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Thione vs. ketone: The influence of the chalcogenide on weak intermolecularinteractions in crystal packing of 4,5-bis(bromomethyl)-1,3-dithiole-2-thioneand 4,5-bis(bromomethyl)-1,3-dithiol-2-one

Vladimir A. Azov a,⇑, Matthias Zeller b, Michèle-Laure Lieunang Watat a, Ying Xin a

a University of Bremen, Department of Chemistry, Leobener Strasse NW 2C, D-28359 Bremen, Germanyb Youngstown State University, One University Plaza, Youngstown, OH 44555-3663, USA

a r t i c l e i n f o

Article history:Received 1 June 2011Received in revised form 11 August 2011Accepted 12 August 2011Available online 23 August 2011

Keywords:CrystallographyNon-covalent interactionsWeak hydrogen bondsHalogen–halogen contactsHirshfeld surfacesFingerprint plots

a b s t r a c t

Crystal structures of 4,5-bis(bromomethyl)-1,3-dithiole-2-thione (1) and 4,5-bis(bromomethyl)-1,3-dithiol-2-one (2) were determined and analyzed. Both compounds pack in the same C2/c space groupand adopt very similar molecular geometries. Patterns of intermolecular contacts, analyzed with the helpof Hirshfeld surfaces and fingerprint plots, on the other hand, are remarkably different. The dominantinteractions in the packing of 1 are short Br� � �Br contacts and non-classical CAH� � �Br hydrogen bonds.For 2, the packing is governed by short CAH� � �O@C hydrogen bonds, and longer CAH� � �Br and S� � �Br con-tacts play only a secondary role.

� 2011 Elsevier B.V. All rights reserved.

1. Introduction

The study of noncovalent interactions plays an increasinglyimportant role in modern chemical research [1]. They are consid-ered nowadays keystones in supramolecular chemistry, materialsscience, and even biochemistry. The importance of such interac-tions, which include weak hydrogen bonds [2], halogen bonds[3], and various types of interactions involving p-systems [4], inshaping the formation of crystal lattices of organic compounds isnow fully recognized, which makes deeper investigations into thenature of these weak H-bonds and halogen interactions in crystal-line materials an area of current interest.

Herein we analyze the molecular structures and crystal packingof two five-membered heterocyclic derivatives, 4,5-bis(bromo-methyl)-1,3-dithiole-2-thione (1) and 4,5-bis(bromomethyl)-1,3-dithiol-2-one (2). Both compounds were used as intermediatesfor the preparation of various pyrrolo-tetrathiafulvalene deriva-tives [5–7]. Packing motifs for the two reported compounds showan interesting interplay of CAH� � �O@C and CAH� � �Br non-classicalhydrogen bonds and Br� � �Br and Br� � �S soft–soft close contacts. De-spite the similarity of molecular architectures, packing motifs for 1and 2 are strikingly different. Hirshfeld surface analysis [8] is used

to decipher the intermolecular interactions in the crystal packingof 1 and 2.

2. Experimental

2.1. Synthesis and crystallization

4,5-Bis(bromomethyl)-1,3-dithiole-2-thione 1 was prepared bybromination of the corresponding diol, 4,5-bis(hydroxymethyl)-1,3-dithiole-2-thione, using phosphorous tribromide, as describedbefore [5]. Large X-ray quality yellow transparent crystals weregrown by slow evaporation of a chloroform/heptane solution.Mp: 128–128.5 �C; 1H NMR (200 MHz, CDCl3): d = 4.33 (s, 4H);13C NMR (50 MHz, CDCl3): d = 20.3, 139.4, 208.3.

4,5-Bis(bromomethyl)-1,3-dithiol-2-one 2 was prepared by rad-ical bromination of 4,5-dimethyl-1,3-dithiol-2-one with N-bromosuccinimide (NBS) as described elsewhere [6]. Large X-ray qualitycolorless transparent crystals were grown by slow evaporation ofa chloroform solution in an NMR tube. Mp: 153–154 �C; 1H NMR(200 MHz, CDCl3): d = 4.38 (s, 4H); 13C NMR (50 MHz, CDCl3):d = 21.5, 130.0, 187.4.

2.2. X-ray data collection and refinement

X-ray diffraction measurements were performed on a BrukerAXS SMART APEX CCD diffractometer with graphite monochroma-

0022-2860/$ - see front matter � 2011 Elsevier B.V. All rights reserved.doi:10.1016/j.molstruc.2011.08.026

⇑ Corresponding author. Tel.: +49 421 218 63126; fax: +49 421 218 63120.E-mail address: vazov@uni-bremen.de (V.A. Azov).

