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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2016 Jan 16;72(Pt 2):188–190. doi: 10.1107/S2056989015024755

Crystal structure and conformational analysis of 2-hy­droxy-3-(2-methyl­prop-1-en-1-yl)naphthalene-1,4-dione

Sannyele Alcantara Emiliano a, Sheyla Welma Duarte Silva a, Mariano Alves Pereira a, Valeria Rdos Santos Malta a, Tatiane Luciano Balliano a,*
PMCID: PMC4770963  PMID: 26958384

In the structure of the naphtho­quinone derivative 2-hy­droxy-3-(2-methyl­prop-1-en-1-yl)naphthalene-1,4-dione, the mol­ecules form a centrosymmetric cyclic dimer through inter­molecular O—H⋯O hydrogen bonds which, together with inter­molecular C—H⋯O hydrogen bonds and weak π–π ring inter­actions, give rise to an overall two-dimensional structure.

Keywords: crystal structure, naphtho­quinone derivative, mol­ecular conformation, hydrogen bonding

Abstract

In the structure of the title compound, C14H12O3, the substituent side chain, in which the H atoms of both methyl groups are disordered over six equivalent sites, lies outside of the plane of the naphthalene­dione ring. The ring-to-chain C—C—C—C torsion angles are 50.7 (3), −176.6 (2) and 4.9 (4)°. An intra­molecular meth­yl–hy­droxy C—H⋯O hydrogen bond is present. In the crystal, mol­ecules are primarily connected by inter­molecular O—H⋯O hydrogen bonds, forming a centrosymmetric cyclic dimer motif [graph set R 2 2(10)]. Also present is a weak inter­molecular C—H⋯O hydrogen bond linking the dimers and a weak π–π ring inter­action [ring centroid separation = 3.7862 (13) Å], giving layers parallel to (10-3).

Chemical context  

Naphtho­quinone compounds exhibit several biological activities, being utilized for the treatment of parasitic diseases (Salas et al., 2008) some types of cancer (Tonholo et al., 1998) and cardiovascular disease (Silva & Torres, 2013). The compound in this study, 2-hy­droxy-3-(2-metilprop-1-enol)naphthalene-1,4-dione, C14H12O3, is a naphthoquinone deriv­ative and the structure is reported herein.graphic file with name e-72-00188-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound is shown in Fig. 1. In this structure the side chain is rotated out of the plane of the naphthalene­dione ring, with torsion angles C2—C3—C9—C10, C3—C9—C10—C12 and C3—C9—C10—C22 of 50.7 (3), −176.6 (2) and 4.9 (4)°, respectively. Present also in the mol­ecule is an intra­molecular methyl C22⋯O3 [2.959 (3) Å; see Table 1] and a short O3⋯O1 contact [2.665 (2) Å]. When compared with other analogous structures in the literature, e.g. 2-chloro-3-(4-chloro­benzamido)-1,4-naphtho­quinone (Brandy et al., 2009), it is observed that the title compound has similar conformational features with respect to the side chain, which lies out of the naphtho­quinone plane.

Figure 1.

Figure 1

Mol­ecular conformation and atom-numbering scheme, with non-H atoms drawn at the 50% probability level. The H atoms of the rotationally disordered methyl groups are shown as six equivalent half-occupancy sites.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H1O3⋯O1i 0.97 (3) 1.93 (3) 2.770 (2) 143 (3)
C7—H7⋯O2ii 0.93 2.43 3.339 (3) 164
C22—H22C⋯O3 0.96 2.21 2.959 (3) 134

Symmetry codes: (i) Inline graphic; (ii) Inline graphic.

Supra­molecular features  

In the crystal, the mol­ecules are connected by classic inter­molecular O3—H⋯O1i hydrogen bonds (Table 1), forming a centrosymmetric cyclic dimer [graph set Inline graphic(10)] (Bernstein et al., 1995) (Fig. 2 a). Also present in the structure is a weak inter­molecular C7—H⋯O2ii hydrogen bond [3.339 (3) Å], linking the dimers and a weak π–π ring inter­action between the benzene and quinone ring moieties of the parent ring system [ring centroid separation Cg⋯Cg iii = 3.7862 (13) Å; symmetry code: (iii) x + 1, y, z], giving layers parallel to (10Inline graphic) (Figs. 2 b and 3).

Figure 2.

