 (10)	0.6028 (4)	0.186 (4)
O7	0.8263 (6)	0.6326 (9)	0.6088 (3)	0.164 (3)
N1	0.9188 (4)	0.6158 (7)	0.3144 (3)	0.0759 (12)
N2	0.5562 (4)	0.6100 (9)	0.2968 (4)	0.0960 (17)
N3	0.7418 (8)	0.6266 (9)	0.5726 (3)	0.119 (2)
C1	0.8306 (3)	0.6201 (7)	0.4414 (3)	0.0608 (13)
H5'	0.8919	0.6209	0.4727	0.073*	0.50
O1	0.9103 (5)	0.6204 (14)	0.4914 (5)	0.0961 (17)	0.50
H1	0.9593	0.6254	0.4646	0.144*	0.50
C2	0.8259 (3)	0.6157 (7)	0.3572 (3)	0.0512 (11)
C3	0.7366 (3)	0.6136 (6)	0.3097 (3)	0.0515 (11)
H3	0.7349	0.6108	0.2520	0.062*
C4	0.6500 (3)	0.6158 (7)	0.3481 (3)	0.0536 (11)
C5	0.6509 (4)	0.6177 (8)	0.4336 (4)	0.0698 (15)
H5	0.5921	0.6154	0.4599	0.084*	0.50
O1'	0.5742 (5)	0.6155 (15)	0.4771 (5)	0.0961 (17)	0.50
H1'	0.5932	0.6105	0.5266	0.144*	0.50
C6	0.7447 (5)	0.6233 (7)	0.4791 (3)	0.0664 (14)
N4	0.2733 (4)	0.6127 (6)	0.1969 (3)	0.0819 (14)
H4	0.3211	0.6082	0.2357	0.098*
C7	0.1746 (5)	0.6148 (9)	0.2074 (4)	0.0861 (17)
H7	0.1496	0.6126	0.2593	0.103*
C8	0.1178 (5)	0.6204 (8)	0.1379 (4)	0.0781 (16)
H8	0.0485	0.6226	0.1312	0.094*
C9	0.1872 (4)	0.6226 (7)	0.0726 (4)	0.0733 (15)
C10	0.1728 (6)	0.6264 (8)	−0.0118 (5)	0.110 (3)
H10	0.1094	0.6302	−0.0397	0.132*
C11	0.2606 (8)	0.6241 (10)	−0.0542 (4)	0.100 (2)
H11	0.2541	0.6246	−0.1120	0.120*
C12	0.3545 (6)	0.6212 (9)	−0.0144 (4)	0.094 (2)
H12	0.4095	0.6213	−0.0456	0.113*
C13	0.3690 (4)	0.6181 (7)	0.0700 (4)	0.0744 (15)
H13	0.4324	0.6156	0.0978	0.089*
C14	0.2836 (3)	0.6189 (7)	0.1114 (3)	0.0541 (11)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O2	0.059 (2)	0.184 (5)	0.154 (4)	−0.002 (3)	0.007 (3)	0.001 (4)
O3	0.106 (3)	0.138 (5)	0.107 (3)	−0.001 (3)	0.049 (3)	0.001 (3)
O4	0.117 (4)	0.294 (10)	0.139 (5)	0.003 (5)	−0.055 (4)	−0.019 (6)
O5	0.062 (3)	0.299 (9)	0.178 (5)	0.012 (5)	−0.001 (3)	−0.001 (6)
O6	0.346 (11)	0.112 (4)	0.124 (5)	−0.030 (6)	0.152 (6)	−0.017 (4)
O7	0.296 (8)	0.118 (4)	0.068 (3)	0.028 (5)	−0.038 (4)	−0.010 (3)
N1	0.074 (3)	0.063 (3)	0.092 (3)	0.007 (3)	0.017 (3)	0.006 (3)
N2	0.067 (3)	0.105 (4)	0.112 (4)	−0.007 (4)	−0.016 (3)	0.009 (4)
N3	0.245 (9)	0.043 (3)	0.067 (4)	0.003 (6)	0.004 (5)	0.006 (4)
C1	0.066 (3)	0.041 (3)	0.072 (3)	−0.004 (3)	−0.012 (3)	0.002 (3)
O1	0.084 (3)	0.089 (4)	0.112 (4)	0.005 (4)	−0.008 (3)	0.011 (5)
C2	0.057 (3)	0.041 (3)	0.057 (3)	0.000 (3)	0.009 (2)	0.002 (3)
C3	0.071 (3)	0.033 (2)	0.050 (2)	0.008 (3)	0.001 (2)	0.002 (3)
C4	0.054 (3)	0.037 (3)	0.070 (3)	−0.003 (3)	0.003 (2)	0.002 (3)
C5	0.078 (3)	0.041 (3)	0.099 (4)	−0.003 (3)	0.050 (3)	0.001 (4)
O1'	0.084 (3)	0.089 (4)	0.112 (4)	0.005 (4)	−0.008 (3)	0.011 (5)
C6	0.120 (5)	0.034 (3)	0.045 (3)	0.000 (4)	0.005 (3)	0.003 (3)
N4	0.116 (4)	0.058 (3)	0.071 (3)	0.008 (3)	−0.002 (3)	−0.001 (3)
C7	0.107 (5)	0.061 (4)	0.095 (5)	0.012 (4)	0.039 (4)	0.006 (4)
C8	0.081 (4)	0.042 (3)	0.116 (5)	−0.003 (3)	0.035 (4)	0.001 (4)
C9	0.089 (4)	0.030 (3)	0.097 (4)	0.002 (3)	−0.017 (3)	−0.001 (4)
C10	0.161 (7)	0.038 (3)	0.119 (6)	0.000 (5)	−0.054 (5)	0.002 (4)
C11	0.183 (7)	0.061 (4)	0.058 (4)	−0.001 (6)	0.024 (5)	−0.004 (4)
C12	0.147 (6)	0.049 (3)	0.096 (5)	0.000 (5)	0.066 (4)	0.001 (4)
C13	0.079 (3)	0.048 (3)	0.100 (5)	0.000 (3)	0.027 (3)	−0.006 (4)
C14	0.071 (3)	0.036 (2)	0.054 (3)	0.009 (3)	−0.002 (2)	0.001 (3)

