Home Selective biocatalytic synthesis and crystal structure of (2R,6R)-hydroxyketaminium chloride, C13H17Cl2NO2
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Selective biocatalytic synthesis and crystal structure of (2R,6R)-hydroxyketaminium chloride, C13H17Cl2NO2

  • U. Joost Luelf ORCID logo EMAIL logo , Guido J. Reiss , Ansgar Bokel and Vlada B. Urlacher
Published/Copyright: April 8, 2021
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 236 Issue 4

Abstract

C13H17Cl2NO2, triclinic, P1 (no. 1), a = 7.1486(3) Å, b = 7.8265(3) Å, c = 13.6579(5) Å, α = 81.085(3)°, β = 77.487(4)°, γ = 73.335(4)°, Z = 2, V = 711.13(5) Å3, Rgt(F) = 0.0536, wRref = 0.0878, T = 290 K.

CCDC no.: 2071277

A part of the hydrogen bonded polymeric title 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:Colorless needle
Size:0.52 × 0.15 × 0.04 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.45 mm−1
Diffractometer, scan mode:Xcalibur, ω
θmax, completeness:30.8°, >99%
N(hkl)measured, N(hkl)unique, Rint:23,627, 8214, 0.056
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 5570
N(param)refined:335
Programs:Bruker [1], SHELX [2], [3], Diamond [4]
Table 2:

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

AtomxyzUiso*/Ueq
Cl10.45305 (17)0.52741 (15)0.19624 (10)0.0536 (3)
Cl20.38590 (17)0.73388 (14)0.41362 (9)0.0502 (3)
Cl30.54115 (16)0.79443 (17)0.83816 (10)0.0527 (3)
Cl40.65298 (15)1.10762 (13)0.60081 (9)0.0442 (3)
O10.4597 (5)0.0086 (5)0.2198 (3)0.0531 (10)
H1O0.418 (9)−0.048 (8)0.278 (5)0.09 (2)*
O20.4485 (5)0.2071 (4)0.3715 (3)0.0503 (9)
O30.5377 (6)0.3198 (5)0.7969 (3)0.0589 (11)
H3O0.578 (7)0.287 (7)0.744 (4)0.053 (18)*
O40.5709 (4)0.5911 (4)0.6453 (3)0.0468 (9)
N10.7089 (5)0.3655 (4)0.3989 (3)0.0379 (9)
H110.6061640.4568250.3867750.045*
H120.6661310.2986240.4532460.045*
N20.3252 (5)0.9046 (4)0.6130 (3)0.0323 (8)
H210.4236040.9347840.6303540.039*
H220.3769020.8427640.5596210.039*
C10.5951 (6)0.1825 (5)0.3067 (3)0.0344 (10)
C20.7736 (6)0.2536 (5)0.3103 (3)0.0319 (9)
C30.9361 (6)0.0830 (5)0.3364 (3)0.0378 (10)
H3A1.0553680.1164870.3389580.045*
H3B0.8908210.0275560.4024850.045*
C40.9853 (6)−0.0523 (6)0.2590 (4)0.0451 (11)
H4A1.042621−0.0007530.1941760.054*
H4B1.083658−0.1585380.2793740.054*
C50.8035 (7)−0.1054 (6)0.2481 (4)0.0505 (13)
H5A0.759193−0.1741170.3097270.061*
H5B0.839594−0.1819550.1937920.061*
C60.6309 (6)0.0572 (6)0.2259 (4)0.0409 (10)
H6A0.6746640.1196390.1607220.049*
C70.8404 (6)0.3655 (5)0.2135 (3)0.0337 (9)
C81.0412 (7)0.3481 (6)0.1752 (3)0.0447 (11)
H8A1.1346190.2685650.2098350.054*
C91.1064 (7)0.4451 (7)0.0874 (4)0.0530 (13)
H9A1.2418350.4278340.0631720.064*
C100.9733 (9)0.5658 (7)0.0361 (4)0.0603 (14)
H10A1.0173920.632335−0.0223820.072*
C110.7724 (8)0.5886 (6)0.0715 (4)0.0501 (12)
H11A0.6806240.6706670.0369370.060*
C120.7083 (6)0.4893 (6)0.1584 (3)0.0389 (10)
C130.8622 (7)0.4391 (6)0.4229 (4)0.0482 (12)
H13A0.9699360.3421960.4413110.072*
H13B0.8045040.5116620.4779380.072*
H13C0.9111490.5110220.3648290.072*
C210.4192 (6)0.6108 (5)0.7063 (3)0.0343 (10)
C220.2461 (5)0.7826 (5)0.6987 (3)0.0307 (9)
C230.0877 (6)0.7155 (5)0.6653 (3)0.0352 (10)
H23A−0.0280840.8150400.6587360.042*
H23B0.1410210.6708880.5997210.042*
C240.0255 (6)0.5664 (6)0.7408 (4)0.0437 (11)
H24A−0.0360570.6128710.8052490.052*
H24B−0.0716110.5263240.7168860.052*
C250.2044 (7)0.4081 (6)0.7543 (4)0.0500 (12)
H25A0.1623030.3191560.8053700.060*
H25B0.2559050.3533350.6915480.060*
C270.1694 (6)0.8801 (5)0.7943 (3)0.0306 (9)
C260.3676 (6)0.4632 (5)0.7849 (4)0.0433 (11)
H26A0.3143240.5142110.8495280.052*
C28−0.0342 (6)0.9715 (5)0.8182 (3)0.0382 (10)
H28A−0.1192390.9679910.7761810.046*
C29−0.1098 (6)1.0649 (6)0.9012 (4)0.0455 (11)
H29A−0.2442061.1240120.9143980.055*
C300.0120 (7)1.0718 (6)0.9650 (4)0.0488 (12)
H30A−0.0399441.1338771.0217920.059*
C310.2115 (7)0.9861 (6)0.9442 (3)0.0448 (11)
H31A0.2953750.9905350.9865790.054*
C320.2858 (6)0.8937 (5)0.8600 (3)0.0356 (10)
C330.1791 (6)1.0727 (5)0.5820 (4)0.0429 (11)
H33A0.0806221.0428860.5548030.064*
H33B0.2468901.1451510.5316130.064*
H33C0.1159201.1380320.6395000.064*

