Literature DB >> 21201722

N-(Hydroxymethyl)ibogaine.

Raoudha Mezghani Jarraya, Amira Bouaziz, Besma Hamdi, Abdelhamid Ben Salah, Mohamed Damak.   

Abstract

THE TITLE COMPOUND (SYSTEMATIC NAME: 16-hydroxy-methyl-12-methoxy-ibogamine), C(21)H(28)N(2)O(2), was prepared by reaction of ibogaine with a formaldehyde-acetic acid solution (pH = 4). The crystal structure of this new product, belonging to the iboga indole family, is stabilized by an inter-molecular O-H⋯N hydrogen bond. The identity of the compound was confirmed by one- and two-dimensional NMR spectroscopic techniques.

Entities:  

Year:  2008        PMID: 21201722      PMCID: PMC2960727          DOI: 10.1107/S1600536808025324

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For related literature on ibogaine and its derivatives, see: Alper et al. (2008 ▶); Levant & Pazdernik (2004 ▶); Maisonneuve et al. (1991 ▶); Soriano-García (1992 ▶).

Experimental

Crystal data

C21H28N2O2 M = 340.45 Orthorhombic, a = 8.4990 (10) Å b = 10.2537 (11) Å c = 20.676 (3) Å V = 1801.8 (4) Å3 Z = 4 Mo Kα radiation μ = 0.08 mm−1 T = 293 (2) K 0.47 × 0.33 × 0.26 mm

Data collection

Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (Coppens et al., 1965 ▶) T min = 0.962, T max = 0.981 9906 measured reflections 2131 independent reflections 1225 reflections with I > 2σ(I) R int = 0.079

