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Weakly diffracting crystals of benz[
cd]indol-2(1
H)-one (naphtholactam), C
11H
7NO, were unsuitable for data collection by early photographic methods. However, a diffractometer data set collected at room temperature in 1989 was solved and refined. The peak scans were broad, and the results indicated disorder or a satellite crystal. Recent data collection (on another crystal from the same sample) with an area detector at 100 K revealed the same disorder, and made it possible to refine two different, more complete, disorder models. Both models assume an occasional 180° rotation of the nearly planar centrosymmetric
cis-lactam dimer. The refinements differ, especially in the anisotropic displacement parameters for the -C(=O)-NH- portion of the molecule. Both models at 100 K give a C-N (`amide') bond distance of 1.38 Å, about 0.04 Å longer than the average distance in saturated
-lactams in the Cambridge Structural Database. Cohesive packing interactions between molecules include opposing-dipole dimers; the packing may explain the 10:1 ratio favoring the major-occupancy molecule.
Supporting information
CCDC references: 866747; 866748; 866749
The sample was synthesized by Professor Cyril A. Grob (Grob & Schmid, 1950).
At room temperature [(Ia)], a peak of 0.59 e- Å-3 in the
difference map after refinement of the 20 C, H, N and O atoms, close to atom
H1N, was assumed to be a second partial O atom (O1A) in the model
described above (Fig. 1). Occupancies for the two O atoms refined to 0.921 (4)
and 0.079 (4). The C1—O1 distance in Table 1 is for the major orientation. At
100 K [(Ib)] (Fig. 2), a more detailed model for refinement of the
disorder was employed, using restraints SIMU, EADP, DFIX, SADI and FLAT
(SHELXL97; Sheldrick, 2008) in the O1A, C1A, N1A
and H1NA region. The occupancies refined to 0.919 (4) for atoms C1, O1,
N1 and H1N, and to 0.081 (4) for atoms C1A, O1A, N1A and
H1NA. Restraints were not completely successful, as shown in the
selected bond lengths reported in Table 2. In addition, checkCIF
reported a Hirshfeld test greater than five times the s.u., as was also true
at room temperature. A second model for the 100 K data [(Ic)] (Fig. 3)
employed a rigid-body refinement (constructed using the instruction SAME
O1A > H11A) for the entire minor-occupancy orientation.
Occupancies refined to 0.912 (3) and 0.088 (3). Changes in bond lengths, angles,
R and Rw for the major-occupancy molecule were minor (Table
3). Anisotropic displacement parameters were significantly improved; see Fig.
3.
Data collection: UCLA Crystallographic Package (Strouse, 1994) for Ia298K; APEX2 (Bruker, 2005) for Ib100K, Ic100K. Cell refinement: UCLA Crystallographic Package (Strouse, 1994) for Ia298K; SAINT (Bruker, 2005) for Ib100K, Ic100K. Data reduction: UCLA Crystallographic Package (Strouse, 1994) for Ia298K; SAINT (Bruker, 2005) for Ib100K, Ic100K. Program(s) used to solve structure: SHELXS90 (Sheldrick, 2008) for Ia298K; SHELXS97 (Sheldrick, 2008) for Ib100K, Ic100K. For all compounds, program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
(Ia298K) Benz[
cd]indol-2(1
H)-one
top
Crystal data top
C11H7NO | F(000) = 352 |
Mr = 169.18 | Dx = 1.355 Mg m−3 |
Monoclinic, P21/n | Melting point = 448–450 K |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
a = 9.251 (3) Å | Cell parameters from 19 reflections |
b = 6.7748 (17) Å | θ = 4.8–10.2° |
c = 13.256 (4) Å | µ = 0.09 mm−1 |
β = 93.196 (8)° | T = 298 K |
V = 829.5 (4) Å3 | Cut plate, yellow |
Z = 4 | 0.35 × 0.25 × 0.10 mm |
Data collection top
Modified Hubers diffractometer | Rint = 0.000 |
Radiation source: fine-focus sealed tube | θmax = 25.0°, θmin = 2.6° |
Graphite monochromator | h = 0→11 |
θ/2θ scans | k = 0→8 |
1462 measured reflections | l = −15→15 |
1462 independent reflections | 3 standard reflections every 97 reflections |
992 reflections with I > 2σ(I) | intensity decay: 0.4% |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0523P)2 + 0.0789P] where P = (Fo2 + 2Fc2)/3 |
1462 reflections | (Δ/σ)max < 0.001 |
128 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.14 e Å−3 |
Crystal data top
C11H7NO | V = 829.5 (4) Å3 |
Mr = 169.18 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.251 (3) Å | µ = 0.09 mm−1 |
b = 6.7748 (17) Å | T = 298 K |
c = 13.256 (4) Å | 0.35 × 0.25 × 0.10 mm |
β = 93.196 (8)° | |
Data collection top
Modified Hubers diffractometer | Rint = 0.000 |
1462 measured reflections | 3 standard reflections every 97 reflections |
1462 independent reflections | intensity decay: 0.4% |
992 reflections with I > 2σ(I) | |
Refinement top
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.19 e Å−3 |
1462 reflections | Δρmin = −0.14 e Å−3 |
128 parameters | |
Special details top
Experimental. The alternate space group setting P 21/n was chosen because the cell angle beta
is close to 90 degrees. |
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. Data were collected in 1989;
negative intensities were set to zero. F and σ(F) were input,
and F2 and σ(F2) were calculated by SHELXL97. When
refinement was complete, a residual peak of about 0.59 suggested disorder. The
disorder model assumes this peak is due to an occasional rotation of the
H-bonded pair of molecules; O1 (major) and O1A (minor) have occupancies which
refined to 0.921 (4) and 0.079 (4). The positions of C1, N1 and H1N are not
corrected for the partial occupancies assumed. For this reason H1N appears to
be connected to two atoms (N1 and O1A) and C1 has a short intermolecular
contact (C1···O1A, 2.64). Hirshfeld test differences greater than 5 s.u.