Source of material

The mutated variant I238Q/V286G/L289T/M388A of the cytochrome P450 monooxygenase CYP154E1 from Thermobifida fusca YX was used to catalyze the oxidation of 120 μmol (R)-ketamine hydrochloride to (2R,6R)-hydroxyketamine and -hydroxynorketamine as described by Bokel et al. [5]. The reaction mixture was incubated for 24 h at 25 °C, 250 revolutions per minute. After addition of sodium carbonate, the product mixture was extracted using ethyl acetate. A semi-preparative HPLC was used to purify the (2R,6R)-hydroxy-ketamine as previously described [5]. The solvents (acetonitrile/water) were removed via evaporation and lyophilization. Afterwards, the residue was dissolved in chloroform with hydrochloric acid to form the title compound. The solvent was removed again, and the title compound was dissolved in 2-propanol. Slow evaporation over night at room temperature gave colorless needle crystals.

Experimental details

All hydrogen atoms were added using different riding models depending on the chemical surroundings [3]. The Flack parameter [−0.02(3)] was determined using 1973 quotients ([I+] − [I−])/([I+] + [I−]) using the post-refinement Parsons’ quotients method [3], [6].

Comment

(2R,6R)-hydroxyketamine is one of the minor human metabolites of the anesthetic drug (R,S)-ketamine [7], [8], [9]. Whereas the hepatic metabolism by cytochrome P450s (CYPs) leads to a mixture of several hydroxynorketamines and hydroxyketamines, mutagenesis of the bacterial CYP154E1 allowed the selective synthesis of (2S,6S)- hydroxynorketamine from (S)-ketamine [10] as well as (2R,6R)-hydroxynorketamine from (R)-ketamine [5]. In this study, the crystal structure of one of the side products of the latter reaction is presented.

