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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
CCDC reference: 259617
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (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
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
C8H6N4S2·2H2O | F(000) = 536 |
Mr = 258.32 | Dx = 1.444 Mg m−3 |
Monoclinic, P21/n | Melting point = 407–409 K |
Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71069 Å |
a = 11.824 (1) Å | Cell parameters from 3253 reflections |
b = 6.9357 (6) Å | θ = 2.2–27.2° |
c = 14.4896 (12) Å | µ = 0.44 mm−1 |
β = 90.423 (2)° | T = 295 K |
V = 1188.27 (17) Å3 | Block, colourless |
Z = 4 | 0.50 × 0.40 × 0.25 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2693 independent reflections |
Radiation source: sealed tube | 2273 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.019 |
φ and ω scans | θmax = 27.5°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | h = −11→15 |
Tmin = 0.805, Tmax = 0.900 | k = −9→7 |
7142 measured reflections | l = −18→18 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.037 | H 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 reflections | Δρmax = 0.24 e Å−3 |
162 parameters | Δρmin = −0.30 e Å−3 |
0 restraints | Extinction correction: SHELXTL (Bruker, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction 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 | x | y | z | Uiso*/Ueq | |
S1 | 0.81272 (4) | 0.24618 (7) | 0.67802 (3) | 0.0612 (2) | |
S11 | 0.64568 (4) | 0.19049 (8) | 0.67050 (3) | 0.0587 (2) | |
N1 | 0.99098 (11) | 0.0485 (2) | 0.64350 (10) | 0.0543 (5) | |
N3 | 0.82001 (11) | −0.1066 (2) | 0.59711 (9) | 0.0485 (4) | |
N11 | 0.49724 (11) | 0.2193 (2) | 0.54032 (10) | 0.0490 (4) | |
N31 | 0.68397 (11) | 0.3017 (2) | 0.49421 (10) | 0.0524 (5) | |
C2 | 0.87891 (12) | 0.0354 (2) | 0.63365 (9) | 0.0425 (4) | |
C4 | 0.88207 (17) | −0.2573 (3) | 0.56898 (13) | 0.0602 (6) | |
C5 | 0.99750 (18) | −0.2624 (3) | 0.57714 (14) | 0.0692 (7) | |
C6 | 1.04927 (15) | −0.1040 (3) | 0.61428 (14) | 0.0660 (7) | |
C21 | 0.60788 (12) | 0.2452 (2) | 0.55445 (11) | 0.0421 (4) | |
C41 | 0.64392 (16) | 0.3365 (3) | 0.40953 (12) | 0.0602 (6) | |
C51 | 0.53207 (16) | 0.3154 (3) | 0.38644 (13) | 0.0597 (6) | |
C61 | 0.46055 (15) | 0.2549 (2) | 0.45438 (14) | 0.0563 (6) | |
O1W | 0.33143 (17) | 0.1492 (4) | 0.68490 (19) | 0.1120 (9) | |
O2W | 0.14638 (14) | 0.3737 (2) | 0.67776 (11) | 0.0708 (5) | |
H4 | 0.8452 | −0.3626 | 0.5429 | 0.0720* | |
H5 | 1.0389 | −0.3692 | 0.5582 | 0.0830* | |
H6 | 1.1277 | −0.1025 | 0.6193 | 0.0790* | |
H41 | 0.6941 | 0.3766 | 0.3643 | 0.0720* | |
H51 | 0.5058 | 0.3412 | 0.3271 | 0.0720* | |
H61 | 0.3843 | 0.2379 | 0.4404 | 0.0680* | |
H1A | 0.379 (3) | 0.157 (5) | 0.649 (2) | 0.122 (12)* | |
H1B | 0.340 (2) | 0.070 (5) | 0.720 (2) | 0.095 (11)* | |
H2A | 0.201 (3) | 0.298 (5) | 0.679 (2) | 0.121 (12)* | |
H2B | 0.096 (2) | 0.297 (4) | 0.6733 (18) | 0.084 (8)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0557 (3) | 0.0594 (3) | 0.0682 (3) | 0.0125 (2) | −0.0202 (2) | −0.0202 (2) |
S11 | 0.0507 (3) | 0.0795 (3) | 0.0458 (2) | 0.0181 (2) | 0.0019 (2) | 0.0002 (2) |
N1 | 0.0401 (7) | 0.0633 (9) | 0.0593 (8) | 0.0008 (6) | −0.0093 (6) | −0.0011 (7) |
N3 | 0.0465 (7) | 0.0514 (8) | 0.0475 (7) | −0.0017 (6) | −0.0022 (5) | −0.0039 (6) |