Geometric parameters (Å, º) top

O2—N1	1.174 (5)	C5—H5	0.9300
O3—N1	1.211 (6)	O1'—H1'	0.8200
O4—N2	1.178 (7)	N4—C7	1.353 (7)
O5—N2	1.175 (7)	N4—C14	1.400 (6)
O6—N3	1.141 (10)	N4—H4	0.8600
O7—N3	1.234 (9)	C7—C8	1.303 (8)
N1—C2	1.480 (6)	C7—H7	0.9300
N2—C4	1.450 (6)	C8—C9	1.468 (7)
N3—C6	1.514 (7)	C8—H8	0.9300
C1—O1	1.286 (7)	C9—C10	1.361 (8)
C1—C6	1.353 (7)	C9—C14	1.392 (7)
C1—C2	1.358 (6)	C10—C11	1.417 (10)
C1—H5'	0.9300	C10—H10	0.9300
O1—H1	0.8200	C11—C12	1.369 (9)
C2—C3	1.369 (6)	C11—H11	0.9300
C3—C4	1.367 (6)	C12—C13	1.360 (8)
C3—H3	0.9300	C12—H12	0.9300
C4—C5	1.380 (7)	C13—C14	1.379 (6)
C5—O1'	1.298 (7)	C13—H13	0.9300
C5—C6	1.406 (7)