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tized Mo Ka radiation at 100 K using APEX2 software [9] for datacollection. Cell refinement, data reduction and absorption correc-tion employing the multi-scan method were performed usingSAINT [9]. The structure was solved by direct methods with thehelp of SIR92 [10], refinements were carried out by full-matrixleast-square techniques using CRYSTALS [11]. All non hydrogenatoms were refined anisotropically. The H atoms were located froma difference map and initially refined with soft restraints on thebond lengths and angles to regularize their geometry (CAH inthe range 0.93–0.98 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq

of the parent atom), after which the positions were refined withriding constraints [12]. Crystal data together with collection andrefinement details for compounds 1 and 2 are presented in Table 1.

ORTEP diagrams were drawn using Ortep-3 for Windows [13].Crystal structures were analyzed using the PLATON package [14].Packing diagrams were prepared with the help of Mercury v. 2.2[15].

2.3. Hirshfeld surface analysis

Molecular Hirshfeld surfaces in crystal structures are based onthe electron distribution calculated as the sum of spherical atomelectron densities of a molecule [16]. The Hirshfeld surface enclos-ing a molecule is defined by points where the contribution to theelectron density from the molecule of interest is equal to the con-tribution from all the other molecules. For each point on such anisosurface two distances are defined: de, the distance from thepoint to the nearest nucleus external to the surface, and di, the dis-tance to the nearest nucleus internal to the surface. The distancesde and di provide a three-dimensional picture of close intermolec-ular contacts in a crystal structure [8]. The normalized contact dis-tance, dnorm, is a symmetric function based on both de and di, andthe van der Waals (vdW) radii of atoms internal or external tothe surface:

dnorm ¼ ðdi � rvdWi Þ=rvdW

i þ ðde � rvdWe Þ=rvdW

e

The value of dnorm is negative/positive when intermolecular con-tacts are shorter/longer than vdW separations, enabling identifica-

tion of the regions of particular interest in relation tointermolecular interactions [8b,c]. Graphical plots of the molecularHirshfeld surfaces mapped with dnorm use the red–white–blue colorscheme with red highlighting the shorter intermolecular contacts,white showing the contacts around the vdW separation, and bluebeing used to indicate the longer contact distances.

The combination of di and de in the form of a 2D fingerprint plotaffords a concise summary of intermolecular contacts in the crystal[17]. Such plots are generated by binning of (di, de) pairs in inter-vals of 0.01 Å and coloring each bin (a single pixel on the plot) ofthe resulting 2D histogram as a function of the fraction of surfacepoints in that bin. Color ranges from blue (few points) throughgreen to red (many points). Resolved fingerprint plots are used toidentify particular close contacts in the crystal structure, such asH-bonds or halogen–halogen interactions.

Hirshfeld surfaces became a useful tool for the analysis of inter-molecular interactions in crystals and were employed in studies ofphenomena such as polymorphism [18], inclusion complexes [19],pressure-induced effects [18a,20], and others. The Hirshfeld sur-faces and fingerprint plots presented in this paper were preparedusing the program Crystal Explorer 2.1 [21].

3. Results and discussion

3.1. Molecular structures

Both compounds 1 and 2 crystallize in monoclinic system inC2/c space group with crystallographically imposed twofold sym-metry. For that reason, the common IUPAC numbering schemecould not be applied. The molecular structures with atom number-ing schemes are shown in Fig. 1 and selected geometrical parame-ters are summarized in Table 2. Bond lengths and distances may beconsidered normal. The molecular frameworks excluding Br6 areessentially planar, with maximum and r.m.s. deviations of fittedatoms from the least-squares plane of 0.009(1) (S3) and 0.002 Å,for 1, and of 0.025(2) (C5) and 0.002 Å for 2, respectively. The bro-mine atoms are directed to the opposite sides of the ring systems,with S3AC4AC5ABr6 torsion angles of 64.63(18)� for 1 and

Table 1Crystal data, collection and refinement details for compounds 1 and 2.

