organic compounds
N-[2-(Acetamido)ethyl]-2-hydroxybenzamide
aDepartment of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
*Correspondence e-mail: mkubicki@amu.edu.pl
In the title molecule, C11H14N2O3, an intramolecular O—H⋯O hydrogen bond closes an almost planar [maximum deviation = 0.022 (13) Å] six-membered ring and enforces the cis conformation of the keto group with respect to the hydroxy substituent. In the crystal, intermolecular N—H⋯O hydrogen bonds link the moleclues into ribbons extended along [10]. Weak intermolecular C—H⋯O interactions further consolidate the crystal packing.
Related literature
For general background to ribonucleic acid, see: Franklin (2001); Komiyama et al. (1999); Kuzuya et al. (2006); Morrow & Iranzo (2004); Nüttymäki & Lönnberg (2006). Some crystal structures of similar molecules have been reported, for instance N-salicyloylglycine (Smeets et al., 1985), 2-(N-(2-(2-hydroxybenzamido)ethylammonioethyl)aminocarbonyl) phenolate (Liu et al., 2006) and N-(2-Aminoethyl)-2-hydroxybenzamide picrate (Yu et al., 2003). More crystal structures of analogs can be found in Cambridge Structural Database (Allen, 2002).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536811003680/cv5045sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811003680/cv5045Isup2.hkl
To a solution of ethylenediamine (0,3972 g, 2 mmol) in THF (7 ml) O-acetylsalicyloyl chloride (0,268 ml, 4 mmol) in THF (7 ml) was added dropwise with stirring. The reaction was carried out for 24 h in ambient temperature. The reaction mixture was evaporated to dryness and purified by silica gel
by elution with CH2Cl2/methanol (98:2). Crystals suitable for X-ray were formed by slow evaporation from CH2Cl2/methanol (1:1) after one week.ESI-MS m/z (%) = 221 (100 {C11H13N2O3-}); 245 (100 {C11H14N2O3+Na+}).
Elemental analysis calculated for C11H14N2O3: C, 59.45; H, 6.35; N, 12.60; found C, 58.95; H, 6.00; N, 12.20.
1H-NMR p.p.m.: 12.46 (s); 7.90 (s); 7.48 (d); 7.38 (t); 6.98 (d); 6.89 (t); 6.10 (s); 3.56 (t); 2.05 (s).
C-bound H atoms were geometrically positioned (C—H 0.95-0.99 Å) and refined as riding, with Uiso(H) = 1.2-1.5 Ueq(C). The rest H atoms were found in the diffrence Fourier maps and isotropically refined.
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).Fig. 1. View of I showing the atomic numbering and 50% probability displacement ellipsoids. Hydrogen atoms are depicted as spheres with arbitrary radii. Intramolecular hydrogen bond is shown as dashed line. | |
Fig. 2. Two views: (a) face-on and (b) side-on of the hydrogen-bonded chain of molecules of I. Hydrogen bonds are shown as dashed lines. | |
Fig. 3. A portion of the crystal packing as seen approximately along b-direction. Hydrogen bonds are shown as dashed lines. |
C11H14N2O3 | F(000) = 472 |
Mr = 222.24 | Dx = 1.38 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 990 reflections |