O2—N1—O3	125.2 (5)	C1—C6—C5	121.8 (4)
O2—N1—C2	119.0 (5)	C1—C6—N3	123.0 (6)
O3—N1—C2	115.7 (5)	C5—C6—N3	115.1 (6)
O5—N2—O4	121.4 (6)	C7—N4—C14	107.8 (5)
O5—N2—C4	120.3 (7)	C7—N4—H4	126.1
O4—N2—C4	118.3 (6)	C14—N4—H4	126.1
O6—N3—O7	126.5 (8)	C8—C7—N4	113.7 (6)
O6—N3—C6	121.6 (9)	C8—C7—H7	123.2
O7—N3—C6	111.9 (8)	N4—C7—H7	123.2
O1—C1—C6	114.6 (6)	C7—C8—C9	104.9 (5)
O1—C1—C2	126.5 (6)	C7—C8—H8	127.6
C6—C1—C2	118.9 (4)	C9—C8—H8	127.6
C6—C1—H5'	120.5	C10—C9—C14	120.0 (6)
C2—C1—H5'	120.5	C10—C9—C8	132.4 (6)
C1—O1—H1	109.5	C14—C9—C8	107.6 (5)
C1—C2—C3	121.7 (4)	C9—C10—C11	115.6 (6)
C1—C2—N1	119.9 (4)	C9—C10—H10	122.2
C3—C2—N1	118.3 (4)	C11—C10—H10	122.2
C4—C3—C2	119.1 (4)	C12—C11—C10	123.2 (6)
C4—C3—H3	120.4	C12—C11—H11	118.4
C2—C3—H3	120.4	C10—C11—H11	118.4
C3—C4—C5	121.4 (4)	C13—C12—C11	121.3 (6)
C3—C4—N2	118.3 (5)	C13—C12—H12	119.4
C5—C4—N2	120.3 (5)	C11—C12—H12	119.4
O1'—C5—C4	127.1 (6)	C12—C13—C14	115.6 (5)
O1'—C5—C6	115.9 (6)	C12—C13—H13	122.2
C4—C5—C6	117.0 (5)	C14—C13—H13	122.2
C4—C5—H5	121.5	C13—C14—C9	124.4 (5)
C6—C5—H5	121.5	C13—C14—N4	129.5 (5)
C5—O1'—H1'	109.5	C9—C14—N4	106.1 (5)

O1—C1—C2—C3	179.3 (7)	C4—C5—C6—C1	−2.2 (8)
C6—C1—C2—C3	−0.3 (8)	O1'—C5—C6—N3	−0.2 (8)
O1—C1—C2—N1	−1.6 (10)	C4—C5—C6—N3	179.6 (5)
C6—C1—C2—N1	178.9 (5)	O6—N3—C6—C1	−179.5 (7)
O2—N1—C2—C1	−7.0 (8)	O7—N3—C6—C1	2.3 (9)
O3—N1—C2—C1	170.9 (5)	O6—N3—C6—C5	−1.4 (10)
O2—N1—C2—C3	172.1 (6)	O7—N3—C6—C5	−179.6 (6)
O3—N1—C2—C3	−10.0 (8)	C14—N4—C7—C8	0.5 (7)
C1—C2—C3—C4	−0.1 (7)	N4—C7—C8—C9	−0.1 (7)
N1—C2—C3—C4	−179.2 (4)	C7—C8—C9—C10	179.4 (6)
C2—C3—C4—C5	−0.8 (7)	C7—C8—C9—C14	−0.3 (6)
C2—C3—C4—N2	−178.9 (5)	C14—C9—C10—C11	0.6 (8)
O5—N2—C4—C3	−171.6 (7)	C8—C9—C10—C11	−179.0 (6)
O4—N2—C4—C3	6.6 (9)	C9—C10—C11—C12	−0.9 (10)
O5—N2—C4—C5	10.3 (10)	C10—C11—C12—C13	0.7 (11)
O4—N2—C4—C5	−171.6 (7)	C11—C12—C13—C14	−0.2 (9)
C3—C4—C5—O1'	−178.4 (7)	C12—C13—C14—C9	0.0 (8)
N2—C4—C5—O1'	−0.3 (11)	C12—C13—C14—N4	178.7 (5)
C3—C4—C5—C6	1.9 (8)	C10—C9—C14—C13	−0.2 (8)
N2—C4—C5—C6	180.0 (5)	C8—C9—C14—C13	179.5 (5)
O1—C1—C6—C5	−178.1 (7)	C10—C9—C14—N4	−179.1 (5)
C2—C1—C6—C5	1.5 (8)	C8—C9—C14—N4	0.6 (6)
O1—C1—C6—N3	−0.1 (9)	C7—N4—C14—C13	−179.5 (5)
C2—C1—C6—N3	179.5 (5)	C7—N4—C14—C9	−0.6 (6)
O1'—C5—C6—C1	178.0 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···O5	0.86	2.50	3.346 (7)	168
C13—H13···O4	0.93	2.56	3.423 (8)	155
C7—H7···O2ⁱ	0.93	2.69	3.524 (8)	150
C8—H8···O3ⁱ	0.93	2.70	3.391 (7)	132
O1—H1···O2	0.82	1.90	2.590 (6)	142
O1′—H1′···O6	0.82	1.53	2.302 (6)	156

Symmetry code: (i) x−1, y, z.

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