In the title compound, C17H25N6O4+·Cl−·CH4O, the cation adopts a bowed conformation with π-conjugation via two pyrrole rings and and two peptide groups.
Supporting information
CCDC reference: 209918
Key indicators
- Single-crystal X-ray study
- T = 183 K
- Mean (C-C) = 0.005 Å
- R factor = 0.068
- wR factor = 0.097
- Data-to-parameter ratio = 12.7
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
The literature procedure for the preparation of 3-[1-methyl-4-(1-methyl-4-nitropyrrole-2-carboxamido)pyrrole-2- carboxamido]dimethylaminopropane was followed (Nishiwaki et al., 1988), with a little modification, and the compound obtained was dissolved in methanol (100%) with a few drops of 1 N HCl. The solution was left at 277 K and the crystals of (I) appeared after several months.
H atoms attached to C and O atoms were placed in geometrically idealized positions, with Csp2—H = 0.95 Å, Csp3—H = 0.98 Å, Csp3—H = 0.98 Å, and Osp3—H = 0.84 Å, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C) and Uiso(H)= 1.5Ueq(O). H atoms on N atoms were located in difference Fourier maps and refined with a common Uiso value. The N—H distances are in the range 0.77–0.86 Å.
Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2000); program(s) used to refine structure: SHELXL97 (Sheldrick, 2000); molecular graphics: SHELXTL/PC (Sheldrick, 1999); software used to prepare material for publication: SHELXTL/PC.
Dimethyl{3-[1-methyl-4-(1-methyl-4-nitropyrrole-2-carboxamido)pyrrole-2- carboxamido]propyl}ammonium chloride monomethanol
top
Crystal data top
C17H25N6O4+·Cl−·CH4O | F(000) = 944 |
Mr = 444.92 | Dx = 1.374 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1027 reflections |
a = 6.2129 (13) Å | θ = 2.4–19.6° |
b = 17.801 (4) Å | µ = 0.22 mm−1 |
c = 19.442 (4) Å | T = 183 K |
β = 90.765 (4)° | Block, yellow |
V = 2150.1 (8) Å3 | 0.20 × 0.20 × 0.20 mm |
Z = 4 | |
Data collection top
SMART 1K CCD area-detector diffractometer | 2335 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.074 |
Graphite monochromator | θmax = 24.8°, θmin = 2.1° |
ω scans | h = −7→6 |
8201 measured reflections | k = −20→19 |
3529 independent reflections | l = −22→21 |
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)] = 0.068 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 0.98 | w = 1/[σ2(Fo2) + (0.0108P)2] where P = (Fo2 + 2Fc2)/3 |
3529 reflections | (Δ/σ)max < 0.001 |
278 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
Crystal data top
C17H25N6O4+·Cl−·CH4O | V = 2150.1 (8) Å3 |
Mr = 444.92 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.2129 (13) Å | µ = 0.22 mm−1 |
b = 17.801 (4) Å | T = 183 K |
c = 19.442 (4) Å | 0.20 × 0.20 × 0.20 mm |
β = 90.765 (4)° | |
Data collection top
