Bis(2 pyrimidinyl) di­sulfide dihydrate: a redetermination

organic papers

o2438

Structure Reports

Online ISSN 1600-5368

Bis(2-pyrimidinyl) disulfide dihydrate:

a redetermination

Gayleen B. Jensen,a_Graham

Smith,a_{* Dalius S. Sagatys,}a

Peter C. Healyb_{and Jonathan M.}

Whitec

a_{School of Physical and Chemical Sciences,} Queensland University of Technology, GPO Box 2434, Brisbane 4001, Australia, b_{School of Science, Griffith University, Nathan} 4111, Australia, andc_{School of Chemistry,} University of Melbourne, Parkville 3052, Australia

Correspondence e-mail: [email protected]

Key indicators Single-crystal X-ray study

T= 295 K

Mean(C±C) = 0.003 AÊ

Rfactor = 0.037

wRfactor = 0.103

Data-to-parameter ratio = 16.6

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2004 International Union of Crystallography Printed in Great Britain ± all rights reserved

The crystal structure of bis(2-pyrimidinyl) disul®de dihydrate, C8H6N4S22H2O, has been redetermined using CCD diffract-ometer 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 disul®de molecules. The structural chemistry of aromatic disul®des has also been reviewed.

Comment

Aromatic disul®des of the type ArÐSÐSÐAr have been known for some considerable time, the bis(2-chlorophenyl) analogue having been reported as being easily obtained from the oxidation of 2-chlorothiophenol (Friedlander & Mauthner, 1904). This facile conversion of thiols to disul®des, which may be achieved with mild oxidizing agents such as iodine, is accelerated by the presence of bases and probably proceedsviathioxy free radicals (Roberts & Caserio, 1965).

Organic disul®des are of commercial importance for their anti-wear properties as additives in lubricating oils (Allum & Ford, 1965; Allum & Forbes, 1967; Meyer, 1977), and are also important in biological function, being present in molecules such as cystine, ribonuclease and insulin. The structures of l-cystine (Oughton & Harrison, 1959), l-cystine hydro-chloride (Steinrauf et al., 1958) and l-cystine hydrobromide (Peterson et al., 1960) have been determined, as has that of insulin, where the two peptide chains are held together by disul®de bridges (Adamset al., 1969). The crystal structures of many disul®des have also been reported, with Ar = phenyl (Lee & Bryant, 1969a; Sacerdotiet al., 1975), 2-aminophenyl (Gomes de Mesquita, 1967; Lee & Bryant, 1970), 2-nitro-phenyl (Ricci & Bernal, 1970), 2-chloro2-nitro-phenyl (Mak et al., 1989), 3-carboxy-4-nitrophenyl (from Ellman reagent; Shefter & Kalman, 1969), 4-tolyl (Vorontsovaet al., 1967), 4-chloro-phenyl (Spirletet al., 1979), 4-bromophenyl (Toussaint, 1945), benzyl (Lee & Bryant, 1969b), cinnamyl (Lee & Bryant, 1971) and 2-chlorophenylaminomethyl (Pierrotet al., 1984).

There are fewer structures of the analogous aromatic diselenides and ditellurides. For ArÐSeÐSeÐAr, structures have been published with Ar = phenyl (Marsh, 1952) and 4-chlorophenyl (Llabres et al., 1972), and for ArÐTeÐTeÐ Ar, structures have been published with Ar = phenyl (Kruseet al., 1957) and 4-chlorophenyl (Llabreset al., 1972). Structures of the heteroaromatic disul®des are also less common, with those of bis(4-uridinyl) disul®de (Shefter & Kalman, 1968), bis(2-methyl-4-uridinyl) disul®de (Shefter, 1970), the disul®de from 5-[1-(20_{-deoxy--d-ribofuranosidyl)uracil (Shefteret al.,} 1968) and the title compound, bis(2-pyrimidinyl) disul®de

dihydrate, (I) (Furberg & Solbakk, 1973), having been previously reported. In (I), although the water molecules appear to be quite strongly associated, they exhibit signi®cant lability, resulting in almost total crystal deterioration (92%) in the X-ray beam, commencing rapidly afterca 18 h of room-temperature exposure in air using a conventional four-circle diffractometer. This seemingly time-related X-ray-enhanced property prompted recollection of data using a diffractometer with a CCD area-detector, and the results are presented here.

The present structure of (I) (Fig. 1, Table 1) is unusual among the aromatic disul®des because of the presence of solvent water molecules in the crystal structure. This is largely the result of the presence of the four N heteroatom acceptors in the two pyrimidinyl residues of the disul®de, which require additional H-donor molecules to balance the donor±acceptor ratio for hydrogen-bonding interactions. The absorption-corrected CCD diffraction data used for the structure rede-termination reported here, together with the use of the more orthogonal cell setting compared with the original analysis, allow a more precise picture of the hydrogen bonding in (I) and the role of water in the crystal structure.