a = 8.642 (3) Å | θ = 3.0–29.0° |
b = 4.9702 (18) Å | µ = 0.10 mm−1 |
c = 24.972 (3) Å | T = 90 K |
β = 95.14 (2)° | Block, yellow |
V = 1068.3 (6) Å3 | 0.3 × 0.2 × 0.15 mm |
Z = 4 |
Oxford Diffraction Xcalibur Eos diffractometer | 2439 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 1504 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
Detector resolution: 16.1544 pixels mm-1 | θmax = 29.2°, θmin = 3.3° |
ω scans | h = −11→6 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | k = −4→6 |
Tmin = 0.111, Tmax = 1.000 | l = −28→33 |
4347 measured reflections |
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) = 0.162 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0581P)2 + 0.0266P] where P = (Fo2 + 2Fc2)/3 |
2439 reflections | (Δ/σ)max < 0.001 |
158 parameters | Δρmax = 0.29 e Å−3 |
0 restraints | Δρmin = −0.34 e Å−3 |
C11H14N2O3 | V = 1068.3 (6) Å3 |
Mr = 222.24 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 8.642 (3) Å | µ = 0.10 mm−1 |
b = 4.9702 (18) Å | T = 90 K |
c = 24.972 (3) Å | 0.3 × 0.2 × 0.15 mm |
β = 95.14 (2)° |
Oxford Diffraction Xcalibur Eos diffractometer | 2439 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | 1504 reflections with I > 2σ(I) |
Tmin = 0.111, Tmax = 1.000 | Rint = 0.039 |
4347 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.162 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.29 e Å−3 |
2439 reflections | Δρmin = −0.34 e Å−3 |
158 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4433 (3) | 0.3212 (5) | 0.31898 (9) | 0.0195 (5) | |
O1 | 0.3176 (2) | 0.4713 (3) | 0.32788 (7) | 0.0273 (5) | |
H1 | 0.357 (4) | 0.597 (7) | 0.3630 (15) | 0.078 (12)* | |
C2 | 0.5847 (3) | 0.3520 (4) | 0.34941 (9) | 0.0163 (5) | |
C3 | 0.7073 (3) | 0.1857 (5) | 0.33760 (10) | 0.0211 (6) | |
H3 | 0.8049 | 0.2046 | 0.3579 | 0.025* | |
C4 | 0.6913 (3) | −0.0051 (5) | 0.29741 (10) | 0.0237 (6) | |
H4 | 0.7763 | −0.1170 | 0.2904 | 0.028* | |
C5 | 0.5507 (3) | −0.0306 (5) | 0.26766 (10) | 0.0239 (6) | |
H5 | 0.5385 | −0.1613 | 0.2398 | 0.029* | |
C6 | 0.4275 (3) | 0.1306 (5) | 0.27763 (10) | 0.0233 (6) | |
H6 | 0.3313 | 0.1127 | 0.2564 | 0.028* | |
C7 | 0.5993 (3) | 0.5583 (4) | 0.39258 (9) | 0.0165 (5) | |
O7 | 0.48629 (18) | 0.7039 (3) | 0.40218 (6) | 0.0215 (4) | |
N8 | 0.7353 (2) | 0.5851 (4) | 0.42095 (8) | 0.0191 (5) | |
H8 | 0.815 (3) | 0.471 (5) | 0.4157 (10) | 0.030 (8)* | |
C9 | 0.7594 (3) | 0.7863 (5) | 0.46326 (10) | 0.0204 (5) | |
H9A | 0.7091 | 0.9568 | 0.4508 | 0.024* | |
H9B | 0.8722 | 0.8209 | 0.4706 | 0.024* | |
C10 | 0.6929 (3) | 0.6963 (5) | 0.51550 (9) | 0.0214 (6) | |
H10A | 0.5782 | 0.6873 | 0.5095 | 0.026* | |
H10B | 0.7316 | 0.5136 | 0.5251 | 0.026* | |
N11 | 0.7358 (2) | 0.8778 (4) | 0.55967 (8) | 0.0212 (5) | |
H11 | 0.666 (3) | 0.991 (5) | 0.5708 (11) | 0.028 (7)* | |
C12 | 0.8726 (3) | 0.8603 (5) | 0.58797 (10) | 0.0208 (6) | |
