Home Crystal structure of methyl (E)-N2-((3-methylquinolin-8-yl)sulfonyl)-Nω′-nitro-L-argininate - ethanol (1/1), C19H28N6O7S
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Crystal structure of methyl (E)-N2-((3-methylquinolin-8-yl)sulfonyl)-Nω-nitro-L-argininate - ethanol (1/1), C19H28N6O7S

  • Binli Jiang ORCID logo and Guo-Chun Zhou EMAIL logo
Published/Copyright: October 25, 2019

Abstract

C19H28N6O7S, monoclinic, P21 (no. 4), a = 8.1573(1) Å, b = 17.4823(1) Å, c = 9.1162(1) Å, β = 116.432(1)°, V = 1164.14(2) Å3, Z = 2, Rgt(F) = 0.0273, wRref(F2) = 0.0732, T = 170(2) K.

CCDC no.: 1922467

The crystal 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:Block, colorless
Size:0.31 × 0.25 × 0.22 mm
Wavelength:Cu Kα radiation (1.54184 Å)
μ:1.69 mm−1
Diffractometer, scan mode:XtaLAB Synergy R, ω-scans
θmax, completeness:75.5°, >99%
N(hkl)measured, N(hkl)unique, Rint:21113, 4394, 0.019
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 4350
N(param)refined:302
Programs:CrysAlisPRO [1], SHELX [2], [3], DIAMOND [4]
Table 2:

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

AtomxyzUiso*/Ueq
S10.85986(6)0.37651(3)0.28561(5)0.01876(12)
O1−0.3533(3)0.65911(14)0.2025(3)0.0560(6)
O2−0.1375(3)0.71613(14)0.4088(3)0.0587(6)
O30.4740(3)0.50527(11)−0.0885(2)0.0422(5)
O40.4055(2)0.38181(11)−0.09722(18)0.0349(4)
O50.7888(2)0.31740(9)0.3507(2)0.0295(4)
O61.0424(2)0.40402(9)0.38129(17)0.0259(3)
N1−0.1905(3)0.66482(12)0.3028(3)0.0348(5)
N2−0.0780(3)0.61244(11)0.2883(3)0.0285(4)
N30.1913(3)0.66470(11)0.5140(2)0.0260(4)
H3A0.3101830.6605620.5745240.031*
H3B0.1303770.7021120.5320390.031*
N40.1968(2)0.55826(11)0.3690(2)0.0260(4)
H40.1363620.5262890.2882890.031*
N50.7264(2)0.45014(10)0.2511(2)0.0177(3)
H50.7729610.4958320.2855170.021*
N60.9252(2)0.46816(11)0.0431(2)0.0210(4)
C10.1039(3)0.61466(13)0.3957(3)0.0222(4)
C20.3924(3)0.54635(15)0.4655(3)0.0282(5)
H2A0.4187710.5336800.5797160.034*
H2B0.4588110.5940000.4672020.034*
C30.4586(3)0.48193(14)0.3938(3)0.0254(5)
H3C0.3921530.4344500.3933060.030*
H3D0.5904480.4731060.4647810.030*
C40.4304(3)0.49857(14)0.2203(3)0.0245(4)
H4A0.4782110.5502160.2165720.029*
H4B0.2977410.4982260.1451880.029*
C50.5270(3)0.43976(12)0.1620(2)0.0204(4)
H5A0.4954510.3873210.1851750.024*
C60.4652(3)0.44737(12)−0.0218(2)0.0224(4)
C70.3542(5)0.3810(2)−0.2722(3)0.0489(7)
H7A0.2503330.415568−0.3291600.073*
H7B0.3195610.328988−0.3147190.073*
H7C0.4582390.398010−0.2902960.073*
C80.8428(3)0.34286(12)0.0965(2)0.0208(4)
C90.7882(3)0.26874(14)0.0494(3)0.0320(5)
H90.7583530.2359600.1171080.038*
C100.7769(4)0.24199(17)−0.1011(4)0.0435(6)
H100.7402430.190735−0.1340140.052*
C110.8181(4)0.28883(17)−0.1994(3)0.0405(6)
H110.8121470.269419−0.2989630.049*
C120.8694(3)0.36586(14)−0.1558(3)0.0277(5)
C130.9044(3)0.41828(17)−0.2564(3)0.0331(5)
H130.9017240.401232−0.3564230.040*
C140.9418(3)0.49288(16)−0.2117(3)0.0321(5)
C150.9493(3)0.51471(14)−0.0593(3)0.0262(5)
H150.9735430.566946−0.0285660.031*
C160.8826(3)0.39381(12)−0.0049(2)0.0203(4)
C170.9782(4)0.5516(2)−0.3143(3)0.0499(8)
H17A1.1061810.568157−0.2578810.075*
H17B0.8976570.595800−0.3314600.075*
H17C0.9542920.529222−0.4205090.075*
O70.5473(3)0.65204(13)0.8022(2)0.0552(6)
H70.5477950.6259400.8797710.083*
C180.6725(5)0.7570(2)0.7241(5)0.0571(9)
H18A0.5495940.7758870.6516620.086*
H18B0.7139030.7223150.6629880.086*
H18C0.7571690.8003280.7652710.086*
C190.6675(4)0.71484(18)0.8660(4)0.0485(7)
H19A0.7917000.6966630.9415590.058*
H19B0.6236750.7491520.9275020.058*