N11 | 0.0366 (6) | 0.0477 (7) | 0.0627 (8) | 0.0031 (5) | 0.0011 (6) | −0.0021 (6) |
N31 | 0.0409 (7) | 0.0620 (9) | 0.0542 (8) | 0.0007 (6) | 0.0017 (6) | 0.0023 (6) |
C2 | 0.0410 (7) | 0.0489 (8) | 0.0375 (7) | 0.0032 (6) | −0.0051 (5) | 0.0019 (6) |
C4 | 0.0670 (11) | 0.0541 (10) | 0.0594 (10) | 0.0025 (8) | −0.0027 (9) | −0.0086 (8) |
C5 | 0.0682 (12) | 0.0686 (13) | 0.0709 (13) | 0.0239 (10) | −0.0015 (10) | −0.0115 (9) |
C6 | 0.0435 (9) | 0.0853 (14) | 0.0692 (11) | 0.0143 (9) | −0.0047 (8) | −0.0014 (10) |
C21 | 0.0375 (7) | 0.0404 (8) | 0.0483 (8) | 0.0072 (6) | −0.0004 (6) | −0.0049 (6) |
C41 | 0.0629 (11) | 0.0655 (12) | 0.0524 (9) | 0.0028 (9) | 0.0045 (8) | 0.0076 (8) |
C51 | 0.0662 (11) | 0.0595 (11) | 0.0533 (9) | 0.0115 (9) | −0.0129 (8) | −0.0022 (8) |
C61 | 0.0449 (9) | 0.0497 (9) | 0.0741 (12) | 0.0060 (7) | −0.0158 (8) | −0.0103 (8) |
O1W | 0.0760 (12) | 0.1295 (18) | 0.1311 (18) | 0.0449 (12) | 0.0462 (12) | 0.0562 (15) |
O2W | 0.0548 (8) | 0.0633 (9) | 0.0945 (11) | −0.0031 (7) | 0.0040 (7) | −0.0002 (7) |
Geometric parameters (Å, º) top
S1—S11 | 2.0147 (7) | N31—C41 | 1.334 (2) |
S1—C2 | 1.7806 (15) | N31—C21 | 1.318 (2) |
S11—C21 | 1.7777 (16) | C4—C5 | 1.370 (3) |
O1W—H1A | 0.77 (3) | C5—C6 | 1.366 (3) |
O1W—H1B | 0.76 (3) | C41—C51 | 1.370 (3) |
O2W—H2A | 0.83 (4) | C51—C61 | 1.368 (3) |
O2W—H2B | 0.80 (3) | C4—H4 | 0.9294 |
N1—C6 | 1.333 (2) | C5—H5 | 0.9304 |
N1—C2 | 1.3349 (19) | C6—H6 | 0.9298 |
N3—C2 | 1.3153 (19) | C41—H41 | 0.9299 |
N3—C4 | 1.342 (2) | C51—H51 | 0.9294 |
N11—C61 | 1.339 (2) | C61—H61 | 0.9301 |
N11—C21 | 1.3348 (19) | | |
| | | |
S11—S1—C2 | 104.86 (5) | S11—C21—N31 | 121.46 (11) |
S1—S11—C21 | 104.46 (5) | N31—C41—C51 | 122.75 (17) |
H1A—O1W—H1B | 114 (3) | C41—C51—C61 | 117.24 (17) |
H2A—O2W—H2B | 99 (3) | N11—C61—C51 | 121.87 (16) |
C2—N1—C6 | 115.29 (14) | C5—C4—H4 | 118.62 |
C2—N3—C4 | 114.60 (14) | N3—C4—H4 | 118.65 |
C21—N11—C61 | 115.37 (14) | C4—C5—H5 | 121.42 |
C21—N31—C41 | 115.06 (14) | C6—C5—H5 | 121.41 |
S1—C2—N3 | 121.82 (11) | N1—C6—H6 | 118.95 |
S1—C2—N1 | 110.13 (11) | C5—C6—H6 | 118.92 |
N1—C2—N3 | 128.05 (14) | C51—C41—H41 | 118.67 |
N3—C4—C5 | 122.73 (18) | N31—C41—H41 | 118.58 |
C4—C5—C6 | 117.17 (19) | C41—C51—H51 | 121.39 |
N1—C6—C5 | 122.13 (17) | C61—C51—H51 | 121.36 |
N11—C21—N31 | 127.71 (15) | C51—C61—H61 | 119.04 |
S11—C21—N11 | 110.83 (11) | N11—C61—H61 | 119.09 |
| | | |
C2—S1—S11—C21 | −82.50 (7) | C61—N11—C21—N31 | 0.2 (2) |
S11—S1—C2—N1 | −174.06 (9) | C61—N11—C21—S11 | −179.30 (11) |
S11—S1—C2—N3 | 6.17 (13) | C21—N11—C61—C51 | −0.6 (2) |
S1—S11—C21—N11 | −178.32 (10) | C41—N31—C21—N11 | 0.1 (2) |
S1—S11—C21—N31 | 2.12 (13) | C41—N31—C21—S11 | 179.54 (13) |
C6—N1—C2—S1 | 178.61 (13) | C21—N31—C41—C51 | 0.0 (3) |
C2—N1—C6—C5 | −0.2 (3) | N3—C4—C5—C6 | −1.1 (3) |
C6—N1—C2—N3 | −1.6 (2) | C4—C5—C6—N1 | 1.4 (3) |
C4—N3—C2—N1 | 1.9 (2) | N31—C41—C51—C61 | −0.4 (3) |
C4—N3—C2—S1 | −178.38 (12) | C41—C51—C61—N11 | 0.7 (3) |
C2—N3—C4—C5 | −0.4 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1W—H1A···N11 | 0.77 (3) | 2.16 (3) | 2.921 (3) | 171 (3) |
O1W—H1B···O2Wi | 0.76 (3) | 2.02 (3) | 2.770 (3) | 174 (3) |
O2W—H2A···O1W | 0.83 (4) | 1.86 (4) | 2.687 (3) | 175 (3) |
O2W—H2B···N1ii | 0.80 (3) | 2.17 (3) | 2.949 (2) | 166 (3) |
Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) x−1, y, z. |
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