O12 | 0.97079 (19) | 0.6959 (3) | 0.57683 (7) | 0.0249 (4) | |
C13 | 0.8981 (3) | 1.0561 (5) | 0.63381 (11) | 0.0296 (6) | |
H13A | 0.9890 | 1.0007 | 0.6575 | 0.044* | |
H13B | 0.8062 | 1.0589 | 0.6541 | 0.044* | |
H13C | 0.9157 | 1.2363 | 0.6196 | 0.044* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0211 (12) | 0.0222 (13) | 0.0154 (12) | 0.0028 (10) | 0.0029 (10) | 0.0010 (10) |
O1 | 0.0243 (10) | 0.0317 (10) | 0.0247 (10) | 0.0087 (8) | −0.0043 (8) | −0.0064 (9) |
C2 | 0.0225 (12) | 0.0153 (11) | 0.0117 (11) | 0.0012 (10) | 0.0051 (10) | 0.0011 (10) |
C3 | 0.0221 (13) | 0.0245 (13) | 0.0172 (13) | −0.0004 (10) | 0.0038 (10) | −0.0019 (11) |
C4 | 0.0285 (14) | 0.0230 (13) | 0.0213 (13) | 0.0025 (11) | 0.0110 (11) | −0.0018 (11) |
C5 | 0.0318 (15) | 0.0245 (13) | 0.0164 (13) | −0.0070 (12) | 0.0081 (11) | −0.0029 (11) |
C6 | 0.0243 (13) | 0.0309 (14) | 0.0142 (12) | −0.0034 (11) | −0.0005 (10) | 0.0009 (11) |
C7 | 0.0206 (12) | 0.0162 (12) | 0.0130 (12) | 0.0003 (10) | 0.0043 (9) | 0.0038 (10) |
O7 | 0.0210 (9) | 0.0265 (9) | 0.0170 (9) | 0.0046 (7) | 0.0022 (7) | −0.0016 (7) |
N8 | 0.0200 (11) | 0.0226 (11) | 0.0148 (11) | 0.0031 (9) | 0.0014 (8) | −0.0037 (9) |
C9 | 0.0245 (13) | 0.0208 (12) | 0.0158 (12) | −0.0018 (10) | 0.0015 (10) | −0.0015 (11) |
C10 | 0.0220 (12) | 0.0261 (13) | 0.0164 (13) | −0.0029 (11) | 0.0024 (10) | −0.0027 (11) |
N11 | 0.0184 (11) | 0.0301 (12) | 0.0152 (11) | 0.0051 (9) | 0.0019 (9) | −0.0060 (9) |
C12 | 0.0217 (13) | 0.0242 (13) | 0.0168 (13) | −0.0007 (11) | 0.0036 (10) | 0.0011 (11) |
O12 | 0.0212 (9) | 0.0308 (10) | 0.0228 (10) | 0.0061 (8) | 0.0021 (7) | −0.0068 (8) |
C13 | 0.0240 (14) | 0.0373 (15) | 0.0262 (15) | 0.0070 (12) | −0.0051 (11) | −0.0109 (13) |
C1—O1 | 1.352 (3) | N8—C9 | 1.456 (3) |
C1—C2 | 1.389 (3) | N8—H8 | 0.91 (3) |
C1—C6 | 1.399 (3) | C9—C10 | 1.538 (4) |
O1—H1 | 1.11 (4) | C9—H9A | 0.9900 |
C2—C3 | 1.395 (3) | C9—H9B | 0.9900 |
C2—C7 | 1.485 (3) | C10—N11 | 1.447 (3) |
C3—C4 | 1.379 (3) | C10—H10A | 0.9900 |
C3—H3 | 0.9500 | C10—H10B | 0.9900 |
C4—C5 | 1.372 (4) | N11—C12 | 1.325 (3) |
C4—H4 | 0.9500 | N11—H11 | 0.89 (3) |
C5—C6 | 1.373 (3) | C12—O12 | 1.228 (3) |
C5—H5 | 0.9500 | C12—C13 | 1.504 (3) |
C6—H6 | 0.9500 | C13—H13A | 0.9800 |
C7—O7 | 1.255 (3) | C13—H13B | 0.9800 |
C7—N8 | 1.323 (3) | C13—H13C | 0.9800 |
O1—C1—C2 | 122.0 (2) | N8—C9—C10 | 112.0 (2) |
O1—C1—C6 | 117.9 (2) | N8—C9—H9A | 109.2 |
C2—C1—C6 | 120.1 (2) | C10—C9—H9A | 109.2 |
C1—O1—H1 | 104.2 (18) | N8—C9—H9B | 109.2 |
C1—C2—C3 | 117.8 (2) | C10—C9—H9B | 109.2 |
C1—C2—C7 | 119.1 (2) | H9A—C9—H9B | 107.9 |
C3—C2—C7 | 123.1 (2) | N11—C10—C9 | 112.1 (2) |
C4—C3—C2 | 122.2 (2) | N11—C10—H10A | 109.2 |
C4—C3—H3 | 118.9 | C9—C10—H10A | 109.2 |
C2—C3—H3 | 118.9 | N11—C10—H10B | 109.2 |
C5—C4—C3 | 118.9 (2) | C9—C10—H10B | 109.2 |
C5—C4—H4 | 120.5 | H10A—C10—H10B | 107.9 |