Figure 2

The centrosymmetric dimers formed from the O3—H⋯O1i hydrogen bonds, viewed (a) along a and (b) along b. For symmetry code (i), see Table 1.

Figure 3.

Figure 3

The crystal packing in the unit cell, showing intra- and inter­molecular inter­actions as dashed lines.

Database survey  

A search of the Cambridge Structural Database (Groom & Allen, 2014) revealed the presence of 40 structures containing the 2-hy­droxy­naphthalene-1,4-dione core moiety. There were 787 structures which possess the naphthalene-1,4-dione moiety. There are structures similar to the title compound, whichvary depending on the oxidant used in the synthesis.

Synthesis and crystallization  

The compound was obtained through to the lapachol oxidation product as can be seen in the scheme below (Hooker, 1936). The sample was subjected to an ethyl acetate solution at 301 K for crystallization.graphic file with name e-72-00188-scheme2.jpg

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. The O3-bound H atom was located in a difference Fourier map and was freely refined. The remaining H atoms were positioned geometrically with aromatic C—H = 0.93 Å and U iso(H) = 1.2U eq(C). Rotational disorder was identified in the hydrogen atoms of the methyl carbon atoms C12 and C22 and these were included in the refinement over six equivalent 60° sites with 50% occupation, with C—H = 0.96 Å and U iso(H) = 1.5U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula C14H12O3
M r 228.24
Crystal system, space group Monoclinic, P21/c
Temperature (K) 293
a, b, c (Å) 4.3564 (2), 16.4069 (8), 15.8598 (7)
β (°) 94.793 (2)
V3) 1129.62 (9)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.14 × 0.11 × 0.10
 
Data collection
Diffractometer Nonius KappaCCD
No. of measured, independent and observed [I > 2σ(I)] reflections 4661, 2585, 1802
R int 0.041
(sin θ/λ)max−1) 0.650
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.061, 0.191, 1.03
No. of reflections 2585
No. of parameters 158
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.31, −0.30

Computer programs: COLLECT (Enraf–Nonius, 2001), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 and SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows and WinGX (Farrugia, 2012), Mercury (Macrae et al., 2008), publCIF (Westrip, 2010) and PLATON (Spek, 2009).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989015024755/zs2357sup1.cif

e-72-00188-sup1.cif (22.7KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015024755/zs2357Isup2.hkl

e-72-00188-Isup2.hkl (124.4KB, hkl)

Supporting information file. DOI: 10.1107/S2056989015024755/zs2357Isup3.cml

CCDC reference: 1444109

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

UFAL, IQB, LabCriMM, CNPq and FAPEAL are acknowledged for support. We thank Professor Dr Antonio Ventura Pinto (in memorium) for his collaboration in the works of this research group, specifically for the synthesis of the title compound.

supplementary crystallographic information

Crystal data

C14H12O3 F(000) = 480
Mr = 228.24 Dx = 1.342 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc Cell parameters from 2659 reflections
a = 4.3564 (2) Å θ = 1.0–27.5°
b = 16.4069 (8) Å µ = 0.09 mm1
c = 15.8598 (7) Å T = 293 K
β = 94.793 (2)° Block, red
V = 1129.62 (9) Å3 0.14 × 0.11 × 0.10 mm
Z = 4

Data collection

Nonius KappaCCD diffractometer 1802 reflections with I > 2σ(I)
Radiation source: Enraf-Nonius FR590 Rint = 0.041
Graphite monochromator θmax = 27.5°, θmin = 2.6°
Detector resolution: 9 pixels mm-1 h = −5→5
CCD rotation images, thick slices scans k = −19→21
4661 measured reflections l = −20→20
2585 independent reflections

Refinement

Refinement on F2 Primary atom site location: structure-invariant direct methods
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.061 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.191 H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0946P)2 + 0.4119P] where P = (Fo2 + 2Fc2)/3
2585 reflections (Δ/σ)max < 0.001
158 parameters Δρmax = 0.31 e Å3
0 restraints Δρmin = −0.30 e Å3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.
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 > 2σ(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)

