organic compounds
3-Nitrophenylacetic acid: a three-dimensional hydrogen-bonded framework structure containing substructures in zero, one and two dimensions
aInstituto de Tecnologia em Fármacos, Far-Manguinhos, FIOCRUZ, 21041-250 Rio de Janeiro, RJ, Brazil, bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and dSchool of Chemistry, University of St Andrews, Fife, KY16 9ST, Scotland
*Correspondence e-mail: cg@st-andrews.ac.uk
In the title compound, C8H7NO4, the molecules are linked into a three-dimensional framework structure by a combination of O—H⋯O, C—H⋯O(carbonyl) and C—H⋯O(nitro) hydrogen bonds. Comparisons are made between the supramolecular structures of the three isomeric nitrophenylacetic acids.
Comment
We have recently reported the structure of 2-nitrophenylacetic acid, (I) (Wardell et al., 2006), and here we report the structure of the isomeric compound 3-nitrophenylacetic acid, (II). The structure of 4-nitrophenylacetic acid, (III), was reported some years ago (Grabowski et al., 1990), and the for (II) now permits a comparison of all three isomers, (I)–(III).
The exocyclic substituents in compound (II) are both twisted out of the plane of the aryl ring (Fig. 1 and Table 1), so that the molecules are chiral. However, the accommodates equal numbers of the two enantiomeric forms. The C—O bond distances are consistent with full ordering of the acidic H atom, as deduced from difference maps.
The molecules of (II) are linked by a combination of O—H⋯O, C—H⋯O(carbonyl) and C—H⋯O(nitro) hydrogen bonds (Table 2) into a three-dimensional framework structure, whose formation is readily analysed in terms of a series of substructures of lower dimensionality: a finite zero-dimensional dimer unit, which can be regarded as the basic building unit within the structure, and two independent substructures, one of which is one-dimensional and the other of which is two-dimensional, which result from different modes of linkage of the dimers.
Hydroxyl atom O12 in the molecule at (x, y, z) acts as hydrogen-bond donor to carbonyl atom O11 in the molecule at (1 − x, −y, 1 − z), so generating by inversion a dimer characterized by the usual R22(8) (Bernstein et al., 1995) motif (Fig. 2). This dimer can be regarded as the basic building unit within the structure, from which the other two substructures are built. The one-dimensional involves a C—H⋯O(carbonyl) hydrogen bond: aryl atom C6 in the molecule at (x, y, z), part of the dimer centred at (, 0, ), acts as hydrogen-bond donor to carbonyl atom O11 in the molecule at (1 − x, y, − z), which is part of the dimer centred at (, 0, 1). Propagation by inversion and rotation then generates a chain of R22(8) rings generated by inversion alternating with R22(12) rings generated by rotation, running parallel to the [001] direction (Fig. 3).
The two-dimensional involves a C—H⋯O(nitro) hydrogen bond. The aryl atoms C2 in the molecules at (x, y, z) and (1 − x, −y, 1 − z), which comprise the R22(8) dimer centred at (, 0, ), act as hydrogen-bond donors to the nitro atoms O32 in the molecules at (, − x, − + y, − z) and ( + x, − y, + z), respectively, which themselves form parts of the dimers centred at (0, −, 0) and (1, , 1). Similarly, nitro atoms O32 in the molecules at (x, y, z) and (1 − x, −y, 1 − z) accept hydrogen bonds from atoms C2 in the molecules at ( − x, + y, − z) and ( + x, − − y, + z), respectively, which form parts of the dimers centred at (0, , 0) and (1, −, 1). Hence, each dimer is linked in this manner to four adjacent dimers, and propagation of this C—H⋯O(nitro) hydrogen bond then generates a sheet parallel to (10) built of alternating R22(8) and R66(40) rings (Fig. 4). The combination of [001] chains and (10) sheets suffices to generate a single continuous three-dimensional framework structure.
of compound (II)It is of interest to compare briefly the supramolecular structure of (II) with those of the two isomers, (I) and (III). In 2-nitropheylacetic acid, (I), the molecules are linked into sheets of R22(8) and R44(18) rings by one O—H⋯O hydrogen bond and two independent C—H⋯O hydrogen bonds, both of which involve nitro O atoms as acceptors (Wardell et al., 2006). Thus, although the hydrogen bonds deployed in the structures of (I) and (II) are similar, differing principally in the identity of one of the acceptors, the dimensionality of the resulting structures differs. In 4-nitrophenylacetic acid, (III) (Grabowski et al., 1990), the centrosymmetric R22(8) dimers are linked into sheets by an aromatic π–π stacking interaction but, in contrast with the structures of (I) and (II), C—H⋯O hydrogen bonds are absent (Wardell et al., 2006). Hence, significant changes in the supramolecular structures of isomers (I)–(III) result from a simple shift of a single substituent between the various sites on the aryl ring, posing a keen test for the predictability of structures from first principles.