C3—C4—H4 | 120.5 | C12—N11—C10 | 121.4 (2) |
C4—C5—C6 | 120.8 (2) | C12—N11—H11 | 118.2 (17) |
C4—C5—H5 | 119.6 | C10—N11—H11 | 120.0 (18) |
C6—C5—H5 | 119.6 | O12—C12—N11 | 121.6 (2) |
C5—C6—C1 | 120.2 (2) | O12—C12—C13 | 123.1 (2) |
C5—C6—H6 | 119.9 | N11—C12—C13 | 115.2 (2) |
C1—C6—H6 | 119.9 | C12—C13—H13A | 109.5 |
O7—C7—N8 | 120.6 (2) | C12—C13—H13B | 109.5 |
O7—C7—C2 | 121.3 (2) | H13A—C13—H13B | 109.5 |
N8—C7—C2 | 118.1 (2) | C12—C13—H13C | 109.5 |
C7—N8—C9 | 121.4 (2) | H13A—C13—H13C | 109.5 |
C7—N8—H8 | 120.5 (16) | H13B—C13—H13C | 109.5 |
C9—N8—H8 | 118.1 (17) | ||
O1—C1—C2—C3 | 179.3 (2) | C1—C2—C7—O7 | 0.3 (3) |
C6—C1—C2—C3 | −0.8 (3) | C3—C2—C7—O7 | −179.8 (2) |
O1—C1—C2—C7 | −0.8 (3) | C1—C2—C7—N8 | −179.7 (2) |
C6—C1—C2—C7 | 179.1 (2) | C3—C2—C7—N8 | 0.2 (3) |
C1—C2—C3—C4 | −0.2 (3) | O7—C7—N8—C9 | −1.2 (3) |
C7—C2—C3—C4 | 179.9 (2) | C2—C7—N8—C9 | 178.81 (19) |
C2—C3—C4—C5 | 0.7 (4) | C7—N8—C9—C10 | 78.9 (3) |
C3—C4—C5—C6 | −0.1 (4) | N8—C9—C10—N11 | 171.87 (19) |
C4—C5—C6—C1 | −0.9 (4) | C9—C10—N11—C12 | −82.2 (3) |
O1—C1—C6—C5 | −178.7 (2) | C10—N11—C12—O12 | 2.5 (4) |
C2—C1—C6—C5 | 1.4 (4) | C10—N11—C12—C13 | −177.9 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O7 | 1.11 (4) | 1.51 (4) | 2.534 (3) | 150 (3) |
N8—H8···O12i | 0.91 (3) | 2.02 (3) | 2.895 (3) | 160 (2) |
N11—H11···O7ii | 0.89 (3) | 2.16 (3) | 3.040 (3) | 174 (2) |
C3—H3···O12i | 0.95 | 2.47 | 3.404 (4) | 169 |
C6—H6···O1iii | 0.95 | 2.47 | 3.325 (4) | 150 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y+2, −z+1; (iii) −x+1/2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H14N2O3 |
Mr | 222.24 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 90 |
a, b, c (Å) | 8.642 (3), 4.9702 (18), 24.972 (3) |
β (°) | 95.14 (2) |
V (Å3) | 1068.3 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.3 × 0.2 × 0.15 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Eos diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.111, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4347, 2439, 1504 |
Rint | 0.039 |
(sin θ/λ)max (Å−1) | 0.686 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.162, 1.04 |
No. of reflections | 2439 |
No. of parameters | 158 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.29, −0.34 |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O7 | 1.11 (4) | 1.51 (4) | 2.534 (3) | 150 (3) |
N8—H8···O12i | 0.91 (3) | 2.02 (3) | 2.895 (3) | 160 (2) |
N11—H11···O7ii | 0.89 (3) | 2.16 (3) | 3.040 (3) | 174 (2) |
C3—H3···O12i | 0.95 | 2.47 | 3.404 (4) | 168.7 |
C6—H6···O1iii | 0.95 | 2.47 | 3.325 (4) | 150.1 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y+2, −z+1; (iii) −x+1/2, y−1/2, −z+1/2. |
Acknowledgements
This work was supported by the Polish Ministry of Science and Higher Education (grant NN204 0317 33).