The two water molecules and their n-glide-related neigh-bours participate in unusual hydrogen-bonded column struc-tures which spiral down the b axial direction [O1WÐ H1B O2Wi _{2.770 (3) and O2WÐH2A O1W 2.687 (3) AÊ;} symmetry code: (i)1

2ÿx,yÿ12,32ÿz] (Fig. 2). The second H atom of each of these water molecules acts as a donor to one N-acceptor atom of each of the pyrimidinyl residues (atoms N1 and N11) of separate disul®de molecules, linking the columns [O1WÐH1A N11 2.921 (3) and O2WÐH2B N1ii 2.949 (2) AÊ; symmetry code: (ii) xÿ1, y, z]. The other N heteroatoms (N3 and N31) are unassociated. The result is a hydrogen-bonded network polymer structure.

The disul®de molecules, which adopt an eclipsed confor-mation with the pyrimidyl residuescis-related [torsion angles

C2ÐS1ÐS11ÐC21 ÿ82.50 (7), S1ÐS11ÐC21ÐN11

ÿ178.3 (1) and S11ÐS1ÐC2ÐN1 ÿ174.1 (1)_{], are} essen-tially unchanged compared with the original determination. This conformation is more common among the disul®des, but examples with the extended trans-related ring systems are known,e.g.dibenzyl disul®de (Lee & Bryant, 1969b).

Experimental

Compound (I) was formed as the sole product from the attempted synthesis of a bismuth complex of 2-pyrimidinethiol (2-mercapto-pyrimidine), by adding 2-pyrimidinethiol (3.0 g) to a stirred solution

of freshly prepared bismuth(III) hydroxide (1.2 g) in 28% w/v

ammonia solution (100 ml). Partial room temperature evaporation of the ®ltered solution gave colourless prisms of (I) (m.p. 407±409 K). IR spectroscopic data (KBr pressed disc,, cmÿ1_{): 3400 (m,br), 1553}

(s), 1427 (m), 1376 (s), 1196 (m), 1165 (s), 800 (m), 767 (m), 741 (m), 626 (m), 448 (m); CHN elemental analysis indicated a bis-pyrimidine-substituted disul®de dihydrate. The previously reported synthesis of (I) (Furberg & Solbakk, 1973) involved heating 2-pyrimidinethiol in aqueous ammonia solution.

Crystal data

C8H6N4S22H2O

Mr= 258.32

Monoclinic, P21=n

a= 11.824 (1) AÊ

b= 6.9357 (6) AÊ

c= 14.4896 (12) AÊ = 90.423 (2) V= 1188.27 (17) AÊ3

Z= 4

Dx= 1.444 Mg mÿ3

MoKradiation Cell parameters from 3253

re¯ections = 2.2±27.2

= 0.44 mmÿ1

T= 295 (2) K Block, colourless 0.500.400.25 mm

organic papers

Acta Cryst.(2004). E60, o2438±o2440 Gayleen B. Jensenet al. C8H6N4S22H2O

o2439

Figure 1

The structure of (I), showing the atom-numbering scheme for the disul®de and water molecules. This follows the scheme employed by Furberg & Solbakk (1973). Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Figure 2

The chain structure of (I) viewed downb, showing then-glide-related

Data collection

Bruker SMART CCD area-detector diffractometer

'and!scans

Absorption correction: multi-scan (SADABS; Bruker, 1999)

Tmin= 0.805,Tmax= 0.900

7142 measured re¯ections

2693 independent re¯ections 2273 re¯ections withI> 2(I)

Rint= 0.019 max= 27.5

h=ÿ11!15

k=ÿ9!7

l=ÿ18!18

Refinement

Re®nement onF2

R[F2_{> 2(F}2_{)] = 0.037}

wR(F2_{) = 0.103}

S= 1.03 2693 re¯ections 162 parameters

H atoms treated by a mixture of independent and constrained re®nement

w= 1/[2_(F

o2) + (0.1574P)2

+ 0.2085P]

whereP= (Fo2+ 2Fc2)/3

(/)max= 0.001

max= 0.24 e AÊÿ3

min=ÿ0.30 e AÊÿ3

Extinction correction:SHELXTL

(Bruker, 1997)

Extinction coef®cient: 0.0103 (19)

Table 1

Hydrogen-bonding geometry (AÊ,_).