Source of materials

Procedures for preparation of methyl (E)-N2-((3-methylquinolin-8-yl)sulfonyl)-Nω-nitro-L-argininate was adapted from the reported paper [5], [6]. Sodium carbonate (3.64 g, 34.3 mmol) was added to a solution of methyl Nω-nitro-L-argininate (4.00 g, 17.15 mmol) in water (40 mL) under stirring. The mixture was stirred for 1 hour at 0 °C. Then a solution of 3-methylquinoline-8-sulfonyl chloride (7.46 g, 30.87 mmol) in tetrahydrofuran (40 mL) was added and the mixture was warmed up to room temperature and stirred for 4 hours.

The crude residue was purified by flash column chromatography with an appropriate eluting solvent system. Off-white, Yield, 85%. 1H NMR (400 MHz, DMSO) δ 8.86 (d, J = 2.2 Hz, 1H), 8.27 (s, 1H), 8.21 (dd, J = 7.3, 1.3 Hz, 1H), 8.17 (dd, J = 8.3, 1.2 Hz, 1H), 7.90 (d, J = 8.5 Hz, 1H), 7.72–7.64 (m, 1H), 4.36– 4.26 (m, 1H), 3.18 (s, 3H), 3.11–2.99 (m, 2H), 2.53 (s, 3H), 1.72–1.33 (m, 5H), 1.23 (s, 2H). 13C NMR (101 MHz, CDCl3): δ 171.34, 159.25, 153.11, 141.17, 135.66, 135.52, 133.08, 132.36, 129.51, 128.66, 125.52, 55.71, 52.13, 40.35, 30.19, 24.33, 18.74. HR-MS(ESI+) m/z calcd. for C17H23N6O6S [M + H]+: 439.1400, Found: 439.1422 (M + H); IR (cm−1): 3408(w), 3295(w), 3250(w), 1737(s), 1623(s), 1596(s), 1538(w), 1418(m), 1331(m), 1253(s), 1221(m), 1160(s), 1138(m), 1008(w), 937(w), 886(w), 770(m), 679(m), 582(s), 536(m), 489(w).

The ethanol solvate was synthesized by the following procedure. An amount of 1 mmol methyl(E)-N2-((3-methylquinolin-8-yl)sulfonyl)-Nω-nitro-L-argininate was dissolved in a mixed solvent of 5 mL absolute ethanol and 1 mL dichloromethane, then the solution was stayed in room temperature for slow evaporation. Colorless crystals were formed after three days. Yield: 80%.

Experimental details

The structure was solved with the ShelXT [2] structure solution program and refined with the XL [3] refinement package. The positions of the hydrogen atoms were generated geometrically. The figure was drawn by Diamond 4.0 [4].

Comment

The title compound is an important intermediate for the thrombin inhibitor argatroban. Argatroban was synthesized in 1970 [7]. The crystal structure of this intermediate is benefit to understand the reaction mechanism. Two related structures were found in the CSD: One is Nη-nitro-L-arginine methyl ester hydrochloride, and the other is L-nitroargininium picrate [8], [9].

The asymmetric unit contains one tite molecule and one ethanol. The bond lengths and angles within these moieties are in the expected ranges. The S1—N5 distance is 1.6237(17) Å. The C5—N5 distance is 1.470(3) Å. Viewing nitroguanidine part closer. For C—N bond, the distance of C1—N2, C1—N3, C1—N4 is 1.367(3) Å, 1.324(3) Å and 1.330(3) Å, respectively. For N—N bond, the distance of N1—N2 is 1.344(3) Å.

