Startseite Crystal structure of phenarsazine chloride dimethylsulfoxide solvate, C14H15AsClNOS
Artikel Open Access

Crystal structure of phenarsazine chloride dimethylsulfoxide solvate, C14H15AsClNOS

  • Arthur Averdunk , Eric C. Hosten ORCID logo und Richard Betz ORCID logo EMAIL logo
Veröffentlicht/Copyright: 2. Oktober 2020

Abstract

C14H15AsClNOS, monoclinic, P21 (no. 4), a = 5.2852(2) Å, b = 13.3035(6) Å, c = 10.7522(5) Å, β = 90.130(2) Å, V = 756.00(6) Å3, Z = 2, Rgt(F) = 0.0200, wRref(F2) = 0.0503, T = 200(2) K.

CCDC no.: 2031796

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:Yellow block
Size:0.50 × 0.40 × 0.30 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:2.55 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:28.3°, >99%
N(hkl)measured, N(hkl)unique, Rint:6536, 3458, 0.015
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3278
N(param)refined:212
Programs:Bruker [1], SHELX [2], WinGX/ORTEP [3], Mercury [4], PLATON [5]
Table 2:

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

AtomxyzUiso*/Ueq
As1−0.09517 (4)0.48504 (3)0.15347 (2)0.03070 (8)
Cl10.15457 (17)0.37728 (7)0.04100 (8)0.0564 (2)
N10.2992 (4)0.5005 (2)0.38523 (19)0.0305 (5)
C110.1646 (5)0.58025 (19)0.1905 (2)0.0276 (5)
C120.3254 (4)0.57271 (19)0.2939 (2)0.0263 (5)
C130.5254 (5)0.6424 (2)0.3066 (3)0.0313 (6)
H130.6372500.6375270.3755890.038*
C140.5598 (6)0.7166 (2)0.2209 (3)0.0391 (6)
H140.6969350.7621790.2300160.047*
C150.3948 (6)0.7261 (3)0.1197 (3)0.0448 (7)
H150.4162790.7788480.0611090.054*
C160.2009 (6)0.6578 (2)0.1063 (3)0.0392 (6)
H160.0889260.6640680.0374690.047*
C21−0.0752 (5)0.41224 (19)0.3068 (2)0.0285 (5)
C220.1151 (5)0.4282 (2)0.3951 (2)0.0294 (5)
C230.1230 (5)0.3652 (2)0.5008 (3)0.0371 (6)
H230.2524290.3742640.5611850.045*
C24−0.0542 (6)0.2912 (2)0.5171 (3)0.0447 (7)
H24−0.0446850.2490490.5882500.054*
C25−0.2487 (6)0.2767 (2)0.4306 (3)0.0453 (8)
H25−0.3728250.2260990.4430290.054*
C26−0.2566 (5)0.3373 (2)0.3272 (3)0.0383 (6)
H26−0.3883630.3281780.2680400.046*
H10.405 (5)0.508 (2)0.438 (2)0.030 (7)*
S3a0.8146 (3)0.55342 (12)0.67438 (15)0.0454 (5)
O3a0.598 (5)0.5610 (12)0.5898 (17)0.060 (3)
C31a0.7704 (17)0.6574 (5)0.7760 (7)0.069 (2)
H31Aa0.8012140.7200470.7306260.104*
H31Ba0.8891560.6523370.8459000.104*
H31Ca0.5966270.6570150.8075830.104*
C32a0.749 (3)0.4560 (6)0.7822 (7)0.109 (4)
H32Aa0.7317270.3920780.7377810.164*
H32Ba0.5906800.4710540.8259280.164*
H32Ca0.8874730.4511930.8425600.164*
S4b0.7087 (5)0.50598 (18)0.7137 (2)0.0537 (9)
O4b0.605 (7)0.5364 (18)0.596 (2)0.060 (3)
C41b0.9955 (18)0.5644 (11)0.7441 (10)0.089 (4)
H41Ab1.1182140.5457310.6799650.133*
H41Bb1.0583490.5430670.8257610.133*
H41Cb0.9719650.6374880.7438020.133*
C42b0.535 (2)0.5638 (14)0.8342 (8)0.094 (5)
H42Ab0.4719460.6291170.8056070.140*
H42Bb0.6449690.5735290.9067400.140*
H42Cb0.3919340.5208520.8571130.140*
  1. aOccupancy: 0.578(4).