(N1—C1, C7—C8) show that displacement parameters are affected by the
disorder. 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 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 | Uiso*/Ueq | Occ. (<1) |
C1 | 0.1261 (2) | 0.2398 (3) | 0.48386 (16) | 0.0562 (6) | |
N1 | 0.0140 (2) | 0.2077 (3) | 0.41424 (13) | 0.0628 (5) | |
H1N | −0.0409 | 0.1052 | 0.4135 | 0.075* | |
O1 | 0.16442 (18) | 0.1308 (2) | 0.55565 (12) | 0.0664 (6) | 0.921 (4) |
O1A | −0.1084 (19) | 0.056 (3) | 0.3873 (15) | 0.072 (8) | 0.079 (4) |
C2 | −0.0007 (2) | 0.3644 (3) | 0.34337 (15) | 0.0561 (6) | |
C3 | 0.1094 (2) | 0.4996 (3) | 0.37131 (15) | 0.0500 (5) | |
C4 | 0.1920 (2) | 0.4308 (3) | 0.45642 (15) | 0.0542 (6) | |
C5 | 0.3055 (3) | 0.5417 (4) | 0.49434 (17) | 0.0660 (7) | |
H5 | 0.3619 | 0.5006 | 0.5507 | 0.079* | |
C6 | 0.3341 (3) | 0.7198 (4) | 0.44545 (18) | 0.0724 (7) | |
H6 | 0.4118 | 0.7963 | 0.4701 | 0.087* | |
C7 | 0.2517 (3) | 0.7865 (4) | 0.36223 (17) | 0.0690 (7) | |
H7 | 0.2744 | 0.9064 | 0.3328 | 0.083* | |
C8 | 0.1340 (2) | 0.6757 (3) | 0.32145 (15) | 0.0557 (6) | |
C9 | 0.0365 (3) | 0.7161 (4) | 0.23668 (16) | 0.0677 (7) | |
H9 | 0.0453 | 0.8321 | 0.2000 | 0.081* | |
C10 | −0.0698 (3) | 0.5836 (4) | 0.20974 (17) | 0.0735 (7) | |
H10 | −0.1314 | 0.6126 | 0.1539 | 0.088* | |
C11 | −0.0918 (2) | 0.4040 (4) | 0.26195 (17) | 0.0665 (7) | |
H11 | −0.1655 | 0.3172 | 0.2413 | 0.080* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0574 (12) | 0.0589 (13) | 0.0524 (12) | 0.0084 (11) | 0.0048 (10) | 0.0032 (11) |
N1 | 0.0677 (12) | 0.0587 (11) | 0.0623 (11) | −0.0041 (9) | 0.0064 (9) | 0.0084 (9) |
O1 | 0.0720 (12) | 0.0647 (11) | 0.0614 (11) | 0.0026 (9) | −0.0080 (8) | 0.0154 (9) |
O1A | 0.045 (11) | 0.097 (16) | 0.073 (14) | −0.037 (10) | −0.001 (9) | 0.000 (11) |
C2 | 0.0514 (12) | 0.0656 (13) | 0.0518 (12) | 0.0040 (11) | 0.0083 (10) | 0.0019 (11) |
C3 | 0.0506 (12) | 0.0564 (12) | 0.0439 (11) | 0.0052 (10) | 0.0091 (9) | 0.0007 (10) |
C4 | 0.0526 (12) | 0.0616 (13) | 0.0492 (12) | 0.0055 (10) | 0.0097 (10) | 0.0001 (10) |
C5 | 0.0624 (14) | 0.0850 (17) | 0.0505 (13) | 0.0015 (13) | 0.0010 (11) | −0.0070 (12) |
C6 | 0.0720 (16) | 0.0800 (17) | 0.0660 (15) | −0.0172 (14) | 0.0106 (13) | −0.0138 (14) |
C7 | 0.0820 (17) | 0.0633 (15) | 0.0639 (15) | −0.0074 (13) | 0.0250 (13) | −0.0017 (12) |
C8 | 0.0594 (13) | 0.0569 (13) | 0.0525 (12) | 0.0024 (10) | 0.0176 (10) | 0.0021 (11) |
C9 | 0.0744 (15) | 0.0727 (15) | 0.0571 (14) | 0.0128 (13) | 0.0137 (12) | 0.0191 (12) |
C10 | 0.0645 (15) | 0.101 (2) | 0.0549 (14) | 0.0141 (15) | 0.0017 (12) | 0.0128 (13) |
C11 | 0.0557 (13) | 0.0849 (17) | 0.0588 (14) | −0.0005 (12) | 0.0021 (11) | 0.0031 (12) |
Geometric parameters (Å, º) top
C1—O1 | 1.241 (2) | C5—H5 | 0.9300 |
C1—N1 | 1.367 (3) | C6—C7 | 1.381 (3) |
C1—C4 | 1.484 (3) | C6—H6 | 0.9300 |
N1—C2 | 1.419 (3) | C7—C8 | 1.405 (3) |
N1—H1N | 0.8600 | C7—H7 | 0.9300 |
C2—C11 | 1.359 (3) | C8—C9 | 1.428 (3) |
C2—C3 | 1.404 (3) | C9—C10 | 1.363 (3) |
C3—C8 | 1.389 (3) | C9—H9 | 0.9300 |
C3—C4 | 1.406 (3) | C10—C11 | 1.420 (3) |
C4—C5 | 1.364 (3) | C10—H10 | 0.9300 |
C5—C6 | 1.402 (3) | C11—H11 | 0.9300 |
| | | |
O1—C1—N1 | 126.6 (2) | C7—C6—C5 | 122.7 (2) |
O1—C1—C4 | 127.1 (2) | C7—C6—H6 | 118.6 |
N1—C1—C4 | 106.25 (18) | C5—C6—H6 | 118.6 |
C1—N1—C2 | 111.65 (18) | C6—C7—C8 | 120.9 (2) |
C1—N1—H1N | 124.2 | C6—C7—H7 | 119.6 |
C2—N1—H1N | 124.2 | C8—C7—H7 | 119.6 |
C11—C2—C3 | 119.3 (2) | C3—C8—C7 | 114.8 (2) |
C11—C2—N1 | 134.9 (2) | C3—C8—C9 | 115.2 (2) |
C3—C2—N1 | 105.80 (18) | C7—C8—C9 | 130.0 (2) |
C8—C3—C2 | 124.8 (2) | C10—C9—C8 | 119.7 (2) |
C8—C3—C4 | 124.8 (2) | C10—C9—H9 | 120.2 |
C2—C3—C4 | 110.43 (19) | C8—C9—H9 | 120.2 |
C5—C4—C3 | 119.1 (2) | C9—C10—C11 | 123.9 (2) |
C5—C4—C1 | 135.1 (2) | C9—C10—H10 | 118.1 |
C3—C4—C1 | 105.86 (19) | C11—C10—H10 | 118.1 |
C4—C5—C6 | 117.7 (2) | C2—C11—C10 | 117.2 (2) |
C4—C5—H5 | 121.1 | C2—C11—H11 | 121.4 |
C6—C5—H5 | 121.1 | C10—C11—H11 | 121.4 |
| | | |
O1—C1—N1—C2 | 179.1 (2) | C3—C4—C5—C6 | −0.3 (3) |
C4—C1—N1—C2 | −0.8 (2) | C1—C4—C5—C6 | −179.9 (2) |
C1—N1—C2—C11 | −179.8 (2) | C4—C5—C6—C7 | 0.7 (3) |
C1—N1—C2—C3 | 0.2 (2) | C5—C6—C7—C8 | −0.6 (4) |
C11—C2—C3—C8 | 0.0 (3) | C2—C3—C8—C7 | −179.22 (19) |
N1—C2—C3—C8 | 179.96 (18) | C4—C3—C8—C7 | 0.2 (3) |
C11—C2—C3—C4 | −179.52 (19) | C2—C3—C8—C9 | 0.6 (3) |
N1—C2—C3—C4 | 0.5 (2) | C4—C3—C8—C9 | −179.97 (19) |
C8—C3—C4—C5 | −0.1 (3) | C6—C7—C8—C3 | 0.2 (3) |
C2—C3—C4—C5 | 179.34 (19) | C6—C7—C8—C9 | −179.6 (2) |
C8—C3—C4—C1 | 179.59 (18) | C3—C8—C9—C10 | −0.9 (3) |
C2—C3—C4—C1 | −0.9 (2) | C7—C8—C9—C10 | 178.9 (2) |
O1—C1—C4—C5 | 0.8 (4) | C8—C9—C10—C11 | 0.6 (4) |
N1—C1—C4—C5 | −179.3 (2) | C3—C2—C11—C10 | −0.3 (3) |
O1—C1—C4—C3 | −178.8 (2) | N1—C2—C11—C10 | 179.7 (2) |
N1—C1—C4—C3 | 1.0 (2) | C9—C10—C11—C2 | 0.0 (4) |
(Ib100K) Benz[
cd]indol-2(1
H)-one
top
Crystal data top
C11H7NO | F(000) = 352 |
Mr = 169.18 | Dx = 1.407 Mg m−3 |
Monoclinic, P21/n | Melting point = 448–450 K |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
a = 9.0551 (19) Å | Cell parameters from 6093 reflections |
b = 6.7287 (14) Å | θ = 4.0–28.3° |
c = 13.120 (3) Å | µ = 0.09 mm−1 |
β = 92.600 (2)° | T = 100 K |
V = 798.5 (3) Å3 | Platelet, yellow |
Z = 4 | 0.20 × 0.10 × 0.05 mm |
Data collection top