Experimental
A commercial sample (Aldrich) of 3-nitrophenylacetic acid was recrystallized from water.
Crystal data
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Refinement
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The Cc and C2/c as possible space groups; C2/c was selected and confirmed by the successful structure analysis. All H atoms were located in difference maps and then treated as riding atoms, with C—H distances of 0.95 (aromatic) or 0.99 Å (CH2) and O—H distances of 0.84 Å, and with UisoH = 1.2Ueq(C) or 1.5Ueq(O).
permittedData collection: COLLECT (Nonius, 1999); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Supporting information
10.1107/S0108270106039205/sk3059sup1.cif
contains datablocks global, II. DOI:Structure factors: contains datablock II. DOI: 10.1107/S0108270106039205/sk3059IIsup2.hkl
A commercial sample (Aldrich) of 3-nitrophenylacetic acid was recrystallized from water.
The
permitted Cc and C2/c as possible space groups; C2/c was selected, and was confirmed by the successful structure analysis. All H atoms were located in difference maps and then treated as riding atoms, with C—H distances of 0.95 (aromatic) or 0.99 Å (CH2) and O—H distances of 0.84 Å, and with UisoH = 1.2Ueq(C) or 1.5Ueq(O).Data collection: COLLECT (Nonius, 1999); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).C8H7NO4 | F(000) = 752 |
Mr = 181.15 | Dx = 1.542 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 1798 reflections |
a = 21.9690 (6) Å | θ = 2.4–27.6° |
b = 9.2901 (7) Å | µ = 0.13 mm−1 |
c = 7.9642 (2) Å | T = 120 K |
β = 106.216 (2)° | Needle, colourless |
V = 1560.78 (13) Å3 | 0.62 × 0.07 × 0.05 mm |
Z = 8 |
Bruker Nonius KappaCCD area-detector diffractometer | 1798 independent reflections |
Radiation source: Bruker Nonius FR591 rotating anode | 1426 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.041 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.6°, θmin = 2.4° |
ϕ and ω scans | h = −28→28 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −12→12 |
Tmin = 0.957, Tmax = 0.994 | l = −10→9 |
16903 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)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0605P)2 + 0.8287P] where P = (Fo2 + 2Fc2)/3 |
1798 reflections | (Δ/σ)max < 0.001 |
119 parameters | Δρmax = 0.23 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
C8H7NO4 | V = 1560.78 (13) Å3 |
Mr = 181.15 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 21.9690 (6) Å | µ = 0.13 mm−1 |
b = 9.2901 (7) Å | T = 120 K |
c = 7.9642 (2) Å | 0.62 × 0.07 × 0.05 mm |
β = 106.216 (2)° |
Bruker Nonius KappaCCD area-detector diffractometer | 1798 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1426 reflections with I > 2σ(I) |
Tmin = 0.957, Tmax = 0.994 | Rint = 0.041 |
16903 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.23 e Å−3 |
1798 reflections | Δρmin = −0.26 e Å−3 |
119 parameters |
