The absolute configuration of strictosidinic acid, (2
S,3
R,4
S)-3-ethenyl-2-(β-
D-glucopyranosyloxy)-4-{[(1
S)-2,3,4,9-tetrahydro-1
H-pyrido[3,4-
b]indol-1-yl]methyl}-3,4-dihydro-2
H-pyran-5-carboxylate, was determined from its sodium chloride trihydrate, poly[[diaqua((2
S,3
R,4
S)-3-ethenyl-2-(β-
D-glucopyranosyloxy)-4-{[(1
S)-2,3,4,9-tetrahydro-1
H-pyrido[3,4-
b]indol-2-ium-1-yl]methyl}-3,4-dihydro-2
H-pyran-5-carboxylate)sodium] chloride monohydrate], {[Na(C
26H
32N
2O
9)(H
2O)
2]Cl·H
2O}
n. The strictosidinic acid molecule participates in intermolecular hydrogen bonds of the O—H
O and O—H
Cl types. The solid-state conformation was observed as a zwitterion, based on a charged pyridine N atom and a carboxylate group, the latter mediating the packing through coordination with the sodium cation.
Supporting information
CCDC reference: 879430
The air-dried and powdered leaves (362 g) were successively extracted with EtOH
(1.5 l for 48 h). The resulting extract was filtered and concentrated under
reduced pressure to give 41.3 g to which was then added a 10% HOAc solution
(250 ml) and the suspension was kept at 278 K overnight. The suspension was
filtered and the acidic aqueous phase was partitioned with CH2Cl2. The
resulting aqueous layer was basificated (pH 8–9) with saturated NaHCO3
solution, and was then again extracted with CH2Cl2. The combined organic
layers were treated with Na2SO4 and filtered, affording a CH2Cl2 basic
fraction. Strictosidinic acid (29 mg) was obtained from a crude methanolic
extract of the leaves after repeated fractionation using column chromatography
(CHCl3/MeOH eluent system on gradient form) followed by preparative
thin-layer chromatography on silica gel (n-butanol/HOAc/H2O
4:1:5–organic phase). Crystals suitable for single-crystal X-ray diffraction
studies were obtained as yellow block-shaped crystals by recrystallization
from chloroform and methanol (1:1v/v) (m.p. 482–485 K).
All water H atoms were located in a difference Fourier map, and refined with
restraints on bond distances using O—H = 0.84 (2) Å, while being allowed to
ride on their parent atoms. The remaining H atoms were positioned
geometrically (aromatic C—H = 0.95 Å, methine C—H = 1.00 Å, alkyl
C—H = 0.99 Å, ethylene C—H = 0.95 Å, N—H= 0.92 Å, aromatic N—H =
0.88 Å and hydroxy O—H = 0.84 Å) and refined using a riding model, with
Uiso(H) = 1.2Ueq(C,N,Owater) and
1.5Ueq(Ohydroxy). Hydroxy groups were allowed to rotate in order to
fit the difference electron-density map.
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
poly[[diaqua((2
S,3
R,4
S)-3-ethenyl-2-(
β-D-
glucopyranosyloxy)-4-{[(1
S)-2,3,4,9-tetrahydro-1
H-
pyrido[3,4-
b]indol-2-ium-1-yl]methyl}-3,4-dihydro-2
H-
pyran-5-carboxylate)sodium] chloride monohydrate]
top
Crystal data top
[Na(C26H32N2O9)(H2O)2]Cl·H2O | F(000) = 1328 |
Mr = 629.02 | Dx = 1.439 Mg m−3 |
Orthorhombic, P212121 | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 4095 reflections |
a = 7.6419 (4) Å | θ = 3.3–66.6° |
b = 16.2205 (8) Å | µ = 1.89 mm−1 |
c = 23.4299 (12) Å | T = 100 K |
V = 2904.3 (3) Å3 | Plate, colourless |
Z = 4 | 0.2 × 0.15 × 0.1 mm |
Data collection top
Bruker SMART APEX DUO diffractometer | 4390 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.078 |
ω scans | θmax = 66.6°, θmin = 3.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −9→8 |
Tmin = 0.706, Tmax = 0.835 | k = −18→17 |
22917 measured reflections | l = −26→27 |
5062 independent reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.063 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.159 | w = 1/[σ2(Fo2) + (0.0921P)2 + 0.2377P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max < 0.001 |