Refinement

R[F 2 > 2σ(F 2)] = 0.049 wR(F 2) = 0.123 S = 1.00 2131 reflections 228 parameters H-atom parameters constrained Δρmax = 0.25 e Å−3 Δρmin = −0.17 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 1998 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808025324/zl2132sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808025324/zl2132Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H28N2O2Dx = 1.255 Mg m3
Mr = 340.45Melting point: 436 K
Orthorhombic, P212121Mo Kα radiation λ = 0.71070 Å
Hall symbol: P 2ac 2abCell parameters from 2130 reflections
a = 8.4990 (10) Åθ = 3.2–24.5º
b = 10.2537 (11) ŵ = 0.08 mm1
c = 20.676 (3) ÅT = 293 (2) K
V = 1801.8 (4) Å3Prism, colourless
Z = 40.47 × 0.33 × 0.26 mm
F000 = 736
Bruker Kappa APEXII CCD diffractometer2131 independent reflections
Radiation source: fine-focus sealed tube1225 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.079
T = 296 Kθmax = 26.4º
φ and ω scansθmin = 2.0º
Absorption correction: multi-scan(Coppens et al., 1965)h = −10→10
Tmin = 0.962, Tmax = 0.981k = −12→11
9906 measured reflectionsl = −25→25
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.049  w = 1/[σ2(Fo2) + (0.06P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.123(Δ/σ)max < 0.001
S = 1.00Δρmax = 0.25 e Å3
2131 reflectionsΔρmin = −0.17 e Å3
228 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.013 (2)
Secondary atom site location: difference Fourier map
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All esds are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles
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.
xyzUiso*/Ueq
O10.3015 (3)0.7399 (3)0.67173 (13)0.0699 (10)
O20.4685 (2)0.3819 (3)0.37616 (16)0.0749 (10)
N10.2906 (3)0.5196 (3)0.42942 (14)0.0473 (10)
N4−0.2039 (3)0.3716 (3)0.39872 (13)0.0444 (10)
C20.1436 (4)0.4598 (4)0.42969 (16)0.0438 (10)
C3−0.1969 (4)0.2289 (4)0.4092 (2)0.0647 (16)
C5−0.2164 (3)0.4504 (4)0.45746 (15)0.0466 (12)
C6−0.0883 (3)0.4396 (4)0.50880 (17)0.0578 (13)
C70.0731 (4)0.4847 (4)0.48818 (15)0.0465 (12)
C80.1799 (4)0.5612 (4)0.52547 (15)0.0451 (11)
C90.1706 (4)0.6143 (4)0.58812 (16)0.0478 (10)
C100.2951 (4)0.6835 (4)0.61088 (18)0.0529 (13)
C110.4272 (4)0.7052 (4)0.5718 (2)0.0566 (15)
C120.4392 (4)0.6560 (4)0.51093 (19)0.0558 (15)
C130.3148 (3)0.5818 (3)0.48816 (16)0.0449 (13)
C14−0.0654 (4)0.1689 (4)0.36909 (19)0.0612 (15)
C15−0.0987 (5)0.1998 (5)0.2990 (2)0.0750 (18)
C160.0864 (3)0.3789 (4)0.37486 (16)0.0454 (12)
C170.0882 (4)0.2308 (4)0.38900 (18)0.0586 (13)
C18−0.2517 (6)0.3734 (8)0.1820 (3)0.140 (4)
C19−0.2565 (4)0.3954 (7)0.2521 (2)0.100 (3)
C20−0.1088 (4)0.3479 (5)0.28785 (18)0.0602 (16)
C21−0.0813 (3)0.4137 (4)0.35298 (14)0.0431 (12)
C220.4069 (4)0.5073 (4)0.37864 (17)0.0572 (13)
C230.1784 (5)0.7078 (5)0.71452 (18)0.0777 (16)
H20.562200.385400.366950.1121*
H3A−0.296650.189870.397140.0776*
H3B−0.178740.211050.454670.0776*
H5A−0.315770.429010.477960.0558*
H5B−0.222400.541070.444370.0558*
H6A−0.120320.490330.546160.0692*
H6B−0.081020.349260.522340.0692*
