Home Physical Sciences Crystal structure of methyl (3R)-1-(2-bromo-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate hydrochloride hydrate, C19H19BrClFN2O3
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Crystal structure of methyl (3R)-1-(2-bromo-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate hydrochloride hydrate, C19H19BrClFN2O3

  • Feijuan Wang , Yanjiao Wang , Xiaojuan Han and Wenqiang Tang ORCID logo EMAIL logo
Published/Copyright: June 5, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 4

Abstract

C19H19BrClFN2O3, orthorhombic, P212121 (no. 19), a = 9.4940(6) Å, b = 10.8303(9) Å, c = 17.7300(14) Å, V = 1823.0(2) Å3, Z = 2, Rgt (F) = 0.0615 wRref (F 2) = 0.1077, T = 150 K.

CCDC no.: 2333947

The molecular structure is shown in the figure. 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: 0.16 × 0.11 × 0.05 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 2.43 mm−1
Diffractometer, scan mode: Bruker D8 VENTURE, φ and ω
θ max, completeness: 26.4°, 99 %
N(hkl)measured, N(hkl)unique, R int: 8,069, 3,617, 0.081
Criterion for I obs, N(hkl)gt: I obs > 2 σ (I obs), 2,342
N(param)refined: 248
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
Br1 0.67404 (10) 0.44166 (8) 0.26614 (6) 0.0435 (3)
C1 0.1374 (8) 0.3513 (7) 0.2229 (5) 0.026 (2)
C2 0.0691 (10) 0.3876 (8) 0.1573 (5) 0.029 (2)
H2 0.106687 0.450726 0.125926 0.034*
C3 −0.0560 (9) 0.3284 (8) 0.1391 (5) 0.032 (2)
H3 −0.104697 0.351172 0.094413 0.039*
C4 −0.1124 (9) 0.2351 (8) 0.1857 (6) 0.031 (2)
H4 −0.198780 0.196542 0.172340 0.037*
C5 −0.0431 (8) 0.1994 (7) 0.2504 (5) 0.026 (2)
H5 −0.081382 0.136992 0.281981 0.032*
C6 0.0835 (8) 0.2560 (6) 0.2687 (5) 0.0219 (18)
C7 0.1829 (9) 0.2400 (7) 0.3295 (5) 0.0218 (19)
C8 0.1850 (9) 0.1474 (7) 0.3922 (5) 0.027 (2)
H8A 0.145984 0.067806 0.374429 0.033*
H8B 0.126749 0.177035 0.434797 0.033*
C9 0.3388 (10) 0.1300 (7) 0.4180 (5) 0.028 (2)
H9 0.390951 0.088518 0.376040 0.033*
C10 0.3474 (8) 0.0474 (8) 0.4862 (5) 0.028 (2)
C11 0.4779 (10) −0.0004 (8) 0.5949 (6) 0.038 (3)
H11A 0.503641 −0.082383 0.575923 0.057*
H11B 0.392753 −0.006915 0.625885 0.057*
H11C 0.555191 0.032549 0.625484 0.057*
C12 0.4210 (9) 0.3316 (8) 0.3619 (5) 0.027 (2)
H12 0.498237 0.296045 0.330348 0.032*
C13 0.2875 (9) 0.3205 (7) 0.3182 (5) 0.026 (2)
C14 0.4612 (9) 0.4627 (8) 0.3809 (5) 0.026 (2)
C15 0.3866 (8) 0.5317 (7) 0.4344 (5) 0.029 (2)
H15 0.312443 0.493049 0.461505 0.034*
C16 0.4172 (10) 0.6543 (8) 0.4493 (5) 0.032 (2)
H16 0.365214 0.699850 0.485627 0.039*
C17 0.5264 (10) 0.7081 (8) 0.4091 (6) 0.036 (2)
C18 0.6014 (10) 0.6465 (8) 0.3559 (6) 0.036 (3)
H18 0.675442 0.686239 0.329345 0.043*
C19 0.5677 (9) 0.5245 (7) 0.3413 (5) 0.027 (2)
Cl1 0.2225 (2) 0.3205 (2) 0.56986 (16) 0.0486 (8)
F1 0.5591 (6) 0.8275 (5) 0.4233 (4) 0.0564 (18)
N1 0.2623 (6) 0.3903 (5) 0.2539 (4) 0.0256 (18)
H1 0.316890 0.449144 0.236103 0.031*
N2 0.4079 (7) 0.2528 (6) 0.4318 (4) 0.0264 (18)
H2A 0.495425 0.239752 0.451201 0.032*
H2B 0.357064 0.294825 0.466965 0.032*
O1 0.4517 (6) 0.0807 (5) 0.5325 (3) 0.0347 (16)
O2 0.2764 (7) −0.0420 (6) 0.4938 (4) 0.0451 (19)
O3a 0.3826 (14) 0.6126 (12) 0.2119 (9) 0.051 (4)
H3Aa 0.368691 0.685601 0.230878 0.077*
H3Ba 0.466396 0.591960 0.227226 0.077*

  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 2-bromo-4-fluorobenzaldehyde (2.42 g, 12 mmol). The mixture was refluxed for 3 h, until the TLC indicated the reaction was completed. The solvent was evaporated to dryness using a rotary evaporator, yielding the crude product that was purified to obtain a single crystal. For crystal growth, the crude product was dissolved in a minimal amount of hot ethanol and slowly cooled to room temperature.

