Inter­molecular C—H...O, Cl...Cl and π–π inter­actions in the 2-di­chloro­methyl derivative of vitamin K₃

The title 1,4-naphtho­quinone, 2-di­chloro­methyl-3-methyl-1,4-di­hydro­naphthalene-1,4-dione, C₁₂H₈Cl₂O₂, is a chlorinated derivative of vitamin K₃, which is a synthetic compound also known as menadione. Mol­ecules of (I) are planar and lie on a crystallographic mirror plane (Z′ = 0.5) in the space group Pnma. They are connected to each other by C—H...O hydrogen bonds, forming two-dimensional layers parallel to the ac plane. In addition, Cl...Cl and π–π inter­actions link adjacent mol­ecules in different layers, thus forming zigzag ribbons along the b axis, such that a three-dimensional architecture is generated.

S1. Introduction

1,4-Naphtho­quinones are one of the most important and widely distributed of the chemical classes in the quinone family, a family which is widespread in nature. For example, quinones play an integral role in many biological electron-transfer processes, particularly respiration and photosynthesis (Boudalis et al., 2008). Naphtho­quinones can (i) generate reactive oxygen species, such as superoxides and hydroxyl radicals, (ii) serve as electrophile compounds and (iii) react with different biological targets in various species, including humans (Bhashin et al., 2013), resulting in a variety of pharmacological properties. These include anti­fungal (Tandon et al., 2004), anti­viral (Dasilva et al., 2002), anti-inflammatory (Checker et al., 2009), anti­artherosclerotic (Ding et al., 2005) and anti­cancer effects (Seshadri et al., 2011). The methyl derivative of 1,4 naphtho­quinone, namely vitamin K₃ or Menadione, and has been considered in the last decade for its anti­hemorragic and anti­cancer activities (Lamson & Plaza, 2003) and was structurally characterized for the first time in 2004 through X-ray powder diffraction techniques (Nowell & Attfield, 2004). The crystal structures of both the form discovered by Nowell & Attfield and of a new polymorph have recently been reported (Rane et al., 2008), as obtained by single-crystal X-ray diffraction. A survey of the Cambridge Structural Database (CSD; 2012 Version; Allen, 2002) identified only 39 other derivatives of vitamin K₃, with substituents in the quinone moiety, half of which include a thiol­ate -SR substituent (Kinuta et al., 2010; Jali & Baruah, 2012) at the 2-position in the naphtho­quinone system. The structures of some simple compounds related to vitamin K₃ (a 2-chloro, a 2-methyl, a 2-hy­droxy and a 2-NH₂ derivative) are known from early studies in the literature (Breton-Lacombe, 1964, 1967; Gaultier & Hauw, 1965, 1966), but these crystallographic studies are rather inaccurate and hardly accessible.

The structure of the title compound has never appeared in the literature; our inter­est here is to find out which changes, with respect to Menadione [Rane et al., 2008, polymorph (1b)], occur in the naphtho­quinone skeleton and in the crystal packing of (I), due to the presence of the bulky di­chloro­methyl substituent at the 2-position of the quinone moiety. Indeed, considering the very high importance of these compounds, there is obviously significant inter­est in finding key structural features to optimize and widen their multifunctional applications.

S2. Experimental

S2.1. Synthesis and crystallization

The title compound, (I), was prepared as an unexpected product. The parent compound 2-methyl-1,4-naphtho­quinone (menadione, 0.02 mmol) (which is a commercial product and was used without further purification) was dissolved in CH₂Cl₂ (2 ml) and the resulting quinonic solution was added to a perfluorodi­acyl peroxide solution (Sansotera et al., 2013). The reaction mixture was heated at 303 K under reflux for 6 h. The crude product obtained was recrystallized from a 1:1 solution of ethanol and chloro­form at room temperature, and a crystal of (I) suitable for X-ray diffraction analysis was obtained by slow evaporation of this solution

S2.2. Refinement

Crystal data, data collection and structure refinement details are summarized in Table1. H atoms were included in the model at geometrically calculated positions and in riding modes, with C—H = 0.96 Å for methyl groups, 0.93 Å for aromatic CH and 0.98 Å for the -CHCl₂ group. The torsion angle of the methyl group was allowed to refine. This gave H-atom positions that were disordered about the mirror plane. The U_iso values of the H atoms were constrained to 1.2 (aromatic C) and 1.5 times (aliphatic C) U_eq of the parent C atom.