H90.081220.602190.613370.0573*
H110.509660.755010.588040.0679*
H120.527560.671520.485560.0670*
H14−0.061430.074300.375740.0738*
H15A−0.197140.159430.286290.0903*
H15B−0.015750.163690.272190.0903*
H160.156780.394450.338130.0547*
H17A0.174110.190260.365530.0701*
H17B0.105510.216570.434830.0701*
H18A−0.346560.406160.162670.2104*
H18B−0.242680.281700.173450.2104*
H18C−0.162700.418110.163880.2104*
H19A−0.347610.350950.269800.1201*
H19B−0.269620.487970.260160.1201*
H20−0.018940.371120.260500.0723*
H21−0.088480.508360.347300.0517*
H22A0.358970.528300.337370.0686*
H22B0.491450.569000.386240.0686*
H23A0.198680.746050.756080.1165*
H23B0.171770.614790.718820.1165*
H23C0.080780.740870.697830.1165*
U11U22U33U12U13U23
O10.0692 (14)0.082 (2)0.0586 (15)−0.0123 (17)−0.0034 (16)−0.0077 (18)
O20.0368 (11)0.078 (2)0.110 (2)−0.0021 (13)0.0146 (16)−0.023 (2)
N10.0333 (14)0.051 (2)0.0577 (17)−0.0022 (14)0.0062 (15)−0.0010 (17)
N40.0345 (12)0.046 (2)0.0527 (17)−0.0025 (13)0.0077 (14)0.0075 (17)
C20.0309 (14)0.048 (2)0.0525 (18)−0.0080 (15)0.0009 (16)0.008 (2)
C30.061 (2)0.055 (3)0.078 (3)−0.003 (2)0.012 (2)0.011 (2)
C50.0295 (14)0.062 (3)0.0484 (17)−0.0091 (15)0.0095 (16)0.000 (2)
C60.0319 (15)0.087 (3)0.0545 (19)−0.0096 (18)0.0043 (18)0.008 (2)
C70.0367 (15)0.058 (3)0.0449 (16)0.0021 (17)0.0018 (17)0.007 (2)
C80.0375 (16)0.047 (2)0.0508 (19)0.0016 (16)−0.0019 (16)0.007 (2)
C90.0363 (14)0.052 (2)0.0551 (19)0.0004 (16)−0.0013 (17)0.004 (2)
C100.0477 (17)0.053 (3)0.058 (2)0.0073 (19)−0.007 (2)0.001 (2)
C110.0418 (15)0.051 (3)0.077 (3)−0.0054 (19)−0.003 (2)−0.008 (2)
C120.0453 (18)0.054 (3)0.068 (3)−0.0033 (18)0.005 (2)−0.002 (2)
C130.0349 (16)0.047 (3)0.0529 (19)−0.0033 (16)0.0003 (18)0.004 (2)
C140.0517 (19)0.054 (3)0.078 (3)0.002 (2)0.008 (2)0.001 (2)
C150.058 (2)0.090 (4)0.077 (3)−0.009 (2)−0.008 (2)−0.022 (3)
C160.0328 (14)0.058 (3)0.0455 (17)0.0030 (17)0.0000 (17)0.005 (2)
C170.0548 (18)0.055 (3)0.066 (2)0.0097 (19)−0.005 (2)−0.002 (2)
C180.089 (4)0.248 (9)0.084 (4)−0.016 (5)−0.013 (3)0.027 (5)
C190.041 (2)0.198 (7)0.061 (3)−0.001 (3)−0.0052 (19)−0.016 (4)
C200.0376 (16)0.089 (4)0.054 (2)0.0018 (19)0.0005 (18)0.002 (3)
C210.0339 (15)0.052 (3)0.0433 (16)−0.0035 (16)0.0012 (16)0.009 (2)
C220.0332 (16)0.081 (3)0.0575 (19)−0.0033 (18)0.0057 (18)−0.001 (3)
C230.077 (2)0.105 (4)0.051 (2)−0.002 (3)0.002 (2)−0.007 (3)
O1—C101.386 (5)C20—C211.524 (5)
O1—C231.409 (5)C3—H3A0.9701
O2—C221.389 (5)C3—H3B0.9701
O2—H20.8196C5—H5A0.9701
N1—C21.392 (4)C5—H5B0.9696
N1—C221.447 (4)C6—H6A0.9702
N1—C131.387 (4)C6—H6B0.9697
N4—C31.480 (5)C9—H90.9301
N4—C211.472 (4)C11—H110.9299
N4—C51.463 (4)C12—H120.9297
C2—C71.374 (5)C14—H140.9803
C2—C161.486 (5)C15—H15A0.9697
C3—C141.522 (5)C15—H15B0.9702
C5—C61.525 (4)C16—H160.9798
C6—C71.509 (4)C17—H17A0.9703
C7—C81.426 (5)C17—H17B0.9700
C8—C131.398 (4)C18—H18A0.9605
C8—C91.407 (5)C18—H18B0.9598
C9—C101.358 (5)C18—H18C0.9606
C10—C111.401 (5)C19—H19A0.9702
C11—C121.360 (6)C19—H19B0.9701
C12—C131.385 (5)C20—H200.9797
C14—C151.510 (6)C21—H210.9796
C14—C171.509 (5)C22—H22A0.9698
