Home Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
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Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9

  • Yueru Wang , Xiaolin Dang , Changhua Yang , Wenqiang Tang ORCID logo and Bin Liu ORCID logo EMAIL logo
Published/Copyright: February 27, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 3

Abstract

C40H48Cl2N4O9, monoclinic, C2 (no. 5), a = 13.434(2) Å, b = 7.2089(11) Å, c = 20.691(3) Å, β = 95.931(4)°, V = 1993.0(5) Å3, Z = 2, R gt (F) = 0.0478, wRref (F 2) = 0.1091, T = 173 K.

CCDC no.: 2313844

Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.19 × 0.15 × 0.12 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.22 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θ max, completeness: 27.5°, >99 %
N (hkl)measured, N(hkl)unique, R int: 8183, 4444, 0.034
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 3624
N(param)refined: 265
Programs: Bruker [1], SHELX [2, 3], Olex2 [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
C1 0.8650 (3) 0.4984 (6) 0.15598 (19) 0.0387 (9)
H1A 0.886449 0.542666 0.114847 0.058*
H1B 0.877907 0.364900 0.160272 0.058*
H1C 0.902342 0.564067 0.192212 0.058*
C2 0.7213 (3) 0.5209 (5) 0.21375 (17) 0.0301 (8)
C3 0.6111 (2) 0.5675 (6) 0.20534 (15) 0.0288 (7)
H3 0.604186 0.704552 0.198981 0.035*
C4 0.5537 (2) 0.4711 (5) 0.14694 (16) 0.0311 (8)
H4A 0.569809 0.530713 0.106200 0.037*
H4B 0.573856 0.339111 0.145804 0.037*
C5 0.4434 (3) 0.4844 (5) 0.15213 (16) 0.0280 (7)
C6 0.4039 (2) 0.5295 (5) 0.20799 (15) 0.0266 (8)
C7 0.4616 (2) 0.5822 (6) 0.27136 (15) 0.0286 (7)
H7 0.461642 0.720505 0.275251 0.034*
C8 0.4246 (2) 0.5009 (5) 0.33159 (15) 0.0278 (8)
C9 0.4082 (3) 0.6138 (6) 0.38395 (18) 0.0379 (9)
H9 0.415802 0.744248 0.380184 0.046*
C10 0.3810 (3) 0.5399 (6) 0.44181 (18) 0.0415 (10)
H10 0.369527 0.619400 0.476909 0.050*
C11 0.3708 (3) 0.3511 (6) 0.44769 (17) 0.0361 (9)
C12 0.3857 (3) 0.2348 (6) 0.39526 (19) 0.0388 (9)
H12 0.378455 0.104267 0.399099 0.047*
C13 0.4111 (3) 0.3114 (5) 0.33787 (17) 0.0326 (8)
H13 0.419411 0.232466 0.302051 0.039*
C14 0.3344 (4) 0.3728 (9) 0.55796 (18) 0.0598 (14)
H14A 0.273599 0.448083 0.550423 0.090*
H14B 0.392647 0.454308 0.566603 0.090*
H14C 0.329423 0.291382 0.595422 0.090*
C15 0.3604 (3) 0.4517 (5) 0.10363 (16) 0.0279 (8)
C16 0.3523 (3) 0.3941 (5) 0.03896 (16) 0.0354 (9)
H16 0.410478 0.373430 0.017519 0.043*
C17 0.2581 (3) 0.3675 (6) 0.00656 (18) 0.0412 (10)
H17 0.251640 0.325293 −0.037163 0.049*
C18 0.1720 (3) 0.4021 (6) 0.03748 (18) 0.0400 (10)
H18 0.108213 0.385056 0.013873 0.048*
C19 0.1773 (3) 0.4602 (5) 0.10112 (17) 0.0334 (8)
H19 0.118612 0.483805 0.121771 0.040*
C20 0.2731 (3) 0.4831 (5) 0.13415 (16) 0.0281 (8)
Cl1 0.59735 (7) 0.08162 (14) 0.26183 (5) 0.0398 (3)
N1 0.3018 (2) 0.5304 (4) 0.19803 (14) 0.0303 (7)
H1 0.263 (2) 0.562 (5) 0.2229 (15) 0.019 (9)*
N2 0.5687 (2) 0.5173 (4) 0.26732 (13) 0.0283 (7)
H2A 0.608439 0.567074 0.301208 0.034*
H2B 0.570778 0.391801 0.271935 0.034*
O1 0.76796 (19) 0.4776 (5) 0.26421 (12) 0.0469 (7)
O2 0.75906 (18) 0.5329 (4) 0.15690 (12) 0.0377 (7)
O3 0.6492 (3) 0.7667 (4) 0.35930 (15) 0.0537 (9)
H3A 0.632534 0.799750 0.396134 0.080*
H3B 0.638099 0.855110 0.332354 0.080*
O4a 0.5890 (5) 0.9115 (9) 0.4713 (3) 0.0529 (15)
H4Ca 0.600931 1.027111 0.474550 0.079*
H4Da 0.525843 0.903092 0.471240 0.079*
O5 0.3454 (2) 0.2634 (5) 0.50206 (13) 0.0528 (8)

  1. aOccupancy: 0.5.