Molecular description and comparison. The asymmetric unit of the title structure contains two crystallographically independent (2R,6R)-hydroxyketaminium cations (systematic name: (1R,3R)-1-(2-chlorophenyl)-3-hydroxy-N-methyl-2-oxocyclohexan-1-aminium; the protonation at the methylamino group shifts the numbering scheme which includes the chiral centers) and two chloride counter anions (see the figure). In contrast to our previously published structure of (2R,4S)-hydroxyketamine [11], the cyclohexanone ring is in a different chair conformation, which rules out an intramolecular hydrogen bond between the aminium and the hydroxy group. Instead, the conformation of the title cation is very similar to that of the cation seen in the crystal structure of (2R,6R)-hydroxynorketaminium chloride [12]. In general, all molecular geometric parameters are in the expected ranges [11], [12].

Supramolecular aspects. In the title crystal structure each cation donates three classical hydrogen bonds. In detail, each cation donates two NH ··· Cl bonds and one OH ··· Cl hydrogen bond (see the figure). Thus, the (2R,6R)-hydroxyketaminium cation exclusively donates hydrogen bonds. The fact that the carbonyl group is not involved in any classical hydrogen bond is the result of a surplus of hydrogen bond acceptors in this structure. Obviously, the charge-supported hydrogen bonds (NH+···Cl− and NH+···O) are preferred. There are two prominent hydrogen bonding motifs, which should be mentioned and classified using so-called graph set descriptors [13]. There are 12-membered rings consisting of two cation and two chloride anions (graph set descriptor: R24(12); see the figure). Furthermore, a simple chain motif is seen, which is formed by the NH2 groups and the chloride anions (see the figure; graph set descriptor: C12(4)). Consequently, a chain-type polymer is formed, which propagates along the crystallographic b axis (red line in the figure).

A further comparison with the aforementioned crystal structure of (2R,6R)-hydroxynorketaminium chloride [12] shows that NH3 group instead of the H3C–NH2 moiety allows a further hydrogen bonding connection leading to a two-dimensional framework.

Corresponding author: U. Joost Luelf, Institut für Biochemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225Düsseldorf, Germany, E-mail:

Funding source: Federal Ministry of Education and Research

Award Identifier / Grant number: 031A223A

Funding source: Ministry of Innovation, Science and Research of North-Rhine Westphalia

Funding source: German Research Foundation

Award Identifier / Grant number: 162659349

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

  2. Research funding: Federal Ministry of Education and Research, Germany (grant number 031A223A), the Ministry of Innovation, Science and Research of North-Rhine Westphalia and the German Research Foundation (DFG) (Xcalibur diffractometer; INST208/533-1, project no. 162659349).

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

References

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Received: 2021-02-05
Accepted: 2021-02-18
Published Online: 2021-04-08
Published in Print: 2021-07-27