x y z Uiso*/Ueq Occ. (<1)
O3 0.3690 (4) 0.37038 (10) 0.48362 (10) 0.0407 (4)
O1 0.2205 (4) 0.52143 (9) 0.43377 (9) 0.0404 (4)
O2 −0.3406 (4) 0.27382 (9) 0.26721 (10) 0.0481 (5)
C10 0.0940 (5) 0.19603 (13) 0.47932 (13) 0.0395 (5)
C9 0.0749 (5) 0.23006 (12) 0.40272 (13) 0.0386 (5)
H9 0.1126 0.1961 0.3578 0.046*
H1O3 0.448 (7) 0.424 (2) 0.5005 (19) 0.073 (9)*
C4A −0.3114 (5) 0.41650 (12) 0.28476 (13) 0.0349 (5)
C8A −0.1689 (5) 0.48205 (13) 0.32860 (13) 0.0348 (5)
C2 0.1441 (5) 0.38047 (12) 0.42115 (13) 0.0351 (5)
C1 0.0733 (5) 0.46622 (12) 0.39675 (13) 0.0350 (5)
C5 −0.5333 (5) 0.43122 (14) 0.21845 (13) 0.0400 (5)
H5 −0.6268 0.3879 0.1885 0.048*
C3 0.0007 (5) 0.31557 (12) 0.38155 (12) 0.0358 (5)
C4 −0.2235 (5) 0.33077 (13) 0.30859 (13) 0.0369 (5)
C6 −0.6151 (5) 0.51093 (14) 0.19709 (14) 0.0426 (5)
H6 −0.7628 0.5207 0.1524 0.051*
C8 −0.2532 (5) 0.56203 (13) 0.30691 (14) 0.0386 (5)
H8 −0.1584 0.6056 0.3362 0.046*
C7 −0.4789 (5) 0.57607 (13) 0.24159 (14) 0.0413 (5)
H7 −0.5389 0.6291 0.2277 0.05*
C12 0.1899 (6) 0.10858 (13) 0.49043 (15) 0.0475 (6)
H12A 0.1919 0.0939 0.5491 0.071* 0.5
H12B 0.3923 0.1015 0.4718 0.071* 0.5
H12C 0.0468 0.0744 0.4575 0.071* 0.5
H12D 0.2288 0.086 0.4365 0.071* 0.5
H12E 0.0283 0.0784 0.5138 0.071* 0.5
H12F 0.3738 0.1055 0.5281 0.071* 0.5
C22 0.0189 (6) 0.23815 (14) 0.55869 (14) 0.0452 (6)
H22A 0.0507 0.2013 0.6056 0.068* 0.5
H22B −0.1923 0.2554 0.553 0.068* 0.5
H22C 0.1503 0.2848 0.5684 0.068* 0.5
H22D −0.0449 0.2931 0.5457 0.068* 0.5
H22E 0.1981 0.2389 0.5983 0.068* 0.5
H22F −0.1445 0.2095 0.583 0.068* 0.5

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O3 0.0435 (9) 0.0323 (8) 0.0450 (9) −0.0013 (6) −0.0051 (6) −0.0002 (7)
O1 0.0456 (9) 0.0318 (8) 0.0431 (8) −0.0041 (6) −0.0005 (6) −0.0022 (6)
O2 0.0651 (11) 0.0308 (8) 0.0460 (9) −0.0033 (7) −0.0096 (7) −0.0026 (7)
C10 0.0438 (12) 0.0302 (10) 0.0439 (12) −0.0025 (8) −0.0013 (9) −0.0004 (9)
C9 0.0462 (12) 0.0282 (10) 0.0409 (11) 0.0009 (9) 0.0011 (9) −0.0027 (9)
C4A 0.0422 (11) 0.0292 (10) 0.0340 (10) −0.0011 (8) 0.0061 (8) 0.0012 (8)
C8A 0.0398 (11) 0.0305 (11) 0.0346 (10) −0.0016 (8) 0.0057 (8) −0.0001 (8)
C2 0.0384 (11) 0.0314 (11) 0.0355 (10) 0.0003 (8) 0.0035 (8) 0.0009 (8)
C1 0.0398 (11) 0.0288 (10) 0.0367 (10) −0.0019 (8) 0.0055 (8) −0.0034 (8)
C5 0.0486 (13) 0.0343 (11) 0.0368 (11) −0.0025 (9) 0.0015 (9) −0.0004 (9)
C3 0.0431 (11) 0.0292 (10) 0.0355 (10) −0.0006 (8) 0.0064 (8) −0.0006 (8)
C4 0.0453 (12) 0.0299 (10) 0.0357 (11) −0.0025 (9) 0.0040 (9) −0.0011 (8)
C6 0.0500 (13) 0.0383 (12) 0.0391 (11) 0.0013 (9) 0.0003 (9) 0.0039 (9)
C8 0.0460 (12) 0.0293 (10) 0.0410 (11) −0.0005 (8) 0.0062 (9) −0.0002 (8)
C7 0.0493 (12) 0.0312 (11) 0.0436 (11) 0.0027 (9) 0.0060 (9) 0.0055 (9)
C12 0.0651 (15) 0.0315 (11) 0.0447 (12) 0.0020 (10) −0.0024 (10) 0.0011 (9)
C22 0.0587 (14) 0.0346 (11) 0.0420 (12) 0.0006 (10) 0.0033 (10) 0.0011 (9)