5062 reflections | Δρmax = 0.53 e Å−3 |
402 parameters | Δρmin = −0.26 e Å−3 |
6 restraints | Absolute structure: Flack (1983), 2134 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.04 (3) |
Crystal data top
[Na(C26H32N2O9)(H2O)2]Cl·H2O | V = 2904.3 (3) Å3 |
Mr = 629.02 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 7.6419 (4) Å | µ = 1.89 mm−1 |
b = 16.2205 (8) Å | T = 100 K |
c = 23.4299 (12) Å | 0.2 × 0.15 × 0.1 mm |
Data collection top
Bruker SMART APEX DUO diffractometer | 5062 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 4390 reflections with I > 2σ(I) |
Tmin = 0.706, Tmax = 0.835 | Rint = 0.078 |
22917 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.063 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.159 | Δρmax = 0.53 e Å−3 |
S = 1.14 | Δρmin = −0.26 e Å−3 |
5062 reflections | Absolute structure: Flack (1983), 2134 Friedel pairs |
402 parameters | Absolute structure parameter: 0.04 (3) |
6 restraints | |
Special details top
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell s.u.'s are taken
into account individually in the estimation of s.u.'s in distances, angles
and torsion angles; correlations between s.u.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell s.u.'s is used for estimating s.u.'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 | x | y | z | Uiso*/Ueq | |
Na1 | 0.3561 (2) | 0.93046 (11) | 0.25270 (7) | 0.0395 (4) | |
Cl1 | 0.39910 (14) | 0.56856 (6) | 0.85273 (5) | 0.0396 (3) | |
O1S | 0.6199 (5) | 1.0006 (2) | 0.23657 (15) | 0.0457 (8) | |
H1SB | 0.692 (7) | 0.981 (4) | 0.213 (2) | 0.055* | |
H1SA | 0.647 (8) | 0.992 (4) | 0.2710 (12) | 0.055* | |
O2S | 0.4540 (5) | 0.7986 (2) | 0.23217 (16) | 0.0456 (8) | |
H2SA | 0.426 (9) | 0.761 (3) | 0.255 (2) | 0.055* | |
H2SB | 0.562 (3) | 0.799 (4) | 0.232 (3) | 0.055* | |
O3S | 0.5825 (7) | 1.1638 (3) | 0.1994 (2) | 0.0681 (12) | |
H3SA | 0.652 (9) | 1.142 (5) | 0.223 (3) | 0.082* | |
H3SB | 0.627 (10) | 1.158 (5) | 0.1665 (17) | 0.082* | |
O18 | 0.5223 (4) | 0.81992 (19) | 0.50674 (14) | 0.0390 (7) | |
O22 | 0.4343 (4) | 0.92329 (19) | 0.35024 (14) | 0.0389 (7) | |
O23 | 0.6989 (4) | 0.97840 (17) | 0.34759 (13) | 0.0354 (6) | |
O26 | 0.6861 (4) | 0.79487 (17) | 0.58525 (13) | 0.0316 (6) | |
O32 | 0.5138 (4) | 0.83495 (17) | 0.65931 (13) | 0.0346 (7) | |
O33 | 0.6190 (4) | 0.62765 (18) | 0.61009 (13) | 0.0360 (6) | |
H33 | 0.6999 | 0.5954 | 0.6197 | 0.054* | |
O34 | 0.5649 (4) | 0.60366 (19) | 0.72886 (14) | 0.0409 (7) | |
H34 | 0.5387 | 0.6066 | 0.7636 | 0.061* | |
O35 | 0.3178 (4) | 0.72449 (19) | 0.77836 (14) | 0.0412 (7) | |
H35 | 0.3456 | 0.681 | 0.7956 | 0.062* | |
O37 | 0.2931 (5) | 0.95967 (19) | 0.70205 (15) | 0.0415 (7) | |
H37 | 0.3731 | 0.9749 | 0.6798 | 0.062* | |
N3 | 0.6804 (5) | 1.1997 (2) | 0.54195 (17) | 0.0346 (8) | |
H3 | 0.6665 | 1.1622 | 0.5687 | 0.041* | |
N13 | 0.7853 (5) | 1.1094 (2) | 0.40300 (16) | 0.0365 (8) | |
H13A | 0.9004 | 1.1203 | 0.4116 | 0.044* | |
H13B | 0.7814 | 1.0602 | 0.3834 | 0.044* | |
C1 | 0.6827 (5) | 1.1009 (2) | 0.45771 (19) | 0.0328 (9) | |
H1 | 0.5581 | 1.0886 | 0.4478 | 0.039* | |
C2 | 0.6905 (6) | 1.1850 (3) | 0.48518 (19) | 0.0320 (8) | |
C4 | 0.6957 (6) | 1.2834 (3) | 0.5505 (2) | 0.0350 (9) | |
C5 | 0.6970 (6) | 1.3297 (3) | 0.6007 (2) | 0.0378 (9) | |
H5 | 0.6878 | 1.3038 | 0.6369 | 0.045* | |
C6 | 0.7122 (6) | 1.4145 (3) | 0.5961 (2) | 0.0360 (10) | |
H6 | 0.7134 | 1.4472 | 0.6297 | 0.043* | |
C7 | 0.7259 (6) | 1.4528 (3) | 0.5426 (2) | 0.0377 (10) | |