1 2

Formula C5H4Br2S3 C5H4Br2OS2

Mr 320.09 304.03Crystal system, space group Monoclinic, C2/c Monoclinic, C2/ca (Å), b (Å), c (Å) 7.510(2), 16.984(5), 7.532(2) 14.910(5), 7.894(3), 7.414(3)b (�) 111.234(4) 104.974(4)V (Å3) 895.5(4) 843.0(5)Z 4 4Dcalc (g cm�3) 2.374 2.395l (mm�1) 9.673 10.039F(000) 608 576Crystal color, habit Yellow, block Colorless, blockCrystal size (mm) 0.40 � 0.45 � 0.55 0.39 � 0.47 � 0.52Temperature (K) 100 100Radiation type, wavelength (Å) Mo Ka, 0.71073 Mo Ka, 0.71073H range (�) 2.4–30.9 2.8–30.9Index range �10 6 h 6 10 �21 6 h 6 21

�24 6 k 6 24 �11 6 k 6 11�10 6 l 6 10 �10 6 l 6 10

Absorption correction Multi-scan, Bruker APEX2 [9]Tmin, Tmax 0.376, 0.746 0.411, 0746Reflections collected/unique/observed [I > 2.0r(I)] 4390/1338 4028/1257Rint 0.024 0.035Data/restraints/parameters 1338/0/48 1257/0/48R[F2 > 2r(F2)] 0.0210 0.0225wR(F2) 0.0527 0.0566Goodness-of-fit, S 1.03 1.04Dqmax, Dqmin (e �3) �0.62, 1.19 �0.71, 0.60

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78.64(17)� for 2, representing the major difference between themolecular geometries of the two compounds.

3.2. Crystal packing

The main focus of the structure analyses concerns the details ofmolecular packing of the title compounds. Presence of several hea-vy atoms per molecule and availability of H-bonding sites gaveexpectations for various types of weak intermolecular interactions.Although the two compounds differ from each other essentially inone atom, replacement of the large and soft sulfur atom with themore electronegative and hard oxygen atom was expected to beable to lead to significant changes in pattern of intermolecularinteractions.

Due to the planarity of the molecular backbones, molecules ofboth compounds form p-stacks in the crystal phase. Planes of theC2AS3AC4AC4iAS3i (for symmetry codes (i), see Table 2) ringsof 1 form layers parallel to [001] with an interplanar distance of3.5276(6) Å (Table 3). The separation between the centroids (Cg)of the rings of two stacked molecules amounts to 3.8152(14) Ådue to the offset along the a axis (S2AS2i vectors) and antiparallelorientation of molecules in the adjacent layers. Compound 2 formsstacks along the c axis with an interval of 3.4126(6) Å between the

planes of the C2AS3AC4AC4iAS3i rings. The distance between thecentroids of the neighboring 5-membered rings increases to3.7254(17) Å due to the intermolecular offset.

For the analysis of short contacts in 1 and 2, Hirshfeld surfacesmapped with dnorm were drawn (Fig. 2). The red-colored areas onthe isosurfaces (distances shorter than the sum of the vdW radii)are grouped in the regions of CH2Br as well as of C@O/C@S groups,highlighting their involvement in short directional intermolecularinteractions. On the other hand, the five-membered backbones of1 and 2 show almost no close contacts.

Fingerprint plots for 1 and 2 are remarkably different (Fig. 3a).Their shapes indicate that the pattern of close contacts of thetwo compounds do not show much similarity. Analysis of the fin-gerprint plots (Fig. 3b), resolved for various types of intermolecularinteractions [22], and of dnorm isosurfaces allowed us to draw thefollowing conclusions: (a) Although the areas for Br� � �Br contactsin crystals of 1 and 2 are comparable, in the fingerprint plot of 1

Fig. 1. Structures and ORTEP plots of 1 and 2 with atom numbering schemes.Displacement ellipsoids are represented at 50% probability levels. H atoms areshown as small spheres of arbitrary radius. Symmetry codes (i): (1) 1 � x, y, 3/2 � z;(2) 1 � x, y, 1/2 � z.

Table 2Selected geometric parameters for compounds 1 and 2.

1 2

Bond lengths (Å)S1AC2 1.644(3) O1AC2 1.213(4)C2AS3 1.7331(16) C2AS3 1.7677(19)S3AC4 1.7443(18) S3AC4 1.7499(19)C4AC4i 1.348(2) C4AC4i 1.347(3)C4AC5 1.488(3) C4AC5 1.490(3)C5ABr6 1.974(2) C5ABr6 1.975(2)

Angles (�)S3AC2AS3i 112.54(14) S3AC2AS3i 112.68(17)C2AS3AC4 97.63(9) C2AS3AC4 96.53(11)S3AC4AC4i 116.10(13) S3AC4AC4i 117.13(13)C4iAC4AC5 126.76(17) C4iAC4AC5 125.78(16)C4AC5ABr6 109.59(14) C4AC5ABr6 110.75(14)

Torsion angles (�)C4AS3AC2AS3i 0.10(8) C4AS3AC2AS3i 0.17(7)C2AS3AC4AC4i �0.36(18) C2AS3AC4AC4i �0.58(17)S3AC4AC4iAS3i 0.5(2) S3AC4AC4iAS3i 0.8(2)C2AS3AC4AC5 179.41(15) C2AS3AC4AC5 178.10(15)S3AC4AC5ABr6 �64.63(18) S3AC4AC5ABr6 78.64(17)