  2. bOccupancy: 0.422(4).

Source of material

The title compound was synthesized upon the recrystallization of phenarsazine chloride from warm dimethyl sulfoxide. Crystals suitable for the diffraction studies were obtained upon cooling of the solution to room temperature.

Experimental details

The position of the H atom attached to N1 was refined subject to a distance restraint. All other H atoms were placed geometrically and refined as riding with Uiso(H) = 1.2-1.5 Ueq (C) using the appropriate SHELXL AFIX commands. The dimethylsufoxide molecule was found to be disordered over two positions with refined occupancies of 0.578(4) and 0.422(4), respectively. The Flack parameter [6] refined to 0.023(10) and was determined using full-matrix least squares.

Comment

The effect of size and steric presence of large ions on chemical and spectroscopic properties of compounds have been a focus of research for many decades. Among the many effects that can be attributed to the spatial requirements of counterions are the glass transition temperature in ionomers [7], surfactant modifying properties [8], the charge transfer in radical ions [9] and polymer-modified electrodes [10], as well as the structural and vibrational spectroscopic behavior of DNA building blocks [11]. Furthermore, the benefit of chosing the adequate size of counterions to crystallize ionic compounds has been confirmed and reviewed on many occasions [12]. Gaining crystallographic information about a vast variety of large anions has seen significant growth upon the introduction of bulky cations that have simplified the crystallization of these compounds. A remarkable example in this aspect for instance the group of chlorido coordination compounds of gallium that apply cations derived from the phenarsazine scaffold [13], [14]. At the onset of a research project aimed at the characterization of large anionic compounds, we set out to create a novel set of phenarsazine-inspired cations via phenarsazine chloride as the starting material. To confirm the successful synthesis of the latter, a diffraction study of the recrystallized compound was conducted. The crystal structures of solvent - free phenarsazine chloride [15], [16] and phenarsazine bromide [15] have been reported earlier; however, no hydrogen atoms had been included in the refinement process. Furthermore, the crystal structure of the para-xylene solvate of phenarsazine chloride has been mentioned earlier [16]; however, no structural data has been deposited with the Cambridge Structural Database.

The structure solution from the experimental data collected in this study shows the presence of the desired phenarsazine chloride product as well as one molecule of dimethyl sulfoxide in the asymmetric unit. The solvent molecule is disordered over two positions, as described in the experimental section. The As–Cl bond length of 2.2950(8) Å is slightly longer than the most commonly-reported arsenic–chlorine bond lengths deposited with the Cambridge Structural Database [17]. The angles around the arsenic atom were measured at 96.32(8)° and 96.76(11)° towards the chlorine atom as well as 96.14(8)° for the intracyclic angle thus ruling out classical hybridization of the heavier pnicogen atom. The least-squares planes as defined by the respective atoms of the two aromatic moieties on the one hand as well as the central six-membered heterocyclic ring on the other hand enclose angles of 2.93(11)° and 3.82(12)° while the two planes of the outer aromatic moieties intersect at an angle of 3.99(13)°. A puckering analysis [18] of the central six-membered ring shows the latter to adopt a 4C1 conformation on atoms N1 and As1 [19]. In the crystal structure, classical hydrogen bonds of the N–H···O type as well as C–H···O and C–H···Cl contacts are observed. The classical hydrogen bonds employ the oxygen atom of the disordered solvent molecule as an acceptor. The latter atom also serves as an acceptor for the C–H···O contacts that are supported by a) one of the hydrogen atoms in ortho-position to the N–H group and b) one of the hydrogen atoms in para-position to the N–H group in the other phenyl ring. The C–H···Cl contacts stem from one of the hydrogen atoms on one of the methyl groups of the solvent molecule as well as the remaining hydrogen atom in para-position to the N–H group. In total, these contacts connect the entities in the crystal structure to a three-dimensional network. In terms of graph-set analysis [20], [21], the classical hydrogen bonds requires a D descriptor on the unary level while the C–H···O are to be described by means of a DD descriptor on the same level. The graph-set descriptor for C–H···Cl contacts is DC11(6) on the unary level. π-Stacking is not a prominent feature in the crystal structure of the title compound as the shortest distance between two centers of gravity was measured at 4.5864(15) Å. However, one could debate the presence of one C–H···π interaction that is supported by one of the hydrogen atoms on the disordered solvent molecule as donor and one of the phenyl moieties as acceptor.