© 2021 U. Joost Luelf et al., published by De Gruyter, Berlin/Boston

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

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  54. The crystal structure of catena-poly[bis(µ2-1,2-bis((1H-imidazol-1-yl)methyl)benzene- κ2N:N′)-bis(nitrato-κO)copper(II)], C28H28N10O6Cu
  55. Synthesis and crystal structure of the novel chiral acetyl-3-thiophene-5-(9-anthryl)-2-pyrazoline, C23H18N2OS
  56. Crystal structure of (E)-3-(dimethylamino)-1-(thiophen-3-yl)prop-2-en-1-one, C9H11NOS
  57. Crystal structure of catena-poly[aqua-(4-iodopyridine-2,6-dicarboxylato-κ3N,O,O′)-(μ2-4-amino-4H-1,2,4-triazole-κ2N:N′) copper(II)], C9H8N5O5CuI
  58. Crystal structure of cyclopropane-1,2,3-triyltris(phenylmethanone), C24H18O3
  59. Crystal structure of bis(amino(thioureido)methaniminium) terephthalate, C12H18N8O4S2
  60. A three-dimensional Eu(III) framework in the crystal structure of dimethylaminium poly[dimethylformamide-κ1N)bis(μ4-terephthalato-κ4O:O′:O′′:O′′′)europium(III)] monohydrate, C21H25EuN2O10
  61. Crystal structure of 2-methoxyphenyl 2-(6-methoxynaphthalen-2-yl)propanoate, C21H20O4
  62. The crystal structure of Hexakis(diethylamido)dimolybdenum, Mo2(NEt2)6
https://doi.org/10.1515/ncrs-2021-0055
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of poly[(μ2-aqua-tetraaqua-(μ3-glutarato-κ4O,O′:O′:O′′)-(μ5-glutarato-κ6O:O,O′:O′:O′′:O′′′)distrontium(II)], C10H22O13Sr2
  4. The crystal structure of acetato-κ1O-{(2-(2-(2-aminophenoxy)ethoxy)phenyl)(4-oxo-4-phenylbut-2-en-2-yl)amido-κ2N,N′,O}copper(II), C26H26CuN2O5
  5. Crystal structure of dimethanolato-k2O:O-bis(1-((2-methyl-1H-benzo[d]imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κN)-bis(thiocyanato-κN)dicopper(II), C34H32Cu2N12O2S2
  6. Crystal structure of poly[diaqua-bis(μ2-3-(pyrimidin-5-yl)benzoato-κ2N:O)cobalt(II)] dihydrate, [Co(C11H11O2N2)2(H2O)2]
  7. Crystal structure of bis(3,3-dimethyl-1-phenylbut-1-en-2-yl)(trimethylsilyl)amido-k1N)zinc(II), Zn(C15H24NSi)2
  8. Crystal structure of catena-poly[(μ2-methanolato-κ2O:O)-(μ2-1-((2-methyl-1H-benzo[d]imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κ2N:N′)-(thiocyanato-κ1N)copper(II)] 0.25 hydrate, C17H16CuN6OS ⋅ 0.5H2O
  9. The crystal structure of 2-amino-5-nitroanilinium iodide monohydrate, C6H8IN3O2
  10. The crystal structure of 3-amino-5-carboxypyridin-1-ium perchlorate monohydrate, C6H9ClN2O7
  11. Crystal structure of 7-hydroxy-2,4-dimethoxy-9,10-dihydrophenanthrene from Arundina graminifolia, C16H16O3
  12. Crystal structure of 6,6′-((1E, 1′E)-(((1R, 2R)-1,2-diphenylethane-1,2-diyl) bis(azanylylidene))bis(methanylylidene))bis(2-ethylphenol), C32H32N2O2
  13. The crystal structure of 2-amino-5-carboxypyridin-1-ium iodide monohydrate, C6H9IN2O3
  14. The crystal structure of 2-(3,5-difluorophenyl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]diazaborinine, C16H11BF2N2
  15. Crystal structure of bis{(2-pyridinyl)-1-phenyl-1-isopropylmethanolato-κ2N,O}nickel, C30H32N2NiO2