H7 | 0.7319 | 1.5113 | 0.5406 | 0.045* | |
C8 | 0.7306 (6) | 1.4076 (3) | 0.4933 (2) | 0.0382 (10) | |
H8 | 0.7438 | 1.434 | 0.4574 | 0.046* | |
C9 | 0.7154 (6) | 1.3212 (3) | 0.4968 (2) | 0.0348 (9) | |
C10 | 0.7143 (6) | 1.2570 (2) | 0.4554 (2) | 0.0338 (9) | |
C11 | 0.7423 (6) | 1.2607 (3) | 0.3923 (2) | 0.0390 (10) | |
H11A | 0.8626 | 1.2802 | 0.3843 | 0.047* | |
H11B | 0.6592 | 1.3006 | 0.3753 | 0.047* | |
C12 | 0.7155 (7) | 1.1768 (3) | 0.36551 (19) | 0.0399 (10) | |
H12A | 0.5891 | 1.1677 | 0.3588 | 0.048* | |
H12B | 0.7757 | 1.175 | 0.3281 | 0.048* | |
C14 | 0.7520 (6) | 1.0316 (3) | 0.49490 (19) | 0.0352 (9) | |
H14A | 0.6748 | 1.027 | 0.5287 | 0.042* | |
H14B | 0.8693 | 1.0479 | 0.5088 | 0.042* | |
C15 | 0.7677 (5) | 0.9449 (2) | 0.46762 (18) | 0.0321 (9) | |
H15 | 0.8683 | 0.9468 | 0.4404 | 0.039* | |
C16 | 0.6081 (6) | 0.9149 (3) | 0.43428 (19) | 0.0342 (9) | |
C17 | 0.5084 (5) | 0.8542 (2) | 0.45537 (19) | 0.0325 (8) | |
H17 | 0.4188 | 0.8335 | 0.4312 | 0.039* | |
C19 | 0.6458 (6) | 0.8560 (3) | 0.54527 (19) | 0.0340 (9) | |
H19 | 0.5934 | 0.905 | 0.5647 | 0.041* | |
C20 | 0.8126 (6) | 0.8804 (3) | 0.51379 (19) | 0.0340 (9) | |
H20 | 0.8569 | 0.8301 | 0.4937 | 0.041* | |
C21 | 0.5765 (5) | 0.9404 (2) | 0.37354 (18) | 0.0327 (9) | |
C24 | 0.9515 (6) | 0.9067 (2) | 0.5556 (2) | 0.0346 (9) | |
H24 | 0.9209 | 0.9466 | 0.5836 | 0.042* | |
C25 | 1.1120 (6) | 0.8781 (3) | 0.5559 (2) | 0.0422 (10) | |
H25A | 1.1468 | 0.8382 | 0.5285 | 0.051* | |
H25B | 1.1934 | 0.8973 | 0.5835 | 0.051* | |
C27 | 0.5454 (6) | 0.7701 (2) | 0.62002 (18) | 0.0317 (8) | |
H27 | 0.4389 | 0.7588 | 0.5965 | 0.038* | |
C28 | 0.6060 (6) | 0.6926 (2) | 0.65071 (18) | 0.0315 (8) | |
H28 | 0.7244 | 0.703 | 0.6674 | 0.038* | |
C29 | 0.4815 (6) | 0.6694 (3) | 0.69848 (19) | 0.0352 (9) | |
H29 | 0.3687 | 0.6493 | 0.6819 | 0.042* | |
C30 | 0.4466 (6) | 0.7429 (3) | 0.73655 (19) | 0.0345 (9) | |
H30 | 0.5576 | 0.7593 | 0.756 | 0.041* | |
C31 | 0.3807 (6) | 0.8147 (3) | 0.70055 (19) | 0.0342 (9) | |
H31 | 0.2701 | 0.7989 | 0.6806 | 0.041* | |
C36 | 0.3520 (6) | 0.8925 (3) | 0.7348 (2) | 0.0392 (10) | |
H36A | 0.2651 | 0.881 | 0.7652 | 0.047* | |
H36B | 0.4633 | 0.9079 | 0.7537 | 0.047* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Na1 | 0.0395 (9) | 0.0360 (9) | 0.0431 (9) | 0.0008 (7) | −0.0036 (7) | −0.0004 (7) |
Cl1 | 0.0440 (6) | 0.0352 (5) | 0.0396 (5) | 0.0004 (4) | 0.0035 (4) | 0.0001 (4) |
O1S | 0.0441 (18) | 0.0489 (19) | 0.0439 (18) | 0.0014 (15) | 0.0004 (15) | 0.0013 (14) |
O2S | 0.0442 (18) | 0.0402 (17) | 0.0525 (19) | 0.0054 (15) | −0.0010 (16) | 0.0009 (14) |
O3S | 0.080 (3) | 0.048 (2) | 0.076 (3) | −0.014 (2) | 0.028 (2) | −0.009 (2) |
O18 | 0.0331 (16) | 0.0411 (16) | 0.0429 (17) | −0.0043 (13) | −0.0034 (13) | 0.0047 (13) |
O22 | 0.0365 (16) | 0.0388 (15) | 0.0414 (16) | −0.0043 (13) | −0.0054 (13) | 0.0006 (13) |
O23 | 0.0341 (16) | 0.0318 (14) | 0.0402 (15) | −0.0004 (13) | 0.0007 (13) | 0.0009 (13) |
O26 | 0.0294 (14) | 0.0270 (13) | 0.0383 (15) | 0.0007 (12) | 0.0034 (12) | 0.0026 (11) |
O32 | 0.0329 (15) | 0.0322 (15) | 0.0387 (16) | −0.0030 (12) | 0.0057 (12) | −0.0003 (11) |
O33 | 0.0377 (16) | 0.0266 (14) | 0.0436 (16) | 0.0020 (12) | 0.0004 (13) | −0.0049 (12) |
O34 | 0.0419 (17) | 0.0340 (15) | 0.0468 (18) | 0.0042 (13) | 0.0066 (14) | 0.0052 (13) |
O35 | 0.0429 (18) | 0.0362 (16) | 0.0445 (18) | 0.0006 (14) | 0.0051 (15) | 0.0044 (13) |
O37 | 0.0413 (18) | 0.0333 (16) | 0.0498 (18) | 0.0024 (13) | 0.0049 (14) | −0.0017 (13) |
N3 | 0.0326 (18) | 0.0262 (16) | 0.045 (2) | 0.0001 (14) | 0.0020 (16) | 0.0024 (14) |
