Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807042778/pk2041sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807042778/pk2041Isup2.hkl |
CCDC reference: 663708
Key indicators
- Single-crystal X-ray study
- T = 89 K
- Mean (C-C) = 0.003 Å
- R factor = 0.038
- wR factor = 0.103
- Data-to-parameter ratio = 14.0
checkCIF/PLATON results
No syntax errors found
Alert level B ABSTM02_ALERT_3_B The ratio of expected to reported Tmax/Tmin(RR') is < 0.75 Tmin and Tmax reported: 0.672 0.981 Tmin(prime) and Tmax expected: 0.919 0.974 RR(prime) = 0.726 Please check that your absorption correction is appropriate. PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large ............. 0.73
Alert level C PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 100 Deg. PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3 PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 1
0 ALERT level A = In general: serious problem 2 ALERT level B = Potentially serious problem 3 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related literature on the biological activity of polybenzamide DNA binding agents, see: Lelkes & Pollard (1987); Lown et al.(1986); Petering et al. (2000); Storl et al. (1993). For related literature on natural and synthetic minor groove binding agents, see: Arcamone et al. (1964); Atwell et al. (1995); Baraldi et al. (1999, 2004, 2007); Turner & Denny (2000); Turner et al. (1999); Wemmer (2000); Xie et al. (1996); Yan et al. (1997).
To a solution of 3-acetamido-5-nitrobenzyl acetate (990 mg, 3.93 mmol) in ethanol (20 ml), was added a solution of sodium hydroxide (315 mg, 7.85 mmol) in water (5 ml). The resulting solution was stirred at room temperature for 3 h before water (15 ml) was added to quench the reaction. The ethanol was removed in vacuo, and the resulting aqueous solution extracted with ethyl acetate (3 x 20 ml). The organic extracts were combined, dried (Na2SO4), and the solvent removed in vacuo, to give the crude product, which was purified by flash chromatography (9:1 dichloromethane-methanol), to afford the title compound (810 mg, 98%) as white solid which was recrystallized from DMSO for single-crystal analysis. Mp 450–451 K. νmax (NaCl)/cm-1 3298, 1681, 1529, 1348. δH (400 MHz, (CD3)2SO) 2.09 (3H, s, NHCOCH3), 4.58 (2H, s, CH2OH), 5.55 (OH), 7.83 (1H, s, Ar—H), 7.85 (1H, s, Ar—H), 8.49 (1H, br s, Ar—H) and 10.43 (NH). δC (100 MHz, (CD3)2SO) 24.1 (CH3, NHCOCH3), 61.9 (CH2, CH2OH), 111.4 (CH, Ar—C), 115.0 (CH, Ar—C), 122.3 (CH, Ar—C), 140.3 (quat. Ar—C), 145.5 (quat. Ar—C), 147.9 (quat. Ar—C) and 169.1 (C=O). m/z (EI+) 210 (M+, 27%), 168 (M+—C2H2O, 100), 43 (COCH3, 93). Found M+ 210.06318, C9H10N2O4 requires 210.06406.
Hydrogen atoms were placed in calculated positions and refined using the riding model [C—H 0.93–0.97, N—H 0.86 Å), with Uiso(H) = 1.2 or 1.5 times Ueq(C). Atom HO4 was located from a difference map, and refined individually with an isotropic temperature factor.
Oligopeptides are a growing area of interest due to their strong biological activities (Lown et al., 1986, Lelkes & Pollard, 1987, Xie et al., 1996, Turner & Denny, 2000, Petering et al., 2000). Some natural oligopeptides are powerful DNA minor groove-binding agents but their cytotoxity precludes their use as medicines (Arcamone et al., 1964, Baraldi et al., 2004, Wemmer, 2000, Storl et al., 1993). To increase the DNA binding affinity and sequence specificity and to minimize the undesired physiological activities, many synthetic analogues have been prepared (Baraldi et al., 2007). The title compound is a key intermediate required in the synthesis of a novel polybenzamide DNA minor groove-binding agent. For background information on polybenzamide DNA binding agents see (Atwell et al., 1995, Turner et al., 1999, Yan et al., 1997)
For related literature on the biological activity of polybenzamide DNA binding agents, see: Lelkes & Pollard (1987); Lown et al.(1986); Petering et al. (2000); Storl et al. (1993). For related literature on natural and synthetic minor groove binding agents, see: Arcamone et al. (1964); Atwell et al. (1995); Baraldi et al. (1999, 2004, 2007); Turner & Denny (2000); Turner et al. (1999); Wemmer (2000); Xie et al. (1996); Yan et al. (1997).