2 Experimental details

All hydrogen atoms were placed in calculated positions and assigned isotropic displacement parameters. Specifically, hydrogen atoms were refined using a riding model with the isotropic displacement factor U iso(H) set to 1.2 times the equivalent isotropic displacement parameter U eq(C) of the attached atom.

3 Comment

Tryptophan is one of the nine essential amino acids required by the human body, which cannot be synthesized on its own and must be obtained through diet. 5 It is an aromatic amino acid with an indole side chain, featuring a complex double-ring structure, and serves as a precursor for many bioactive molecules. Tryptophan is relatively rare in nature but plays a crucial role in many protein structures. Its derivatives are diverse and have significant physiological and pharmacological effects in organisms. 6 – 11 This paper reports a crystal structure of a tryptophan derivative to assist in the development of new drugs.

As shown, the crystal structure reported in this paper contains the organic molecule (3R)-1-(2-bromo-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b] indole-3-carboxylate and hydrochloride, along with one water molecule. The water molecule forms a hydrogen bond with the hydrogen of the amino group in the indole ring of the organic compound molecule, where the bond angle N1–H1–O3 is 159.5(6)° and the bond length H1–O3 is 1.925(14) Å. The Cl ion is linked to the compound molecule through bonds Cl1–H2B and Cl1–H15, with bond lengths of 2.244(3) and 2.813(3) Å respectively, indicating weak interactions between them. In the organic compound molecule, the phenyl ring and the indole ring are nearly perpendicular to each other, with a dihedral angle of 81.8°. This is consistent with the reported similar crystal structure. 12 – 15

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

Funding source: Scientific Research Project of 2021 Youth Innovation Team of the Shaanxi Province Education Department

Award Identifier / Grant number: 21JP012

Funding source: Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang City

Award Identifier / Grant number: 2021QXNL–PT-0008

Funding source: Scientific Research Plan Project of Shaanxi Provincial Department of Education

Award Identifier / Grant number: 23JK0323

Funding source: Key Research Project of Shaanxi Provincial Department of Education – the Collaborative Innovation Center

Award Identifier / Grant number: 23JY006

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

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

  3. Research funding: This work was financially supported by the Scientific Research Project of 2021 Youth Innovation Team of the Shaanxi Province Education Department (21JP012), the Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang City (2021QXNL–PT-0008), the Scientific Research Plan Project of Shaanxi Provincial Department of Education (23JK0323) and the Key Research Project of Shaanxi Provincial Department of Education – the Collaborative Innovation Center (23JY006).

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Received: 2024-04-27
Accepted: 2024-05-23
Published Online: 2024-06-05
Published in Print: 2024-08-27