N13 | 0.0349 (19) | 0.0344 (18) | 0.040 (2) | −0.0065 (15) | 0.0050 (15) | −0.0002 (15) |
C1 | 0.0258 (19) | 0.0295 (19) | 0.043 (2) | −0.0008 (16) | 0.0030 (18) | −0.0017 (17) |
C2 | 0.0262 (19) | 0.031 (2) | 0.038 (2) | −0.0020 (16) | 0.0017 (17) | −0.0029 (16) |
C4 | 0.030 (2) | 0.030 (2) | 0.045 (2) | 0.0032 (17) | −0.0004 (18) | −0.0020 (17) |
C5 | 0.035 (2) | 0.034 (2) | 0.045 (2) | −0.0038 (18) | −0.0022 (19) | 0.0007 (18) |
C6 | 0.029 (2) | 0.029 (2) | 0.050 (3) | 0.0019 (16) | 0.0019 (18) | −0.0061 (17) |
C7 | 0.030 (2) | 0.029 (2) | 0.053 (3) | −0.0024 (16) | −0.0025 (19) | −0.0016 (18) |
C8 | 0.033 (2) | 0.037 (2) | 0.044 (2) | 0.0005 (17) | −0.0048 (18) | 0.0058 (18) |
C9 | 0.029 (2) | 0.029 (2) | 0.046 (2) | −0.0039 (16) | −0.0023 (18) | −0.0007 (18) |
C10 | 0.030 (2) | 0.0271 (19) | 0.044 (2) | 0.0006 (16) | −0.0029 (18) | 0.0020 (17) |
C11 | 0.042 (2) | 0.028 (2) | 0.047 (2) | −0.0026 (17) | −0.003 (2) | 0.0029 (18) |
C12 | 0.044 (3) | 0.039 (2) | 0.037 (2) | −0.0022 (19) | −0.0016 (19) | −0.0006 (18) |
C14 | 0.029 (2) | 0.035 (2) | 0.041 (2) | 0.0003 (16) | −0.0002 (17) | −0.0068 (18) |
C15 | 0.028 (2) | 0.028 (2) | 0.040 (2) | −0.0026 (16) | 0.0024 (16) | −0.0022 (16) |
C16 | 0.0273 (19) | 0.036 (2) | 0.039 (2) | −0.0009 (17) | 0.0023 (17) | −0.0063 (16) |
C17 | 0.0261 (19) | 0.0297 (19) | 0.042 (2) | 0.0042 (15) | −0.0004 (17) | −0.0005 (17) |
C19 | 0.033 (2) | 0.030 (2) | 0.039 (2) | 0.0038 (16) | −0.0006 (18) | −0.0007 (17) |
C20 | 0.031 (2) | 0.031 (2) | 0.040 (2) | −0.0019 (17) | 0.0035 (18) | −0.0022 (17) |
C21 | 0.032 (2) | 0.0257 (19) | 0.040 (2) | 0.0027 (17) | 0.0019 (18) | −0.0048 (16) |
C24 | 0.033 (2) | 0.0275 (19) | 0.044 (2) | 0.0002 (16) | −0.0005 (18) | 0.0039 (17) |
C25 | 0.040 (2) | 0.037 (2) | 0.050 (3) | 0.000 (2) | −0.006 (2) | 0.0053 (19) |
C27 | 0.031 (2) | 0.0268 (19) | 0.038 (2) | −0.0052 (15) | 0.0013 (17) | −0.0029 (16) |
C28 | 0.031 (2) | 0.0260 (18) | 0.037 (2) | −0.0055 (16) | −0.0011 (18) | 0.0000 (16) |
C29 | 0.034 (2) | 0.032 (2) | 0.040 (2) | 0.0019 (18) | −0.0003 (18) | 0.0006 (17) |
C30 | 0.032 (2) | 0.031 (2) | 0.041 (2) | −0.0013 (16) | 0.0012 (18) | 0.0002 (17) |
C31 | 0.028 (2) | 0.032 (2) | 0.042 (2) | 0.0034 (17) | 0.0014 (17) | −0.0016 (17) |
C36 | 0.039 (2) | 0.039 (2) | 0.040 (2) | 0.0028 (18) | 0.0045 (18) | −0.0028 (19) |
Geometric parameters (Å, º) top
Na1—O2S | 2.316 (4) | C6—C7 | 1.404 (7) |
Na1—O34i | 2.334 (4) | C6—H6 | 0.95 |
Na1—O1S | 2.346 (4) | C7—C8 | 1.369 (7) |
Na1—O22 | 2.365 (4) | C7—H7 | 0.95 |
Na1—O37ii | 2.426 (4) | C8—C9 | 1.409 (6) |
Na1—H1SA | 2.47 (6) | C8—H8 | 0.95 |
O1S—H1SB | 0.84 (2) | C9—C10 | 1.423 (6) |
O1S—H1SA | 0.85 (2) | C10—C11 | 1.495 (7) |
O2S—H2SA | 0.84 (2) | C11—C12 | 1.513 (6) |
O2S—H2SB | 0.83 (2) | C11—H11A | 0.99 |
O3S—H3SA | 0.85 (2) | C11—H11B | 0.99 |
O3S—H3SB | 0.85 (2) | C12—H12A | 0.99 |
O18—C17 | 1.330 (6) | C12—H12B | 0.99 |
O18—C19 | 1.431 (5) | C14—C15 | 1.549 (6) |
O22—C21 | 1.248 (5) | C14—H14A | 0.99 |
O23—C21 | 1.274 (5) | C14—H14B | 0.99 |
O26—C19 | 1.398 (5) | C15—C16 | 1.528 (6) |
O26—C27 | 1.408 (5) | C15—C20 | 1.544 (6) |
O32—C27 | 1.418 (5) | C15—H15 | 1 |
O32—C31 | 1.441 (5) | C16—C17 | 1.341 (6) |
O33—C28 | 1.424 (5) | C16—C21 | 1.501 (6) |
O33—H33 | 0.84 | C17—H17 | 0.95 |
O34—C29 | 1.431 (5) | C19—C20 | 1.525 (6) |
O34—H34 | 0.84 | C19—H19 | 1 |
O35—C30 | 1.420 (6) | C20—C24 | 1.506 (6) |
O35—H35 | 0.84 | C20—H20 | 1 |
O37—C36 | 1.408 (6) | C24—C25 | 1.311 (7) |
O37—H37 | 0.84 | C24—H24 | 0.95 |
N3—C2 | 1.353 (6) | C25—H25A | 0.95 |
N3—C4 | 1.378 (6) | C25—H25B | 0.95 |