Data collection: SMART (Siemens, 1995); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT (Siemens, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXTL (Siemens, 1995).
Fig. 1. The molecular structure showing 50% probability displacement ellipsoids for non-hydrogen atoms and hydrogen atoms as arbitary spheres (Burnett & Johnson, 1996). |
C9H10N2O4·C2H6OS | Z = 2 |
Mr = 288.32 | F(000) = 304 |
Triclinic, P1 | Dx = 1.441 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.2124 (4) Å | Cell parameters from 3933 reflections |
b = 10.1722 (6) Å | θ = 2.2–25.7° |
c = 10.4117 (6) Å | µ = 0.26 mm−1 |
α = 65.904 (1)° | T = 89 K |
β = 76.889 (1)° | Needle, colourless |
γ = 74.014 (1)° | 0.32 × 0.20 × 0.10 mm |
V = 664.62 (7) Å3 |
Siemens SMART CCD diffractometer | 2506 independent reflections |
Radiation source: fine-focus sealed tube | 2078 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.026 |
Area detector ω scans | θmax = 25.7°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1997) | h = −8→8 |
Tmin = 0.672, Tmax = 0.981 | k = −12→12 |
6112 measured reflections | l = −12→12 |
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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.103 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0528P)2 + 0.4021P] where P = (Fo2 + 2Fc2)/3 |
2506 reflections | (Δ/σ)max < 0.001 |
179 parameters | Δρmax = 0.50 e Å−3 |
0 restraints | Δρmin = −0.38 e Å−3 |
C9H10N2O4·C2H6OS | γ = 74.014 (1)° |
Mr = 288.32 | V = 664.62 (7) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.2124 (4) Å | Mo Kα radiation |
b = 10.1722 (6) Å | µ = 0.26 mm−1 |
c = 10.4117 (6) Å | T = 89 K |
α = 65.904 (1)° | 0.32 × 0.20 × 0.10 mm |
β = 76.889 (1)° |
Siemens SMART CCD diffractometer | 2506 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1997) | 2078 reflections with I > 2σ(I) |
Tmin = 0.672, Tmax = 0.981 | Rint = 0.026 |
6112 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.103 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.50 e Å−3 |
2506 reflections | Δρmin = −0.38 e Å−3 |
179 parameters |
Experimental. After primary data collection, a portion of the first block of data was re-measured to check for crystal decay. No decay was detected. |
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 > 2σ(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 | ||
O1 | 0.7428 (2) | 0.74152 (14) | 0.49286 (14) | 0.0194 (3) | |
O2 | 0.7892 (2) | 0.12848 (16) | 0.93095 (15) | 0.0275 (4) | |
O3 | 0.8474 (2) | 0.34423 (16) | 0.87491 (15) | 0.0240 (3) | |