Bruker APEXII CCD area-detector diffractometer | 1969 independent reflections |
Radiation source: fine-focus sealed tube | 1700 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.079 |
ϕ and ω scans | θmax = 28.3°, θmin = 3.8° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −12→11 |
Tmin = 0.982, Tmax = 0.995 | k = −8→8 |
9032 measured reflections | l = −17→17 |
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)] = 0.065 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.180 | H-atom parameters constrained |
S = 1.07 | w = 1/[σ2(Fo2) + (0.1056P)2 + 0.3049P] where P = (Fo2 + 2Fc2)/3 |
1969 reflections | (Δ/σ)max < 0.001 |
135 parameters | Δρmax = 0.48 e Å−3 |
14 restraints | Δρmin = −0.31 e Å−3 |
Crystal data top
C11H7NO | V = 798.5 (3) Å3 |
Mr = 169.18 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.0551 (19) Å | µ = 0.09 mm−1 |
b = 6.7287 (14) Å | T = 100 K |
c = 13.120 (3) Å | 0.20 × 0.10 × 0.05 mm |
β = 92.600 (2)° | |
Data collection top
Bruker APEXII CCD area-detector diffractometer | 1969 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 1700 reflections with I > 2σ(I) |
Tmin = 0.982, Tmax = 0.995 | Rint = 0.079 |
9032 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.065 | 14 restraints |
wR(F2) = 0.180 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.48 e Å−3 |
1969 reflections | Δρmin = −0.31 e Å−3 |
135 parameters | |
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 same disorder is found in this crystal as in a
larger crystal at room temperature. Atoms C1, O1, N1 and H1N and the atoms C1A,
O1A, N1A and H1NA (related by an approximate twofold rotation) are refined with
restraints to occupancies of 0.919 (4) and 0.081 (4), respectively. Restraints in
the final cycles are shown in the iucr_refine_instructions_details section
below. The restraints are inadequate to define the minor-occupancy molecule,
for example, the C1A—O1A distance is 1.31 (C1—O1 is 1.230) and N1A—C1A is
1.34 (N1—C1 is 1.375). Also the Hirshfeld test difference for N1—C2 is 5.2 s.u., indicating poor refinement of displacement parameters in the
major-occupancy molecule (C2···C1A is not a bonded distance). 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 | Uiso*/Ueq | Occ. (<1) |
O1 | 0.16662 (14) | 0.13056 (19) | 0.55699 (10) | 0.0234 (4) | 0.919 (4) |
C1 | 0.1282 (4) | 0.2405 (5) | 0.4857 (3) | 0.0227 (4) | 0.919 (4) |
N1 | 0.0148 (3) | 0.2082 (3) | 0.41439 (19) | 0.0236 (4) | 0.919 (4) |
H1N | −0.0416 | 0.1016 | 0.4129 | 0.028* | 0.919 (4) |
O1A | −0.1009 (16) | 0.066 (2) | 0.3875 (12) | 0.033 (5) | 0.081 (4) |
C1A | 0.003 (3) | 0.196 (3) | 0.411 (2) | 0.0236 (4) | 0.081 (4) |
N1A | 0.117 (4) | 0.244 (4) | 0.475 (3) | 0.0227 (4) | 0.081 (4) |
H1NA | 0.1454 | 0.1646 | 0.5257 | 0.027* | 0.081 (4) |
C2 | −0.00089 (18) | 0.3660 (3) | 0.34374 (13) | 0.0228 (4) | |
C3 | 0.11037 (17) | 0.5037 (2) | 0.37205 (12) | 0.0195 (4) | |
C4 | 0.19355 (19) | 0.4341 (2) | 0.45724 (12) | 0.0216 (4) | |
C5 | 0.3099 (2) | 0.5471 (3) | 0.49643 (13) | 0.0264 (4) | |
H5 | 0.3681 | 0.5051 | 0.5546 | 0.032* | |
C6 | 0.3389 (2) | 0.7278 (3) | 0.44640 (13) | 0.0284 (4) | |
H6 | 0.4197 | 0.8065 | 0.4714 | 0.034* | |
C7 | 0.2554 (2) | 0.7952 (3) | 0.36300 (13) | 0.0256 (4) | |
H7 | 0.2787 | 0.9191 | 0.3329 | 0.031* | |
C8 | 0.13541 (18) | 0.6820 (2) | 0.32180 (12) | 0.0213 (4) | |
C9 | 0.0365 (2) | 0.7238 (3) | 0.23605 (13) | 0.0265 (4) | |
H9 | 0.0456 | 0.8436 | 0.1986 | 0.032* | |
C10 | −0.0720 (2) | 0.5880 (3) | 0.20861 (13) | 0.0287 (4) | |
H10 | −0.1360 | 0.6174 | 0.1512 | 0.034* | |
C11 | −0.09397 (19) | 0.4049 (3) | 0.26171 (13) | 0.0273 (4) | |
H11 | −0.1701 | 0.3147 | 0.2406 | 0.033* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0239 (7) | 0.0236 (7) | 0.0227 (7) | 0.0008 (5) | 0.0018 (5) | 0.0046 (5) |
C1 | 0.0241 (11) | 0.0221 (8) | 0.0227 (11) | 0.0036 (6) | 0.0096 (7) | 0.0017 (7) |
N1 | 0.0251 (9) | 0.0209 (8) | 0.0254 (7) | −0.0018 (5) | 0.0079 (6) | 0.0031 (6) |
O1A | 0.030 (9) | 0.034 (9) | 0.034 (9) | 0.000 (7) | −0.002 (7) | 0.021 (7) |
C1A | 0.0251 (9) | 0.0209 (8) | 0.0254 (7) | −0.0018 (5) | 0.0079 (6) | 0.0031 (6) |
N1A | 0.0241 (11) | 0.0221 (8) | 0.0227 (11) | 0.0036 (6) | 0.0096 (7) | 0.0017 (7) |
C2 | 0.0198 (8) | 0.0252 (8) | 0.0243 (8) | 0.0004 (6) | 0.0103 (6) | −0.0007 (6) |
C3 | 0.0178 (8) | 0.0216 (8) | 0.0198 (7) | 0.0021 (5) | 0.0081 (6) | −0.0007 (6) |
C4 | 0.0232 (8) | 0.0232 (8) | 0.0191 (7) | 0.0047 (6) | 0.0091 (6) | 0.0010 (6) |
C5 | 0.0246 (9) | 0.0355 (10) | 0.0195 (7) | 0.0038 (7) | 0.0043 (6) | −0.0033 (6) |
C6 | 0.0255 (9) | 0.0333 (10) | 0.0270 (8) | −0.0059 (7) | 0.0085 (7) | −0.0081 (7) |
C7 | 0.0276 (9) | 0.0238 (8) | 0.0265 (8) | −0.0027 (6) | 0.0127 (7) | −0.0011 (6) |
C8 | 0.0212 (8) | 0.0231 (8) | 0.0204 (7) | 0.0025 (6) | 0.0108 (6) | 0.0010 (6) |
C9 | 0.0274 (9) | 0.0297 (9) | 0.0232 (8) | 0.0067 (7) | 0.0101 (7) | 0.0071 (7) |
C10 | 0.0225 (9) | 0.0416 (11) | 0.0226 (8) | 0.0074 (7) | 0.0055 (6) | 0.0047 (7) |
C11 | 0.0193 (8) | 0.0365 (10) | 0.0266 (8) | −0.0015 (6) | 0.0063 (6) | −0.0014 (7) |
Geometric parameters (Å, º) top
O1—C1 | 1.230 (3) | C4—C5 | 1.380 (3) |
C1—N1 | 1.375 (3) | C5—C6 | 1.412 (3) |
C1—C4 | 1.485 (3) | C5—H5 | 0.9500 |
N1—C2 | 1.412 (3) | C6—C7 | 1.378 (3) |
N1—H1N | 0.8800 | C6—H6 | 0.9500 |
O1A—C1A | 1.313 (15) | C7—C8 | 1.414 (2) |