1 Source of materials

To a solution of d-tryptophan methyl ester hydrochloride (2.55 g, 10 mmol) in methanol (30 mL) was added 4-methoxybenzaldehyde (1.63 g, 12 mmol). The mixture was refluxed for 3 h, until the TLC indicated the reaction was completed. The solvent was evaporated to dryness, yielding the crude product that was then purified to obtain a single crystal of high quality. For crystal growth, the crude product was dissolved in a minimal amount of hot ethanol and slowly cooled to room temperature.

2 Experimental details

Hydrogen atoms were assigned isotropic displacement factors: U iso(H) = 1.2 times U eq(C). All hydrogen atoms were refined as being bonded to their respective parent atoms.

3 Comment

Tryptophan plays a crucial role in protein functionality as a constituent of both proteins and non-ribosomal peptides. The hydrophobic and electrostatic characteristics of the indole group are of paramount importance [5]. Tryptophan and its derivatives exhibit biological activity and serve as significant building blocks in drug development, with numerous crystal structures having been reported [6], [7], [8], [9], [10]. In this study, we have synthesized and reported the detailed single-crystal structure of a new tryptophan derivative.

The crystal structure, depicted in the figure, reveals that the carbon and nitrogen atoms within the indole group are almost coplanar. The phenyl ring in the benzylmethoxy moiety is nearly orthogonal to the indole plane, with a dihedral angle of 82.1°. The bond lengths, bond angles, and dihedral angles in the molecular structure fall within reasonable ranges [11], [12], [13], [14].

Corresponding author: Bin Liu, Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, China, E-mail:

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: Shaanxi Administration of Traditional Chinese Medicine (2021PY009), the Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang City (2021QXNL-PT-0008), the key research and development project of Shaanxi Provincial Science and Technology Department (2023-YBSF-036) and the youth innovation team of Shaanxi university 2023 – “Key technology development and application innovation team of the industrialization of traditional Chinese medicine with northwest characteristics”.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2024-01-22
Accepted: 2024-02-14
Published Online: 2024-02-27
Published in Print: 2024-06-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/ncrs-2024-0034
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of tris((Z)-2-hydroxy-N-((E)-pyridin-2-ylmethylene)benzohydrazonato-k2O,N)europium(III), C39H30N9O6Eu
  4. Crystal structure of (E)-3-(benzylideneamino)-2-phenylthiazolidin-4-one, C16H14N2OS
  5. The crystal structure of (E)-4-fluoro-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H15FN2O
  6. Crystal structure of (6-chloropyridin-3-yl)methyl 2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  7. Crystal structure of methyl 3-methoxy-4-(2-methoxy-2-oxoethoxy)benzoate, C12H14O6
  8. The crystal structure of bis[(4-methoxyphenyl)(picolinoyl)amido-κ2 N:N′]copper(II), C26H22CuN4O4
  9. The crystal structure of poly[di(μ2-aqua)-diaqua-bis(3-aminopyridine-4-carboxylate-κ2 O: O′)-tetra(μ2-3-aminopyridine-4-carboxylate-κ2 O: O′)-dineodymium(III), [Nd2(C6H5N2O2)6(H2O)4] n
  10. The crystal structure of t-butyl 7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoate, C28H34FNO4
  11. Crystal structure of catena-poly[(benzylamine-κ1 N)-(sorbato-κ1 O)-(μ2-sorbato-κ2 O,O′)-copper(II), C19H23CuNO4
  12. Crystal structure of (4-(2-chlorophenyl)-1H-pyrrol-3-yl)(ferrocenyl) methanone, C21H16ClFeNO
  13. The crystal structure of N-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-3-(2-methylphenyl)-2-sulfanylprop-2-enamide hydrate, C19H17BrN2O2S2
  14. The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate
  15. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C26H24O3
  16. Crystal structure of naphthalen-1-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C25H22O3
  17. Crystal structure of poly[diaqua- (μ4-5-(1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ5N:O,O’:O’’:O’’’)calcium(II), C10H9CaN3O6
  18. Crystal structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-dimethylformimidamide, C14H19N3O2
  19. Crystal structure of (E)-3-(dimethylamino)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one, C13H17NO4
  20. Crystal structure of (2-chloropyridin-3-yl)methyl-2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  21. The crystal structure of diethyl 4-(3,4-dimethylphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, C21H27NO4
  22. Crystal structure of (8R,9S,10R,13S,14S,17S)-17-hydroxy-10,13-dimethyl-17-((4-(2-phenylpropyl)phenyl)ethynyl)-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H42O2
  23. Synthesis and crystal structure of 4-(4-cyclopropylnaphthalen-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C15H13N3S
  24. Crystal structure of catena-poly[aqua-(2,6-di-(2-pyridyl)-pyridine-κ3 N,N′, N″)(μ2-1,4-naphthalene dicarboxylato-κ2 O,O′)nickel(II)], C27H19NiN3O5
  25. Crystal structure of 3-(diphenylphosphoryl)-3-hydroxy-1-phenylpropan-1-one, C21H19O3P
  26. The crystal structure of R,S-{N-[(2-oxidonaphthalen-1-yl)methylidene]phenylglycinato}divinylsilicon, C23H19NO3Si
  27. The crystal structure of 1,2,4-tris(bromomethyl)benzene, C9H9Br3
  28. Crystal structure of chlorido-[4-(pyridin-2-yl)benzaldehyde-κ2 N,C]-(diethylamine-κ1 N)platinum(II), C16H18ClN2OPt
  29. Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
  30. The crystal structure of 1-(2-chlorobenzyl)-3-(3-chlorophenyl)urea, C14H12Cl2N2O
  31. Hydrothermal synthesis and crystal structure of aqua-tris(4-acetamidobenzoato-κ2 O,O′)-(1,10-phenanthroline-κ2 N,N′)terbium(III) hydrate C39H36N5O11Tb
  32. The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2
  33. The crystal structure of bis{[monoaqua-μ2-4-[(pyridine-4-carbonyl)-amino]-phthalato-κ3 N:O,O′-(2,2′-bipyridine κ2 N,N′)copper(II)]}decahydrate, C48H56N8O22Cu2
  34. Crystal structure of poly[μ10-4,4′-methylene-bis(oxy)benzoatodipotassium], C15H10K2O6
  35. The crystal structure of catena-poly[[tetraaqua[(μ2-1,4-di(4-methyl-1-imidazolyl)benzene] cobalt(II)]bis(formate)], C16H24CoN4O8
  36. The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
  37. The crystal structure of (E)-1-(((2-amino-4,5-dimethylphenyl)iminio)methyl)naphthalen-2-olate, C19H18N2O
  38. Crystal structure of N-(acridin-9-yl)-2-(4-methylpiperidin-1-yl) acetamide monohydrate, C21H25N3O2
  39. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2 O,O′)-zinc(II), C14H20Cl2N4O4Zn
  40. The crystal structure of 2,8-diethyl-1,3,7,9-tetramethyl-4λ4,5λ4-spiro[dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine-5,2′-naphtho[1,8-de][1,3,2]dioxaborinine], C25H29BN2O2
  41. The crystal structure of 5-tert-butyl-2-(5-tert-butyl-3-iodo-benzofuran-2-yl)-3-iodobenzofuran, C24H24I2O2
  42. Synthesis and crystal structure of methyl 2-{[4-(4-cyclopropyl-1-naphthyl)-4H-1,2,4-triazole-3-yl]thio} acetate, C18H17N3O2S
  43. The crystal structure of n-propylammonium bis(2,3-dimethylbutane-2,3-diolato)borate-boric acid (1/1), [C3H10N][C12H24BO4]·B(OH)3
  44. Crystal structure of methyl 1-(2-bromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C19H17BrN2O2
  45. Crystal structure of (4-bromobenzyl)triphenylphosphonium bromide ethanol solvate, C52H48Br4OP2
  46. The crystal structure of unsymmetrical BOPHY C26H27BN4
  47. The crystal structure of Tb3B5O11(OH)2
  48. The crystal structure of (Z)-4-ethyl-2-((4-ethyl-3,5-dimethyl-1H-pyrrol-2-yl)methylene)-3,5-dimethyl-2H-pyrrol-1-ium 2,2'-spirobi[naphtho[1,8-de][1,3,2]dioxaborinin]-2-uide, C37H37BN2O4
  49. Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16
  50. The crystal structure of (2-diphenylphosphanylphenyl) 2-[7-(dimethylamino)-2-oxochromen-4-yl]acetate, C31H26NO4P
  51. Crystal structure of (E)-6-(4-ethylpiperazin-1-yl)-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C23H25FN2O
  52. The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
  53. Crystal structure of 4-amino-3,5-dibromobenzonitrile, C7H4Br2N2
  54. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-acetoxybenzoate, C21H18O4
  55. Single-crystal structure determination of Tm3B12O19(OH)7
  56. Crystal structure determination of NdB3.6O7
  57. The crystal structure of NdB6O8(OH)5·H3BO3
  58. Crystal structure of 2-(5-ethylpyridin-2-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H25NO3
  59. Crystal structure of N-(1-(3,4-dimethoxyphenyl)-2-methylpropyl)aniline, C18H23NO2
  60. Crystal structure of Ba6Cd12Mn4SiF48
  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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