© 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-2024-0189
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of hexaquazinc(II) poly[hexakis(μ2-4-methylbenzenesulfinato-κ2O:O′) dizinc(II)]
  4. The crystal structure of poly[((2-(4,5-dihydro-1H-pyrazol-4-yl)-1,3-dioxoisoindoline-5-carbonyl)oxy)(1-(dimethylamino)ethoxy)zinc[II]], C16H14ZnN4O5
  5. Crystal structure of bis[(triaqua-4-iodopyridine-2,6-dicarboxylato-κ 3 N,O,O ″)cobalt(II)] trihydrate, C14H22N2O17I2Co2
  6. Crystal structure of bis(methanol-κO)-bis(nitrato-kO)-bis(1-((2-(2-chloro-4-(4-chlorophenoxy)phenyl)-4-methyl-1,3-dioxolan-2-yl)methyl)-1H-1,2,4-triazole-κN)cadmium(II), C40H42O14N8Cl4Cd
  7. Crystal structure of poly[μ2-dichlorido-(μ2-1-[(2,4-dimethyl-1H-triazole-1-yl)methyl]-1H-benzotriazole-κ2N:N′)cadmium(II)], C11H12CdN6Cl2
  8. The crystal structure of (3aS, 4R, 7S, 7aR)-hexahydro-4, 7-methano-1H-isoindole-1, 3-(2H)-dione, C9H11NO2
  9. The crystal structure of N-(acridin-9-yl)-4-chloro-N-(4-chloro-butanoyl) butanamide, C21H20Cl2N2O2
  10. Crystal structure of 3,3′-dimethoxy-4,4′-oxy-di-benzaldehyde, C16H14O5
  11. The crystal structure of tetrakis(μ 2-2-amino-3,5-dibromobenzoate-κ 2 O:O′)-octakis(n-butyl-κ 1 C)-bis(μ 3-oxo)tetratin(II), C60H92Br8N4O10Sn4
  12. Crystal structure of methyl-1-(naphthalen-1-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b] indole-3-carboxylate, C23H20N2O2
  13. Crystal structure of tetrapropylammonium bicarbonate–1-(diaminomethylene)thiourea(1/1)
  14. Crystal structure of 6,6′-((1E,1′E)-((2-phenylpyrimidine-4,6-diyl)bis(hydrazin-2-yl-1-ylidene))bis(methaneylylidene))bis(2-methoxyphenol)monohydrate, C26H26N6O5
  15. Crystal structure of bis(N,N,N-trimethylbutanaminium) tetrathiotungstate(VI), (BuMe3N)2[WS4]
  16. The crystal structure of 2,3,9-triphenyl-9-(2-phenylbenzofuran-3-yl)-9H-9λ 5-benzo[4,5][1,2]oxaphospholo[2,3-b][1,2,5]oxadiphosphole 2-oxide, C40H28O4P2
  17. Crystal structure of 1–methyl-3-propyl-4-nitro-1H-pyrazole-5-carboxylic acid, C8H11N3O4
  18. Crystal structure of N-(benzo[d]thiazol-2-yl)-2-chloroacetamide, C9H7ClN2OS
  19. The crystal structure of N-benzyl-2-chloro-N-(p-tolyl) acetamide, C16H16ClNO
  20. Crystal structure of 3,4-dimethoxybenzyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H24O5
  21. Crystal structure of 2,5-bis(2,5-dimethoxybenzyl)-3,6-dimethyl-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione, C26H28N2O6
  22. Crystal structure of poly[(μ3-5-bromoisophthalato-κ4 O,O′ :O″,O‴)-(μ2-1,2-bis(1,2,4-triazole-1-ylmethyl)benzene-κ2 N:N′)cobalt(II)], C20H15BrCoN6O4
  23. The crystal structure of bis(2-(piperidin-1-ium-4-yl)-1Hbenzo[d]imidazol-3-ium) dihydrogen decavanadate, C24H36N6O28V10
  24. Crystal structure of diaqua-bis(1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine3-carboxylato-O,O′)-cobalt(ii)dihydrate, C26H36N4O14Co
  25. Crystal structure of poly[(μ2-5-bromoisophthalato-κ4 O,O ′:O ″,O ‴)-(μ2-1,4-bis(2-methylimidazol-1-ylmethyl)benzene-N:N′)cadmium(II)], C24H21BrCdN4O4
  26. The crystal structure of dimethyl 8-(3-methoxy-2-(methoxycarbonyl)-3-oxoprop-1-en-1-yl)-4-methyl-1-(p-tolyl)-1,3a,4,8b-tetrahydro-3H-furo[3,4-b]indole-3,3-dicarboxylate. C28H29NO9
  27. Crystal structure of (3R)-1-(3,5-dimethoxyphenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate chloride, C21H23ClN2O4
  28. Synthesis and crystal structure of 3-(4,5-dihydroisoxazol-3-yl)-2-methyl-4-(methylsulfonyl)benzoic acid, C12H13NO5S
  29. The crystal structure of hexaaquamagnesium(II) bis-3-(1,2,3,4-tetrahydrobenzo[4,5]imidazo[1,2-α]pyridin-1-yl)benzoate, C36H42N4O10Mg
  30. Crystal structure of 4-formyl-2-methoxyphenyl 2-acetoxybenzoate, C17H14O6