N3—H3 | 0.88 | C27—C28 | 1.520 (6) |
N13—C12 | 1.501 (6) | C27—H27 | 1 |
N13—C1 | 1.509 (6) | C28—C29 | 1.516 (6) |
N13—H13A | 0.92 | C28—H28 | 1 |
N13—H13B | 0.92 | C29—C30 | 1.513 (6) |
C1—C2 | 1.510 (6) | C29—H29 | 1 |
C1—C14 | 1.518 (6) | C30—C31 | 1.525 (6) |
C1—H1 | 1 | C30—H30 | 1 |
C2—C10 | 1.371 (6) | C31—C36 | 1.511 (6) |
C4—C5 | 1.394 (7) | C31—H31 | 1 |
C4—C9 | 1.408 (7) | C36—H36A | 0.99 |
C5—C6 | 1.385 (6) | C36—H36B | 0.99 |
C5—H5 | 0.95 | | |
| | | |
O2S—Na1—O34i | 97.32 (14) | N13—C12—H12B | 109.3 |
O2S—Na1—O1S | 97.86 (14) | C11—C12—H12B | 109.3 |
O34i—Na1—O1S | 164.70 (14) | H12A—C12—H12B | 108 |
O2S—Na1—O22 | 94.23 (13) | C1—C14—C15 | 117.6 (4) |
O34i—Na1—O22 | 92.89 (13) | C1—C14—H14A | 107.9 |
O1S—Na1—O22 | 87.84 (13) | C15—C14—H14A | 107.9 |
O2S—Na1—O37ii | 136.77 (14) | C1—C14—H14B | 107.9 |
O34i—Na1—O37ii | 79.43 (13) | C15—C14—H14B | 107.9 |
O1S—Na1—O37ii | 88.21 (14) | H14A—C14—H14B | 107.2 |
O22—Na1—O37ii | 128.87 (13) | C16—C15—C20 | 108.6 (3) |
O2S—Na1—H1SA | 96.7 (15) | C16—C15—C14 | 116.0 (3) |
O34i—Na1—H1SA | 157.0 (11) | C20—C15—C14 | 110.1 (3) |
O1S—Na1—H1SA | 20.0 (7) | C16—C15—H15 | 107.3 |
O22—Na1—H1SA | 67.9 (7) | C20—C15—H15 | 107.3 |
O37ii—Na1—H1SA | 102.3 (12) | C14—C15—H15 | 107.3 |
Na1—O1S—H1SB | 119 (5) | C17—C16—C21 | 117.4 (4) |
Na1—O1S—H1SA | 88 (5) | C17—C16—C15 | 120.0 (4) |
H1SB—O1S—H1SA | 113 (6) | C21—C16—C15 | 121.7 (4) |
Na1—O2S—H2SA | 117 (4) | O18—C17—C16 | 126.5 (4) |
Na1—O2S—H2SB | 108 (4) | O18—C17—H17 | 116.7 |
H2SA—O2S—H2SB | 105 (6) | C16—C17—H17 | 116.7 |
H3SA—O3S—H3SB | 108 (8) | O26—C19—O18 | 106.1 (3) |
C17—O18—C19 | 116.9 (3) | O26—C19—C20 | 108.9 (3) |
C21—O22—Na1 | 129.2 (3) | O18—C19—C20 | 110.6 (4) |
C19—O26—C27 | 114.9 (3) | O26—C19—H19 | 110.4 |
C27—O32—C31 | 112.8 (3) | O18—C19—H19 | 110.4 |
C28—O33—H33 | 109.5 | C20—C19—H19 | 110.4 |
C29—O34—H34 | 109.5 | C24—C20—C19 | 110.3 (4) |
C30—O35—H35 | 109.5 | C24—C20—C15 | 114.9 (3) |
C36—O37—H37 | 109.5 | C19—C20—C15 | 109.2 (3) |
C2—N3—C4 | 108.2 (4) | C24—C20—H20 | 107.4 |
C2—N3—H3 | 125.9 | C19—C20—H20 | 107.4 |
C4—N3—H3 | 125.9 | C15—C20—H20 | 107.4 |
C12—N13—C1 | 112.3 (4) | O22—C21—O23 | 122.5 (4) |
C12—N13—H13A | 109.2 | O22—C21—C16 | 119.6 (4) |
C1—N13—H13A | 109.2 | O23—C21—C16 | 117.9 (4) |
C12—N13—H13B | 109.2 | C25—C24—C20 | 124.2 (4) |
C1—N13—H13B | 109.2 | C25—C24—H24 | 117.9 |
H13A—N13—H13B | 107.9 | C20—C24—H24 | 117.9 |
N13—C1—C2 | 105.1 (3) | C24—C25—H25A | 120 |
N13—C1—C14 | 111.9 (3) | C24—C25—H25B | 120 |
C2—C1—C14 | 114.3 (4) | H25A—C25—H25B | 120 |
N13—C1—H1 | 108.5 | O26—C27—O32 | 107.1 (3) |
C2—C1—H1 | 108.5 | O26—C27—C28 | 106.1 (3) |
C14—C1—H1 | 108.5 | O32—C27—C28 | 111.0 (3) |
N3—C2—C10 | 111.0 (4) | O26—C27—H27 | 110.8 |
N3—C2—C1 | 125.1 (4) | O32—C27—H27 | 110.8 |
C10—C2—C1 | 123.9 (4) | C28—C27—H27 | 110.8 |
N3—C4—C5 | 130.9 (4) | O33—C28—C29 | 110.7 (3) |
N3—C4—C9 | 107.9 (4) | O33—C28—C27 | 108.5 (3) |
C5—C4—C9 | 121.2 (4) | C29—C28—C27 | 111.3 (3) |
C6—C5—C4 | 118.0 (5) | O33—C28—H28 | 108.8 |
C6—C5—H5 | 121 | C29—C28—H28 | 108.8 |
C4—C5—H5 | 121 | C27—C28—H28 | 108.8 |
C5—C6—C7 | 121.1 (4) | O34—C29—C30 | 111.9 (4) |
C5—C6—H6 | 119.5 | O34—C29—C28 | 105.8 (3) |
C7—C6—H6 | 119.5 | C30—C29—C28 | 110.5 (3) |
C8—C7—C6 | 121.2 (4) | O34—C29—H29 | 109.5 |
C8—C7—H7 | 119.4 | C30—C29—H29 | 109.5 |
C6—C7—H7 | 119.4 | C28—C29—H29 | 109.5 |
C7—C8—C9 | 118.8 (5) | O35—C30—C29 | 111.3 (3) |
C7—C8—H8 | 120.6 | O35—C30—C31 | 108.3 (3) |
C9—C8—H8 | 120.6 | C29—C30—C31 | 109.5 (4) |
C4—C9—C8 | 119.6 (4) | O35—C30—H30 | 109.2 |
C4—C9—C10 | 106.9 (4) | C29—C30—H30 | 109.2 |