Symmetry code (i)1 � x, y, 3/2 � z 1 � x, y, 1/2 � z

Table 3Analysis of short ring–ring contacts for compounds 1 and 2.a

Compound CgI–CgJb (Å) CgI–CgJ perp.c (Å) Slippaged (Å)

1 3.8152(14) 3.5276(6) 1.4532 3.7254(17) 3.4126(6) 1.494

a Cg are the centroids of the C2AS3AC4AC4iAS3i rings of the compounds 1 and 2.b Distance between the two neighboring Cg.c Perpendicular distance from Cg(I) to the plane of the neighboring ring J.d Distance between Cg(I) and perpendicular projection of Cg(J) on ring I.

Fig. 2. Hirshfeld surfaces of 1: (a) and 2 (b), mapped with dnorm and showing thenearest neighboring molecules participating in short intermolecular contacts. Suchcontacts are displayed as dark lines penetrating through the red areas of molecularisosurface. (For interpretation of the references to color in this figure legend, thereader is referred to the web version of this article.)

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Fig. 3. (a) Non-resolved fingerprint plots for 1 and 2. (b) Resolved fingerprint plots for the most important modes of intermolecular interactions [22]. The percentage showsthe contribution of a particular contact to the total Hirshfeld surface area of molecules.

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they appear as sharp and long traces reaching low di/de values,indicating a very short and highly directional Br� � �Br interaction.The same contacts in 2 are of much longer range. (b) CAH� � �S@Ccontacts appear as two broad blunt wings in a fingerprint plot of1, meaning large contact areas, but also relatively large contact dis-tances and low directionality. For 2, CAH� � �S@C contacts almostcompletely loose their significance, being replaced by very shortdirectional CAH� � �O@C interactions, which represent a remarkableexample of non-classical hydrogen bonds. (c) Fingerprint plots ofboth 1 and 2 reveal the presence of CAH� � �Br non-classical H-bonds, which appear as two broad and sharp wings [22]. The wingapexes are longer and sharper for 1, indicating substantially short-er CAH� � �Br contacts. (d) Br� � �S contacts occupy large molecularareas with some of them showing short contact distances and pro-nounced directionality. On the other hand, the S� � �S contacts occu-py a much smaller area and are not likely to play an important rolein molecular packing. No carbonyl–carbonyl interactions [23] wereobservable in the fingerprint plots of 2.

Full details of short intermolecular contacts are presented in theTables below, where non-classical H-bonds (Table 4) and soft–softshort interactions (Br� � �Br and Br� � �S, Table 5) are listed. The con-

tacts occurring below or slightly above (‘‘borderline contacts’’)the sum of vdW radii of the involved atoms [24] and non-classicalH-bonds, all complying with the accepted distance/angle criteriafor crystalline substances [2a,c], are included in the Tables.

Packing and patterns of intermolecular interactions for 1 areshown in Figs. 4 and 5. Very short Br6� � �Br6 contacts (motif a) linkmolecular layers, parallel to [001], with matching molecular orien-tation (i.e. every second layer) with each other, forming columnsalong the c axis. Twofold C5AH51� � �Br6 interactions (motif b) withan R2

2ð6Þ graph-set notation [25] link the molecules within the layersalong the a axis. The longer Br6� � �S1 contacts interconnect the mol-ecules within the layers along the b axis (motif c). The C5AH51� � �S1contacts (not shown) link neighboring layers and can be also classi-fied as non-classical H-bonds. The C5ABr6� � �S3AC4 contacts, whichalso link the layers, as well as the C5AH51� � �S1 contacts can be con-sidered as borderline interactions and likely do not play any signif-icant role for molecular packing.

The crystal packing of 2, shown in Fig. 6, is dominated byremarkably short C5AH51� � �O1@C2 acceptor bifurcated hydrogenbonds (motif a), forming chains of molecules along the b axis.The geometry of this interaction displays favorable donor (157�)

Table 4Intermolecular non-classical hydrogen bonds for compounds 1 and 2.

