Home Physical Sciences Crystal structure of sodium morpholine-4-carbodithioate, (C5H12NNaO3S2)
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Crystal structure of sodium morpholine-4-carbodithioate, (C5H12NNaO3S2)

  • Nolwazi Solomane , Peter A. Ajibade and Bernard Omondi EMAIL logo
Published/Copyright: March 26, 2019

Abstract

C5H12NNaO3S2, monoclinic, P21/c (no. 14), a = 28.8222(3) Å, b = 5.6782(3) Å, c = 12.3810(9) Å, β = 102.074(2)°, V = 1987.43(17) Å3, Z = 8, Rgt(F) = 0.0269, wRref(F2) = 0.0591, T = 100(2) K.

CCDC no.: 1855486

The asymmetric unit of the title crystal structure is shown in the figure (The disorder in the morpholine moieties is amitted for clarity.). Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Source of material

The title compound was synthesized by dispersing (4.33 mL, 50 mmol) of morpholine into 20 mL of diethyl ether and stirred for 10 minutes. Followed by the addition of 20 mL of an ice cold methanolic solution of sodium hydroxide (2.00 g, 50 mmol) and stirred for 15 minutes at an ice-cold temperature. To this mixture, cold carbon disulfide (3 mL, 50 mmol) was added dropwise. The mixture was stirred for 4 h while maintaining an ice-cold temperature resulting in a formation of white precipitate which was collected by filtration. The product obtained was rinsed with diethyl ether and dried in a desiccator. The crystals of the title compound were formed after four days of extracting the filtrate with diethyl ether. White powder. Yield = 61%. m.p. 308.4−310.3 °C. 1H NMR D2O: δ = 3.77 (4H, t, N—CH2), 4.36 (4H, t, O—CH2). 13C NMR D2O: δ = 51.40 (N—CH2), 66.13 (O—CH2), 209.36 (C-SSNa). IR v(cm−1): 972 (C—S), 1108 (C=S), 1414 (C—N). MS (m/z): 162.0045 [M+].

Table 1:

Data collection and handling.

Crystal:Yellow block
Size:0.36 × 0.23 × 0.14 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.55 mm−1
Diffractometer, scan mode:Bruker SMART, φ and ω-scans
θmax, completeness:27.4°, >99%
N(hkl)measured, N(hkl)unique, Rint:31639, 4506, 0.024
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 4308
N(param)refined:150
Programs:Bruker programs [1], SHELX [2], WinGX and ORTEP [3]
Table 2:

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

AtomxyzUiso*/Ueq
S10.55623(2)0.03105(6)0.78588(3)0.01240(8)
O10.45297(4)−0.09325(19)0.91778(9)0.0155(2)
S20.63255(2)0.23405(7)0.96360(3)0.01908(9)
S40.94367(2)−0.03262(6)1.23051(3)0.01196(8)
S30.86773(2)−0.24153(6)1.33344(3)0.01535(8)
Na10.49327(2)0.25887(10)0.91592(4)0.01334(12)
Na20.99301(2)0.24134(10)1.07727(4)0.01347(12)
O20.54519(4)0.5878(2)0.94798(9)0.0150(2)
O30.95269(4)0.59302(19)1.03569(9)0.0151(2)
O41.04453(4)−0.0892(2)1.09677(9)0.0155(2)
O1Aa0.71454(6)−0.3683(3)0.76431(14)0.0275(4)
C2Aa0.66508(7)−0.3968(4)0.72608(17)0.0224(4)
H2AAa0.651540−0.4733590.7843750.027*
H2ABa0.659231−0.5013200.6606380.027*
C1Aa0.64031(8)−0.1632(5)0.69550(19)0.0179(5)
H1AAa0.652399−0.0889400.6344800.022*
H1ABa0.605753−0.1886960.6704030.022*
N1Aa0.64941(6)−0.0095(3)0.79245(16)0.0150(4)
C10.61594(5)0.0703(3)0.84542(12)0.0172(3)
C3Ab0.72386(8)−0.2202(5)0.85912(19)0.0268(5)
H3AAb0.758564−0.2000310.8842080.032*
H3ABb0.711654−0.2960280.9196010.032*
C4Ab0.70071(7)0.0202(4)0.83457(18)0.0221(4)
H4AAb0.7063210.1164350.9027480.027*
H4ABb0.7148820.1031370.7789690.027*
C7b0.88425(5)−0.0648(3)1.23605(13)0.0200(3)
N1Bb0.6461(3)−0.1046(17)0.8302(6)0.0229(17)
C3Bb0.6741(3)−0.1908(19)0.6646(7)0.033(2)
H3Ab0.668880−0.2835070.5954100.039*
H3Bb0.670723−0.0216930.6451340.039*
O1Bb0.7211(2)−0.2362(17)0.7295(6)0.0385(19)
C4Bb0.7287(3)−0.083(2)0.8248(7)0.035(2)
H12Ab0.761660−0.1004810.8672080.042*
H12Bb0.7240180.0830560.8004560.042*
C5Bb0.6959(3)−0.1413(18)0.8945(7)0.032(2)
H13Ab0.701842−0.0397840.9609840.038*
H13Bb0.700271−0.3074530.9187040.038*
C2Bb0.6398(3)−0.2571(19)0.7294(8)0.023(2)
H15Ab0.644200−0.4245230.7515030.027*
H15Bb0.607240−0.2379080.6846520.027*
O2Ac0.7808(2)0.3381(8)1.0415(4)0.0241(8)
N2Ac0.85009(7)0.0104(4)1.15107(17)0.0150(4)
C5Ac0.79895(8)−0.0287(5)1.1431(2)0.0213(5)
H5AAc0.793880−0.1127001.2097900.026*
H5ABc0.786137−0.1276701.0778730.026*
C8Ac0.85855(8)0.1566(5)1.0594(2)0.0183(5)
H8AAc0.8489210.0694460.9889920.022*
H8ABc0.8928000.1931851.0701670.022*
C7Ac0.83047(8)0.3831(5)1.0539(2)0.0223(5)
H7ACc0.8418400.4748851.1223100.027*
H7ADc0.8358260.4786900.9907670.027*
C6Ac0.77320(12)0.2054(7)1.1329(3)0.0238(7)
H6ACc0.7387650.1768931.1249810.029*
H6ADc0.7842210.2975181.2013690.029*
N2Bd0.85459(12)0.1221(7)1.1920(3)0.0129(7)
C6Bd0.86342(15)0.2834(9)1.1047(4)0.0178(9)
H2Cd0.8955020.2554111.0903990.021*
H2Dd0.8616390.4488961.1286460.021*
C7Bd0.82628(16)0.2389(9)1.0006(4)0.0217(9)
H9AAd0.8318250.3467240.9417860.026*
H9ABd0.8294970.0754080.9753940.026*
C9Bd0.80589(14)0.1546(8)1.2098(3)0.0172(8)
H6AAd0.8022220.3160161.2370830.021*
H6ABd0.7997140.0414401.2659590.021*
C8Bd0.7710(2)0.1153(12)1.1023(5)0.0211(12)
H7AAd0.773330−0.0496841.0781470.025*
H7ABd0.7383660.1411041.1135470.025*
O2Bd0.7800(4)0.2726(15)1.0174(8)0.0224(15)
H1A0.4492(7)−0.179(4)0.8673(17)0.026(5)*
H3C0.9494(7)0.679(4)1.0831(17)0.026(5)*
H2A0.5467(7)0.691(4)0.9045(17)0.028(5)*
H4A1.0458(7)−0.198(4)1.1437(18)0.033(6)*
H2B0.5699(8)0.514(4)0.9506(16)0.030(6)*
H4B1.0680(8)−0.015(4)1.1179(17)0.034(6)*
H3D0.9294(8)0.608(4)0.9877(18)0.032(6)*
H1B0.4288(8)−0.110(4)0.9439(18)0.039(6)*
  1. Occupancies: a = 0.8, b = 0.2, c = 0.65, d = 0.35.

Experimental details

Crystal evaluation and data collection were done on a Bruker Smart APEX2 diffractometer [1]. The structure was solved by the direct method using the SHELXS [2] program and refined using SHELXL [2]. The visual crystal structure information was obtained using ORTEP-3 [3] system software. All hydrogen atoms were placed in idealized positions and refined in riding models with Uiso assigning values of 1.2 times those of their parent atoms and the distances of C—Hs were constrained to 0.99 Å for all the methylene H atoms and 0.84 Å for water hydrogens.

Both morpholine moieties are disordered over two positions (Table 2).

Discussion

Dithiocarbamate ligands are known to be flexible ligands that are able to form diverse types of complexes and be able to stabilize transition metal in various oxidation states [4], [5]. They may possess electrochemical and optical properties because of their redox behaviour and strong coordination ability [6]. They are known to be planar and sterically non-demanding ligands that can be automatically changed by having choices of substituents [7]. Their functionalization of substituents on the nitrogen atom of the dithiocarbamate moeity, can result in various complex structures through secondary interactions hence desirable physical properties [8]. The ease of formation of metal complexes is due to the electron delocalization around the N(CSS)- moiety which is also transferred to the metal centre [9]. This ability is recognized to the approval of dithiocarbamates and thioureide tautomers [10]. In dithiocarbamates, the sulfur atoms act as soft donor atoms containing a lone pair of electron localized on nitrogen (sp3) resulting in pyramidal arrangement of substituents. In thioureide systems there are donor ligands which are planar with lone pair of electron localized in the backbone of carbon-nitrogen bond and onto the sulfur atoms [10]. Dithiocarbamate ligands have been widely used in coordination chemistry due to diverse applications, for example used in dyes, agricultural and pharmaceutical industries and to chelate with heavy metals [11], [12], [13].

Dithiocarbamate ligands are mostly synthesized from nucleophilic addition reaction of primary or secondary amines with carbon disulfide in the presence of a strong base i.e. sodium/ potassium hydroxide acting as a proton acceptor [14]. The formation of these compounds is often accompanied by release of heat, hence the syntheses are carried out at low temperatures [15]. The title compound was as such prepared by the reaction morpholine 4-dithiocarbamate with sodium hydroxide in ethanol.

The asymmetric unit of the title compound contains two fragments of two chains of coordination polymers (see the figure). The fragments contain a morpholine 4-dithiocarbamate moiety and two water molecules coordinated to a sodium centre. The coordination of the two water molecules to the Na center results in four member metallacycles connected in alternating orthogonal fashion in the b crystallographic direction. Two S atoms from two morpholine moieties also in the same chains occupy the other coordination sites such that adjacent chains have the O containing sides of the chair conformed morpholine facing each other. The interaction between the sodium cation and water molecules does not disturb the geometric conformation of the ligand [16]. The S—Na bond distances are 3.0291(7) Å, while the S—C ones are 1.7151(15) Å and 1.7390(15) Å indicating a tendency towards a double bond character of electron density in the S—C—S group [17]. The C—S—Na bond angle is 132.42(5)°, while the S—C—S bond angle is 120.40(8)° and is similar to what is observed for similar complexes.

Acknowledgements

We acknowledge the University of KwaZulu-Natal and National Research Foundation of South Africa for financial support for Ekemini Akpan and Sizwe J. Zamisa.

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Received: 2018-11-19
Accepted: 2019-02-14
Published Online: 2019-03-26
Published in Print: 2019-06-26

© 2019 Nolwazi Solomane 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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  45. The crystal structure of aqua-bis(3-acetyl-2-oxo-2H-chromen-4-olato-κ2O,O′)zinc(II) monohydrate, C22H18O10Zn
  46. Crystal structure of poly[bis(μ2-4-bromoisophthalate-κ2O:O′)-tris(μ2-1-(3-((1H-1,2,4-triazol-1-yl)methyl)benzyl)-1H-1,2,4-triazole-κ2N:N′)dicobalt(II)] monohydrate, C26H23CoN9O5Br
  47. A cyclic I102− anion in the layered crystal structure of theophyllinium pentaiodide, C7H9I5N4O2
  48. Crystal structure of catena-poly[diaqua-bis(μ2-4-((4-(pyridin-2-ylmethoxy)phenyl)diazenyl)benzoato-κ3O,O′:N)cadmium(III)], Cd(C19H14O3N3)2(H2O)
  49. Crystal structure of catena-poly[(μ2-4,4′-bipyridyl-κN,N′)-bis(O,O′-dimethyldithiophosphato-κS)-zinc(II)], {C14H20N2O4P2S4Zn}n
  50. Crystal structure of 3-amino-2-hydroxy-6-methoxybenzamide hydrate, C16H22N4O7
  51. Crystal structure of hemikis(cyclohexane-1,4-diammonium) (pyridine-2-carboxylate), [C6H16N2]0.5[C6H4NO2]
  52. Crystal structure of 2-chloro-4-(prop-2-yn-1-yloxy)-6-(thiophen-2-yl)-1,3,5-triazine, C10H6ClN3OS
  53. The crystal structure of 3-butyl-1-methyl-1H-imidazol-3-ium catena-poly[tris(μ2-bromido-κ2Br:Br)lead(II)], C8H15Br3N2Pb
  54. Crystal structure of 3-(5-amino-1H-1,2,4-triazol-3-yl)-1-(piperidin-1-yl)propan-1-one, C10H17N5O
  55. Crystal structure of aqua-2,2′,2′′-(((nitrilo-κN-tris(ethane-2,1-diyl))tris(azanylylidene-κ3N′,N′′,N′′′))tris(methanylylidene))tris(4-chlorophenolato-κ3O,O′,O′′)neodymium(III), C27H26Cl3N4NdO4
  56. Crystal structure of dichlorido-(μ2-2,2′-(diazene-1,2-diyl)bis(benzen-1-ido)-κ2C:C′)dimercury(II), C12H8Cl2Hg2N2
  57. Crystal structure of (3E,5E)-3,5-bis(4-cyanobenzylidene)-1-((4-fluorophenyl)sulfonyl)piperidin-4-one, C27H18FN3O3S
  58. Crystal structure of dichlorido(pyridine-κN)(2,4,6-tri-2-pyridyl-1,3,5-triazine-κ3N2,N1,N6)nickel(II), C23H17Cl2N7Ni
  59. Redetermination of the crystal structure of tetrakis(4-chlorobenzyl)tin(IV), C28H24Cl4Sn
  60. The crystal structure of 2,6-bis(pyridin-1-ium-3-ylmethyl)hexahydro-4,8-ethenopyrrolo-[3,4-f] isoindole-1,3,5,7-tetrone tetrachloridocuprate(II) monohydrate, C24H24Cl4CuN4O5
  61. Crystal structure of cyclo-[octaaqua-tetrakis(μ2-5,5′-(1H-imidazole-4,5-diyl)bis(tetrazol-2-ido)-κ4N,N′,N′′,N′′′)tetramagnesium(II)], C20H24N40O8Mg4
  62. The crystal structure of a matrine derivative, 13-(4-Cl-pyrrole)-matrine, C18H26ClN4O
  63. Crystal structure of (dibenzyl sulphoxide-κO)bis(2-chlorobenzyl-κC1)dichloridotin(IV), C28H26Cl4OSSn
  64. Crystal structure of catena-poly[(μ2-azido-κ2N:N)(μ2-4-cyanobenzoato-κ2O:O′)-(μ2-methanol-κ2O:O)copper(II)], C9H8CuN4O3
  65. Crystal structure of 1,1′-dibenzyl-3,3′-dicyano-1,1′,4,4′-tetrahydro-4,4′-bipyridine, C26H22N4
  66. Crystal structure of (2-bromobenzyl)((1-bromonaphthalen-2-yl)methyl)sulfane, C18H14Br2S
  67. Crystal structure of 2-(4-ammoniocyclohexyl)-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium 2-[(2-carboxylatophenyl)disulfanyl]benzoate dihydrate, [C18H22N4][C14H8O4S2] ⋅ 2H2O
  68. Crystal structure of (E)-N-((3R,5S,10S, 13S,14S,17S)-17-((S)-1-(dimethylamino)ethyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-3-yl)-2-methylbut-2-enamide – water – methanol (1/1/1), C29H54N2O3
  69. Crystal structure of methyl 2-(4-(3-(2,4-difluorophenyl)pyrazolo[1,5-a]pyrimidin-6-yl)phenyl)acetate, C21H15F2N3O2
  70. Crystal structure of poly[triaqua-(μ4-benzene-1,3,5-tricarboxylato-κ5O1,O2:O3:O4:O5)-(μ2-5-(3-pyridyl)tetrazolato-κ2N1:N3)dizinc(II)], C15H13N5O9Zn2
  71. Crystal structure of N-(3-methylphenyl)(propan-2-yloxy)carbothioamide, C11H15NOS
  72. Crystal structure of poly[(μ2-1,3-bis(imidazol-1-ylmethyl)benzene-κ2N:N′)(nitrato-κ1O)cadmium(II)] — water (2/1), C28H32CdN10O7
  73. Crystal structure of 4-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, C8H7N3S
  74. Crystal structure of benzyltrichloridobis(1H-pyrazole-κ2N)tin(IV), C13H15Cl3N4Sn
  75. Crystal structure of chlorido-4-fluorobenzyl-bis(2-methylquinolin-8-olato-κ2N,O)tin(IV), C27H22ClFN2O2Sn
  76. Crystal structure of tetrakis(O,O′-diisopropyldithiophosphato-κ2S,S′)-(μ2-1,2-bis(4-pyridylmethylene)hydrazine-κ2N:N′)zinc(II), C36H66N4O8P4S8Zn2
  77. Crystal structure of tetrabutylammonium 4,4-oxydibenzoate – boric acid – water (1/2/6) C46H98B2N2O17
  78. Redetermination of the crystal structure of catena-poly[[tribenzyltin(IV)]-(μ2-pyridine-4-carboxylato-κ2N:O)], C27H25NO2Sn
  79. The synthysis and crystal structure of cyclohexyl 5-amino-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-((trifluoromethyl)sulfinyl)-1H-pyrazole-3-carboxylate, C18H15N3Cl2F6O3S
  80. The crystal structure of 5,7-bis(2-hydroxyethoxy)-2-phenyl-4H-chromen-4-one, C19H18O6
  81. Synthesis and crystal structure of (±)-Ethyl 5′-(difluoromethyl)-2-oxo-4′,5′-dihydrospiro[indoline-3,3′-pyrazole]-4′-carboxylate, C14H13F2N3O3
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