x | y | z | Uiso*/Ueq | ||
O11 | 0.47049 (5) | 0.16282 (10) | 0.51651 (13) | 0.0268 (3) | |
O12 | 0.43311 (5) | −0.04557 (10) | 0.58490 (15) | 0.0323 (3) | |
O31 | 0.22765 (5) | 0.56092 (11) | 0.29531 (14) | 0.0331 (3) | |
O32 | 0.28282 (5) | 0.75666 (10) | 0.35972 (13) | 0.0289 (3) | |
N3 | 0.27493 (5) | 0.62691 (12) | 0.37843 (15) | 0.0230 (3) | |
C1 | 0.37313 (6) | 0.32274 (14) | 0.61287 (17) | 0.0206 (3) | |
C2 | 0.32437 (6) | 0.39825 (14) | 0.49749 (16) | 0.0202 (3) | |
C3 | 0.32499 (6) | 0.54757 (13) | 0.50499 (17) | 0.0200 (3) | |
C4 | 0.37157 (6) | 0.62561 (14) | 0.62303 (17) | 0.0219 (3) | |
C5 | 0.41941 (6) | 0.54895 (14) | 0.73923 (18) | 0.0237 (3) | |
C6 | 0.42016 (6) | 0.39950 (14) | 0.73416 (17) | 0.0219 (3) | |
C11 | 0.37434 (6) | 0.16061 (14) | 0.60971 (18) | 0.0238 (3) | |
C12 | 0.43087 (6) | 0.09578 (13) | 0.56546 (16) | 0.0205 (3) | |
H2 | 0.2913 | 0.3487 | 0.4153 | 0.024* | |
H4 | 0.3708 | 0.7278 | 0.6244 | 0.026* | |
H5 | 0.4519 | 0.5990 | 0.8228 | 0.028* | |
H6 | 0.4532 | 0.3486 | 0.8146 | 0.026* | |
H11A | 0.3354 | 0.1263 | 0.5232 | 0.029* | |
H11B | 0.3734 | 0.1246 | 0.7259 | 0.029* | |
H12 | 0.4644 | −0.0782 | 0.5561 | 0.048* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O11 | 0.0286 (5) | 0.0167 (5) | 0.0395 (6) | 0.0009 (4) | 0.0169 (4) | 0.0001 (4) |
O12 | 0.0315 (6) | 0.0152 (5) | 0.0572 (7) | 0.0026 (4) | 0.0240 (5) | 0.0032 (4) |
O31 | 0.0257 (5) | 0.0283 (6) | 0.0403 (6) | 0.0008 (4) | 0.0010 (4) | 0.0007 (4) |
O32 | 0.0345 (6) | 0.0182 (5) | 0.0370 (6) | 0.0031 (4) | 0.0152 (5) | 0.0065 (4) |
N3 | 0.0252 (6) | 0.0196 (6) | 0.0272 (6) | 0.0034 (4) | 0.0121 (5) | 0.0022 (4) |
C1 | 0.0201 (7) | 0.0184 (7) | 0.0269 (7) | 0.0014 (5) | 0.0127 (5) | 0.0000 (5) |
C2 | 0.0183 (6) | 0.0188 (7) | 0.0257 (6) | −0.0012 (5) | 0.0098 (5) | −0.0015 (5) |
C3 | 0.0201 (7) | 0.0182 (7) | 0.0245 (6) | 0.0024 (5) | 0.0110 (5) | 0.0023 (5) |
C4 | 0.0242 (7) | 0.0151 (6) | 0.0305 (7) | −0.0012 (5) | 0.0144 (6) | −0.0015 (5) |
C5 | 0.0212 (7) | 0.0233 (7) | 0.0281 (7) | −0.0014 (5) | 0.0094 (5) | −0.0053 (5) |
C6 | 0.0189 (6) | 0.0230 (7) | 0.0253 (6) | 0.0025 (5) | 0.0086 (5) | −0.0004 (5) |
C11 | 0.0218 (7) | 0.0166 (7) | 0.0345 (7) | 0.0006 (5) | 0.0102 (6) | 0.0016 (5) |
C12 | 0.0223 (6) | 0.0153 (6) | 0.0227 (6) | 0.0002 (5) | 0.0044 (5) | −0.0003 (5) |
C1—C2 | 1.3908 (18) | C4—H4 | 0.95 |
C1—C6 | 1.3971 (18) | C5—C6 | 1.3893 (18) |
C1—C11 | 1.5067 (18) | C5—H5 | 0.95 |
C2—C3 | 1.3884 (17) | C6—H6 | 0.95 |
C2—H2 | 0.95 | C11—C12 | 1.5079 (18) |
C3—C4 | 1.3854 (18) | C11—H11A | 0.99 |
C3—N3 | 1.4662 (17) | C11—H11B | 0.99 |
N3—O31 | 1.2284 (15) | C12—O11 | 1.2194 (16) |
N3—O32 | 1.2327 (14) | C12—O12 | 1.3216 (15) |
C4—C5 | 1.3874 (19) | O12—H12 | 0.84 |
C2—C1—C6 | 118.94 (12) | C4—C5—H5 | 119.8 |
C2—C1—C11 | 120.47 (12) | C6—C5—H5 | 119.8 |
C6—C1—C11 | 120.57 (12) | C5—C6—C1 | 121.18 (12) |
C3—C2—C1 | 118.62 (12) | C5—C6—H6 | 119.4 |