SMART 1K CCD area-detector diffractometer | 2335 reflections with I > 2σ(I) |
8201 measured reflections | Rint = 0.074 |
3529 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.068 | 0 restraints |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 0.98 | Δρmax = 0.19 e Å−3 |
3529 reflections | Δρmin = −0.21 e Å−3 |
278 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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.1155 (6) | 0.52134 (19) | 0.8850 (2) | 0.0355 (10) | |
H1A | −0.0087 | 0.5295 | 0.9154 | 0.043* | |
H1B | 0.1747 | 0.5713 | 0.8733 | 0.043* | |
C2 | 0.2860 (6) | 0.47772 (19) | 0.9244 (2) | 0.0358 (10) | |
H2A | 0.4151 | 0.4732 | 0.8954 | 0.043* | |
H2B | 0.3277 | 0.5067 | 0.9660 | 0.043* | |
C3 | 0.2176 (5) | 0.40062 (19) | 0.94611 (19) | 0.0290 (10) | |
H3A | 0.1020 | 0.4050 | 0.9804 | 0.035* | |
H3B | 0.1581 | 0.3735 | 0.9057 | 0.035* | |
C4 | 0.4357 (6) | 0.35272 (19) | 1.0438 (2) | 0.0258 (9) | |
C5 | 0.6261 (5) | 0.30744 (19) | 1.06192 (19) | 0.0227 (9) | |
C6 | 0.7847 (5) | 0.28059 (18) | 1.02045 (19) | 0.0238 (9) | |
H6 | 0.7933 | 0.2880 | 0.9722 | 0.029* | |
C7 | 0.9313 (6) | 0.24071 (18) | 1.0608 (2) | 0.0248 (9) | |
C8 | 0.8599 (6) | 0.24328 (18) | 1.1281 (2) | 0.0274 (9) | |
H8 | 0.9280 | 0.2207 | 1.1670 | 0.033* | |
C9 | 0.5459 (6) | 0.29557 (19) | 1.18982 (19) | 0.0346 (10) | |
H9A | 0.6077 | 0.2661 | 1.2278 | 0.052* | |
H9B | 0.3975 | 0.2792 | 1.1809 | 0.052* | |
H9C | 0.5468 | 0.3489 | 1.2022 | 0.052* | |
C10 | 1.2441 (5) | 0.15836 (19) | 1.07096 (19) | 0.0224 (9) | |
C11 | 1.4251 (5) | 0.12558 (19) | 1.0313 (2) | 0.0272 (10) | |
C12 | 1.4636 (6) | 0.12780 (17) | 0.9627 (2) | 0.0280 (9) | |
H12 | 1.3748 | 0.1498 | 0.9281 | 0.034* | |
C13 | 1.6589 (6) | 0.09136 (19) | 0.9534 (2) | 0.0272 (9) | |
C14 | 1.7379 (6) | 0.06712 (18) | 1.0158 (2) | 0.0305 (10) | |
H14 | 1.8687 | 0.0407 | 1.0238 | 0.037* | |
C15 | 1.6255 (6) | 0.0724 (2) | 1.1371 (2) | 0.0393 (11) | |
H15A | 1.5202 | 0.0349 | 1.1518 | 0.059* | |
H15B | 1.6062 | 0.1187 | 1.1635 | 0.059* | |
H15C | 1.7713 | 0.0530 | 1.1450 | 0.059* | |
C16 | 0.2105 (6) | 0.4578 (2) | 0.7743 (2) | 0.0418 (11) | |
H16A | 0.2967 | 0.5007 | 0.7592 | 0.063* | |
H16B | 0.1467 | 0.4327 | 0.7340 | 0.063* | |
H16C | 0.3029 | 0.4223 | 0.7995 | 0.063* | |
C17 | −0.1120 (6) | 0.5362 (2) | 0.7823 (2) | 0.0460 (12) | |
H17A | −0.2183 | 0.5565 | 0.8141 | 0.069* | |
H17B | −0.1861 | 0.5086 | 0.7453 | 0.069* | |
H17C | −0.0292 | 0.5776 | 0.7624 | 0.069* | |
N1 | 0.0362 (5) | 0.48461 (16) | 0.82003 (16) | 0.0286 (8) | |
H1 | −0.0375 | 0.4474 | 0.8339 | 0.023* | |
N2 | 0.3939 (4) | 0.35759 (16) | 0.97553 (16) | 0.0324 (8) | |
H2 | 0.4832 | 0.3442 | 0.9513 | 0.023* | |
N3 | 0.6736 (4) | 0.28424 (14) | 1.12818 (15) | 0.0233 (7) | |