There are four intermolecular hydrogen bonds: N3—H3A⋯O7 (dN⋯O = 2.932(1) Å; ∠NHO = 153°, ′′ = 1 − x; +1/2 + y; 1 − z), N4—H4⋯N6 (dN⋯N = 3.218(1) Å; ∠NHN = 165°, ′′ = −1 + x; y; z), N5—H5⋯N2 (dN⋯N = 3.198(1) Å; ∠NHN = 157°, ′′ = 1 + x; y; z) and O7—H7⋯O3 (dO⋯O = 2.909(1) Å; ∠OHO = 136°, ′′ = 1 − x; −1/2 + y; −z). Intermolecular hydrogen bonds extend the structure to a three dimensional framework.

Acknowledgements

We gratefully acknowledge the financial support from Doctoral Scientific Research Foundation of Guangxi University of Chinese Medicine (XB017022) and Cultivating High-level Talent Teams in the Qi Huang Project of Guangxi University of Chinese Medicine, China (2018002). Xin-Ting Yan is supported by Undergraduate Student Scientific Research Training Project of Guangxi University of Chinese Medicine (2018DXS17).

References

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Received: 2019-08-17
Accepted: 2019-10-08
Published Online: 2019-10-25
Published in Print: 2020-02-25

© 2019 Binli Jiang et al., published by De Gruyter, Berlin/Boston

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

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  67. Crystal structure of (E)-2-cyano-N′-(1-(3-ethylpyrazin-2-yl)ethylidene)acetohydrazide, C11H3N5O
  68. Crystal structure of (2,7-dihexyl-9,9-dimethyl-9H-xanthene-4,5-diyl)bis(diphenylphosphane), C51H56OP2
  69. Crystal structure of 5-((bis(pyridin-2-ylmethyl)amino)methyl)quinolin-8-ol, C22H20N4O
  70. Crystal structure of 3-(2-(5-(4-fluorophenyl)-3-(4-methylphenyl)-4,5-dihydro-1H-pyrazol-1-yl)thiazol-4-yl)-2H-chromen-2-one, C28H20FN3O2S
  71. The crystal structure of [(tetra-μ2-2,6-difluorobenzoato-κ2O:O′)-bis-(2,6-difluorobenzoato-κ2O:O′)-bis-(1,10-phenanthroline-κ2N:N′)]dierbium(III) C66H34N4O12F12Er2
  72. Crystal structure of bis(3-chloro-N-(1-(pyrazin-2-yl)ethylidene)benzohydrazonato-k3N,N′,O)nickel(II), C26H20N8O2Cl2Ni
  73. Crystal structure of (E)-3-(3-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)-1-phenyl-1H-pyrazol-4-yl)-1-phenylprop-2-en-1-one, C27H21N5O
  74. Crystal structure of (E)-N′-((4-aminophenyl)sulfonyl)-N,N-dimethylformimidamide, C9H13N3O2S
  75. Crystal structure of η6-p-cymene-iodido-(N-isopropyl-1-(pyridin-2-yl)methanimine-κ2N,N′)ruthenium(II) hexafluorophosphate(V), C19H26IN2F6Ru
  76. Crystal structure of 6-iodo-3-phenyl-2-propylquinazolin-4(3H)-one, C17H15IN2O
  77. Low temperature redetermination of the crystal structure of catena-poly[[tri-4-fluorobenzyltin(IV)]μ2-pyridine-4-carboxylato-κ2N:O], {C27H22F3NO2Sn}n
  78. Crystal structure of bis(2-propyl-1H-benzo[d]imidazol-3-ium) tetrachloridozincate(II), C10H13Cl4N2Zn
  79. The crystal structure of (Z)-3-hydrazono-5-nitroindolin-2-one – dimethyl sulfoxide (1/1), C8H6N4O3
  80. Crystal structure of bis-[N-(1-pyrazin-2-yl-ethylidene)-cyanoacetic acid-hydrazonato-κ3O,N,N′)]-zinc(II), C18H16N10O2Zn
  81. Crystal structure and photochromism of 1-(2,5-dimethyl-3-thienyl)-2-[2-methyl-5-(benzaldoxime)-3-thienyl] perfluorocyclopentene, C23H17F6NOS2
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