C3—C2—H2 | 120.7 | C1—C6—H6 | 119.4 |
C1—C2—H2 | 120.7 | C1—C11—C12 | 115.01 (11) |
C4—C3—C2 | 123.27 (12) | C1—C11—H11A | 108.5 |
C4—C3—N3 | 118.26 (11) | C12—C11—H11A | 108.5 |
C2—C3—N3 | 118.44 (11) | C1—C11—H11B | 108.5 |
O31—N3—O32 | 123.31 (11) | C12—C11—H11B | 108.5 |
O31—N3—C3 | 118.60 (11) | H11A—C11—H11B | 107.5 |
O32—N3—C3 | 118.09 (11) | O11—C12—O12 | 122.58 (12) |
C3—C4—C5 | 117.54 (12) | O11—C12—C11 | 125.36 (12) |
C3—C4—H4 | 121.2 | O12—C12—C11 | 112.06 (11) |
C5—C4—H4 | 121.2 | C12—O12—H12 | 109.5 |
C4—C5—C6 | 120.43 (12) | ||
C6—C1—C2—C3 | 1.27 (18) | N3—C3—C4—C5 | −178.54 (11) |
C11—C1—C2—C3 | 179.88 (12) | C3—C4—C5—C6 | 0.67 (18) |
C1—C2—C3—C4 | −0.61 (19) | C4—C5—C6—C1 | 0.00 (19) |
C1—C2—C3—N3 | 177.55 (11) | C2—C1—C6—C5 | −1.00 (19) |
C4—C3—N3—O31 | −166.97 (12) | C11—C1—C6—C5 | −179.61 (12) |
C2—C3—N3—O31 | 14.78 (17) | C2—C1—C11—C12 | 117.89 (13) |
C4—C3—N3—O32 | 13.74 (17) | C6—C1—C11—C12 | −63.52 (16) |
C2—C3—N3—O32 | −164.51 (11) | C1—C11—C12—O11 | −7.75 (19) |
C2—C3—C4—C5 | −0.37 (19) | C1—C11—C12—O12 | 172.54 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
O12—H12···O11i | 0.84 | 1.86 | 2.6980 (13) | 175 |
C2—H2···O32ii | 0.95 | 2.49 | 3.4099 (16) | 164 |
C6—H6···O11iii | 0.95 | 2.52 | 3.4474 (17) | 166 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1/2, y−1/2, −z+1/2; (iii) −x+1, y, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C8H7NO4 |
Mr | 181.15 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 120 |
a, b, c (Å) | 21.9690 (6), 9.2901 (7), 7.9642 (2) |
β (°) | 106.216 (2) |
V (Å3) | 1560.78 (13) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.62 × 0.07 × 0.05 |
Data collection | |
Diffractometer | Bruker Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.957, 0.994 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16903, 1798, 1426 |
Rint | 0.041 |
(sin θ/λ)max (Å−1) | 0.651 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.108, 1.03 |
No. of reflections | 1798 |
No. of parameters | 119 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.23, −0.26 |
Computer programs: COLLECT (Nonius, 1999), DENZO (Otwinowski & Minor, 1997) and COLLECT, DENZO and COLLECT, OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997), OSCAIL and SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).
C12—O11 | 1.2194 (16) | C12—O12 | 1.3216 (15) |
C2—C3—N3—O31 | 14.78 (17) | C1—C11—C12—O12 | 172.54 (11) |
C2—C1—C11—C12 | 117.89 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
O12—H12···O11i | 0.84 | 1.86 | 2.6980 (13) | 175 |
C2—H2···O32ii | 0.95 | 2.49 | 3.4099 (16) | 164 |
C6—H6···O11iii | 0.95 | 2.52 | 3.4474 (17) | 166 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1/2, y−1/2, −z+1/2; (iii) −x+1, y, −z+3/2. |
Acknowledgements
The X-ray data were collected at the EPSRC National Crystallography Service, University of Southampton, England; the authors thank the staff of the Service for all their help and advice.
References
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We have recently reported the structure of 2-nitrophenylacetic acid, (I) (Wardell et al., 2006), and here we report the structure of the isomeric compound 3-nitrophenylacetic acid, (II). The structure of 4-nitrophenylacetic acid, (III), was reported some years ago (Grabowski et al., 1990), and the structure determination for (II) now permits a comparison of all three isomers, (I)–(III).
The exocyclic substituents in compound (II) are both twisted out of the plane of the aryl ring (Fig. 1, Table 1), so that the molecules are chiral. However, the space group accommodates equal numbers of the two enantiomeric forms. The C—O bond distances are consistent with full ordering of the acidic H atom, as deduced from difference maps.
The molecules of (II) are linked by a combination of O—H···O, C—H···O(carbonyl) and C—H···O(nitro) hydrogen bonds (Table 2) into a three-dimensional framework structure, whose formation is readily analysed in terms of a series of sub-structures of lower dimensionality: a finite zero-dimensional dimer unit, which can be regarded as the basic building unit within the structure, and two independent sub-structures, one of which is one-dimensional and the other of which is two-dimensional, which result from different modes of linkage of the dimers.
Hydroxyl atom O12 in the molecule at (x, y, z) acts as hydrogen-bond donor to carbonyl atom O11 in the molecule at (1 − x, −y, 1 − z), so generating by inversion a dimer characterized by the usual R22(8) (Bernstein et al., 1995) motif (Fig. 2). This dimer can be regarded as the basic building unit within the structure, from which the other two sub-structure are built. The one-dimensional sub-structure involves a C—H···O(carbonyl) hydrogen bond: aryl atom C6 in the molecule at (x, y, z), part of the dimer centred at (1/2, 0, 1/2), acts as hydrogen-bond donor to carbonyl atom O11 in the molecule at (1 − x, y, 3/2 − z), which is part of the dimer centred at (1/2, 0, 1). Propagation by inversion and rotation then generates a chain of R22(8) rings generated by inversion alternating with R22(12) rings generated by rotation, running parallel to the [001] direction (Fig. 3).
The two-dimensional sub-structure of compound (II) involves a C—H···O(nitro) hydrogen bond. The aryl atoms C2 in the molecules at (x, y, z) and (1 − x, −y, 1 − z), which comprise the R22(8) dimer centred at (1/2, 0, 1/2), act as hydrogen-bond donors to the nitro atoms O32 in the molecules at (1/2, − x, −1/2 + y, 1/2 − z) and (1/2 + x, 1/2 − y, 1/2 + z), respectively, which themselves form parts of the dimers centred at (0, −1/2, 0) and (1, 1/2, 1). Similarly, the nitro atoms O32 in the molecules at (x, y, z) and (1 − x, −y, 1 − z) accept hydrogen bonds from the atoms C2 in the molecules at (1/2 − x, 1/2 + y, 1/2 − z) and (1/2 + x, −1/2 − y, 1/2 + z), respectively, which form parts of the dimers centred at (0, 1/2, 0) and (1, −1/2, 1). Hence each dimer is linked in this manner to four adjacent dimers, and propagation of this C—H···O(nitro) hydrogen bond then generates a sheet parallel to (101) built of alternating R22(8) and R66(40) rings (Fig. 4). The combination of [001] chains and (101) sheets suffices to generate a single and continuous three-dimensional framework structure.
It is of interest to compare briefly the supramolecular structure of (II) with those of the two isomers, (I) and (III). In 2-nitropheylacetic acid, (I), the molecules are linked into sheets of R22(8) and R44(18) rings by one O—H···O hydrogen bond and two independent C—H···O hydrogen bonds, both of which involve nitro O atoms as acceptors (Wardell et al., 2006). Thus, although the hydrogen bonds deployed in the structures of (I) and (II) are similar, differing principally in the identity of one of the acceptors, the dimensionality of the resulting structures differs. In 4-nitrophenylacetic acid, (III) (Grabowski et al., 1990), the centrosymmetric R22(8) dimers are linked into sheets by an aromatic π–π stacking interaction but, in contrast with the structures of (I) and (II), C—H···O hydrogen bonds are absent (Wardell et al., 2006). Hence significant changes in the supramolecular structures of isomers (I)–(III) result from a simple shift of a single substituent between the various sites on the aryl ring, posing a keen test for the predictability of structures from first principles.