C1A—N1A | 1.339 (16) | C7—H7 | 0.9500 |
C1A—C2 | 1.445 (18) | C8—C9 | 1.434 (2) |
N1A—C4 | 1.481 (11) | C9—C10 | 1.377 (3) |
N1A—H1NA | 0.8800 | C9—H9 | 0.9500 |
C2—C11 | 1.362 (3) | C10—C11 | 1.433 (3) |
C2—C3 | 1.406 (2) | C10—H10 | 0.9500 |
C3—C8 | 1.393 (2) | C11—H11 | 0.9500 |
C3—C4 | 1.400 (2) | | |
| | | |
O1—C1—N1 | 126.8 (2) | C5—C4—C1 | 134.08 (17) |
O1—C1—C4 | 128.1 (2) | C3—C4—C1 | 106.75 (17) |
N1—C1—C4 | 105.14 (18) | C4—C5—C6 | 117.13 (16) |
C1—N1—C2 | 112.18 (18) | C4—C5—H5 | 121.4 |
C1—N1—H1N | 123.9 | C6—C5—H5 | 121.4 |
C2—N1—H1N | 123.9 | C7—C6—C5 | 123.09 (17) |
O1A—C1A—N1A | 146.2 (17) | C7—C6—H6 | 118.5 |
O1A—C1A—C2 | 112.8 (15) | C5—C6—H6 | 118.5 |
N1A—C1A—C2 | 101.0 (10) | C6—C7—C8 | 120.68 (16) |
C1A—N1A—C4 | 117.4 (12) | C6—C7—H7 | 119.7 |
C1A—N1A—H1NA | 121.3 | C8—C7—H7 | 119.7 |
C4—N1A—H1NA | 121.3 | C3—C8—C7 | 114.96 (16) |
C11—C2—C3 | 119.49 (16) | C3—C8—C9 | 115.51 (16) |
C11—C2—N1 | 134.69 (17) | C7—C8—C9 | 129.53 (16) |
C3—C2—N1 | 105.81 (16) | C10—C9—C8 | 119.22 (16) |
C11—C2—C1A | 129.2 (7) | C10—C9—H9 | 120.4 |
C3—C2—C1A | 111.3 (7) | C8—C9—H9 | 120.4 |
C8—C3—C4 | 124.95 (16) | C9—C10—C11 | 123.78 (16) |
C8—C3—C2 | 124.94 (16) | C9—C10—H10 | 118.1 |
C4—C3—C2 | 110.10 (15) | C11—C10—H10 | 118.1 |
C5—C4—C3 | 119.17 (16) | C2—C11—C10 | 117.05 (17) |
C5—C4—N1A | 140.6 (6) | C2—C11—H11 | 121.5 |
C3—C4—N1A | 100.2 (6) | C10—C11—H11 | 121.5 |
(Ic100K) Benz[
cd]indol-2(1
H)-one
top
Crystal data top
C11H7NO | F(000) = 352 |
Mr = 169.18 | Dx = 1.407 Mg m−3 |
Monoclinic, P21/n | Melting point = 448–450 K |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
a = 9.0551 (19) Å | Cell parameters from 6093 reflections |
b = 6.7287 (14) Å | θ = 4.0–28.3° |
c = 13.120 (3) Å | µ = 0.09 mm−1 |
β = 92.600 (2)° | T = 100 K |
V = 798.5 (3) Å3 | Platelet, yellow |
Z = 4 | 0.20 × 0.10 × 0.05 mm |
Data collection top
Bruker APEXII CCD area-detector diffractometer | 1969 independent reflections |
Radiation source: fine-focus sealed tube | 1700 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.079 |
ϕ and ω scans | θmax = 28.3°, θmin = 3.8° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −12→11 |
Tmin = 0.982, Tmax = 0.995 | k = −8→8 |
9032 measured reflections | l = −17→17 |
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)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.164 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.1076P)2 + 0.0449P] where P = (Fo2 + 2Fc2)/3 |
1969 reflections | (Δ/σ)max = 0.002 |
138 parameters | Δρmax = 0.45 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
Crystal data top
C11H7NO | V = 798.5 (3) Å3 |
Mr = 169.18 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.0551 (19) Å | µ = 0.09 mm−1 |
b = 6.7287 (14) Å | T = 100 K |
c = 13.120 (3) Å | 0.20 × 0.10 × 0.05 mm |
β = 92.600 (2)° | |
Data collection top
Bruker APEXII CCD area-detector diffractometer | 1969 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 1700 reflections with I > 2σ(I) |
Tmin = 0.982, Tmax = 0.995 | Rint = 0.079 |
9032 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.164 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.45 e Å−3 |
1969 reflections | Δρmin = −0.27 e Å−3 |
138 parameters | |
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. After refinement of a disorder model with four minor-occupancy
atoms (data_Ib), with 135 parameters and 14 restraints, resulting in R
= 0.0651 and wR = 0.1725, Hirshfeld (Hirshfeld, 1976) tests of the ADPs
for the major conformer were poor. A rigid-body refinement was tried, first
with six minor-occupancy atoms and finally with the entire minor molecule. The
rigid body was constructed using SAME O1A > H11A at the beginning of the atom
list. In the final cycles the major conformer and occupancy were fully refined,
while AFIX 6 was used for the minor conformer, with isotropic U values. The
result presented here (138 parameters, 0 restraints) gave improved Hirshfeld
tests, a reduced R and wR, and a slightly reduced major-occupancy
factor [0.912 (3) versus 0.919 (4)]. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
O1 | 0.16659 (11) | 0.13084 (14) | 0.55695 (7) | 0.0241 (3) | 0.912 (3) |
C1 | 0.12932 (18) | 0.2418 (2) | 0.48603 (11) | 0.0191 (3) | 0.912 (3) |
N1 | 0.01491 (17) | 0.20721 (17) | 0.41482 (10) | 0.0206 (3) | 0.912 (3) |
H1N | −0.0412 | 0.1004 | 0.4135 | 0.025* | 0.912 (3) |
C2 | 0.0001 (2) | 0.3649 (2) | 0.34490 (18) | 0.0205 (4) | 0.912 (3) |
C3 | 0.1117 (4) | 0.5040 (2) | 0.37240 (12) | 0.0193 (9) | 0.912 (3) |
C4 | 0.1947 (2) | 0.4356 (3) | 0.45732 (10) | 0.0188 (3) | 0.912 (3) |
C5 | 0.31064 (16) | 0.5485 (3) | 0.49643 (10) | 0.0223 (3) | 0.912 (3) |
H5 | 0.3689 | 0.5070 | 0.5546 | 0.027* | 0.912 (3) |
C6 | 0.33907 (17) | 0.7301 (3) | 0.44569 (11) | 0.0242 (4) | 0.912 (3) |
H6 | 0.4197 | 0.8096 | 0.4703 | 0.029* | 0.912 (3) |
C7 | 0.2541 (2) | 0.7967 (2) | 0.36159 (16) | 0.0232 (4) | 0.912 (3) |
H7 | 0.2767 | 0.9204 | 0.3310 | 0.028* | 0.912 (3) |
C8 | 0.1346 (3) | 0.6821 (2) | 0.32122 (18) | 0.0195 (6) | 0.912 (3) |
C9 | 0.0360 (2) | 0.7232 (3) | 0.23569 (13) | 0.0229 (4) | 0.912 (3) |
H9 | 0.0448 | 0.8430 | 0.1981 | 0.027* | 0.912 (3) |
C10 | −0.07256 (17) | 0.5859 (3) | 0.20847 (10) | 0.0248 (4) | 0.912 (3) |
H10 | −0.1366 | 0.6141 | 0.1509 | 0.030* | 0.912 (3) |
C11 | −0.09390 (16) | 0.4029 (3) | 0.26237 (12) | 0.0238 (3) | 0.912 (3) |