O4 | 0.7515 (2) | −0.04223 (15) | 0.57626 (15) | 0.0223 (3) | |
HO4 | 0.751 (4) | −0.107 (3) | 0.547 (3) | 0.033 (7)* | |
N1 | 0.7253 (2) | 0.61369 (17) | 0.36153 (16) | 0.0143 (3) | |
H1 | 0.7122 | 0.6232 | 0.2779 | 0.017* | |
N2 | 0.8098 (2) | 0.25090 (18) | 0.84407 (17) | 0.0176 (4) | |
C1 | 0.7568 (3) | 0.2115 (2) | 0.5149 (2) | 0.0144 (4) | |
C2 | 0.7386 (3) | 0.3575 (2) | 0.4214 (2) | 0.0139 (4) | |
H2 | 0.7207 | 0.3813 | 0.3282 | 0.017* | |
C3 | 0.7466 (2) | 0.4693 (2) | 0.4645 (2) | 0.0130 (4) | |
C4 | 0.7726 (3) | 0.4339 (2) | 0.6049 (2) | 0.0144 (4) | |
H4 | 0.7801 | 0.5056 | 0.6362 | 0.017* | |
C5 | 0.7867 (3) | 0.2879 (2) | 0.6955 (2) | 0.0148 (4) | |
C6 | 0.7804 (3) | 0.1751 (2) | 0.6555 (2) | 0.0152 (4) | |
H6 | 0.7915 | 0.0785 | 0.7201 | 0.018* | |
C7 | 0.7482 (3) | 0.0950 (2) | 0.4630 (2) | 0.0174 (4) | |
H7A | 0.6301 | 0.1233 | 0.4201 | 0.021* | |
H7B | 0.8583 | 0.0868 | 0.3913 | 0.021* | |
C8 | 0.7231 (3) | 0.7392 (2) | 0.3791 (2) | 0.0150 (4) | |
C9 | 0.6964 (3) | 0.8784 (2) | 0.2486 (2) | 0.0200 (4) | |
H9A | 0.5845 | 0.9475 | 0.2689 | 0.030* | |
H9B | 0.6779 | 0.8556 | 0.1721 | 0.030* | |
H9C | 0.8098 | 0.9204 | 0.2219 | 0.030* | |
S | 0.67034 (7) | 0.73548 (5) | 0.95105 (5) | 0.02010 (16) | |
O5 | 0.6536 (2) | 0.62318 (16) | 1.10091 (14) | 0.0233 (3) | |
C10 | 0.9074 (3) | 0.6815 (2) | 0.8663 (2) | 0.0250 (5) | |
H10A | 1.0039 | 0.6890 | 0.9118 | 0.038* | |
H10B | 0.9197 | 0.7450 | 0.7681 | 0.038* | |
H10C | 0.9260 | 0.5817 | 0.8735 | 0.038* | |
C11 | 0.5368 (3) | 0.6896 (2) | 0.8558 (2) | 0.0239 (5) | |
H11A | 0.5771 | 0.5865 | 0.8722 | 0.036* | |
H11B | 0.5612 | 0.7457 | 0.7562 | 0.036* | |
H11C | 0.4003 | 0.7118 | 0.8879 | 0.036* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0281 (8) | 0.0156 (7) | 0.0178 (7) | −0.0067 (6) | −0.0044 (6) | −0.0074 (6) |
O2 | 0.0426 (9) | 0.0201 (8) | 0.0169 (8) | −0.0079 (7) | −0.0058 (7) | −0.0019 (6) |
O3 | 0.0330 (8) | 0.0257 (8) | 0.0206 (8) | −0.0106 (6) | −0.0079 (6) | −0.0107 (6) |
O4 | 0.0395 (9) | 0.0121 (7) | 0.0175 (8) | −0.0085 (6) | −0.0073 (6) | −0.0038 (6) |
N1 | 0.0188 (8) | 0.0137 (8) | 0.0115 (8) | −0.0041 (6) | −0.0035 (6) | −0.0044 (7) |
N2 | 0.0187 (8) | 0.0191 (9) | 0.0141 (9) | −0.0033 (7) | −0.0019 (6) | −0.0059 (7) |
C1 | 0.0116 (9) | 0.0157 (10) | 0.0175 (10) | −0.0024 (7) | −0.0012 (7) | −0.0082 (8) |
C2 | 0.0140 (9) | 0.0158 (9) | 0.0118 (9) | −0.0031 (7) | −0.0032 (7) | −0.0043 (8) |
C3 | 0.0109 (9) | 0.0140 (9) | 0.0141 (9) | −0.0029 (7) | −0.0018 (7) | −0.0049 (8) |
C4 | 0.0151 (9) | 0.0144 (9) | 0.0153 (10) | −0.0034 (7) | −0.0020 (7) | −0.0069 (8) |