N4 | 1.1142 (4) | 0.20392 (15) | 1.03479 (15) | 0.0284 (8) | |
H4 | 1.1276 | 0.2084 | 0.9910 | 0.023* | |
N5 | 1.5937 (5) | 0.08810 (15) | 1.06375 (16) | 0.0289 (8) | |
N6 | 1.7679 (5) | 0.07992 (17) | 0.88990 (18) | 0.0369 (9) | |
O1 | 0.3218 (4) | 0.38337 (13) | 1.08637 (13) | 0.0354 (7) | |
O2 | 1.2177 (4) | 0.14425 (14) | 1.13204 (14) | 0.0424 (7) | |
O3 | 1.6775 (5) | 0.10320 (15) | 0.83639 (15) | 0.0508 (8) | |
O4 | 1.9404 (4) | 0.04654 (14) | 0.89035 (14) | 0.0474 (8) | |
Cl1 | 0.27650 (15) | 0.64975 (5) | 0.16446 (5) | 0.0355 (3) | |
C18 | 0.8187 (7) | 0.7770 (2) | 0.1817 (2) | 0.0514 (13) | |
H18A | 0.9187 | 0.7853 | 0.2204 | 0.077* | |
H18B | 0.7393 | 0.7302 | 0.1890 | 0.077* | |
H18C | 0.7171 | 0.8190 | 0.1786 | 0.077* | |
O5 | 0.9346 (4) | 0.77204 (15) | 0.12045 (13) | 0.0427 (8) | |
H5 | 1.0456 | 0.7460 | 0.1271 | 0.064* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.046 (3) | 0.029 (2) | 0.032 (3) | −0.003 (2) | −0.004 (2) | −0.005 (2) |
C2 | 0.032 (2) | 0.031 (2) | 0.044 (3) | 0.0031 (19) | −0.010 (2) | 0.001 (2) |
C3 | 0.022 (2) | 0.040 (2) | 0.026 (2) | 0.0023 (18) | 0.0016 (18) | 0.0000 (19) |
C4 | 0.032 (2) | 0.021 (2) | 0.025 (2) | −0.0104 (18) | 0.0042 (19) | 0.0016 (19) |
C5 | 0.025 (2) | 0.022 (2) | 0.021 (2) | −0.0046 (17) | 0.0023 (17) | 0.0004 (17) |
C6 | 0.022 (2) | 0.027 (2) | 0.023 (2) | −0.0050 (17) | 0.0059 (17) | 0.0030 (18) |
C7 | 0.025 (2) | 0.023 (2) | 0.027 (2) | −0.0024 (17) | 0.0083 (18) | −0.0002 (18) |
C8 | 0.033 (2) | 0.022 (2) | 0.027 (2) | 0.0056 (18) | 0.0001 (18) | 0.0042 (17) |
C9 | 0.043 (3) | 0.038 (2) | 0.022 (2) | 0.004 (2) | 0.0068 (19) | 0.002 (2) |
C10 | 0.020 (2) | 0.024 (2) | 0.023 (2) | −0.0007 (17) | 0.0072 (17) | 0.0037 (18) |
C11 | 0.025 (2) | 0.028 (2) | 0.029 (3) | −0.0006 (18) | 0.0062 (19) | −0.0028 (18) |
C12 | 0.032 (2) | 0.024 (2) | 0.028 (3) | 0.0088 (18) | −0.0046 (19) | 0.0003 (18) |
C13 | 0.033 (2) | 0.025 (2) | 0.024 (2) | 0.0016 (18) | 0.0070 (19) | −0.0020 (18) |
C14 | 0.025 (2) | 0.029 (2) | 0.038 (3) | 0.0018 (18) | 0.0038 (19) | 0.000 (2) |
C15 | 0.031 (2) | 0.055 (3) | 0.031 (3) | 0.011 (2) | 0.000 (2) | 0.009 (2) |
C16 | 0.050 (3) | 0.048 (3) | 0.028 (3) | 0.008 (2) | 0.017 (2) | 0.002 (2) |
C17 | 0.061 (3) | 0.049 (3) | 0.028 (3) | 0.026 (2) | −0.006 (2) | −0.001 (2) |
N1 | 0.0324 (19) | 0.0314 (18) | 0.022 (2) | 0.0008 (15) | 0.0070 (15) | −0.0030 (15) |
N2 | 0.0297 (19) | 0.0396 (19) | 0.028 (2) | 0.0121 (16) | 0.0063 (16) | −0.0008 (17) |
N3 | 0.0249 (18) | 0.0225 (17) | 0.023 (2) | 0.0034 (14) | −0.0001 (14) | −0.0031 (15) |
N4 | 0.0243 (18) | 0.0357 (19) | 0.025 (2) | 0.0041 (15) | 0.0042 (15) | 0.0051 (16) |