C8—C9—C10 | 133.5 (5) | C31—C30—H30 | 109.2 |
C2—C10—C9 | 106.1 (4) | O32—C31—C36 | 105.6 (4) |
C2—C10—C11 | 123.8 (4) | O32—C31—C30 | 108.2 (3) |
C9—C10—C11 | 130.1 (4) | C36—C31—C30 | 113.1 (4) |
C10—C11—C12 | 110.8 (4) | O32—C31—H31 | 110 |
C10—C11—H11A | 109.5 | C36—C31—H31 | 110 |
C12—C11—H11A | 109.5 | C30—C31—H31 | 110 |
C10—C11—H11B | 109.5 | O37—C36—C31 | 113.7 (4) |
C12—C11—H11B | 109.5 | O37—C36—H36A | 108.8 |
H11A—C11—H11B | 108.1 | C31—C36—H36A | 108.8 |
N13—C12—C11 | 111.4 (4) | O37—C36—H36B | 108.8 |
N13—C12—H12A | 109.3 | C31—C36—H36B | 108.8 |
C11—C12—H12A | 109.3 | H36A—C36—H36B | 107.7 |
| | | |
O2S—Na1—O22—C21 | 87.7 (4) | C21—C16—C17—O18 | 176.1 (4) |
O34i—Na1—O22—C21 | −174.8 (3) | C15—C16—C17—O18 | 6.9 (7) |
O1S—Na1—O22—C21 | −10.1 (4) | C27—O26—C19—O18 | −64.7 (4) |
O37ii—Na1—O22—C21 | −96.0 (4) | C27—O26—C19—C20 | 176.2 (3) |
C12—N13—C1—C2 | −56.5 (4) | C17—O18—C19—O26 | −158.0 (3) |
C12—N13—C1—C14 | 179.0 (4) | C17—O18—C19—C20 | −40.0 (5) |
C4—N3—C2—C10 | 0.7 (5) | O26—C19—C20—C24 | −55.5 (4) |
C4—N3—C2—C1 | 178.9 (4) | O18—C19—C20—C24 | −171.7 (3) |
N13—C1—C2—N3 | −152.3 (4) | O26—C19—C20—C15 | 177.4 (3) |
C14—C1—C2—N3 | −29.2 (6) | O18—C19—C20—C15 | 61.1 (4) |
N13—C1—C2—C10 | 25.6 (6) | C16—C15—C20—C24 | −171.8 (4) |
C14—C1—C2—C10 | 148.7 (4) | C14—C15—C20—C24 | −43.8 (5) |
C2—N3—C4—C5 | −178.6 (5) | C16—C15—C20—C19 | −47.2 (4) |
C2—N3—C4—C9 | 0.2 (5) | C14—C15—C20—C19 | 80.8 (4) |
N3—C4—C5—C6 | −179.1 (4) | Na1—O22—C21—O23 | 11.7 (6) |
C9—C4—C5—C6 | 2.2 (7) | Na1—O22—C21—C16 | −167.5 (3) |
C4—C5—C6—C7 | 0.0 (7) | C17—C16—C21—O22 | 20.1 (6) |
C5—C6—C7—C8 | −2.2 (7) | C15—C16—C21—O22 | −170.9 (4) |
C6—C7—C8—C9 | 2.1 (7) | C17—C16—C21—O23 | −159.2 (4) |
N3—C4—C9—C8 | 178.8 (4) | C15—C16—C21—O23 | 9.8 (6) |
C5—C4—C9—C8 | −2.3 (7) | C19—C20—C24—C25 | 129.4 (5) |
N3—C4—C9—C10 | −0.9 (5) | C15—C20—C24—C25 | −106.7 (5) |
C5—C4—C9—C10 | 178.0 (4) | C19—O26—C27—O32 | −73.1 (4) |
C7—C8—C9—C4 | 0.1 (6) | C19—O26—C27—C28 | 168.4 (3) |
C7—C8—C9—C10 | 179.7 (5) | C31—O32—C27—O26 | −175.5 (3) |
N3—C2—C10—C9 | −1.3 (5) | C31—O32—C27—C28 | −60.1 (4) |
C1—C2—C10—C9 | −179.5 (4) | O26—C27—C28—O33 | −69.6 (4) |
N3—C2—C10—C11 | 175.8 (4) | O32—C27—C28—O33 | 174.4 (3) |
C1—C2—C10—C11 | −2.4 (7) | O26—C27—C28—C29 | 168.3 (3) |
C4—C9—C10—C2 | 1.3 (5) | O32—C27—C28—C29 | 52.3 (4) |
C8—C9—C10—C2 | −178.3 (5) | O33—C28—C29—O34 | 67.4 (4) |
C4—C9—C10—C11 | −175.5 (4) | C27—C28—C29—O34 | −171.9 (3) |
C8—C9—C10—C11 | 4.9 (8) | O33—C28—C29—C30 | −171.4 (3) |
C2—C10—C11—C12 | 7.9 (6) | C27—C28—C29—C30 | −50.6 (5) |
C9—C10—C11—C12 | −175.8 (4) | O34—C29—C30—O35 | −67.8 (5) |
C1—N13—C12—C11 | 66.8 (5) | C28—C29—C30—O35 | 174.5 (3) |
C10—C11—C12—N13 | −37.9 (5) | O34—C29—C30—C31 | 172.5 (4) |
N13—C1—C14—C15 | −54.1 (5) | C28—C29—C30—C31 | 54.8 (5) |
C2—C1—C14—C15 | −173.4 (4) | C27—O32—C31—C36 | −174.7 (3) |
C1—C14—C15—C16 | −47.5 (5) | C27—O32—C31—C30 | 64.0 (4) |
C1—C14—C15—C20 | −171.3 (3) | O35—C30—C31—O32 | 178.3 (3) |
C20—C15—C16—C17 | 15.7 (5) | C29—C30—C31—O32 | −60.2 (4) |
C14—C15—C16—C17 | −108.9 (5) | O35—C30—C31—C36 | 61.7 (5) |
C20—C15—C16—C21 | −153.0 (4) | C29—C30—C31—C36 | −176.8 (4) |
C14—C15—C16—C21 | 82.4 (5) | O32—C31—C36—O37 | 61.2 (5) |
C19—O18—C17—C16 | 5.8 (6) | C30—C31—C36—O37 | 179.3 (4) |
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) −x+1/2, −y+2, z−1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1S—H1SB···Cl1iii | 0.84 (2) | 2.35 (2) | 3.192 (4) | 177 (6) |
O1S—H1SA···O23 | 0.85 (2) | 1.85 (2) | 2.694 (5) | 176 (7) |
O2S—H2SA···O3Siv | 0.84 (2) | 1.90 (3) | 2.726 (6) | 165 (7) |