  16. Crystal structure of poly[(m3-3-carboxyadamantane-1-carboxylato-κ3O:O′:O″)-(phenanthroline-κ2N,N′)sodium(II)], C24H23N2NaO4
  17. Crystal structure of 2-phenylethynyl-1,3,6,8-tetramethylBOPHY (BOPHY = bis(difluoroboron)-1,2-bis((1H-pyrrol-2-yl)methylene)hydrazine), C22H20B2F4N4
  18. Crystal structure of 4-tert-butyl-2-N-(2-pyridylmethyl)aminophenol, C16H20N2O
  19. The crystal structure of (3Z,3′Z)-4,4′-((1,4-phenylenebis(methylene))bis(azanediyl))bis(pent-3-en-2-one), C18H24N2O2
  20. Crystal structure of (morpholine-1-carbodithioato-κ2-S,S′)bis(triphenylphosphine-κ-P)gold(I), C41H38AuNOP2S2
  21. Crystal structure of 1,4-bis(4-bromobenzyl)-4-(4-chlorophenyl)-1,4-dihydropyridine-3-carbonitrile, C26H19Br2ClN2
  22. The crystal structure of fac-tricarbonyl (N′-benzoyl-N,N-diphenylcarbamimidothioato-κ2S,O)-(pyrazole-κN)rhenium(I) — methanol (1/1) C26H23O4N4SRe
  23. The crystal structure of Ba2Mn(SeO3)2Cl2 containing 1∞[Mn(SeO3)2Cl2]4− chains
  24. Crystal structure of 3,3′,3″-((1E,1′E,1″E)-((nitrilotris(ethane-2,1-diyl))tris(azaneylylidene)) tris(methaneylylidene))tris(4-hydroxy-1-naphthaldehyde) monohydrate, C42H36N4O6·H2O
  25. The crystal structure of 4-(6-acetyl-5-methyl-4,7-dihydrotetrazolo[1,5-a]pyrimidin-7-yl)benzonitrile, C14H12N6O
  26. Crystal structure of benzo[d][1,3]dioxol-5-yl-2-(6-methoxynaphthalen-2-yl)propanoate, C21H18O5
  27. The crystal structure of ethyl 5-methyl-7-(4-(phenylthio)phenyl)-4,7-dihydrotetrazolo[1,5-a]pyrimidine-6-carboxylate, C20H19N5O2S
  28. Crystal structure of N′,N‴-((propane-2,2-diylbis(1H-pyrrole-5,2-diyl))bis(methaneylylidene))-di(isonicotinohydrazide)– water – dimethylformamide (1/4/2), C25H24N8O2·4H2O·2C3H7NO
  29. Synthesis and crystal structure of 4-(2,4-dinitrophenoxy)benzaldehyde, C13H8N2O6
  30. The crystal structure of 1-dodecylpyridin-1-ium bromide monohydrate, C17H32BrNO
  31. Crystal structure of (E)-amino(2-(4-(dimethylamino)benzylidene)hydrazineyl)methaniminium nitrate, C10H16N6O3
  32. Crystal structure of (E)-(2-((1H-pyrrol-2-yl)methylene)hydrazineyl)(amino)methaniminium nitrate monohydrate, C6H12N6O4
  33. The crystal structure of hexakis(1-propylimidazole-κ1N)copper(II) dichloride, C36H60Cl2CuN12
  34. The crystal structure of bis{(μ2-3,3-dimethyl-1-phenylbut-1-en-2-yl)((dimethylamino)dimethylsilyl)amido-κ3N,N′:N′}dilithium, C32H54Li2N4Si2
  35. The crystal structure of methyl 4-(1H-naphtho[1,8-de][1,3,2]diazaborinin-2(3H)-yl)benzoate, C18H15BN2O2
  36. Crystal structure of (E)-N-(1-((2-chlorothiazol-5-yl)methyl)pyridin-2(1H)-ylidene)-2,2,2-trifluoroacetamide, C11H7ClF3N3OS
  37. Crystal structure of N′, N‴-((propane-2,2-diylbis(1H-pyrrole-5,2-diyl))bis (methaneylylidene))di(picolinohydrazide) – water – methanol (1/1/1), C25H24N8O2·H2O·CH3OH
  38. Crystal structure of 3-(2-chloro-benzyl)-7-[4-(2-chloro-benzyl)-piperazin-1-yl]-5,6,8-trifluoro-3H-quinazolin-4-one, C26H21Cl2F3N4O
  39. Crystal structure of N1,N2-bis(2-fluorobenzyl)benzene-1,2-diamine,C20H18F2N2