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Ribonucleic acid, which mediates genetic information encoded in DNA, is one of the most important compounds in life. If only one RNA can be chosen from many RNAs in cells and selectively cleaved at desired site, it opens the way to new RNA science (e.g. regulation of expression of a specific gene, advanced therapy, RNA manipulation) (Kuzuya et al., 2006). During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, have received special attention (Nüttymäki et al., 2006). The first artificial nucleases capable of cleaving RNA oligonucleotides in a selective manner were DNA conjugates of lanthanide(III) ion complexes (Komiyama et al., 1999; Franklin, 2001; Morrow et al., 2004). The title compound (I, Scheme 1) was isolated during efforts to prepare new synthetic ribonuclease precursors as part of our research program involving the study of the nonselective and selective hydrolysis of RNA by lanthanide complexes.
The conformation of the CNCCNCC chain in (I) is tg+tg-t (t - trans, g - gauche), as can be seen from the values of the torsion angles. Intramolecular hydrogen bond between hydroxy group and O7 oxygen atom causes closing of the six-membered nearly planar (within 0.022 (13) Å) ring (Fig. 1). This bond is strong and causes the changes in the geometry of involved fragments: lengthening of both O—H (1.11 (4) Å) and C=O (1.255 (3) Å) bonds. This ring is almost coplanar with the phenyl ring plane, the dihedral angle between the two planes is 1.6 (9)°. In the Cambridge Structural Database (Allen, 2002; Version 5.31 of Nov. 2009, updated August 2010) there are 229 fragments of 2-hydroxy-N-monosubstituted- benzamide, and both O—H···O and N—H···O (with hydroxy group as an acceptor) are almost equally represented in the sample. Of course, the different hydrogen bond schemes are connected with the different C1—C2—C7—N8 torsion angles, which are close to 180° for the former and close to 0° for the latter possibility (cf. Fig. 2). The overall conformation of the molecule can be described as two almost planar (within 0.022 (2) Å) and nearly parallel (the dihedral angle is 5.65 (16)°) fragments C1···C9 and C10···C13.
In the crystal structure, the variety of hydrogen bonds connects the molecules of I into the hydrogen-bonded chains of molecules (cf. Table 1). The pairs of almost linear N11—H11···O7(1 - x,2 - y,1 - z) and N8—H8···O12(2 - x,1 - y,1 - z) hydrogen bonds join the molecules in centrosymmetric dimers, the graph set connected with these interactions are R22(14). Each of these bonds is accompanied by secondary however still relatively short and directional C—H···O interactions (Table 1). As can be seen in Fig. 3 these bonds in general join two different "storeys" of the molecules in alternating manner. Therefore these interactions create the double ribbons of molecules which expand approximately along [-110] direction. The interactions between these motifs are only very week.