  31. Crystal structure of poly[octakis(μ-oxido)-tris(μ-1,1′-[[1,1′-biphenyl]-4,4′-diylbis(methylene)]bis(1H-imidazole))-tetrakis(oxido)-tetra-vanadium-dimanganese(II)dihydrate], C30H29MnN6O7V2
  32. Crystal structure of 4,8a-bis(4-chlorophenyl)-1,5,6-tris(4-fluorobenzyl)-1,4,4a,4b,5,6,8a,8b-octahydrocyclobuta[1,2-b:3,4-c′]dipyridine-3,8-dicarbonitrile, C45H33Cl2F3N4
  33. Crystal structure of benzo[d][1,3]dioxol-5-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C22H20O5
  34. Crystal structure of N-benzoyl-N-phenylhydroxylaminato-dicarbonylrhodium(I), [Rh(BNA)CO2]
  35. The crystal structure of N-(2-((2-methoxynaphthalen-1-yl)ethynyl)phenyl)-4-methylbenzenesulfonamide, C26H21NO3S
  36. The crystal structure of methyl ((4-aminobenzyl)sulfonyl)-d-prolinate, C13H18N2O4S
  37. The crystal structure of dichlorido-(N-isopropyl-N-(pyridin-2-ylmethyl)propan-2-amine-κ 2 N, N′)palladium(II), C12H20N2PdCl2
  38. Crystal structure of poly[(μ 2-5-hydroxyisophthalato-κ4 O,O′:O″,O‴)-(μ 2-1,4-bis(2-methylimidazolyl)-1-butene-N:N′)nickel(II)], C20H20NiN4O5
  39. The crystal structure of {hexakis(1-methyl-1H-imidazole-κ 1 N)cobalt(II)}(μ 2-oxido)-hexaoxido-dimolybdenum(VI)— 1-methyl-1H-imidazole (1/2), C32H48CoMo2N16O7
  40. Synthesis, crystal structure and nonlinear optical property of 1-((propan-2-ylideneamino)oxy)propan-2-yl-4-methylbenzenesulfonate, C13H19O4NS
  41. The crystal structure of N,N-(ethane-1,1-diyl)dibenzamide, C16H16N2O2
  42. Crystal structure of 1-(4-bromophenyl)-3-(diphenylphosphoryl)-3-hydroxypropan-1-one, C21H18BrO3P
  43. The crystal structure of fac-tricarbonyl(bis(3,5-dimethyl-4H-pyrazole)-κ1 N)-((nitrato)-κ1 O)-rhenium(I)— 3,5-dimethyl-4H-pyrazole(1/1), C18H23N7O6Re
  44. The crystal structure of 4′-chloro-griseofulvin: (2S,6′R)-4′,7-dichloro-4,6-dimethoxy-6′-methyl-3H-spiro[benzofuran-2,1′-cyclohexan]-3′-ene-2′,3-dione, C16H14Cl2O5
  45. Crystal structure of tetraethylammonium bicarbonate–1-(diaminomethylene)thiourea(1/1)
  46. Crystal structure of 1-cyclohexyl-4-p-tolyl-1,4-dihydropyridine-3,5-dicarboxylic acid dimethyl ester, C22H27NO4
  47. The crystal structure of catena-poly(μ2-1,4-bis-(1H-imidazol-1-yl)benzene-copper(I)) dichloridocopper(I), {[CuC12H10N4]+[CuCl2]−} n
  48. The crystal structure of propane-1-aminium-2-carbamate, C4H10N2O2
  49. Crystal structure of 5,6,3′,4′,5′-pentamethoxy-flavone dihydrate, C20H24O9
  50. Crystal structure of (E)-N-(2-bromophenyl)-4-(4-(3,5-dimethoxystyryl)phenoxy)pyrimidin-2-amine, C26H22BrN3O3
  51. Crystal structure of methyl (3R)-1-(2-bromo-4-fluorophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate hydrochloride hydrate, C19H19BrClFN2O3
  52. The crystal structure of 1-(2-chlorophenyl)-3-(p-tolyl)urea, C14H13ClN2O
  53. The crystal structure of 1-cyclohexyl-3-(p-tolyl)urea, C14H20N2O
  54. Crystal structure of ((benzyl(hydroxy)-amino)(4-chlorophenyl)methyl)-diphenylphosphine oxide, C26H23ClNO2P
  55. The crystal structure of ethyl 3-(1-methyl-1H-indole-2-carbonyl)-2-phenylquinoline-4-carboxylate, C28H22N2O3
  56. The crystal structure of 1,4-bis(1H-imidazol-3-ium-1-yl)benzene dinitrate, C12H12N4 2+·2(NO3 −)
  57. Crystal structure of tris(hexafluoroacetylacetonato-κ2O,O′) bis(triphenylphosphine oxide-κ1O)samarium(III), C51H33F18O8P2Sm
  58. Crystal structure of 1-(4-(dimethylamino)phenyl)-2,3-bis(diphenylphosphoryl)propan-1-one, C35H33NO3P2
  59. Crystal structure of diaqua[bis(μ 2-pyridine 2,6-dicarboxylato) bismuth(III) potassium(I)], C14H10BiKN2O10
  60. Crystal structure of (R)-N, N ′-dimethyl-[1, 1′-binaphthalene]-2, 2′-diamine, C22H20N2
  61. Crystal structure of 1-phenyl-4-(2-furoyl)-3-furyl-1H-pyrazol-5-ol, C18H12N2O4
  62. Crystal structure of bis(14,34-dimethyl[11,21:23,31-terphenyl]-22-yl)diselane, C40H34Se2
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