S3. Results and discussion

The title compound, (I), crystallizes in the Pnma space group, resulting in molecules lying on a crystallographic mirror plane, with the asymmetric unit consisting of half a molecule. Its molecular structure at 150 K, with the atom-labeling scheme, is shown in Fig. 1. The main deviation from planarity is the two Cl atoms at C12, which are symmetry-related through the mirror plane perpendicular to the b axis, and which lie 1.466 (1) Å from the mean plane of the molecule. The torsion angles Cl1—C12—C10—C1 and Cl1—C12—C10—C9 measure their orientation with respect to the adjacent carbonyl and methyl groups and are 62.22 (18) and 117.78 (18)°, respectively. Examination of the C—O and C—C bond lengths and of the C—C—C and C—C—O angles (Table 2) confirms the quinonoid nature of the C1/C2/C7–C10 ring in the planar 1,4 naphtho­quinone moiety; the two carbonyl bonds are the same within s.u. deviation, with bond lengths typical of C═O bonds. The C2—C7 [1.391 (5) Å] and C9—C10 [1.338 (5) Å] bonds are significantly shorter than the other four bonds of the ring [in the range 1.482 (5)–1.499 (5) Å], as expected for C═C compared with C—C bonds. In addition, the C—C—C and C—C—O angles are in the range 118.4 (3)–122.3 (3)°, very close to the ideal value of 120° for sp²-hybridized atoms. These features perfectly match those observed in the parent Menadione molecule (Rane et al., 2008) and in some carboxyl-substituted 1,4-naphtho­quinones (Boudalis et al., 2008). As regards the exocyclic bond angles at atom C9, the steric repulsion between the methyl and di­chloro­methyl substituents results in a marked difference in the angular values at atom C9 [124.9 (3) versus 115.0 (3)° for C11—C9—C10 and C11—C9—C8, respectively], significantly larger than the analogue difference observed in Menadione [122.7 (4) versus 118.1 (4)°]. As a consequence, the C···O distance between the methyl group and carbonyl atom O2 is shorter in (I) than in the parent Menadione molecule [2.764 (5) versus 2.806 (6) Å].

The C12—Cl1 bond length is 1.781 (2) Å, slightly longer than the equivalent value of 1.776 Å reported in Inter­national Tables for Crystallography (Allen et al., 1995), suggesting that the halogen atom could be involved in some intra- or inter­molecular inter­actions. Actually, atom Cl1 is only 3.069 (1) Å distant from carbonyl atom O1 (Table 2), an intra­molecular value well below the sum of the van der Waals radii of these atomic species (Bondi, 1964); nonetheless the C12—Cl1···O1 angle is so narrow [64.5 (2)°] that this intra­molecular inter­action cannot be classified among those of C—X···O type, where X is a halogen atom, which are called halogen bonds (XBs) (Desiraju et al., 2013) and which are considered similar to conventional hydrogen bonds (Cukiernik et al., 2009). Conversely, the C12—Cl1···Cl1ⁱ—C12ⁱ inter­molecular inter­action [symmetry code: (i) -x, -y, -z+1], which is present in the crystal between molecules related by an inversion center and a translation along the c cell axis, can be considered a true XB. The torsion angle between the atoms involved in the inter­action amounts to 180°, while the Cl···Cl separation is as long as 3.546 (1) Å, i.e. just barely above the sum of van der Waals radii. Angles θ₁ and θ₂, i.e. C12—Cl1···Cl1ⁱ and Cl1···Cl1ⁱ—C12ⁱ, are equal to one another due to crystallographic symmetry and are 131.09 (4)°. This inter­action can therefore be classified as a symmetrical type-I trans-XB contact (Hathwar & Guru Row, 2010).