Compound DAH� � �A DH� � �A (Å) D� � �A (Å) \DAH� � �A (�) Symmetry codes

1 C5AH51� � �Br6(motif a) 2.95 3.820(2) 155 2 � x, y, 3/2 � zC5AH52� � �Br6 3.09 3.9220(18) 147 �1/2 + x, 3/2 � y, �1/2 + zC5AH51� � �S1 2.99 3.554(2) 120 1 � x, 1 � y, 1 � z; x, 1 � y, �1/2 + z

2 C5AH51� � �O1(motif a) 2.40 3.317(3) 157 x, 1 + y, z; 1 � x, 1 + y, 1/2 � zC5AH52� � �Br6(motif b) 3.04 3.823(2) 140 3/2 � x, 3/2 � y, 1 � z

Table 5Short bromine–bromine and bromine–sulfur contacts for compounds 1 and 2.

Compound CABr� � �YAC Br� � �Y (Å) CABr� � �Y, Br� � �YAC (�) Symmetry codes

1 C5ABr6� � �Br6AC5(motif b) 3.5610(11) 143.97(7) 2 � x, y, 5/2 � zC5ABr6� � �S1AC2(motif c) 3.7356(13) 77.21(6), 145.66(1) 1/2 + x, 1/2 + y, z; 3/2 � x, 1/2 + y, 3/2 � zC5ABr6� � �S3AC4 3.7594(12) 132.52(6), 149.30(7) 2 � x, 1 � y, 2 � z

2 C5ABr6� � �S3AC2(motif c) 3.6320(16) 166.56(6), 111.28(5) 3/2 � x, 1/2 + y, 1/2 � z

Fig. 4. Crystal packing of 1 highlighting intermolecular stacking of the title compound. Two principal intermolecular interactions, CAH� � �Br (motif a) and Br� � �Br (motif b), areshown as dashed lines only for the molecules of one particular orientation (with C@S bond directed to a reader). p–p interactions are shown as solid lines only for the leftcolumn of stacked molecules for the sake of clarity.

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and acceptor (152�) directionalities, which are indicative for astrong hydrogen bond. Soft–soft C5ABr6� � �S3AC2 interactions(motif c) link the molecules together in layers parallel to [001]. Fi-nally, double C5AH52� � �Br6 contacts with an R2

2ð6Þ graph-set motif(motif b) interconnect the molecules in layers parallel to [10�1].

4. Conclusions

To sum up, the crystal structures of 1 and 2 were determinedand analyzed. Both thione 1 and ketone 2 demonstrate interestingfeatures in their molecular packing. Compound 1 displays veryclose Br� � �Br interactions as well as CAH� � �Br non-classical hydro-

gen bonds. In the packing of 2, notably short CAH� � �O@C hydro-gen bonds represent the dominant interaction, which issupplemented by close CAH� � �Br and Br� � �S contacts. We can con-clude that for both 1 and 2 crystal packing is dominated by thecontacts involving bromomethylene as well as carbonyl/thiocar-bonyl groups. Nevertheless, the roles of carbonyl and thiocarbonylgroups are notably different: whereas the carbonyl group tend toform short and directed hydrogen bonds, the thiocarbonyl groupprefer to participate in relatively long-range contacts, both withsoft bromine atoms as well as with hydrogens. Examination ofthe Hirshfeld surfaces and fingerprint plots afforded effectivedetermination of the dominant intermolecular contacts and

Fig. 5. Crystal packing of 1 viewed along the c axis. Close S� � �Br (motif c) are shown as dashed lines.

Fig. 6. Crystal packing of 2 viewed along the c axis (a) and along the b axis (b). Principal intermolecular interactions, CAH� � �O (motif a), CAH� � �Br (motif b), and S� � �Br (motifc), are shown as dashed lines; p–p interactions are shown as solid lines. For clarity, motifs b and c are shown only for the upper/lower rows of molecules, and p–p interactionsare shown only for the central row of molecules, respectively.

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served as a handy complement to classical methods of crystalstructure analysis.

Acknowledgements

We are grateful to Dr. C. Vande Velde (Karel de Grote UniversityCollege, Antwerp, Belgium) for helpful discussions. The X-ray dif-fractometer (M.Z.) was funded by NSF Grant 0087210, Ohio Boardof Regents Grant CAP-491 and Youngstown State University.

Appendix A. Supplementary data

Supplementary data contains the Hirshfeld surfaces of 1 and 2,mapped with di and de, and dnorm, as well as the decomposed fin-gerprint plots for all important intermolecular interactions. CCDC827694 and 827695 contain the supplementary crystallographicdata for 1 and 2. These crystallographic data can be obtained freeof charge from via http://www.ccdc.cam.ac.uk/conts/retriev-ing.html, or from the Cambridge Crystallographic Data Centre, 12Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336 033. Sup-plementary data associated with this article can be found, in theonline version, at doi:10.1016/j.molstruc.2011.08.026.

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[22] For additional fingerprint plots, resolved for several other types of interactions,see ESI.

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