Corresponding author: Richard Betz, Department of Chemistry, Nelson Metropolitan University, Summerstrand Campus (South) University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa,

Acknowledgments

The authors thank Ms Andiswa Mfakadolo for helpful discussions.

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

  2. Research funding: None declared.

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

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Received: 2020-07-23
Accepted: 2020-09-14
Published Online: 2020-10-02
Published in Print: 2021-01-26

© 2020 Arthur Averdunk et al., published by De Gruyter, Berlin/Boston

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

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of 3-oxo-urs-12-en-28-oic acid, C30H46O3·1/6H2O
  4. The crystal structure of (3S,12R,20R,24R)-3,12-diacetyl-20,24-epoxy-dammarane-3,12,25–triol–ethyl acetate (4/1), C34H56O6⋅ 0.25(C4H8O2)
  5. A new polymorph of tetrakis(dimethylammonium) catena-poly[tetrakis(μ2-sulfato-κ2O:O′)dizinc(II)], Zn2C8H32N4O16S4
  6. Crystal structure of 10-oxysophoridine, C15H22N2O2
  7. The crystal structure of (5R,8R,9R,10R,12R,13R,14R)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl)tetradecahydro-3H-cyclopenta[a]phenanthrene-3,6(2H)-dione, C30H48O4
  8. Synthesis, crystal structure and optical property of 1,6-bis(p-tolylthio)pyrene, C30H22S2
  9. The crystal structure of hexakis(2-(pyridin-2-ylamino)pyridin-1-ium) decavanadate(V) dihydrate, C60H64N18O30V10
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  19. Crystal structure of N,N-diphenylformamide, C13H11NO
  20. Crystal structure of (E)-2-(3,5-bis(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen- 1(2H)-one, C20H14F6O2
  21. Crystal structure of ortho-methoxy benzaldehyde, C8H8O2 – a second polymorph and deposition of 3D coordinates
  22. Crystal structure of catena-poly[diaqua-bis(μ2-2-(4-(2,4,4-trimethylpentan-2-yl)phenoxy)propanoato-κ2O:O')-(2-(4-(2,4,4-trimethylpentan-2-yl)phenoxy)propanoato-κ2O,O')yttrium(III)], C51H79O11Y
  23. Crystal structure of benzylthiouronium chloride, C8H11ClN2S
  24. Synthesis and crystal structure of tert-butyl (2′R,3R,3′R,4aR,9aS)-1-acetyl-5-chloro-3″-methyl-2,5″,9′-trioxo-1″-phenyl-1″,4a′,5″,9a′-tetrahydro-1′H,3′H,9′H-dispiro[indoline-3,4′-xanthene-2′,4″-pyrazole]-3′-carboxylate, C36H32ClN3O7
  25. Crystal structure of 2-hydroxy-4-methoxy benzaldehyde, C8H8O3
  26. Crystal structure of poly[diaqua-(m3-3′,5′-dicarboxy-[1,1′-biphenyl]-3,4-dicarboxylato-K4O,O′:O″:O‴) cadmium(II)], C16H11O10Cd
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  28. Synthesis and crystal structure of bis{2-bromo-6-((E)-((4-((E)-1-(methoxy-imino)ethyl)phenyl)imino)methyl)phenolato- κ2N,O}zinc(II)-methanol(1/2), C65H60Br4N8O9Zn2
  29. Crystal structure of benzenesulphonic acid
  30. Crystal structure of N-benzyl-N-nicotinoyl-nicotine amide C19H15N3O2
  31. Crystal structure of poly[aqua(μ3-2,4-diamino-benzenesulfonato-κ4N:N′,O:O′)silver(I)], C12H18O8N4S2Ag2
  32. Crystal structure of 1,4-bis(methylpyridinium benzene) bis(1,2-dicyanoethene-1,2-dithiolato-κ2S:S)nickel(II), C26H18N6NiS4
  33. Crystal structure of the Cu(II) complex chlorido-(6-oxo-2-phenyl-1,6-dihydropyrimidine-4-carboxylato-k2N,O)-(phenanthroline-k2N,N')copper(II), C23H15ClCuN4O3