O2S—H2SB···O35iii | 0.83 (2) | 2.00 (3) | 2.816 (5) | 167 (6) |
O3S—H3SA···O1S | 0.85 (2) | 2.33 (8) | 2.801 (6) | 115 (7) |
O3S—H3SB···O26v | 0.85 (2) | 2.50 (4) | 3.276 (5) | 152 (7) |
O33—H33···O22iii | 0.84 | 1.95 | 2.711 (4) | 151 |
O34—H34···Cl1 | 0.84 | 2.42 | 3.217 (3) | 158 |
O35—H35···Cl1 | 0.84 | 2.30 | 3.134 (3) | 172 |
O37—H37···Cl1vi | 0.84 | 2.43 | 3.209 (4) | 154 |
N3—H3···Cl1vi | 0.88 | 2.44 | 3.314 (4) | 173 |
N13—H13B···O23 | 0.92 | 1.69 | 2.576 (5) | 160 |
Symmetry codes: (iii) x+1/2, −y+3/2, −z+1; (iv) −x+1, y−1/2, −z+1/2; (v) −x+3/2, −y+2, z−1/2; (vi) −x+1, y+1/2, −z+3/2. |
Experimental details
Crystal data |
Chemical formula | [Na(C26H32N2O9)(H2O)2]Cl·H2O |
Mr | 629.02 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 7.6419 (4), 16.2205 (8), 23.4299 (12) |
V (Å3) | 2904.3 (3) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 1.89 |
Crystal size (mm) | 0.2 × 0.15 × 0.1 |
|
Data collection |
Diffractometer | Bruker SMART APEX DUO diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.706, 0.835 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 22917, 5062, 4390 |
Rint | 0.078 |
(sin θ/λ)max (Å−1) | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.063, 0.159, 1.14 |
No. of reflections | 5062 |
No. of parameters | 402 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.53, −0.26 |
Absolute structure | Flack (1983), 2134 Friedel pairs |
Absolute structure parameter | 0.04 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1S—H1SB···Cl1i | 0.84 (2) | 2.35 (2) | 3.192 (4) | 177 (6) |
O1S—H1SA···O23 | 0.85 (2) | 1.85 (2) | 2.694 (5) | 176 (7) |
O2S—H2SA···O3Sii | 0.84 (2) | 1.90 (3) | 2.726 (6) | 165 (7) |
O2S—H2SB···O35i | 0.83 (2) | 2.00 (3) | 2.816 (5) | 167 (6) |
O3S—H3SA···O1S | 0.85 (2) | 2.33 (8) | 2.801 (6) | 115 (7) |
O3S—H3SB···O26iii | 0.85 (2) | 2.50 (4) | 3.276 (5) | 152 (7) |
O33—H33···O22i | 0.84 | 1.95 | 2.711 (4) | 151 |
O34—H34···Cl1 | 0.84 | 2.42 | 3.217 (3) | 158 |
O35—H35···Cl1 | 0.84 | 2.30 | 3.134 (3) | 172 |
O37—H37···Cl1iv | 0.84 | 2.43 | 3.209 (4) | 154 |
N3—H3···Cl1iv | 0.88 | 2.44 | 3.314 (4) | 173 |
N13—H13B···O23 | 0.92 | 1.69 | 2.576 (5) | 160 |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+3/2, −y+2, z−1/2; (iv) −x+1, y+1/2, −z+3/2. |
Exceptional tryptoline moiety bond lengths (Å). topBond | (I) | DOJBIN | HOPNOQ |
N3—C2 | 1.353 (6) | 1.389 (4) | 1.374 (3) |
N13—C1 | 1.509 (6) | 1.477 (4) | 1.483 (3) |
N13—C12 | 1.501 (6) | 1.487 (5) | 1.471 (3) |
CSD codes: DOJBIN (Piper et al., 1985) and HOPNOQ (Zhang et
al., 2009). |
The Palicourea coriacea (Rubiaceae), popularly known as Douradinha, is a typical plant of the Brazilian savanna (Cerrado), whose tea is popularly used in folk medicine for kidney stones treatment, kidney and urethra inflammation, as well as having effective diuretic action. Previous studies of this genus have yielded triterpenes (Bolzani et al., 1992), alkaloids (do Nascimento et al., 2006), fluoroacetate (Kemmerling, 1996), coumarins (El-Seedi, 1999) and macrocyclic peptides (Bokesch et al., 2001), many of them possessing interesting biological properties such as anti-HIV (Bokesch et al., 2001) and anticancer activities (Hartwell, 1971). As part of our continued interest in plants from the Brazilian Cerrado (Lião et al., 2001) we have investigated the leaves of P. coriacea. Strictosidinic acid, an alkaloid that has important biological properties, was isolated and its structure has been elucidated based on NMR and IR spectroscopic data, and its absolute structure was obtained by X-ray crystallographic analysis.