Halogen–halogen inter­actions provide weak but highly directional packing motifs, which aid in the evaluation of supra­molecular assemblies in the solid state; in the present case, the Cl···Cl inter­action gives rise to a zigzag ribbon that propogates parallel to the crystallographic b axis. The ribbon is formed between molecules which are stacked perpendicularly to the axis in a head-to-tail fashion (Fig. 2). Comparing the crystal structures of (I) and Menadione, it is evident that this XB packing motif is of course completely absent in Menadione, due to the lack of the chloro­methyl substituent. Conversely, in both the structures the crystal packing, along b and along a, respectively, is stabilized by inter­molecular π–π stacking inter­actions involving adjacent quinone and aromatic rings (Fig. 3). In the title compound, the inter­planar distance defined by half the b dimension corresponds to the closest C···C inter­actions and amounts to a separation of 3.441 (3) Å between adjacent molecules related by (-x+1, y+1/2, -z+1), while in Menadione, the equivalent inter­action measures 3.483 (5) Å and links parent molecules with those at (-x+1, -y+1, -z)

Other inter­molecular inter­actions involve the two carbonyl O atoms. In (I), atom O1 acts as an acceptor in weak acceptor-bifurcated nonclassical hydrogen bonds, having as donors the neighbouring C4—H4 and C5—H5 groups of the aromatic ring of the molecule that is symmetry-related through the 2₁ screw axis along a. The same symmetry operator links the C12—H12 group to carbonyl atom O2, forming a C—H···O hydrogen bond (Table 3). These structural features form a two-dimensional perfectly planar sheet architecture in the ac plane (Fig. 4), similar to that already observed in the bc plane in vitamin K₃ (Rane et al., 2008), in which each parent molecule acts as a linker for four neighbouring molecules. These planar structures are stacked parallel one to each other and inter­linked by the π–π contacts described above (Fig. 5), so that a three-dimensional network is generated.

Related literature

For related literature, see: Allen (2002); Allen et al. (1995); Bhashin et al. (2013); Bondi (1964); Boudalis et al. (2008); Breton-Lacombe (1964, 1967); Checker et al. (2009); Cukiernik et al. (2009); Dasilva et al. (2002); Desiraju et al. (2013); Ding et al. (2005); Gaultier & Hauw (1965, 1966); Hathwar & Guru Row (2010); Jali & Baruah (2012); Kinuta et al. (2010); Lamson & Plaza (2003); Nowell & Attfield (2004); Rane et al. (2008); Seshadri et al. (2011); Tandon et al. (2004).

Computing details

Data collection: SAINT-Plus (Bruker, 1999); cell refinement: SAINT-Plus (Bruker, 1999); data reduction: SAINT-Plus (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2012).

Figures

	Fig. 1. The molecular structure of (I) at 150 K, showing the atom-numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level and H atoms are shown as spheres of arbitrary size. Primed atoms are related by the symmetry operation (x, -y+1/2, z).
	Fig. 2. Partial view of the crystal packing of (I), viewed down the c axis, showing the intermolecular Cl···Cl interactions. H atoms have been omitted for clarity.
	Fig. 3. Space-filling diagram of (I), viewed down the c axis, showing the layers formed by π–π interactions along the b-axis direction. H atoms have been omitted for clarity.
	Fig. 4. View of the crystal packing of (I) down the b axis. C—H···O hydrogen bonds linking molecules of (I) into two-dimensional sheets are shown as dashed lines. The symmetry codes are as in Table 3.
	Fig. 5. The crystal packing of (I), showing the stacking of layers down the b axis.

2-Dichloromethyl-3-methyl-1,4-dihydronaphthalene-1,4-dione

Crystal data

C12H8Cl2O2	Dx = 1.564 Mg m^−3
Mr = 255.08	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pnma	Cell parameters from 2767 reflections
a = 13.166 (3) Å	θ = 4.6–43.1°
b = 6.8812 (14) Å	µ = 0.58 mm^−1
c = 11.958 (2) Å	T = 150 K
V = 1083.4 (4) Å^3	Prism, dark orange
Z = 4	0.22 × 0.08 × 0.05 mm
F(000) = 520

Data collection

Bruker APEX CCD area-detector diffractometer	1703 independent reflections
Radiation source: fine-focus sealed X-ray tube	908 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.073
ω scan	θmax = 30.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −18→18
Tmin = 0.785, Tmax = 0.862	k = −9→9
25336 measured reflections	l = −16→16