C15—C201.538 (7)C22—H22B0.9702
C16—C171.547 (6)C23—H23A0.9602
C16—C211.537 (4)C23—H23B0.9595
C18—C191.467 (8)C23—H23C0.9604
C19—C201.536 (6)
O2···C3i3.319 (4)H5A···O2iv2.8329
O2···C5i3.239 (4)H5A···H2iv2.5581
O2···N4i2.825 (3)H5A···H3B2.5657
O2···C163.248 (3)H5A···H17Bv2.4346
O1···H20ii2.8425H5B···H212.3315
O1···H21iii2.7735H5B···C10vii3.0501
O2···H3Ai2.8371H5B···C11vii2.9150
O2···H5Ai2.8329H6A···C92.9124
O2···H162.7665H6A···H92.4861
O2···H19Ai2.7165H6B···C32.8223
N4···O2iv2.825 (3)H6B···H3B2.1577
N4···H2iv2.0984H9···C63.0870
N4···H19A2.9397H9···C232.4957
C3···O2iv3.319 (4)H9···H6A2.4861
C3···C8v3.431 (6)H9···H23B2.3157
C5···O2iv3.239 (4)H9···H23C2.2520
C8···C3vi3.431 (6)H9···H18Aix2.2414
C16···O23.248 (3)H12···C222.9621
C3···H2iv2.7441H12···H22B2.3273
C3···H6B2.8223H12···C8iii3.0396
C5···H2iv2.7362H12···C9iii2.9363
C6···H93.0870H14···C9v3.0798
C6···H3B2.7084H14···C10v2.9242
C7···H17B2.9751H14···C11v3.0658
C8···H3Avi3.0377H15A···H3A2.4629
C8···H12vii3.0396H15A···H19A2.3682
C8···H3Bvi3.0667H15B···H17A2.5303
C9···H23B2.7024H16···O22.7665
C9···H23C2.7226H16···C153.0582
C9···H6A2.9124H16···C222.5611
C9···H14vi3.0798H16···H202.2054
C9···H12vii2.9363H16···H22A2.1993
C10···H5Biii3.0501H16···C23x3.0973
C10···H14vi2.9242H16···H23Ax2.5422
C11···H5Biii2.9150H17A···H15B2.5303
C11···H14vi3.0658H17A···H23Ax2.5916
C11···H18Cii3.0380H17B···C72.9751
C12···H22B2.7640H17B···H3B2.4511
C15···H163.0582H17B···H5Avi2.4346
C15···H18B2.9902H18A···H9viii2.2414
C16···H22A2.8834H18B···C152.9902
C18···H23Cviii3.0500H18C···H202.3908
C19···H2iv2.8326H18C···C11x3.0380
C21···H2iv3.0574H19A···O2iv2.7165
C22···H122.9621H19A···N42.9397
C22···H162.5611H19A···H2iv2.1788
C23···H92.4957H19A···H15A2.3682
C23···H16ii3.0973H19A···C23viii3.0941
C23···H19Aix3.0941H19B···H212.3791
H2···N4i2.0984H20···H162.2054
H2···C3i2.7441H20···H18C2.3908
H2···C5i2.7362H20···O1x2.8425
H2···C19i2.8326H21···H5B2.3315
H2···C21i3.0574H21···H19B2.3791
H2···H3Ai2.4183H21···O1vii2.7735
H2···H5Ai2.5581H22A···C162.8834
H2···H19Ai2.1788H22A···H162.1993
H3A···O2iv2.8371H22B···C122.7640
H3A···H2iv2.4183H22B···H122.3273
H3A···H15A2.4629H23A···H16ii2.5421
H3A···C8v3.0377H23A···H17Aii2.5916
H3B···C62.7084H23B···C92.7024
H3B···H5A2.5657H23B···H92.3157
H3B···H6B2.1577H23C···C92.7226
H3B···H17B2.4511H23C···H92.2520
H3B···C8v3.0667H23C···C18ix3.0500
C10—O1—C23116.3 (3)C5—C6—H6A108.37
C22—O2—H2109.52C5—C6—H6B108.42
C2—N1—C13109.4 (3)C7—C6—H6A108.40
C2—N1—C22125.3 (3)C7—C6—H6B108.44
C13—N1—C22125.0 (3)H6A—C6—H6B107.47
C3—N4—C5115.3 (3)C8—C9—H9120.72
C3—N4—C21110.8 (3)C10—C9—H9120.77
C5—N4—C21115.0 (3)C10—C11—H11118.88
N1—C2—C16122.4 (3)C12—C11—H11118.78
C7—C2—C16129.2 (3)C11—C12—H12121.28
N1—C2—C7108.3 (3)C13—C12—H12121.25
N4—C3—C14110.4 (3)C3—C14—H14110.42
N4—C5—C6119.1 (3)C15—C14—H14110.40
C5—C6—C7115.5 (3)C17—C14—H14110.38
C2—C7—C8107.5 (3)C14—C15—H15A109.40
C6—C7—C8126.5 (3)C14—C15—H15B109.39
C2—C7—C6126.0 (3)C20—C15—H15A109.43
C7—C8—C13107.9 (3)C20—C15—H15B109.37
C9—C8—C13119.7 (3)H15A—C15—H15B108.01
C7—C8—C9132.4 (3)C2—C16—H16107.50