H11 | −0.1699 | 0.3122 | 0.2417 | 0.029* | 0.912 (3) |
O1A | −0.1101 (10) | 0.0612 (11) | 0.3819 (7) | 0.033 (3)* | 0.088 (3) |
C1A | −0.0268 (8) | 0.2094 (10) | 0.3908 (6) | 0.026 (5)* | 0.088 (3) |
N1A | 0.0866 (9) | 0.2198 (11) | 0.4589 (6) | 0.015 (3)* | 0.088 (3) |
H1NA | 0.1109 | 0.1239 | 0.5020 | 0.018* | 0.088 (3) |
C2A | 0.1620 (8) | 0.3990 (11) | 0.4543 (6) | 0.044 (11)* | 0.088 (3) |
C3A | 0.0935 (9) | 0.5004 (10) | 0.3694 (6) | 0.025 (12)* | 0.088 (3) |
C4A | −0.0212 (9) | 0.3853 (11) | 0.3231 (6) | 0.034 (9)* | 0.088 (3) |
C5A | −0.0976 (13) | 0.4653 (15) | 0.2416 (8) | 0.035 (6)* | 0.088 (3) |
H5A | −0.1770 | 0.3968 | 0.2074 | 0.042* | 0.088 (3) |
C6A | −0.0526 (16) | 0.6548 (17) | 0.2109 (9) | 0.045 (8)* | 0.088 (3) |
H6A | −0.1097 | 0.7184 | 0.1579 | 0.053* | 0.088 (3) |
C7A | 0.0653 (16) | 0.7523 (14) | 0.2511 (9) | 0.088 (18)* | 0.088 (3) |
H7A | 0.0915 | 0.8760 | 0.2220 | 0.105* | 0.088 (3) |
C8A | 0.1511 (12) | 0.6796 (11) | 0.3338 (8) | 0.049 (15)* | 0.088 (3) |
C9A | 0.2743 (13) | 0.7741 (13) | 0.3876 (10) | 0.018 (5)* | 0.088 (3) |
H9A | 0.3111 | 0.9009 | 0.3697 | 0.021* | 0.088 (3) |
C10A | 0.3328 (11) | 0.6645 (16) | 0.4664 (9) | 0.022 (4)* | 0.088 (3) |
H10A | 0.4165 | 0.7182 | 0.5029 | 0.027* | 0.088 (3) |
C11A | 0.2815 (10) | 0.4804 (15) | 0.4988 (8) | 0.041 (6)* | 0.088 (3) |
H11A | 0.3327 | 0.4129 | 0.5533 | 0.049* | 0.088 (3) |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0245 (6) | 0.0243 (5) | 0.0234 (5) | 0.0006 (4) | 0.0014 (4) | 0.0037 (4) |
C1 | 0.0178 (8) | 0.0215 (7) | 0.0183 (6) | 0.0004 (5) | 0.0040 (6) | −0.0011 (5) |
N1 | 0.0188 (7) | 0.0226 (6) | 0.0206 (6) | −0.0016 (4) | 0.0014 (6) | 0.0034 (4) |
C2 | 0.0178 (7) | 0.0240 (8) | 0.0205 (7) | 0.0018 (5) | 0.0079 (6) | 0.0008 (6) |
C3 | 0.0160 (8) | 0.0223 (13) | 0.0203 (11) | 0.0017 (4) | 0.0080 (5) | −0.0011 (5) |
C4 | 0.0186 (7) | 0.0203 (6) | 0.0180 (7) | 0.0019 (7) | 0.0080 (5) | −0.0001 (5) |
C5 | 0.0223 (7) | 0.0262 (8) | 0.0188 (6) | −0.0004 (6) | 0.0049 (5) | −0.0022 (5) |
C6 | 0.0253 (8) | 0.0250 (8) | 0.0230 (7) | −0.0063 (5) | 0.0080 (6) | −0.0022 (6) |
C7 | 0.0261 (9) | 0.0237 (8) | 0.0205 (8) | −0.0008 (6) | 0.0088 (7) | 0.0016 (6) |
C8 | 0.0191 (8) | 0.0226 (10) | 0.0177 (6) | 0.0024 (5) | 0.0095 (5) | 0.0013 (5) |
C9 | 0.0229 (8) | 0.0262 (7) | 0.0202 (6) | 0.0051 (6) | 0.0081 (6) | 0.0058 (5) |
C10 | 0.0208 (8) | 0.0324 (10) | 0.0217 (7) | 0.0043 (6) | 0.0056 (5) | 0.0052 (6) |
C11 | 0.0188 (7) | 0.0299 (8) | 0.0232 (7) | −0.0011 (5) | 0.0055 (5) | 0.0028 (7) |
Geometric parameters (Å, º) top
O1—C1 | 1.2283 (17) | O1A—C1A | 1.25 |
C1—N1 | 1.383 (2) | C1A—N1A | 1.33 |
C1—C4 | 1.488 (3) | C1A—C4A | 1.48 |
N1—C2 | 1.405 (3) | N1A—C2A | 1.39 |
N1—H1N | 0.8800 | N1A—H1NA | 0.8800 |
C2—C11 | 1.371 (3) | C2A—C11A | 1.32 |
C2—C3 | 1.413 (3) | C2A—C3A | 1.42 |
C3—C4 | 1.393 (3) | C3A—C8A | 1.40 |
C3—C8 | 1.394 (2) | C3A—C4A | 1.41 |
C4—C5 | 1.376 (3) | C4A—C5A | 1.36 |
C5—C6 | 1.421 (2) | C5A—C6A | 1.40 |
C5—H5 | 0.9500 | C5A—H5A | 0.9500 |
C6—C7 | 1.390 (3) | C6A—C7A | 1.34 |
C6—H6 | 0.9500 | C6A—H6A | 0.9500 |
C7—C8 | 1.412 (3) | C7A—C8A | 1.39 |
C7—H7 | 0.9500 | C7A—H7A | 0.9500 |
C8—C9 | 1.429 (3) | C8A—C9A | 1.44 |
C9—C10 | 1.384 (3) | C9A—C10A | 1.36 |
C9—H9 | 0.9500 | C9A—H9A | 0.9500 |
C10—C11 | 1.437 (2) | C10A—C11A | 1.40 |
C10—H10 | 0.9500 | C10A—H10A | 0.9500 |
C11—H11 | 0.9500 | C11A—H11A | 0.9500 |
| | | |
O1—C1—N1 | 125.53 (14) | O1A—C1A—N1A | 123.2 |
O1—C1—C4 | 128.74 (16) | O1A—C1A—C4A | 128.1 |
N1—C1—C4 | 105.73 (12) | N1A—C1A—C4A | 108.3 |
C1—N1—C2 | 111.12 (13) | C1A—N1A—C2A | 112.5 |
C1—N1—H1N | 124.4 | C1A—N1A—H1NA | 123.8 |
C2—N1—H1N | 124.4 | C2A—N1A—H1NA | 123.8 |
C11—C2—N1 | 133.96 (15) | C11A—C2A—N1A | 137.2 |
C11—C2—C3 | 119.32 (18) | C11A—C2A—C3A | 117.7 |
N1—C2—C3 | 106.7 (2) | N1A—C2A—C3A | 104.6 |
C4—C3—C8 | 125.6 (3) | C8A—C3A—C4A | 127.3 |
C4—C3—C2 | 109.82 (18) | C8A—C3A—C2A | 121.1 |
C8—C3—C2 | 124.5 (3) | C4A—C3A—C2A | 111.1 |
C5—C4—C3 | 119.35 (18) | C5A—C4A—C3A | 117.4 |
C5—C4—C1 | 134.05 (13) | C5A—C4A—C1A | 139.3 |
C3—C4—C1 | 106.59 (19) | C3A—C4A—C1A | 103.0 |
C4—C5—C6 | 116.85 (13) | C4A—C5A—C6A | 116.2 |
C4—C5—H5 | 121.6 | C4A—C5A—H5A | 121.9 |
C6—C5—H5 | 121.6 | C6A—C5A—H5A | 121.9 |
C7—C6—C5 | 122.93 (13) | C7A—C6A—C5A | 124.7 |
C7—C6—H6 | 118.5 | C7A—C6A—H6A | 117.7 |
C5—C6—H6 | 118.5 | C5A—C6A—H6A | 117.7 |
C6—C7—C8 | 120.58 (17) | C6A—C7A—C8A | 122.7 |
C6—C7—H7 | 119.7 | C6A—C7A—H7A | 118.7 |
C8—C7—H7 | 119.7 | C8A—C7A—H7A | 118.7 |
C3—C8—C7 | 114.7 (3) | C7A—C8A—C3A | 111.0 |
C3—C8—C9 | 116.3 (2) | C7A—C8A—C9A | 128.2 |
C7—C8—C9 | 129.03 (17) | C3A—C8A—C9A | 120.5 |
C10—C9—C8 | 118.98 (13) | C10A—C9A—C8A | 113.6 |
C10—C9—H9 | 120.5 | C10A—C9A—H9A | 123.2 |
C8—C9—H9 | 120.5 | C8A—C9A—H9A | 123.2 |
C9—C10—C11 | 123.70 (13) | C9A—C10A—C11A | 126.2 |
C9—C10—H10 | 118.2 | C9A—C10A—H10A | 116.9 |
C11—C10—H10 | 118.2 | C11A—C10A—H10A | 116.9 |
C2—C11—C10 | 117.13 (14) | C2A—C11A—C10A | 120.6 |
C2—C11—H11 | 121.4 | C2A—C11A—H11A | 119.7 |
C10—C11—H11 | 121.4 | C10A—C11A—H11A | 119.7 |
| | | |
O1—C1—N1—C2 | 179.08 (12) | O1A—C1A—N1A—C2A | −179.8 |
C4—C1—N1—C2 | −1.40 (14) | C4A—C1A—N1A—C2A | 7.5 |
C1—N1—C2—C11 | −179.60 (14) | C1A—N1A—C2A—C11A | −176.1 |
C1—N1—C2—C3 | 0.89 (15) | C1A—N1A—C2A—C3A | −4.7 |
