Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
The title compound, C9H10N2O4·C2H6OS, was prepared by the selective hydrolysis of 3-acetamido-5-nitro­benzyl ­acetate with sodium hydroxide in ethanol. The crystal structure contains a dimethyl sulfoxide solvent mol­ecule. The title compound is an inter­mediate in the synthesis of DNA minor-groove-binding polybenzamide agents. N—H...O and O—H...O hydrogen bonds are present in the crystal structure.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807042778/pk2041sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807042778/pk2041Isup2.hkl
Contains datablock I

CCDC reference: 663708

Key indicators

  • Single-crystal X-ray study
  • T = 89 K
  • Mean [sigma](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

Comment top

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)

Related literature top

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).

Experimental top

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.

Refinement top

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.

Structure description top

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).

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structure showing 50% probability displacement ellipsoids for non-hydrogen atoms and hydrogen atoms as arbitary spheres (Burnett & Johnson, 1996).
N-(3-Hydroxymethyl-5-nitrophenyl)acetamide dimethyl sulfoxide solvate top
Crystal data top
C9H10N2O4·C2H6OSZ = 2
Mr = 288.32F(000) = 304
Triclinic, P1Dx = 1.441 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.2124 (4) ÅCell parameters from 3933 reflections
b = 10.1722 (6) Åθ = 2.2–25.7°
c = 10.4117 (6) ŵ = 0.26 mm1
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
Data collection top
Siemens SMART CCD
diffractometer
2506 independent reflections
Radiation source: fine-focus sealed tube2078 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.026
Area detector ω scansθmax = 25.7°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)
h = 88
Tmin = 0.672, Tmax = 0.981k = 1212
6112 measured reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103H 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 parametersΔρmax = 0.50 e Å3
0 restraintsΔρmin = 0.38 e Å3
Crystal data top
C9H10N2O4·C2H6OSγ = 74.014 (1)°
Mr = 288.32V = 664.62 (7) Å3
Triclinic, P1Z = 2
a = 7.2124 (4) ÅMo Kα radiation
b = 10.1722 (6) ŵ = 0.26 mm1
c = 10.4117 (6) ÅT = 89 K
α = 65.904 (1)°0.32 × 0.20 × 0.10 mm
β = 76.889 (1)°
Data collection top
Siemens SMART CCD
diffractometer
2506 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)
2078 reflections with I > 2σ(I)
Tmin = 0.672, Tmax = 0.981Rint = 0.026
6112 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.50 e Å3
2506 reflectionsΔρmin = 0.38 e Å3
179 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.7428 (2)0.74152 (14)0.49286 (14)0.0194 (3)
O20.7892 (2)0.12848 (16)0.93095 (15)0.0275 (4)
O30.8474 (2)0.34423 (16)0.87491 (15)0.0240 (3)
O40.7515 (2)0.04223 (15)0.57626 (15)0.0223 (3)
HO40.751 (4)0.107 (3)0.547 (3)0.033 (7)*
N10.7253 (2)0.61369 (17)0.36153 (16)0.0143 (3)
H10.71220.62320.27790.017*
N20.8098 (2)0.25090 (18)0.84407 (17)0.0176 (4)
C10.7568 (3)0.2115 (2)0.5149 (2)0.0144 (4)
C20.7386 (3)0.3575 (2)0.4214 (2)0.0139 (4)
H20.72070.38130.32820.017*
C30.7466 (2)0.4693 (2)0.4645 (2)0.0130 (4)
C40.7726 (3)0.4339 (2)0.6049 (2)0.0144 (4)
H40.78010.50560.63620.017*
C50.7867 (3)0.2879 (2)0.6955 (2)0.0148 (4)
C60.7804 (3)0.1751 (2)0.6555 (2)0.0152 (4)
H60.79150.07850.72010.018*
C70.7482 (3)0.0950 (2)0.4630 (2)0.0174 (4)
H7A0.63010.12330.42010.021*
H7B0.85830.08680.39130.021*
C80.7231 (3)0.7392 (2)0.3791 (2)0.0150 (4)
C90.6964 (3)0.8784 (2)0.2486 (2)0.0200 (4)
H9A0.58450.94750.26890.030*
H9B0.67790.85560.17210.030*
H9C0.80980.92040.22190.030*
S0.67034 (7)0.73548 (5)0.95105 (5)0.02010 (16)
O50.6536 (2)0.62318 (16)1.10091 (14)0.0233 (3)
C100.9074 (3)0.6815 (2)0.8663 (2)0.0250 (5)
H10A1.00390.68900.91180.038*
H10B0.91970.74500.76810.038*
H10C0.92600.58170.87350.038*