C8—C9—C10118.5 (3)C17—C16—H16107.47
O1—C10—C9124.3 (3)C21—C16—H16107.47
O1—C10—C11115.2 (3)C14—C17—H17A109.54
C9—C10—C11120.5 (3)C14—C17—H17B109.54
C10—C11—C12122.3 (3)C16—C17—H17A109.49
C11—C12—C13117.5 (3)C16—C17—H17B109.50
N1—C13—C8107.0 (3)H17A—C17—H17B108.06
C8—C13—C12121.4 (3)C19—C18—H18A109.51
N1—C13—C12131.6 (3)C19—C18—H18B109.56
C3—C14—C15107.5 (3)C19—C18—H18C109.50
C15—C14—C17109.6 (3)H18A—C18—H18B109.45
C3—C14—C17108.5 (3)H18A—C18—H18C109.38
C14—C15—C20111.2 (4)H18B—C18—H18C109.44
C2—C16—C17113.6 (3)C18—C19—H19A108.82
C2—C16—C21113.5 (3)C18—C19—H19B108.86
C17—C16—C21107.0 (3)C20—C19—H19A108.77
C14—C17—C16110.7 (3)C20—C19—H19B108.75
C18—C19—C20113.8 (4)H19A—C19—H19B107.64
C15—C20—C21107.2 (3)C15—C20—H20106.43
C19—C20—C21114.2 (4)C19—C20—H20106.40
C15—C20—C19115.5 (4)C21—C20—H20106.43
N4—C21—C16113.5 (3)N4—C21—H21108.88
C16—C21—C20107.4 (3)C16—C21—H21108.85
N4—C21—C20109.2 (3)C20—C21—H21108.85
O2—C22—N1111.4 (3)O2—C22—H22A109.35
N4—C3—H3A109.57O2—C22—H22B109.29
N4—C3—H3B109.56N1—C22—H22A109.39
C14—C3—H3A109.57N1—C22—H22B109.36
C14—C3—H3B109.57H22A—C22—H22B107.99
H3A—C3—H3B108.08O1—C23—H23A109.46
N4—C5—H5A107.53O1—C23—H23B109.51
N4—C5—H5B107.56O1—C23—H23C109.47
C6—C5—H5A107.52H23A—C23—H23B109.49
C6—C5—H5B107.55H23A—C23—H23C109.41
H5A—C5—H5B107.04H23B—C23—H23C109.48
C23—O1—C10—C98.4 (6)C6—C7—C8—C13−179.5 (3)
C23—O1—C10—C11−173.2 (4)C6—C7—C8—C90.3 (7)
C13—N1—C2—C16−176.6 (3)C2—C7—C8—C130.2 (4)
C13—N1—C2—C70.6 (4)C7—C8—C13—C12178.5 (3)
C22—N1—C2—C7174.5 (3)C7—C8—C13—N10.2 (4)
C2—N1—C13—C12−178.5 (4)C13—C8—C9—C10−0.7 (6)
C22—N1—C13—C127.5 (6)C7—C8—C9—C10179.5 (4)
C2—N1—C22—O2−68.4 (4)C9—C8—C13—N1−179.7 (3)
C13—N1—C22—O2104.6 (4)C9—C8—C13—C12−1.4 (5)
C22—N1—C2—C16−2.7 (6)C8—C9—C10—C112.3 (6)
C22—N1—C13—C8−174.4 (3)C8—C9—C10—O1−179.5 (4)
C2—N1—C13—C8−0.5 (4)O1—C10—C11—C12179.7 (4)
C5—N4—C21—C1674.8 (4)C9—C10—C11—C12−1.8 (6)
C3—N4—C21—C16−58.2 (4)C10—C11—C12—C13−0.2 (6)
C5—N4—C21—C20−165.3 (3)C11—C12—C13—C81.8 (5)
C5—N4—C3—C14−133.2 (3)C11—C12—C13—N1179.6 (4)
C21—N4—C3—C14−0.3 (4)C17—C14—C15—C20−59.4 (4)
C21—N4—C5—C6−72.2 (4)C3—C14—C17—C16−62.3 (4)
C3—N4—C21—C2061.6 (4)C3—C14—C15—C2058.3 (4)
C3—N4—C5—C658.7 (4)C15—C14—C17—C1654.8 (4)
N1—C2—C7—C6179.2 (3)C14—C15—C20—C19−128.7 (3)
C7—C2—C16—C17−70.8 (5)C14—C15—C20—C21−0.1 (4)
N1—C2—C16—C17105.7 (4)C2—C16—C21—C20166.7 (3)
C16—C2—C7—C8176.5 (4)C17—C16—C21—N453.7 (4)
N1—C2—C16—C21−131.7 (3)C2—C16—C21—N4−72.4 (4)
C16—C2—C7—C6−3.8 (7)C2—C16—C17—C14133.0 (3)
N1—C2—C7—C8−0.5 (4)C17—C16—C21—C20−67.2 (4)
C7—C2—C16—C2151.7 (5)C21—C16—C17—C146.9 (4)
N4—C3—C14—C1759.5 (4)C18—C19—C20—C21157.5 (5)
N4—C3—C14—C15−59.0 (4)C18—C19—C20—C15−77.5 (6)
N4—C5—C6—C764.4 (5)C19—C20—C21—N468.8 (5)
C5—C6—C7—C8137.5 (4)C19—C20—C21—C16−167.7 (4)
C5—C6—C7—C2−42.2 (6)C15—C20—C21—C1663.0 (4)
C2—C7—C8—C9−180.0 (4)C15—C20—C21—N4−60.5 (4)
D—H···AD—HH···AD···AD—H···A
O2—H2···N4i0.82002.10002.825 (3)148.00
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O2—H2⋯N4i0.822.102.825 (3)148

Symmetry code: (i) .

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