The strictosidinic acid molecule is composed of a tryptoline moiety bonded to a pyran ring bonded to a β-glucose group. This molecule crystallized as a sodium chloride trihydrate, (I), with three water molecules, a coordinated sodium cation and a chloride counter-ion. The indole group of the tryptoline moiety shares a double bond [C2═C10 = 1.371 (6) Å] with the six-membered heterocyclic pyridinium ring (N13/C1/C2/C10/C11/C12), which adopts a half-chair conformation with the protonated N13 atom as the flap atom [puckering parameters: Q = 0.513 (4) Å, θ = 49.7 (5)° and ϕ = 349.6 (7)°; Cremer & Pople, 1975; Spek, 2009]. The pyran ring (C20/C19/O18/C17/C16/C15) includes a C═C double bond [C16═C17 = 1.341 (6) Å] which allows for a half-chair conformation with the C20 atom as the flap atom [puckering parameters: Q = 0.501 (5) Å, θ = 125.1 (5)° and ϕ = 198.6 (6)°]. This pyran ring is substituted with a carboxylate group (C21/O22/O23) in the 5-position (on C16), which is coordinated to the sodium cation though the O22 carbonyl group. Atom O23 transfers its proton to the amine atom N13 and is a strong hydrogen-bond acceptor from both N13 and the O1S water molecule (Table 1), which is also coordinated to the sodium cation. The C21═O22 bond is lengthened to 1.248 (5) Å and C21—O23 is shortened to 1.274 (5) Å, indicating that electron delocalization increases in this group. Given that the C15—C16—C21—O23 torsion angle is 9.8 (6)°, there is no resonance between the carboxylate group and the pyran ring C═C double bond, what [which] is reflected in the elongation of the C16—C21 single bond to 1.501 (6) Å, when compared with the expected formal bond distance. The N13—C1 and N13—C12 single bonds of 1.509 (6) and 1.501 (6) Å, respectively, indicate that the N13 atom is sp3-hybridized. The β-glucose group shows a chair conformation [puckering parameters: Q = 0.574 (5) Å, θ = 6.0 (5)°, ϕ = 300 (4)°], with O32 as the pivot atom.
A search of the Cambridge Structural Database (CSD, Version 5.23, May 2011 update; Allen, 2002) gave two structures with the a chiral tryptoline moiety not substituted in the C12 and N13 positions, namely 1(S)-(α-D-arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (CSD refcode DOJBIN; Piper et al., 1985) and 1-[2-(pyrrolidin-1-yl)phenyl]-2,3,4,9-tetrahydro-1H-β-carboline (HOPNOQ; Zhang et al., 2009). In general, the bond lengths are comparable within standard uncertainty, the exceptions (see Table 2) being N3—C2 which is shorter in (I) by 0.036 Å compared to DOJBIN, N13—C1 which is longer in (I) by 0.032 and 0.026 Å, respectively, compared to DOJBIN and HOPNOQ, and N13—C12 which is longer in (I) by 0.03 Å compared to HOPNOQ. These elongated N13—C bonds might be ascribed to the lowered charge density in these bonds due to the quaternary N atom.
Due to the fact that the natural extract contained salt, it allowed the establishment of the absolute configuration of (I) (Flack & Bernardinelli, 1999, 2000); we determined the chiral centers: C1 S, C15 S, C19 S, C20 R, C27 S, C28 R, C29 S, C30 R and C31 R.
The sodium cation is involved in the packing stabilization mediating the intermolecular interactions, being five-coordinated by the hydroxy atom O34i, the methoxy atom O37ii, the carboxylate atom O22 and water molecules O1S and O2S (symmetry codes as in Fig. 1). In the crystal, there are classical intermolecular interactions where the strictosidinate anion acts as a donor (O33—H33···O22iii) and involving the coordinated O2S water molecule (O2S—H2SB···O35iii). There are also nonclassical intermolecular hydrogen-bond interactions, viz. O34—H34···Cl1, O35—H35···Cl1 and O37—H37···Cl1vi (Table 1). The O3S water molecule is involved in intermolecular interactions both as a donor, viz. in O3S—H3SA···O1S and O3S—H3SA···O26v, and as an acceptor, viz. in O2S—H2SA···O3Siv (symmetry codes as in Table 1). All these intermolecular interactions create a three-dimensional polymeric chain.