N5 | 0.0285 (19) | 0.0300 (18) | 0.028 (2) | 0.0033 (15) | 0.0025 (15) | 0.0023 (16) |
N6 | 0.040 (2) | 0.031 (2) | 0.041 (3) | 0.0121 (17) | 0.0058 (19) | −0.0071 (18) |
O1 | 0.0349 (16) | 0.0438 (16) | 0.0280 (18) | 0.0137 (13) | 0.0107 (13) | −0.0065 (14) |
O2 | 0.0386 (16) | 0.0586 (18) | 0.0302 (18) | 0.0122 (15) | 0.0085 (13) | 0.0146 (16) |
O3 | 0.060 (2) | 0.064 (2) | 0.0287 (19) | 0.0261 (17) | −0.0009 (16) | −0.0015 (16) |
O4 | 0.0471 (19) | 0.0509 (18) | 0.045 (2) | 0.0238 (16) | 0.0154 (15) | 0.0001 (15) |
Cl1 | 0.0332 (6) | 0.0392 (6) | 0.0340 (6) | 0.0015 (5) | 0.0020 (4) | −0.0005 (5) |
C18 | 0.056 (3) | 0.066 (3) | 0.032 (3) | 0.019 (2) | 0.014 (2) | −0.002 (2) |
O5 | 0.0449 (19) | 0.0530 (19) | 0.0304 (19) | 0.0163 (15) | 0.0090 (14) | 0.0002 (15) |
Geometric parameters (Å, º) top
C1—N1 | 1.499 (4) | C11—N5 | 1.387 (4) |
C1—C2 | 1.514 (5) | C12—C13 | 1.390 (4) |
C1—H1A | 0.9900 | C12—H12 | 0.9500 |
C1—H1B | 0.9900 | C13—C14 | 1.372 (5) |
C2—C3 | 1.499 (4) | C13—N6 | 1.430 (4) |
C2—H2A | 0.9900 | C14—N5 | 1.355 (4) |
C2—H2B | 0.9900 | C14—H14 | 0.9500 |
C3—N2 | 1.448 (4) | C15—N5 | 1.463 (4) |
C3—H3A | 0.9900 | C15—H15A | 0.9800 |
C3—H3B | 0.9900 | C15—H15B | 0.9800 |
C4—O1 | 1.225 (4) | C15—H15C | 0.9800 |
C4—N2 | 1.351 (4) | C16—N1 | 1.489 (4) |
C4—C5 | 1.470 (5) | C16—H16A | 0.9800 |
C5—C6 | 1.368 (4) | C16—H16B | 0.9800 |
C5—N3 | 1.381 (4) | C16—H16C | 0.9800 |
C6—C7 | 1.389 (5) | C17—N1 | 1.488 (4) |
C6—H6 | 0.9500 | C17—H17A | 0.9800 |
C7—C8 | 1.387 (5) | C17—H17B | 0.9800 |
C7—N4 | 1.411 (4) | C17—H17C | 0.9800 |
C8—N3 | 1.368 (4) | N1—H1 | 0.8515 |
C8—H8 | 0.9500 | N2—H2 | 0.7708 |
C9—N3 | 1.460 (4) | N4—H4 | 0.8598 |
C9—H9A | 0.9800 | N6—O4 | 1.225 (3) |
C9—H9B | 0.9800 | N6—O3 | 1.247 (4) |
C9—H9C | 0.9800 | C18—O5 | 1.403 (4) |
C10—O2 | 1.227 (4) | C18—H18A | 0.9800 |
C10—N4 | 1.337 (4) | C18—H18B | 0.9800 |
C10—C11 | 1.490 (4) | C18—H18C | 0.9800 |
C11—C12 | 1.359 (5) | O5—H5 | 0.8400 |
| | | |
N1—C1—C2 | 115.0 (3) | C12—C13—N6 | 127.1 (4) |
N1—C1—H1A | 108.5 | N5—C14—C13 | 106.9 (3) |
C2—C1—H1A | 108.5 | N5—C14—H14 | 126.6 |
N1—C1—H1B | 108.5 | C13—C14—H14 | 126.6 |
C2—C1—H1B | 108.5 | N5—C15—H15A | 109.5 |
H1A—C1—H1B | 107.5 | N5—C15—H15B | 109.5 |
C3—C2—C1 | 114.4 (3) | H15A—C15—H15B | 109.5 |
C3—C2—H2A | 108.7 | N5—C15—H15C | 109.5 |
C1—C2—H2A | 108.7 | H15A—C15—H15C | 109.5 |
C3—C2—H2B | 108.7 | H15B—C15—H15C | 109.5 |
C1—C2—H2B | 108.7 | N1—C16—H16A | 109.5 |
H2A—C2—H2B | 107.6 | N1—C16—H16B | 109.5 |
N2—C3—C2 | 112.3 (3) | H16A—C16—H16B | 109.5 |
N2—C3—H3A | 109.1 | N1—C16—H16C | 109.5 |
C2—C3—H3A | 109.1 | H16A—C16—H16C | 109.5 |
N2—C3—H3B | 109.1 | H16B—C16—H16C | 109.5 |
C2—C3—H3B | 109.1 | N1—C17—H17A | 109.5 |
H3A—C3—H3B | 107.9 | N1—C17—H17B | 109.5 |