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  36. Crystal structure of catena-poly[(μ2-3-amino-benzenedisulfonato-κ2N:O)-bis (3-methyl-isoquinoline-κN)silver(I)], C26H24N3O3SAg
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  50. Synthesis and crystal structure of 1-octyl-3-phenylquinoxalin-2(1H)-one, C22H26N2O
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  52. 4-(9H-Fluoren-9-yl)-4-methylmorpholin-4-ium bromide, C18H20BrNO
  53. The crystal structure of 2,4-dimethylimidazole monohydrate, C5H10N2O
  54. The crystal structure of 1,2-dimethylimidazole, C5H8N2
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  59. The crystal structure of 2-iso-propylimidazole, C6H10N2
  60. The crystal structure of aqua-tris (1,3-diphenylpropane-1,3-dionato-κ2O,O′)-lanthanum(III), C45H35LaO7
  61. Crystal structure of (3E,5E)-3,5-bis-4-methoxy-3-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
  62. The crystal structure of 3,5-dichloro-6-diazo-2,4-dinitrocyclohexa-2,4-dien-1-one, C6Cl2N4O5
  63. Crystal structure of carbonyl(2-methylquinolin-8-olato-κ2N,O)(triphenylarsine-κAs)rhodium(I), C29H23AsNO2Rh
  64. Crystal structure of (1aS,1a1S,2S)-4a-butoxy-1a,1a1,2,4a,5,6-hexahydro-1H-cyclobuta[de]naphthalen-2-yl-4-nitrobenzoate, C22H25NO5
  65. Crystal structure of carbonyl(2-oxopyridin-1(2H)-olato-k2O,O′)(triphenylarsine-κAs)rhodium(I), C24H19AsNO3Rh
  66. Crystal structure of catena-poly[triqua-bis(μ2-4-carboxy-2-(1H-tetrazol-1-yl)-1H-imidazole-5-carboxylato-k3N,O:O′)barium(II)] tetrahydrate, C14H14BaN12O15
  67. Crystal structure of (E)-3′,6′-bis(ethylamino)-2-((quinoxalin-2-ylmethylene)amino)spiro[isoindoline-1,9′-xanthen]-3-one, C35H32N6O2
  68. Crystal structure of diaqua-bis(μ2-5-chloro-salicylato-κ3O,O′:O′)-bis(5-chloro-salicylato-κ2O,O′)-bis(1,10-phenanthroline-κ2N,N′) dilead(II) – water (1/2), C52H36C14N4O14Pb2·2(H2O)
  69. Crystal structure of (E)-2-(4-ethoxycarbonyl-3,5-dimethyl-2-(pyrrole-2-ylmethyleneamino)-3′,6′-dihydroxylspiro[isoindoline-1,9′-xanthen]-3-one-methanol (1/1), C31H29N3O7
  70. The crystal structure of 5H-dibenzo[b,e]azepine-6,11-dione, C14H9NO2
  71. Crystal structure of (E)-2-(4-fluoro-2-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  72. The crystal structure of N-(2-methoxy-4,5-bis[phenylselanyl]phenyl)picolinamide, C25H20N2O2Se2
  73. The crystal structure of (E)-2-(5-bromo-2-hydroxybenzylidene)-N-phenylhydrazine-1- carboxamide monohydrate, C14H14BrN3O3
  74. Crystal structure of fac-tricarbonyl-(nitrato-k1O)-bis(pyridine-κN)-rhenium, C13H10O6N3Re
  75. Crystal structure of (E)-2-(((1H-pyrrol-2-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one — methanol (1/2), C27H25N3O6
  76. The crystal structure of 4-amino-N′-(4-aminobenzoyl)benzohydrazide monohydrate, C14H16N4O3
  77. Crystal structure of bis(amino(carbamothioylamino)methaniminium) 5-hydroxyisophthalate monohydrate, C12H20N8O6S2
  78. The crystal structure of 2-(chloromethyl)pyridine, C6H6ClN
  79. The crystal structure of 1-bromo-4-iodo-benzene, C6H4BrI
  80. The crystal structure of 2,6-dimethyl-4-nitro-phenol, C8H9NO3
  81. The crystal structure of 3-chloropropionic acid, C3H5ClO2
  82. The crystal structure of 2-(2-methoxyphenyl)acetic acid, C9H10O3
Heruntergeladen am 7.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2020-0394/html
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