C110.5368 (3)0.6896 (2)0.8558 (2)0.0239 (5)
H11A0.57710.58650.87220.036*
H11B0.56120.74570.75620.036*
H11C0.40030.71180.88790.036*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0281 (8)0.0156 (7)0.0178 (7)0.0067 (6)0.0044 (6)0.0074 (6)
O20.0426 (9)0.0201 (8)0.0169 (8)0.0079 (7)0.0058 (7)0.0019 (6)
O30.0330 (8)0.0257 (8)0.0206 (8)0.0106 (6)0.0079 (6)0.0107 (6)
O40.0395 (9)0.0121 (7)0.0175 (8)0.0085 (6)0.0073 (6)0.0038 (6)
N10.0188 (8)0.0137 (8)0.0115 (8)0.0041 (6)0.0035 (6)0.0044 (7)
N20.0187 (8)0.0191 (9)0.0141 (9)0.0033 (7)0.0019 (6)0.0059 (7)
C10.0116 (9)0.0157 (10)0.0175 (10)0.0024 (7)0.0012 (7)0.0082 (8)
C20.0140 (9)0.0158 (9)0.0118 (9)0.0031 (7)0.0032 (7)0.0043 (8)
C30.0109 (9)0.0140 (9)0.0141 (9)0.0029 (7)0.0018 (7)0.0049 (8)
C40.0151 (9)0.0144 (9)0.0153 (10)0.0034 (7)0.0020 (7)0.0069 (8)
C50.0132 (9)0.0186 (10)0.0127 (9)0.0034 (7)0.0021 (7)0.0056 (8)
C60.0141 (9)0.0133 (9)0.0168 (10)0.0026 (7)0.0025 (7)0.0038 (8)
C70.0205 (10)0.0142 (9)0.0177 (10)0.0043 (7)0.0034 (8)0.0052 (8)
C80.0116 (9)0.0142 (9)0.0193 (10)0.0034 (7)0.0008 (7)0.0063 (8)
C90.0242 (10)0.0144 (10)0.0209 (11)0.0046 (8)0.0038 (8)0.0054 (8)
S0.0245 (3)0.0192 (3)0.0170 (3)0.0062 (2)0.00436 (19)0.0052 (2)
O50.0322 (8)0.0263 (8)0.0121 (7)0.0112 (6)0.0045 (6)0.0035 (6)
C100.0227 (11)0.0296 (12)0.0182 (11)0.0070 (9)0.0048 (8)0.0021 (9)
C110.0223 (10)0.0329 (12)0.0165 (11)0.0096 (9)0.0052 (8)0.0052 (9)
Geometric parameters (Å, º) top
O1—C81.235 (2)C5—C61.386 (3)
O2—N21.230 (2)C6—H60.9300
O3—N21.228 (2)C7—H7A0.9700
O4—C71.410 (2)C7—H7B0.9700
O4—HO40.83 (3)C8—C91.512 (3)
N1—C81.357 (2)C9—H9A0.9600
N1—C31.413 (2)C9—H9B0.9600
N1—H10.8600C9—H9C0.9600
N2—C51.473 (2)S—O51.5130 (14)
C1—C21.393 (3)S—C111.785 (2)
C1—C61.394 (3)S—C101.788 (2)
C1—C71.510 (3)C10—H10A0.9600
C2—C31.401 (3)C10—H10B0.9600
C2—H20.9300C10—H10C0.9600
C3—C41.399 (3)C11—H11A0.9600
C4—C51.387 (3)C11—H11B0.9600
C4—H40.9300C11—H11C0.9600
C7—O4—HO4110.7 (18)O4—C7—H7B109.5
C8—N1—C3127.59 (16)C1—C7—H7B109.5
C8—N1—H1116.2H7A—C7—H7B108.1
C3—N1—H1116.2O1—C8—N1123.12 (18)
O3—N2—O2123.43 (17)O1—C8—C9121.40 (17)
O3—N2—C5118.31 (16)N1—C8—C9115.48 (17)
O2—N2—C5118.26 (16)C8—C9—H9A109.5
C2—C1—C6119.66 (17)C8—C9—H9B109.5
C2—C1—C7119.49 (17)H9A—C9—H9B109.5
C6—C1—C7120.85 (17)C8—C9—H9C109.5
C1—C2—C3121.52 (18)H9A—C9—H9C109.5
C1—C2—H2119.2H9B—C9—H9C109.5
C3—C2—H2119.2O5—S—C11105.62 (9)
C4—C3—C2119.39 (17)O5—S—C10106.87 (9)
C4—C3—N1123.66 (16)C11—S—C1097.05 (10)
C2—C3—N1116.94 (16)S—C10—H10A109.5
C5—C4—C3117.43 (17)S—C10—H10B109.5
C5—C4—H4121.3H10A—C10—H10B109.5
C3—C4—H4121.3S—C10—H10C109.5
C6—C5—C4124.38 (18)H10A—C10—H10C109.5
C6—C5—N2118.08 (17)H10B—C10—H10C109.5
C4—C5—N2117.54 (16)S—C11—H11A109.5
C5—C6—C1117.60 (17)S—C11—H11B109.5
C5—C6—H6121.2H11A—C11—H11B109.5
C1—C6—H6121.2S—C11—H11C109.5
O4—C7—C1110.61 (16)H11A—C11—H11C109.5
O4—C7—H7A109.5H11B—C11—H11C109.5
C1—C7—H7A109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.861.982.835 (2)171
O4—HO4···O1ii0.83 (3)1.86 (3)2.6941 (19)177 (3)
Symmetry codes: (i) x, y, z1; (ii) x, y1, z.

Experimental details

Crystal data
Chemical formulaC9H10N2O4·C2H6OS
Mr288.32
Crystal system, space groupTriclinic, 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)
V3)664.62 (7)
Z2
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.32 × 0.20 × 0.10
Data collection
DiffractometerSiemens SMART CCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1997)
Tmin, Tmax0.672, 0.981
No. of measured, independent and
observed [I > 2σ(I)] reflections
6112, 2506, 2078
Rint0.026
(sin θ/λ)max1)0.610
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.103, 1.02
No. of reflections2506
No. of parameters179
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.861.982.835 (2)170.9
O4—HO4···O1ii0.83 (3)1.86 (3)2.6941 (19)177 (3)
Symmetry codes: (i) x, y, z1; (ii) x, y1, z.
 

Subscribe to Acta Crystallographica Section E: Crystallographic Communications

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email support@iucr.org for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds