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The crystal structure of bis(2-pyrimidinyl) di­sulfide dihydrate, C8H6N4S2·2H2O, has been redetermined using CCD diffractometer data. This has allowed for a more precise location of the water H atoms and shows the water mol­ecules forming unusual spiral hydrogen-bonded aqua columns, as well as giving inter-column crosslinks through the pyrimidine N-atom acceptors of the di­sulfide mol­ecules. The structural chemistry of aromatic di­sulfides has also been reviewed.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804029782/tk6197sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536804029782/tk6197Isup2.hkl
Contains datablock I

CCDC reference: 259617

Key indicators

  • Single-crystal X-ray study
  • T = 295 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.037
  • wR factor = 0.103
  • Data-to-parameter ratio = 16.6

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ?
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART; data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXTL (Bruker, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: PLATON (Spek, 1999); software used to prepare material for publication: PLATON.

Bis(2-pyrimidinyl) disulfide dihydrate top
Crystal data top
C8H6N4S2·2H2OF(000) = 536
Mr = 258.32Dx = 1.444 Mg m3
Monoclinic, P21/nMelting point = 407–409 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71069 Å
a = 11.824 (1) ÅCell parameters from 3253 reflections
b = 6.9357 (6) Åθ = 2.2–27.2°
c = 14.4896 (12) ŵ = 0.44 mm1
β = 90.423 (2)°T = 295 K
V = 1188.27 (17) Å3Block, colourless
Z = 40.50 × 0.40 × 0.25 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer
2693 independent reflections
Radiation source: sealed tube2273 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
φ and ω scansθmax = 27.5°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Bruker, 1999)
h = 1115
Tmin = 0.805, Tmax = 0.900k = 97
7142 measured reflectionsl = 1818
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.103 w = 1/[σ2(Fo2) + (0.1574P)2 + 0.2085P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
2693 reflectionsΔρmax = 0.24 e Å3
162 parametersΔρmin = 0.30 e Å3
0 restraintsExtinction correction: SHELXTL (Bruker, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0103 (19)
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.81272 (4)0.24618 (7)0.67802 (3)0.0612 (2)
S110.64568 (4)0.19049 (8)0.67050 (3)0.0587 (2)
N10.99098 (11)0.0485 (2)0.64350 (10)0.0543 (5)
N30.82001 (11)0.1066 (2)0.59711 (9)0.0485 (4)
N110.49724 (11)0.2193 (2)0.54032 (10)0.0490 (4)
N310.68397 (11)0.3017 (2)0.49421 (10)0.0524 (5)
C20.87891 (12)0.0354 (2)0.63365 (9)0.0425 (4)
C40.88207 (17)0.2573 (3)0.56898 (13)0.0602 (6)
C50.99750 (18)0.2624 (3)0.57714 (14)0.0692 (7)
C61.04927 (15)0.1040 (3)0.61428 (14)0.0660 (7)
C210.60788 (12)0.2452 (2)0.55445 (11)0.0421 (4)
C410.64392 (16)0.3365 (3)0.40953 (12)0.0602 (6)
C510.53207 (16)0.3154 (3)0.38644 (13)0.0597 (6)
C610.46055 (15)0.2549 (2)0.45438 (14)0.0563 (6)
O1W0.33143 (17)0.1492 (4)0.68490 (19)0.1120 (9)
O2W0.14638 (14)0.3737 (2)0.67776 (11)0.0708 (5)
H40.84520.36260.54290.0720*
H51.03890.36920.55820.0830*
H61.12770.10250.61930.0790*
H410.69410.37660.36430.0720*
H510.50580.34120.32710.0720*
H610.38430.23790.44040.0680*
H1A0.379 (3)0.157 (5)0.649 (2)0.122 (12)*
H1B0.340 (2)0.070 (5)0.720 (2)0.095 (11)*
H2A0.201 (3)0.298 (5)0.679 (2)0.121 (12)*
H2B0.096 (2)0.297 (4)0.6733 (18)0.084 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0557 (3)0.0594 (3)0.0682 (3)0.0125 (2)0.0202 (2)0.0202 (2)
S110.0507 (3)0.0795 (3)0.0458 (2)0.0181 (2)0.0019 (2)0.0002 (2)
N10.0401 (7)0.0633 (9)0.0593 (8)0.0008 (6)0.0093 (6)0.0011 (7)
N30.0465 (7)0.0514 (8)0.0475 (7)0.0017 (6)0.0022 (5)0.0039 (6)
N110.0366 (6)0.0477 (7)0.0627 (8)0.0031 (5)0.0011 (6)0.0021 (6)
N310.0409 (7)0.0620 (9)0.0542 (8)0.0007 (6)0.0017 (6)0.0023 (6)
C20.0410 (7)0.0489 (8)0.0375 (7)0.0032 (6)0.0051 (5)0.0019 (6)
C40.0670 (11)0.0541 (10)0.0594 (10)0.0025 (8)0.0027 (9)0.0086 (8)
C50.0682 (12)0.0686 (13)0.0709 (13)0.0239 (10)0.0015 (10)0.0115 (9)
C60.0435 (9)0.0853 (14)0.0692 (11)0.0143 (9)0.0047 (8)0.0014 (10)
C210.0375 (7)0.0404 (8)0.0483 (8)0.0072 (6)0.0004 (6)0.0049 (6)
C410.0629 (11)0.0655 (12)0.0524 (9)0.0028 (9)0.0045 (8)0.0076 (8)
C510.0662 (11)0.0595 (11)0.0533 (9)0.0115 (9)0.0129 (8)0.0022 (8)
C610.0449 (9)0.0497 (9)0.0741 (12)0.0060 (7)0.0158 (8)0.0103 (8)
O1W0.0760 (12)0.1295 (18)0.1311 (18)0.0449 (12)0.0462 (12)0.0562 (15)
O2W0.0548 (8)0.0633 (9)0.0945 (11)0.0031 (7)0.0040 (7)0.0002 (7)
Geometric parameters (Å, º) top
S1—S112.0147 (7)N31—C411.334 (2)
S1—C21.7806 (15)N31—C211.318 (2)
S11—C211.7777 (16)C4—C51.370 (3)
O1W—H1A0.77 (3)C5—C61.366 (3)
O1W—H1B0.76 (3)C41—C511.370 (3)
O2W—H2A0.83 (4)C51—C611.368 (3)
O2W—H2B0.80 (3)C4—H40.9294
N1—C61.333 (2)C5—H50.9304
N1—C21.3349 (19)C6—H60.9298
N3—C21.3153 (19)C41—H410.9299
N3—C41.342 (2)C51—H510.9294
N11—C611.339 (2)C61—H610.9301
N11—C211.3348 (19)
S11—S1—C2104.86 (5)S11—C21—N31121.46 (11)
S1—S11—C21104.46 (5)N31—C41—C51122.75 (17)
H1A—O1W—H1B114 (3)C41—C51—C61117.24 (17)
H2A—O2W—H2B99 (3)N11—C61—C51121.87 (16)
C2—N1—C6115.29 (14)C5—C4—H4118.62
C2—N3—C4114.60 (14)N3—C4—H4118.65
C21—N11—C61115.37 (14)C4—C5—H5121.42
C21—N31—C41115.06 (14)C6—C5—H5121.41
S1—C2—N3121.82 (11)N1—C6—H6118.95
S1—C2—N1110.13 (11)C5—C6—H6118.92
N1—C2—N3128.05 (14)C51—C41—H41118.67
N3—C4—C5122.73 (18)N31—C41—H41118.58
C4—C5—C6117.17 (19)C41—C51—H51121.39
N1—C6—C5122.13 (17)C61—C51—H51121.36
N11—C21—N31127.71 (15)C51—C61—H61119.04
S11—C21—N11110.83 (11)N11—C61—H61119.09
C2—S1—S11—C2182.50 (7)C61—N11—C21—N310.2 (2)
S11—S1—C2—N1174.06 (9)C61—N11—C21—S11179.30 (11)
S11—S1—C2—N36.17 (13)C21—N11—C61—C510.6 (2)
S1—S11—C21—N11178.32 (10)C41—N31—C21—N110.1 (2)
S1—S11—C21—N312.12 (13)C41—N31—C21—S11179.54 (13)
C6—N1—C2—S1178.61 (13)C21—N31—C41—C510.0 (3)
C2—N1—C6—C50.2 (3)N3—C4—C5—C61.1 (3)
C6—N1—C2—N31.6 (2)C4—C5—C6—N11.4 (3)
C4—N3—C2—N11.9 (2)N31—C41—C51—C610.4 (3)
C4—N3—C2—S1178.38 (12)C41—C51—C61—N110.7 (3)
C2—N3—C4—C50.4 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1A···N110.77 (3)2.16 (3)2.921 (3)171 (3)
O1W—H1B···O2Wi0.76 (3)2.02 (3)2.770 (3)174 (3)
O2W—H2A···O1W0.83 (4)1.86 (4)2.687 (3)175 (3)
O2W—H2B···N1ii0.80 (3)2.17 (3)2.949 (2)166 (3)
Symmetry codes: (i) x+1/2, y1/2, z+3/2; (ii) x1, y, z.
 

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