  40. The crystal structure of 2-(benzo[d][1,3]dioxol-5-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]diazaborinine, C17H13BN2O2
  41. The crystal structure of 6,6′-((1E,1′E)-hydrazine-1,2-diylidenebis(methaneylylidene)) bis(2-bromo-4-nitrophenol) — dimethylsulfoxide (1/2), C14H8Br2N4O6⋅2(C2H6OS)
  42. Selective biocatalytic synthesis and crystal structure of (2R,6R)-hydroxyketaminium chloride, C13H17Cl2NO2
  43. Crystal structure of bis{tetraaqua-[μ3-1-(4-carboxylatophenyl)-5-methyl-1H-pyrazole-3-carboxylate-κ4N,O,O′,O″] [μ2-1-methyl-1H-pyrazole-3,5-dicarboxylate-κ3N,O:O]dicobalt(II)} dihydrate, C36H44Co4N8O26
  44. Crystal structure of diethyl-2,2′-naphthalene-2,3-diylbis(oxy)diacetate, C18H20O6
  45. Synthesis and crystal structure of poly[(μ3-2-(2-carboxylatophenyl)-1H-benzo[d]imidazole-5-carboxylato-κO,O′:O′;:O″, O″′)-(μ2-1-(4-(1Himidazol-1-yl)phenyl)-1H-imidazole-κ2N:N′)cadmium(II)], C27H18CdN6O4
  46. The crystal structure of catena-poly[diaqua-bis(μ2-2-((2-(2-phenylacetyl)hydrazineylidene)methyl)benzoato-κ2O:O')zinc(II)], C32H30N4O8Zn
  47. The crystal structure of 2-(3,4-dimethoxyphenyl)-2,3-dihydro-1H-naphtho [1,8-de][1,3,2]diazaborinine, C18H17BN2O2
  48. The crystal structure of hexakis(1-ethylimidazole-κ1N)nickel(II) dichloride – 1-ethylimidazole (1/2), C40H64Cl2NiN16
  49. Crystal structure of diaqua-bis(2,4-dinitrophenolato-κ2O,O′)copper(II) 1.5 hydrate, C12H13CuN4O13.5
  50. Crystal structure of N′,N‴-((1E,1′E)-((decane-1,10-diylbis(oxy))bis(2,1-phenylene)) bis(methaneylylidene))di(isonicotinohydrazide), C36H40N6O4
  51. The crystal structure of 2-[(R)-1-(naphthalen-1-yl)ethyl]-2,3,7,7a-tetrahydro-3a,6-epoxyisoindol-1(6H)-one, C19H20NO2
  52. Synthesis and crystal structure of (1E,2E)-3-(anthracen-9-yl)-1-(4-methoxyphenyl)prop-2-en-1-one oxime, C24H19NO2
  53. Synthesis and crystal structure of (2E,2′E)-3,3′-(1,3-phenylene)bis(1-(3-bromophenyl)prop-2-en-1-one), C24H16Br2O2
  54. The crystal structure of catena-poly[bis(µ2-1,2-bis((1H-imidazol-1-yl)methyl)benzene- κ2N:N′)-bis(nitrato-κO)copper(II)], C28H28N10O6Cu
  55. Synthesis and crystal structure of the novel chiral acetyl-3-thiophene-5-(9-anthryl)-2-pyrazoline, C23H18N2OS
  56. Crystal structure of (E)-3-(dimethylamino)-1-(thiophen-3-yl)prop-2-en-1-one, C9H11NOS
  57. Crystal structure of catena-poly[aqua-(4-iodopyridine-2,6-dicarboxylato-κ3N,O,O′)-(μ2-4-amino-4H-1,2,4-triazole-κ2N:N′) copper(II)], C9H8N5O5CuI
  58. Crystal structure of cyclopropane-1,2,3-triyltris(phenylmethanone), C24H18O3
  59. Crystal structure of bis(amino(thioureido)methaniminium) terephthalate, C12H18N8O4S2
  60. A three-dimensional Eu(III) framework in the crystal structure of dimethylaminium poly[dimethylformamide-κ1N)bis(μ4-terephthalato-κ4O:O′:O′′:O′′′)europium(III)] monohydrate, C21H25EuN2O10
  61. Crystal structure of 2-methoxyphenyl 2-(6-methoxynaphthalen-2-yl)propanoate, C21H20O4
  62. The crystal structure of Hexakis(diethylamido)dimolybdenum, Mo2(NEt2)6
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