C11—C2—C3—C4 | −179.55 (12) | C11A—C2A—C3A—C8A | 0.4 |
N1—C2—C3—C4 | 0.05 (16) | N1A—C2A—C3A—C8A | −172.9 |
C11—C2—C3—C8 | 0.2 (2) | C11A—C2A—C3A—C4A | 173.2 |
N1—C2—C3—C8 | 179.77 (14) | N1A—C2A—C3A—C4A | −0.1 |
C8—C3—C4—C5 | −0.2 (2) | C8A—C3A—C4A—C5A | −8.5 |
C2—C3—C4—C5 | 179.50 (12) | C2A—C3A—C4A—C5A | 179.2 |
C8—C3—C4—C1 | 179.40 (14) | C8A—C3A—C4A—C1A | 176.5 |
C2—C3—C4—C1 | −0.88 (16) | C2A—C3A—C4A—C1A | 4.2 |
O1—C1—C4—C5 | 0.4 (2) | O1A—C1A—C4A—C5A | 7.6 |
N1—C1—C4—C5 | −179.07 (13) | N1A—C1A—C4A—C5A | 179.8 |
O1—C1—C4—C3 | −179.12 (14) | O1A—C1A—C4A—C3A | −179.2 |
N1—C1—C4—C3 | 1.38 (14) | N1A—C1A—C4A—C3A | −7.0 |
C3—C4—C5—C6 | −0.60 (19) | C3A—C4A—C5A—C6A | 0.9 |
C1—C4—C5—C6 | 179.90 (13) | C1A—C4A—C5A—C6A | 173.4 |
C4—C5—C6—C7 | 1.2 (2) | C4A—C5A—C6A—C7A | 5.3 |
C5—C6—C7—C8 | −1.0 (2) | C5A—C6A—C7A—C8A | −4.6 |
C4—C3—C8—C7 | 0.4 (2) | C6A—C7A—C8A—C3A | −2.3 |
C2—C3—C8—C7 | −179.24 (13) | C6A—C7A—C8A—C9A | −176.1 |
C4—C3—C8—C9 | −179.91 (14) | C4A—C3A—C8A—C7A | 9.0 |
C2—C3—C8—C9 | 0.4 (2) | C2A—C3A—C8A—C7A | −179.5 |
C6—C7—C8—C3 | 0.19 (19) | C4A—C3A—C8A—C9A | −176.7 |
C6—C7—C8—C9 | −179.40 (13) | C2A—C3A—C8A—C9A | −5.1 |
C3—C8—C9—C10 | −0.89 (19) | C7A—C8A—C9A—C10A | 178.9 |
C7—C8—C9—C10 | 178.70 (13) | C3A—C8A—C9A—C10A | 5.7 |
C8—C9—C10—C11 | 0.9 (2) | C8A—C9A—C10A—C11A | −2.1 |
N1—C2—C11—C10 | −179.72 (13) | N1A—C2A—C11A—C10A | 173.8 |
C3—C2—C11—C10 | −0.26 (19) | C3A—C2A—C11A—C10A | 3.3 |
C9—C10—C11—C2 | −0.3 (2) | C9A—C10A—C11A—C2A | −2.5 |
Experimental details
| (Ia298K) | (Ib100K) | (Ic100K) |
Crystal data |
Chemical formula | C11H7NO | C11H7NO | C11H7NO |
Mr | 169.18 | 169.18 | 169.18 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, P21/n | Monoclinic, P21/n |
Temperature (K) | 298 | 100 | 100 |
a, b, c (Å) | 9.251 (3), 6.7748 (17), 13.256 (4) | 9.0551 (19), 6.7287 (14), 13.120 (3) | 9.0551 (19), 6.7287 (14), 13.120 (3) |
β (°) | 93.196 (8) | 92.600 (2) | 92.600 (2) |
V (Å3) | 829.5 (4) | 798.5 (3) | 798.5 (3) |
Z | 4 | 4 | 4 |
Radiation type | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.09 | 0.09 | 0.09 |
Crystal size (mm) | 0.35 × 0.25 × 0.10 | 0.20 × 0.10 × 0.05 | 0.20 × 0.10 × 0.05 |
|
Data collection |
Diffractometer | Modified Hubers diffractometer | Bruker APEXII CCD area-detector diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | – | Multi-scan (SADABS; Bruker, 2005) | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | – | 0.982, 0.995 | 0.982, 0.995 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1462, 1462, 992 | 9032, 1969, 1700 | 9032, 1969, 1700 |
Rint | 0.000 | 0.079 | 0.079 |
(sin θ/λ)max (Å−1) | 0.595 | 0.668 | 0.668 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.133, 1.09 | 0.065, 0.180, 1.07 | 0.058, 0.164, 1.09 |
No. of reflections | 1462 | 1969 | 1969 |
No. of parameters | 128 | 135 | 138 |
No. of restraints | 0 | 14 | 0 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.19, −0.14 | 0.48, −0.31 | 0.45, −0.27 |
Selected bond lengths (Å) for (Ia298K) topC1—O1 | 1.241 (2) | C1—C4 | 1.484 (3) |
C1—N1 | 1.367 (3) | N1—C2 | 1.419 (3) |
Selected bond lengths (Å) for (Ib100K) topO1—C1 | 1.230 (3) | C1A—N1A | 1.339 (16) |
C1—N1 | 1.375 (3) | C1A—C2 | 1.445 (18) |
C1—C4 | 1.485 (3) | N1A—C4 | 1.481 (11) |
N1—C2 | 1.412 (3) | C2—C3 | 1.406 (2) |
O1A—C1A | 1.313 (15) | C3—C4 | 1.400 (2) |
Selected bond lengths (Å) for (Ic100K) topO1—C1 | 1.2283 (17) | O1A—C1A | 1.25 |
C1—N1 | 1.383 (2) | C1A—N1A | 1.33 |
C1—C4 | 1.488 (3) | C1A—C4A | 1.48 |
N1—C2 | 1.405 (3) | N1A—C2A | 1.39 |
C2—C3 | 1.413 (3) | C2A—C3A | 1.42 |
C3—C4 | 1.393 (3) | C3A—C4A | 1.41 |
C(═O)—N (`amide') distances (Å) and torsion angles (°) (Fig. 4) top2-PD, 2-PD dimers, 2-PD.H2O (ab initio values, HF/6-31G*, s.u. values
not given). Crystal structures (see Fig. 4): 2-PD; (2-PD)3.HBr;
2-PD–succinic acid; 2-PD–fumaric acid; gabapentin-lactam (A1),
gabapentin-lactam–benzoic acid;
(5S*)-1-oxo-2-azaspiro[4.4]non-7-ene-7-carboxylate (A2); 2-PD.H2O (A3); 41
γ-lactams (ave, stdev). Search A: 59 2-PD centrosymmetric dimers (ave, stdev);
146 nondimer 2-PD derivatives (ave, stdev); 39 2-PD derivatives, cocrystals
[dimers and nondimers (ave, stdev)]; 22 2-PD centrosymmetric dimers, 100–200 K
(ave, stdev); 51 nondimer 2-PD derivatives, 100–200 K (ave, stdev), 13 2-PD
derivatives, cocrystals, 93–93 K [dimers and nondimers (ave, stdev)]. Other
examples: 12 primary amides (ave, stdev); three trans secondary amide
groups. Search B: ten derivatives of (I) {benz[cd]indol-2(1H)-one
(ave, stdev)}; three examples from the ten derivatives (see Fig. 4). This work:
(Ia), (Ib) and (Ic). |
Structure | C—N | C═O | C—N + C═O | N···O | O—C—N—H | C—C—N—C | Source |
2-PD, ab initio | 1.356 | 1.196 | 2.552 | N/A | -9.39 | Not given | Yekeler et al. (1999) |
2-PD, cyclic dimer | 1.338 | 1.209 | 2.557 | 3.00* | -6.12 | Not given | Yekeler et al. (1999) |
2-PD, dimer, 1 hydrogen bond | 1.345 | 1.203 | 2.548 | 3.03* | -8.67 | Not given | Yekeler et al. (1999) |
2-PD, 1,2 or 3 H2O | 1.34 (1.344–1.336) | 1.21 (1.206–1.210) | 2.542–2.550 | 3.01, 2.97* (2,3) | -6.36, -5.90 (2,3) | Not given | Yekeler et al. (1999) |
| | | | | | | |
Crystal structures | | | | | | | |
2-PD (NILYAI) | 1.335 (2) | 1.237 (2) | 2.572 | 2.92 | -11 | 4.3 | Goddard et al. (1998) |
(2-PD)3.HBr (FAJHUT) | 1.33 (2) (N1—C1) | 1.20 (2) (C1═O1) | 2.53 | 2.96 (dimer) | -4 | 1 | Boeyens et al. (1986) |