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.048	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.161	H-atom parameters constrained
S = 1.04	w = 1/[σ^2(Fo^2) + (0.064P)^2 + 0.9747P] where P = (Fo^2 + 2Fc^2)/3
1703 reflections	(Δ/σ)max < 0.001
95 parameters	Δρmax = 0.43 e Å^−3
0 restraints	Δρmin = −0.40 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cl1	0.12535 (6)	0.03696 (16)	0.54982 (7)	0.0583 (3)
O1	0.2587 (2)	0.2500	0.3787 (2)	0.0568 (10)
O2	0.5444 (2)	0.2500	0.6919 (2)	0.0494 (9)
C1	0.3241 (3)	0.2500	0.4500 (3)	0.0342 (9)
C2	0.4332 (3)	0.2500	0.4174 (3)	0.0290 (8)
C3	0.4597 (3)	0.2500	0.3052 (3)	0.0363 (10)
H3	0.4094	0.2500	0.2506	0.044*
C4	0.5603 (3)	0.2500	0.2747 (3)	0.0414 (11)
H4	0.5781	0.2500	0.1995	0.050*
C5	0.6347 (3)	0.2500	0.3557 (4)	0.0406 (10)
H5	0.7027	0.2500	0.3345	0.049*
C6	0.6098 (3)	0.2500	0.4677 (4)	0.0373 (10)
H6	0.6606	0.2500	0.5217	0.045*
C7	0.5079 (3)	0.2500	0.4996 (3)	0.0288 (9)
C8	0.4798 (3)	0.2500	0.6195 (3)	0.0324 (9)
C9	0.3694 (3)	0.2500	0.6506 (3)	0.0306 (9)
C10	0.2983 (3)	0.2500	0.5707 (3)	0.0315 (9)
C11	0.3483 (3)	0.2500	0.7744 (3)	0.0439 (11)
H11A	0.4065	0.2993	0.8137	0.066*	0.5
H11B	0.3345	0.1197	0.7988	0.066*	0.5
H11C	0.2906	0.3309	0.7897	0.066*	0.5
C12	0.1873 (3)	0.2500	0.5999 (3)	0.0417 (11)
H12	0.1819	0.2500	0.6816	0.063*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0351 (4)	0.0896 (7)	0.0501 (5)	−0.0192 (4)	0.0015 (3)	−0.0038 (5)
O1	0.0260 (14)	0.119 (3)	0.0252 (14)	0.000	−0.0042 (12)	0.000
O2	0.0353 (16)	0.081 (2)	0.0321 (15)	0.000	−0.0118 (13)	0.000
C1	0.0246 (18)	0.054 (3)	0.0239 (19)	0.000	0.0006 (16)	0.000
C2	0.0249 (18)	0.035 (2)	0.0275 (18)	0.000	0.0015 (15)	0.000
C3	0.031 (2)	0.052 (3)	0.0260 (19)	0.000	0.0004 (16)	0.000
C4	0.037 (2)	0.054 (3)	0.033 (2)	0.000	0.0125 (18)	0.000
C5	0.0244 (19)	0.051 (3)	0.046 (2)	0.000	0.0104 (18)	0.000
C6	0.0270 (19)	0.044 (3)	0.041 (2)	0.000	−0.0026 (17)	0.000
C7	0.0245 (18)	0.033 (2)	0.0288 (18)	0.000	0.0002 (14)	0.000
C8	0.0291 (19)	0.038 (2)	0.030 (2)	0.000	−0.0051 (16)	0.000
C9	0.0302 (18)	0.040 (2)	0.0214 (17)	0.000	−0.0005 (15)	0.000
C10	0.0240 (17)	0.044 (3)	0.0260 (19)	0.000	0.0008 (14)	0.000
C11	0.041 (2)	0.067 (3)	0.0231 (19)	0.000	0.0001 (16)	0.000
C12	0.0256 (19)	0.071 (3)	0.028 (2)	0.000	0.0021 (16)	0.000

Geometric parameters (Å, º)