C5 | 0.0132 (9) | 0.0186 (10) | 0.0127 (9) | −0.0034 (7) | −0.0021 (7) | −0.0056 (8) |
C6 | 0.0141 (9) | 0.0133 (9) | 0.0168 (10) | −0.0026 (7) | −0.0025 (7) | −0.0038 (8) |
C7 | 0.0205 (10) | 0.0142 (9) | 0.0177 (10) | −0.0043 (7) | −0.0034 (8) | −0.0052 (8) |
C8 | 0.0116 (9) | 0.0142 (9) | 0.0193 (10) | −0.0034 (7) | −0.0008 (7) | −0.0063 (8) |
C9 | 0.0242 (10) | 0.0144 (10) | 0.0209 (11) | −0.0046 (8) | −0.0038 (8) | −0.0054 (8) |
S | 0.0245 (3) | 0.0192 (3) | 0.0170 (3) | −0.0062 (2) | −0.00436 (19) | −0.0052 (2) |
O5 | 0.0322 (8) | 0.0263 (8) | 0.0121 (7) | −0.0112 (6) | −0.0045 (6) | −0.0035 (6) |
C10 | 0.0227 (11) | 0.0296 (12) | 0.0182 (11) | −0.0070 (9) | −0.0048 (8) | −0.0021 (9) |
C11 | 0.0223 (10) | 0.0329 (12) | 0.0165 (11) | −0.0096 (9) | −0.0052 (8) | −0.0052 (9) |
O1—C8 | 1.235 (2) | C5—C6 | 1.386 (3) |
O2—N2 | 1.230 (2) | C6—H6 | 0.9300 |
O3—N2 | 1.228 (2) | C7—H7A | 0.9700 |
O4—C7 | 1.410 (2) | C7—H7B | 0.9700 |
O4—HO4 | 0.83 (3) | C8—C9 | 1.512 (3) |
N1—C8 | 1.357 (2) | C9—H9A | 0.9600 |
N1—C3 | 1.413 (2) | C9—H9B | 0.9600 |
N1—H1 | 0.8600 | C9—H9C | 0.9600 |
N2—C5 | 1.473 (2) | S—O5 | 1.5130 (14) |
C1—C2 | 1.393 (3) | S—C11 | 1.785 (2) |
C1—C6 | 1.394 (3) | S—C10 | 1.788 (2) |
C1—C7 | 1.510 (3) | C10—H10A | 0.9600 |
C2—C3 | 1.401 (3) | C10—H10B | 0.9600 |
C2—H2 | 0.9300 | C10—H10C | 0.9600 |
C3—C4 | 1.399 (3) | C11—H11A | 0.9600 |
C4—C5 | 1.387 (3) | C11—H11B | 0.9600 |
C4—H4 | 0.9300 | C11—H11C | 0.9600 |
C7—O4—HO4 | 110.7 (18) | O4—C7—H7B | 109.5 |
C8—N1—C3 | 127.59 (16) | C1—C7—H7B | 109.5 |
C8—N1—H1 | 116.2 | H7A—C7—H7B | 108.1 |
C3—N1—H1 | 116.2 | O1—C8—N1 | 123.12 (18) |
O3—N2—O2 | 123.43 (17) | O1—C8—C9 | 121.40 (17) |
O3—N2—C5 | 118.31 (16) | N1—C8—C9 | 115.48 (17) |
O2—N2—C5 | 118.26 (16) | C8—C9—H9A | 109.5 |
C2—C1—C6 | 119.66 (17) | C8—C9—H9B | 109.5 |
C2—C1—C7 | 119.49 (17) | H9A—C9—H9B | 109.5 |
C6—C1—C7 | 120.85 (17) | C8—C9—H9C | 109.5 |
C1—C2—C3 | 121.52 (18) | H9A—C9—H9C | 109.5 |
C1—C2—H2 | 119.2 | H9B—C9—H9C | 109.5 |
C3—C2—H2 | 119.2 | O5—S—C11 | 105.62 (9) |
C4—C3—C2 | 119.39 (17) | O5—S—C10 | 106.87 (9) |
C4—C3—N1 | 123.66 (16) | C11—S—C10 | 97.05 (10) |
C2—C3—N1 | 116.94 (16) | S—C10—H10A | 109.5 |
C5—C4—C3 | 117.43 (17) | S—C10—H10B | 109.5 |
C5—C4—H4 | 121.3 | H10A—C10—H10B | 109.5 |
C3—C4—H4 | 121.3 | S—C10—H10C | 109.5 |
C6—C5—C4 | 124.38 (18) | H10A—C10—H10C | 109.5 |
C6—C5—N2 | 118.08 (17) | H10B—C10—H10C | 109.5 |
C4—C5—N2 | 117.54 (16) | S—C11—H11A | 109.5 |
C5—C6—C1 | 117.60 (17) | S—C11—H11B | 109.5 |