O1—C4—N2 | 122.0 (4) | H17A—C17—H17B | 109.5 |
O1—C4—C5 | 123.5 (4) | N1—C17—H17C | 109.5 |
N2—C4—C5 | 114.5 (3) | H17A—C17—H17C | 109.5 |
C6—C5—N3 | 107.4 (3) | H17B—C17—H17C | 109.5 |
C6—C5—C4 | 129.3 (4) | C16—N1—C17 | 110.7 (3) |
N3—C5—C4 | 123.3 (3) | C16—N1—C1 | 114.2 (3) |
C5—C6—C7 | 108.5 (3) | C17—N1—C1 | 109.9 (3) |
C5—C6—H6 | 125.7 | C16—N1—H1 | 109.8 |
C7—C6—H6 | 125.7 | C17—N1—H1 | 107.8 |
C8—C7—C6 | 107.5 (3) | C1—N1—H1 | 104.2 |
C8—C7—N4 | 128.5 (3) | C4—N2—C3 | 123.8 (3) |
C6—C7—N4 | 124.0 (3) | C4—N2—H2 | 116.8 |
N3—C8—C7 | 107.4 (3) | C3—N2—H2 | 117.9 |
N3—C8—H8 | 126.3 | C8—N3—C5 | 109.2 (3) |
C7—C8—H8 | 126.3 | C8—N3—C9 | 122.9 (3) |
N3—C9—H9A | 109.5 | C5—N3—C9 | 127.8 (3) |
N3—C9—H9B | 109.5 | C10—N4—C7 | 125.2 (3) |
H9A—C9—H9B | 109.5 | C10—N4—H4 | 120.7 |
N3—C9—H9C | 109.5 | C7—N4—H4 | 113.6 |
H9A—C9—H9C | 109.5 | C14—N5—C11 | 108.8 (3) |
H9B—C9—H9C | 109.5 | C14—N5—C15 | 122.4 (3) |
O2—C10—N4 | 123.0 (3) | C11—N5—C15 | 128.8 (3) |
O2—C10—C11 | 122.1 (3) | O4—N6—O3 | 123.5 (3) |
N4—C10—C11 | 114.8 (3) | O4—N6—C13 | 119.2 (3) |
C12—C11—N5 | 108.6 (3) | O3—N6—C13 | 117.4 (3) |
C12—C11—C10 | 129.8 (4) | O5—C18—H18A | 109.5 |
N5—C11—C10 | 121.6 (3) | O5—C18—H18B | 109.5 |
C11—C12—C13 | 106.3 (3) | H18A—C18—H18B | 109.5 |
C11—C12—H12 | 126.9 | O5—C18—H18C | 109.5 |
C13—C12—H12 | 126.9 | H18A—C18—H18C | 109.5 |
C14—C13—C12 | 109.5 (3) | H18B—C18—H18C | 109.5 |
C14—C13—N6 | 123.4 (3) | C18—O5—H5 | 109.5 |
| | | |
N1—C1—C2—C3 | −58.7 (5) | O1—C4—N2—C3 | 2.0 (5) |
C1—C2—C3—N2 | 172.4 (3) | C5—C4—N2—C3 | −178.6 (3) |
O1—C4—C5—C6 | −168.4 (3) | C2—C3—N2—C4 | 95.4 (4) |
N2—C4—C5—C6 | 12.2 (5) | C7—C8—N3—C5 | 0.1 (4) |
O1—C4—C5—N3 | 11.7 (5) | C7—C8—N3—C9 | 176.7 (3) |
N2—C4—C5—N3 | −167.8 (3) | C6—C5—N3—C8 | 0.0 (4) |
N3—C5—C6—C7 | −0.1 (4) | C4—C5—N3—C8 | 179.9 (3) |
C4—C5—C6—C7 | 180.0 (3) | C6—C5—N3—C9 | −176.4 (3) |
C5—C6—C7—C8 | 0.1 (4) | C4—C5—N3—C9 | 3.5 (5) |
C5—C6—C7—N4 | 178.8 (3) | O2—C10—N4—C7 | −0.7 (5) |
C6—C7—C8—N3 | −0.1 (4) | C11—C10—N4—C7 | 179.2 (3) |
N4—C7—C8—N3 | −178.7 (3) | C8—C7—N4—C10 | 6.3 (6) |
O2—C10—C11—C12 | 171.3 (4) | C6—C7—N4—C10 | −172.1 (3) |
N4—C10—C11—C12 | −8.7 (5) | C13—C14—N5—C11 | −0.2 (4) |
O2—C10—C11—N5 | −11.4 (5) | C13—C14—N5—C15 | −179.3 (3) |
N4—C10—C11—N5 | 168.7 (3) | C12—C11—N5—C14 | 0.2 (4) |
N5—C11—C12—C13 | −0.2 (4) | C10—C11—N5—C14 | −177.6 (3) |
C10—C11—C12—C13 | 177.4 (3) | C12—C11—N5—C15 | 179.3 (3) |
C11—C12—C13—C14 | 0.1 (4) | C10—C11—N5—C15 | 1.5 (5) |
C11—C12—C13—N6 | −179.5 (3) | C14—C13—N6—O4 | 0.4 (5) |
C12—C13—C14—N5 | 0.0 (4) | C12—C13—N6—O4 | 179.9 (3) |
N6—C13—C14—N5 | 179.6 (3) | C14—C13—N6—O3 | 178.5 (3) |
C2—C1—N1—C16 | −48.8 (4) | C12—C13—N6—O3 | −1.9 (6) |