Molecule 2 (FAJHUT) | 1.24 (2) (N2—C5) | 1.29 (2) (C5═O2) | 2.53 | 2.76 (nondimer) | -2 | -3 | Boeyens et al. (1986) |
Molecule 3 (FAJHUT) | 1.30 (2) (N3—C9) | 1.26 (2) (C9═O3) | 2.56 | 3.01 (dimer) | 2 | -1 | Boeyens et al. (1986) |
2-PD–succinic acid (UHACEM) | 1.322 (7) | 1.247 (7) | 2.569 | 2.94 | 4.0 | 4.0 | Callear et al. (2009) |
2-PD–fumaric acid (UHACUC) | 1.321 (3) | 1.254 (3) | 2.575 | 2.92 | 3.0 | 2.0 | Callear et al. (2009) |
A1 (AWUWOE) | 1.331 (2) | 1.234 (3) | 2.565 | 2.91 | -3 | 0.3 | Ananda et al. (2003) |
A1–benzoic acid (XOHXAU) | 1.319 (2) | 1.249 (2) | 2.568 | 2.97 | 0 | 2.3 | Braga et al. (2008) |
A2 (GASSUP) | 1.355 (2) | 1.256 (2) | 2.611 | 2.95 | 0.4 | 5 | Yong et al. (2005) |
A3: 2-PD.H2O (DIPMUK) | 1.319 (3) | 1.257 (3) | 2.576 | 2.83 (H2O) | 0.5 | 0.8 | Pirilä et al. (1999) |
41 γ-lactams | 1.335 (13) | 1.232 (11) | | | | | CSD (Norskov-Lauritsen et al. 1985) |
| | | | | | | |
Search A (Fig. 4) | | | | | | | |
59 2-PD dimers | 1.338 (8) | 1.232 (8) | 2.570 (11) | | | | CSD** |
146 2-PD nondimers | 1.335 (10) | 1.232 (9) | 2.567 (12) | | | | CSD** |
39 2-PD cocrystals | 1.332 (11) | 1.232 (14) | 2.564 (12) | | | | CSD** |
22 2-PD dimers, 100–200 K | 1.341 (9) | 1.235 (7) | 2.576 (12) | | | | CSD** |
51 2-PD nondimers, 100–200 K | 1.337 (9) | 1.235 (8) | 2.571 (9) | | | | CSD** |
13 2-PD cocrystals, 93–193 K | 1.328 (8) | 1.244 (10) | 2.572 (6) | | | | CSD** |
| | | | | | | |
Other examples | | | | | | | |
12 primary amides (dimers and nondimers) | 1.323 (8) | 1.238 (9) | 2.561 (14) | | | | Gavezzotti (2010) |
Three trans amides: unit I | 1.325 (2) | 1.237 (2) | 2.562 | 2.87 (N2···O1) | 177 | -178 | Munro & Wilson (2010) |
Unit I' | 1.338 (2) | 1.226 (2) | 2.564 | 2.93 (N3..O1) | -174 | 177 | ibid. |
Unit II | 1.3382 (12) | 1.2289 (11) | 2.567 | 3.09 | 177 | -175 | ibid. |
| | | | | | | |
Search B (Fig. 4) | | | | | | | |
Ten naphtholactam derivatives | 1.41 (3) | 1.215 (11) | 2.63 (2) | N/A | (O—C—N—R) | (C—C—N—C) | CSD*** |
B1 (QACQOA) | 1.376 (7) | 1.226 (7) | 2.602 | 2.90 | 4 | -1.2 | Wang et al. (1998) |
B2 (RAKYUY) | 1.430 (5) | 1.193 (5) | 2.623 | N/A (Br···O) | -3.1 | -0.2 | Lux et al. (2005) |
B3, molecule 1 (DUXXEA) | 1.42 (1) | 1.219 (8) | 2.634 | N/A (no N···O) | -12 | 1 | Sheik et al. (2010) |
B3, molecule 2 (DUXXEA) | 1.460 (8) | 1.209 (9) | 2.669 | N/A (no N···O) | 4 | 2 | Sheik et al. (2010) |
(Ia) (298 K) | 1.367 (3) | 1.241 (3) | 2.608 | 2.866 | -0.9 | -0.8 | This work |
(Ib) (100 K) | 1.375 (3) | 1.230 (4) | 2.605 | 2.845 | -0.8 | -1.3 | This work |
(Ic) (100 K) | 1.383 (2) | 1.228 (2) | 2.611 | 2.840 | -0.9 | -1.4 | This work |
Notes: (*) Calculated from given N—H and H···O distances and N—H···O angle.
C—C—N—C not given. (**) Search requirements for 2-pyrrolidone (2-PD): a
five-membered ring with the -C(═O)—NH- group and three other C atoms
(Fig. 4), each with a total of four connected atoms. Requirements also included
three-dimensional crystal coordinates, only organics, no powder structures, no
ions, no disorder or errors and R ≤ 0.075. Cambridge Structural
Database (CSD) Version 5.32 (November 2010, four updates) (Allen,
2002). (***)
Search requirements for (I) and derivatives: three-dimensional crystal
coordinates, only organics, no powder structures, no ions, no errors.
N—R allowed, C—R single bond, no solvent. CSD Version 5.32
(November 2010, four updates). Tables S-4, S-5 and S-6 in the
supplementary
material give detailed refcode lists for the CSD searches. |
Crystal packing topMolecule–molecule energies calculated using OPIX (Gavezzotti,
2003);
see Fig. 5 for symmetry codes. |
Symmetry codes | Molecule–molecule distance (centers of mass) (Å) | Molecule–molecule energy (kJ mol-1) |
(i) to (ii) | 7.49 | -65 |
(i) to (iii) | 6.73 | -15 |
(i) to (iv) | 3.78 | -48 |
(i) to (v) | 6.73 | -15 |
(i) to (vii) | 5.51 | -32 |
(i) to (ix) | 5.51 | -32 |
(i) to (xii) | 7.45 | -13 |
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Naphtholactam, (I), may be used as a starting material in the preparation of anticancer and hypotensive agents; an improved large-scale synthesis of the title compound has been published (Marzoni & Varney, 1997). Deprotonation of (I) yields the lactamate, which has been tested as a ligand with fluorophore properties (Limmert et al., 2003). Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei was crystallized with a molecule of (I) in the active site (Bosch et al., 2006) in a study of `fragment cocktail soaks'. The Cambridge Structural Database (CSD, Version 5.32; Allen, 2002; Macrae et al., 2008) contains three-dimensional coordinates for 15 derivatives of (I), but no published crystal structure of the unsubstituted compound was found.
Before our investigation began, it was predicted that the –C(═O)—NH– (`amide') bond in (I) would be longer than that in other amides. But what is the distance in `other amides'? The CIF dictionary contains no reference C—N bond length for amides. Clearly, the C—N and C═O bond lengths are changed by distortion of the amide unit away from planarity (Bennett et al., 1990; Wang et al., 1991, and references therein). In this paper, we examine evidence that, in crystal structures, these distances also depend on the intermolecular hydrogen-bonding pattern.