C5—C6—H6 | 121.2 | H11A—C11—H11B | 109.5 |
C1—C6—H6 | 121.2 | S—C11—H11C | 109.5 |
O4—C7—C1 | 110.61 (16) | H11A—C11—H11C | 109.5 |
O4—C7—H7A | 109.5 | H11B—C11—H11C | 109.5 |
C1—C7—H7A | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O5i | 0.86 | 1.98 | 2.835 (2) | 171 |
O4—HO4···O1ii | 0.83 (3) | 1.86 (3) | 2.6941 (19) | 177 (3) |
Symmetry codes: (i) x, y, z−1; (ii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C9H10N2O4·C2H6OS |
Mr | 288.32 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 89 |
a, b, c (Å) | 7.2124 (4), 10.1722 (6), 10.4117 (6) |
α, β, γ (°) | 65.904 (1), 76.889 (1), 74.014 (1) |
V (Å3) | 664.62 (7) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.32 × 0.20 × 0.10 |
Data collection | |
Diffractometer | Siemens SMART CCD |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1997) |
Tmin, Tmax | 0.672, 0.981 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6112, 2506, 2078 |
Rint | 0.026 |
(sin θ/λ)max (Å−1) | 0.610 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.103, 1.02 |
No. of reflections | 2506 |
No. of parameters | 179 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.50, −0.38 |
Computer programs: SMART (Siemens, 1995), SAINT (Siemens, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPIII (Burnett & Johnson, 1996), SHELXTL (Siemens, 1995).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O5i | 0.86 | 1.98 | 2.835 (2) | 170.9 |
O4—HO4···O1ii | 0.83 (3) | 1.86 (3) | 2.6941 (19) | 177 (3) |
Symmetry codes: (i) x, y, z−1; (ii) x, y−1, z. |
Subscribe to Acta Crystallographica Section E: Crystallographic Communications
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- If you have already subscribed, you may need to register
Oligopeptides are a growing area of interest due to their strong biological activities (Lown et al., 1986, Lelkes & Pollard, 1987, Xie et al., 1996, Turner & Denny, 2000, Petering et al., 2000). Some natural oligopeptides are powerful DNA minor groove-binding agents but their cytotoxity precludes their use as medicines (Arcamone et al., 1964, Baraldi et al., 2004, Wemmer, 2000, Storl et al., 1993). To increase the DNA binding affinity and sequence specificity and to minimize the undesired physiological activities, many synthetic analogues have been prepared (Baraldi et al., 2007). The title compound is a key intermediate required in the synthesis of a novel polybenzamide DNA minor groove-binding agent. For background information on polybenzamide DNA binding agents see (Atwell et al., 1995, Turner et al., 1999, Yan et al., 1997)