C2—C1—N1—C17 | −173.9 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5···Cl1i | 0.84 | 2.34 | 3.152 (3) | 162 |
N1—H1···Cl1ii | 0.85 | 2.28 | 3.099 (3) | 161 |
N4—H4···O5iii | 0.86 | 2.22 | 3.060 (4) | 164 |
N2—H2···Cl1iv | 0.77 | 2.72 | 3.430 (3) | 154 |
Symmetry codes: (i) x+1, y, z; (ii) −x, −y+1, −z+1; (iii) −x+2, −y+1, −z+1; (iv) −x+1, −y+1, −z+1. |
Experimental details
Crystal data |
Chemical formula | C17H25N6O4+·Cl−·CH4O |
Mr | 444.92 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 183 |
a, b, c (Å) | 6.2129 (13), 17.801 (4), 19.442 (4) |
β (°) | 90.765 (4) |
V (Å3) | 2150.1 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.22 |
Crystal size (mm) | 0.20 × 0.20 × 0.20 |
|
Data collection |
Diffractometer | SMART 1K CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8201, 3529, 2335 |
Rint | 0.074 |
(sin θ/λ)max (Å−1) | 0.590 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.068, 0.097, 0.98 |
No. of reflections | 3529 |
No. of parameters | 278 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.19, −0.21 |
Selected geometric parameters (Å, º) topC1—N1 | 1.499 (4) | C10—O2 | 1.227 (4) |
C1—C2 | 1.514 (5) | C10—N4 | 1.337 (4) |
C2—C3 | 1.499 (4) | C10—C11 | 1.490 (4) |
C3—N2 | 1.448 (4) | C11—C12 | 1.359 (5) |
C4—O1 | 1.225 (4) | C11—N5 | 1.387 (4) |
C4—N2 | 1.351 (4) | C12—C13 | 1.390 (4) |
C4—C5 | 1.470 (5) | C13—C14 | 1.372 (5) |
C5—C6 | 1.368 (4) | C13—N6 | 1.430 (4) |
C5—N3 | 1.381 (4) | C14—N5 | 1.355 (4) |
C6—C7 | 1.389 (5) | C15—N5 | 1.463 (4) |
C7—C8 | 1.387 (5) | C16—N1 | 1.489 (4) |
C7—N4 | 1.411 (4) | C17—N1 | 1.488 (4) |
C8—N3 | 1.368 (4) | N6—O4 | 1.225 (3) |
C9—N3 | 1.460 (4) | N6—O3 | 1.247 (4) |
| | | |
N2—C4—C5—C6 | 12.2 (5) | C5—C4—N2—C3 | −178.6 (3) |
N4—C10—C11—C12 | −8.7 (5) | O2—C10—N4—C7 | −0.7 (5) |
O1—C4—N2—C3 | 2.0 (5) | C11—C10—N4—C7 | 179.2 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5···Cl1i | 0.84 | 2.34 | 3.152 (3) | 162 |
N1—H1···Cl1ii | 0.85 | 2.28 | 3.099 (3) | 161 |
N4—H4···O5iii | 0.86 | 2.22 | 3.060 (4) | 164 |
N2—H2···Cl1iv | 0.77 | 2.72 | 3.430 (3) | 154 |
Symmetry codes: (i) x+1, y, z; (ii) −x, −y+1, −z+1; (iii) −x+2, −y+1, −z+1; (iv) −x+1, −y+1, −z+1. |
All living organisms (excluding certain viruses) store their genetic information in the form of double-helical DNA. Biochemical access to this information is based on specific protein–DNA interactions. Despite recent progress using biological selection methods (phage display), predictive chemical principles for protein–DNA recognition are still considered complex (Greisman & Pabo, 1997; Choo & Klug, 1997); thus, this problem has attracted the interest of chemists to synthesize small molecules to the problem of DNA recognition. Inspired by the natural products netropsin and