Cl1—C12	1.781 (2)	C6—C7	1.394 (5)
O1—C1	1.212 (4)	C6—H6	0.9300
O2—C8	1.214 (4)	C7—C8	1.482 (5)
C1—C10	1.483 (5)	C8—C9	1.499 (5)
C1—C2	1.487 (5)	C9—C10	1.338 (5)
C2—C3	1.386 (5)	C9—C11	1.507 (5)
C2—C7	1.391 (5)	C10—C12	1.504 (5)
C3—C4	1.374 (5)	C11—H11A	0.9600
C3—H3	0.9300	C11—H11B	0.9600
C4—C5	1.378 (6)	C11—H11C	0.9600
C4—H4	0.9300	C12—Cl1^i	1.781 (2)
C5—C6	1.379 (6)	C12—H12	0.9800
C5—H5	0.9300
Cl1···Cl1^ii	3.546 (1)	Cl1···O1	3.069 (1)
O1—C1—C10	121.5 (3)	O2—C8—C7	121.0 (3)
O1—C1—C2	120.1 (3)	O2—C8—C9	120.2 (4)
C10—C1—C2	118.4 (3)	C7—C8—C9	118.8 (3)
C3—C2—C7	120.4 (3)	C10—C9—C8	120.1 (3)
C3—C2—C1	119.8 (3)	C10—C9—C11	124.9 (3)
C7—C2—C1	119.9 (3)	C8—C9—C11	115.0 (3)
C4—C3—C2	120.0 (4)	C9—C10—C1	122.3 (3)
C4—C3—H3	120.0	C9—C10—C12	121.0 (3)
C2—C3—H3	120.0	C1—C10—C12	116.7 (3)
C3—C4—C5	119.9 (4)	C9—C11—H11A	109.5
C3—C4—H4	120.0	C9—C11—H11B	109.5
C5—C4—H4	120.0	H11A—C11—H11B	109.5
C4—C5—C6	120.9 (4)	C9—C11—H11C	109.5
C4—C5—H5	119.5	H11A—C11—H11C	109.5
C6—C5—H5	119.5	H11B—C11—H11C	109.5
C5—C6—C7	119.6 (4)	C10—C12—Cl1	111.52 (16)
C5—C6—H6	120.2	C10—C12—Cl1^i	111.52 (16)
C7—C6—H6	120.2	Cl1—C12—Cl1^i	110.8 (2)
C2—C7—C6	119.2 (4)	C10—C12—H12	107.6
C2—C7—C8	120.5 (3)	Cl1—C12—H12	107.6
C6—C7—C8	120.4 (3)	Cl1^i—C12—H12	107.6
O1—C1—C2—C3	0.000 (1)	C6—C7—C8—C9	180.000 (1)
C10—C1—C2—C3	180.000 (1)	O2—C8—C9—C10	180.000 (1)
O1—C1—C2—C7	180.000 (1)	C7—C8—C9—C10	0.000 (1)
C10—C1—C2—C7	0.000 (1)	O2—C8—C9—C11	0.000 (1)
C7—C2—C3—C4	0.000 (1)	C7—C8—C9—C11	180.000 (1)
C1—C2—C3—C4	180.000 (1)	C8—C9—C10—C1	0.000 (1)
C2—C3—C4—C5	0.000 (1)	C11—C9—C10—C1	180.000 (1)
C3—C4—C5—C6	0.000 (1)	C8—C9—C10—C12	180.000 (1)
C4—C5—C6—C7	0.000 (1)	C11—C9—C10—C12	0.000 (1)
C3—C2—C7—C6	0.000 (1)	O1—C1—C10—C9	180.000 (1)
C1—C2—C7—C6	180.000 (1)	C2—C1—C10—C9	0.000 (1)
C3—C2—C7—C8	180.000 (1)	O1—C1—C10—C12	0.000 (1)
C1—C2—C7—C8	0.000 (1)	C2—C1—C10—C12	180.000 (1)
C5—C6—C7—C2	0.000 (1)	C9—C10—C12—Cl1	−117.78 (18)
C5—C6—C7—C8	180.000 (1)	C1—C10—C12—Cl1	62.22 (18)
C2—C7—C8—O2	180.000 (1)	C9—C10—C12—Cl1^i	117.78 (18)
C6—C7—C8—O2	0.000 (1)	C1—C10—C12—Cl1^i	−62.22 (18)
C2—C7—C8—C9	0.000 (1)

Symmetry codes: (i) x, −y+1/2, z; (ii) −x, −y, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C12—H12···O2^iii	0.98	2.36	3.120 (5)	134
C5—H5···O1^iv	0.93	2.65	3.243 (5)	122
C4—H4···O1^iv	0.93	2.55	3.192 (5)	126

Symmetry codes: (iii) x−1/2, −y+1/2, −z+3/2; (iv) x+1/2, −y+1/2, −z+1/2.