DÐH A DÐH H A D A DÐH A

O1WÐH1A N11 0.77 (3) 2.16 (3) 2.921 (3) 171 (3) O1WÐH1B O2Wi _{0.76 (3) 2.02 (3) 2.770 (3) 174 (3)}

O2WÐH2A O1W 0.83 (4) 1.86 (4) 2.687 (3) 175 (3) O2WÐH2B N1ii _{0.80 (3) 2.17 (3) 2.949 (2) 166 (3)}

Symmetry codes: (i)1

2ÿx;yÿ12;32ÿz; (ii)xÿ1;y;z.

The H atoms of the water molecules were located by difference methods and their positional and isotropic displacement parameters were re®ned. Other H atoms were included in the re®nement at calculated positions, with CÐH = 0.93 AÊ, and were treated as riding atoms, withUiso(H) = 1.2Ueq(C).

Data collection:SMART(Bruker, 2000); cell re®nement:SAINT

(Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 1997); program(s) used to re®ne structure: SHELXTL; molecular graphics:PLATON(Spek, 2003); software used to prepare material for publication:PLATON.

The authors acknowledge ®nancial support from the School of Physical and Chemical Sciences, Queensland University of

Technology, the School of Science, Grif®th University, and the School of Chemistry, University of Melbourne.

References

Adams, M. J., Blundell, T. L., Dodson, E. J., Dodson, G. G., Vijayan, M., Baker, E. N., Harding, M. M., Hodgkin, D. C., Rimmer, B. & Sheat, S. (1969).

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B. P. (1984).Acta Cryst.C40, 1931±1934.

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Sacerdoti, M., Gilli, G. & Domiano, P. (1975).Acta Cryst.B31, 327±329. Shefter, E. (1970).J. Chem. Soc. B, pp. 703±706.

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Shefter, E. & Kalman, T. I. (1969).J. Chem. Soc. D, pp. 1027±1029. Shefter, E., Kotick, M. P. & Bardos, T. J. (1968).J. Pharm. Sci.56, 1293±1299. Spek, A. L. (2003).J. Appl. Cryst.36, 7±13.

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organic papers

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sup-1 Acta Cryst. (2004). E60, o2438–o2440

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Acta Cryst. (2004). E60, o2438–o2440 [https://doi.org/10.1107/S1600536804029782]

Bis(2-pyrimidinyl) disulfide dihydrate: a redetermination

Gayleen B. Jensen, Graham Smith, Dalius S. Sagatys, Peter C. Healy and Jonathan M. White

Bis(2-pyrimidinyl) disulfide dihydrate

Crystal data

C8H6N4S2·2H2O Mr = 258.32 Monoclinic, P21/n

Hall symbol: -P 2yn a = 11.824 (1) Å b = 6.9357 (6) Å c = 14.4896 (12) Å β = 90.423 (2)° V = 1188.27 (17) Å3 Z = 4

F(000) = 536 Dx = 1.444 Mg m−3

Melting point = 407–409 K Mo Kα radiation, λ = 0.71069 Å Cell parameters from 3253 reflections θ = 2.2–27.2°

µ = 0.44 mm−1 T = 295 K Block, colourless 0.50 × 0.40 × 0.25 mm

Data collection

Bruker SMART CCD area-detector diffractometer

Radiation source: sealed tube Graphite monochromator φ and ω scans

Absorption correction: multi-scan (SADABS; Bruker, 1999) Tmin = 0.805, Tmax = 0.900

7142 measured reflections 2693 independent reflections 2273 reflections with I > 2σ(I) Rint = 0.019

θmax = 27.5°, θmin = 2.2° h = −11→15

k = −9→7 l = −18→18

Refinement

Refinement on F2

Least-squares matrix: full R[F2 _{> 2σ(F}2_{)] = 0.037} wR(F2_{) = 0.103} S = 1.03 2693 reflections 162 parameters 0 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H atoms treated by a mixture of independent and constrained refinement

w = 1/[σ2_(F

o2) + (0.1574P)2 + 0.2085P]

where P = (Fo2 + 2Fc2)/3

(Δ/σ)max = 0.001

Δρmax = 0.24 e Å−3

Δρmin = −0.30 e Å−3

Extinction correction: SHELXTL (Bruker, 1997), Fc*_{=kFc[1+0.001xFc}2_λ3_/sin(2θ)]-1/4

Extinction coefficient: 0.0103 (19)

Special details

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sup-2 Acta Cryst. (2004). E60, o2438–o2440

Refinement. Refinement of F2 _{against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F}2_,

conventional R-factors R are based on F, with F set to zero for negative F2_{. The threshold expression of F}2 _{> σ(F}2_{) 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₎

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₎

U11 _U22 _U33 _U12 _U13 _U23

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sup-3 Acta Cryst. (2004). E60, o2438–o2440

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)

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)

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sup-4 Acta Cryst. (2004). E60, o2438–o2440

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)

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)}