In the crystal structure of (I) presented here, the structural units are pairs of molecules strongly hydrogen0bonded in dimers. The dimers are shown with atom numbering in Figs. 1, 2 and 3. Tables 1, 2 and 3 give bond lengths for the five-membered ring in (Ia), at 298 K, (Ib), at 100 K, and (Ic), with the same data as (Ib) but using a different disorder model.
As in 2-pyrrolidone (or 2-pyrrolidinone, 2-PD, the saturated γ-lactam), the –C(═O)—NH– conformation in (I) is required to be cis, and planar or nearly so (Fig. 4 and Table 4). To estimate the effect of the naphthalene rings on the lactam portion of (I), we may first examine 2-PD and its derivatives.
The length of the cis-amide C—N bond in cyclic lactam crystal structures was found to be nearly independent of ring size, from four- to eight-membered rings (Yang et al., 1987). For five-membered rings, an average value from 41 crystal structures from the CSD [1.335 (13) Å, Table 4] was quoted. The structures surveyed included both dimeric and nondimeric hydrogen bonding in the crystal packing, and all were considered to be planar.
However, in an ab initio study the `amide' C—N and C═O bond lengths for 2-PD were shown to differ for the single molecule, hydrogen-bonded 2-PD dimers and clusters of 2-PD with water molecules (Yekeler et al., 1999). The C—N distance decreased by about 0.02 Å, and the C═O distance increased by about 0.01 Å, if 2-PD formed N—H···O and C═O···H hydrogen bonds with another 2-PD molecule or with water. [Out-of-plane distortions are also accompanied by a smaller change in the C═O than in the C—N bond lengths (Wang et al., (1991).]
The structure of (2-PD)3.HBr3 , which was referred to by Yekeler et al. (1999), shows different hydrogen-bonding patterns for the three 2-PD molecules in the asymmetric unit (Table 4). The shortest C—N (1.24 Å) and longest C═O (1.29 Å) are attributed to a C═O···H+···O═C interaction (O···O = 2.45 Å); the structure may be better described in terms of three units, 2-PD, (2-PD)2.H+ and Br3- (Boeyens et al., 1986). Ions were excluded from the searches described below.
Table 4 gives the `amide' bond lengths (C—N and C═O) from the ab initio study, from appropriate structures from the CSD and from this work. Fig. 4 shows the models used to search the CSD and some example structures. These examples indicate that, even though there is little or no distortion from planarity, ions and cocrystals may exhibit additional hydrogen bonding that extends the resonance of the –C(═O)—NH– group. The carbonyl O atom may accept two hydrogen bonds, as demonstrated by the structure of 2-PD.H2O (Table 4 and Fig. 4). For these reasons, we have averaged the distances for centrosymmetric dimers, nondimers (including `dimers' with no center of symmetry) and cocrystals separately.
As seen in Table 4, more recent crystal structures are, on average, in agreement with the ab initio cyclic dimer value of 1.338 Å (Yekeler et al., 1999). For example, in a low-temperature phase of 2-PD (CSD refcode NILYAI, Fig. 4) the C—N bond length is 1.335 (2) Å. The average C—N and C═O bond lengths for crystal structures of 2-PD derivatives in the CSD are nearly the same for cyclic dimers and for nondimers.
Examination of the structures with unusually long and unusually short amide bonds suggests explanations for variations from the average. An example of an outlier with `long' amide bonds is A2 in Fig. 4 [(5S*)-1-oxo-2-azaspiro[4.4]non-7-ene-7-carboxylate; GASSUP; Yong et al., 2005]. A centrosymmetric amide–amide dimer is formed, but the carbonyl O atom also accepts a C—H···O hydrogen bond and makes contact with a neighboring –C═C– C atom. The amide C—N and C═O distances are 1.355 (2) and 1.256 (2) Å, respectively, each significantly longer than the average distances in Table 4. On average, however, the sum of these two distances is nearly constant. When structures determined at 200 K and below are separated from the overall search results, the average distances for dimers and nondimers are slightly longer, as expected when thermal motion effects are reduced.
Cocrystals are averaged separately in Table 4 because they generally produce `short' C—N (amide) bonds (and `long' C═O bonds). For 2-PD.H2O (DIPMUK, Table 4), the C—N bond is significantly shorter [1.319 (3) Å] and the C═O bond longer than average. Each water molecule accepts one and donates two H atoms to hydrogen bonds; see A3 in Fig. 4. (This arrangement was not included in the ab initio study.) Similarly, for gabapentin-lactam–benzoic acid (XOHXAU), the C—N bond is shorter than that in gabapentin-lactam (A1, AWUWOE). In the benzoic acid solvate, the –C(═ O)—NH– O atom is hydrogen-bonded to both solvent and another lactam in a cyclic tetramer, while the pure compound is a cyclic dimer. In a recent example, cocrystals of 2-PD with succinic acid and with fumaric acid have different chain arrangements but similarly short C—N bond lengths of 1.322 (7) and 1.321 (3) Å, respectively (Callear et al., 2009). In all of these cases, additional hydrogen bonding to carbonyl O atoms appears to lengthen the C═O bond and shorten the C—N bond by approximately equal amounts.
Bond lengths also vary for primary amides (Table 4). The examples quoted were chosen from a study of molecule–molecule energies (Gavezzotti, 2010). For an illustration of the effect of intermolecular interactions in trans –C(═O)—N(R)—H amides, we cite a recent study of the crystal structures of two symmetrical pyridine-2-carboxamide derivatives (Munro & Wilson, 2010). Chemically identical but crystallographically unique bonds differ by 0.013 Å, six times the s.u. of the distances (Table 4). The shorter C—N distance is correlated to the longer C═O distance, attributable to stronger intermolecular H···O hydrogen bonds.
For naphtholactam, (I), the values for the C—N bond length (in the major orientation) are 1.37–1.38 Å and the corresponding C═O distances are 1.24–1.23 Å (Tables 1, 2, 3 and 4). For the ten naphtholactam derivatives (excluding cocrystals and helicenes) in the CSD, the values for C—N range from 1.38 to 1.46 Å. Again, longer C—N bonds are accompanied by shorter C═O distances. Only one of these derivatives can form the hydrogen-bonded dimeric structure found here; for QACQOA (B1, Fig. 4 and Table 4), the C—N length is 1.376 (7) Å at 228 K (Wang et al., 1998), in agreement with our 100 K results. Derivatives with N—R have longer C—N bonds. In RAKYUY (B2), a Br atom makes contact with the carbonyl O atom. In DUXXEA (B3), the two molecules in the asymmetric unit have C—N distances of 1.42 (1) and 1.460 (8) Å; the corresponding C═O distances are 1.219 (8) and 1.209 (9) Å. The amide O atom in molecule 1 has three C—H···O close contacts, while that in molecule 2 has only two.
Thus, the C—N bond length in (I) is ~0.04 Å longer than that in 2-PD and its derivatives. The replacement of two single C—C bonds in 2-PD (NILYAI; Goddard et al., 1998) with aromatic C≐C bonds in (I) introduces other changes as well: N1—C2 is shorter (1.41 versus 1.46 Å), C1—C4 is shorter (1.48 versus 1.52 Å) and the five-membered ring is more nearly planar.
The crystal packing for (I), shown in Figs. 5 and 6, is strikingly similar to that in 2-PD (NILYAI). Stacks of centrosymmetric dimers result in a packing coefficient of 0.75 (Gavezzotti, 2003). In the stacks, additional `dimers' are formed (Fig. 6), with opposing dipoles resembling those reported for cyclobutanone and cyclopentanone (Yufit & Howard, 2011). Table 5 gives intermolecular cohesive energy values and distances (Gavezzotti, 2003). Though these are summaries of point-to-point energies, including repulsions between the N and O atoms in the centrosymmetric dimer, they are useful for comparison. It is likely that the dimer was present in the benzene solution that was used to prepare the crystals.
In (I), there are two stacks of dimers related by an n-glide (Fig. 5). If a dimer were rotated by ~180° before insertion in a stack, as is proposed in the disorder model, both the cohesive stacking interactions within the stacks and the cohesive interactions between adjacent stacks would be adversely affected. Thus, the packing may explain the 10:1 ratio favoring the major-occupancy molecule.