ditamycin, which bind to the AATT and AAATT sequences, respectively, in the minor grove of DNA, chemists have recently developed polyamides containing N-methylpyrrole and N-methylimidazole amino acids which can recognize and bind in the minor groove of predetermined DNA sequences with high affinity and specificity comparable to naturally occurring DNA-binding proteins (Trauger et al., 1996; Swalley et al., 1997; Turner et al., 1997; Trauger et al., 1998; Dervan & Buril, 1999). The co-crystal structures of netropsin, ditamycin and some polyamides showed that the polyamides exerted an influence on DNA structures, and DNA also influenced the structure of the polyamides (Berman et al., 1979; Kopka et al., 1985; Coll et al., 1987; Balendiran et al., 1995; Kielkopf, Baird et al., 1998; Kielkopf, White et al., 1998; Shi et al., 2002). To understand the principle of the interaction, which is significant for the design of new DNA-binding compounds, more structure information of polyamide–DNA and polyamides alone is needed. In this paper, we discuss the structure of the title polyamide, which contains two N-methylpyrrole rings.
The overall appearance of the cation in the title compound, (I), is a bowed molecule (Fig. 1). The bond lengthes and angles are not unusual (Table 1). There is a π-conjugation bond containing two pyrrole groups and two peptide bonds. Their adjacent atoms are essentially coplanar, forming a plane consisting of 22 atoms (N2–N6, O1–O4 and C3–C15). The maximum deviations from the plane are 0.250 (2) and −0.247 (2) Å for O1 and O2, and the minimum deviations only 0.001 (3) and −0.003 (3) Å for C13 and N5, respectively. The dihedral angle between the two pyrrole portions is 3.7 (2)°, i.e. there is only a slight distortion between the two pyrrole planes. A better planar character can be drawn from the dihedral angles of the pyrrole ring groups (Table 1). Meanwhile, an obvious difference from the similar compound, such as netropsin, is a smaller rotation [8.7 (5)°] about the C10—C11 bond than that of netropsin (26° rotation about the C6—C9 bond), which causes the two pyrrole groups of netropsin to be skewed with respect to one another (Berman et al., 1979). The plane angle between two peptide regions is 16.9 (2)°. This is larger than that between the two pyrrole rings, and may be due to one peptide bond connecting an unconjugated dimethylaminopropyl group.
Hydrogen-bond parameters are listed in Table 2 and a packing diagram is shown in Fig. 2. In the crystal packing, the molecules are held together by a number of intermolecular hydrogen bonds involving atoms N1, N2 and N4 of the cation, as well as the O atom of the sovent methanol molecule and the chlorine anion.