Geometric parameters (Å, º)

O3—C2 1.344 (3) C3—C4 1.472 (3)
O3—H1O3 0.97 (4) C6—C7 1.387 (3)
O1—C1 1.230 (2) C6—H6 0.93
O2—C4 1.228 (2) C8—C7 1.387 (3)
C10—C9 1.333 (3) C8—H8 0.93
C10—C22 1.496 (3) C7—H7 0.93
C10—C12 1.501 (3) C12—H12A 0.96
C9—C3 1.472 (3) C12—H12B 0.96
C9—H9 0.93 C12—H12C 0.96
C4A—C5 1.389 (3) C12—H12D 0.96
C4A—C8A 1.398 (3) C12—H12E 0.96
C4A—C4 1.498 (3) C12—H12F 0.96
C8A—C8 1.398 (3) C22—H22A 0.96
C8A—C1 1.469 (3) C22—H22B 0.96
C2—C3 1.361 (3) C22—H22C 0.96
C2—C1 1.485 (3) C22—H22D 0.96
C5—C6 1.390 (3) C22—H22E 0.96
C5—H5 0.93 C22—H22F 0.96
C2—O3—H1O3 108.3 (18) C10—C12—H12C 109.5
C9—C10—C22 124.9 (2) H12A—C12—H12C 109.5
C9—C10—C12 120.2 (2) H12B—C12—H12C 109.5
C22—C10—C12 114.91 (19) C10—C12—H12D 109.5
C10—C9—C3 127.1 (2) H12A—C12—H12D 141.1
C10—C9—H9 116.5 H12B—C12—H12D 56.3
C3—C9—H9 116.5 H12C—C12—H12D 56.3
C5—C4A—C8A 119.67 (19) C10—C12—H12E 109.5
C5—C4A—C4 120.09 (19) H12A—C12—H12E 56.3
C8A—C4A—C4 120.23 (18) H12B—C12—H12E 141.1
C4A—C8A—C8 120.21 (19) H12C—C12—H12E 56.3
C4A—C8A—C1 119.46 (19) H12D—C12—H12E 109.5
C8—C8A—C1 120.32 (19) C10—C12—H12F 109.5
O3—C2—C3 121.45 (19) H12A—C12—H12F 56.3
O3—C2—C1 115.56 (18) H12B—C12—H12F 56.3
C3—C2—C1 122.95 (19) H12C—C12—H12F 141.1
O1—C1—C8A 122.31 (19) H12D—C12—H12F 109.5
O1—C1—C2 119.00 (18) H12E—C12—H12F 109.5
C8A—C1—C2 118.68 (18) C10—C22—H22A 109.5
C4A—C5—C6 119.8 (2) C10—C22—H22B 109.5
C4A—C5—H5 120.1 H22A—C22—H22B 109.5
C6—C5—H5 120.1 C10—C22—H22C 109.5
C2—C3—C4 118.61 (19) H22A—C22—H22C 109.5
C2—C3—C9 123.83 (19) H22B—C22—H22C 109.5
C4—C3—C9 117.35 (18) C10—C22—H22D 109.5
O2—C4—C3 120.66 (19) H22A—C22—H22D 141.1
O2—C4—C4A 119.58 (18) H22B—C22—H22D 56.3
C3—C4—C4A 119.76 (18) H22C—C22—H22D 56.3
C7—C6—C5 120.7 (2) C10—C22—H22E 109.5
C7—C6—H6 119.6 H22A—C22—H22E 56.3
C5—C6—H6 119.6 H22B—C22—H22E 141.1
C7—C8—C8A 119.7 (2) H22C—C22—H22E 56.3
C7—C8—H8 120.2 H22D—C22—H22E 109.5
C8A—C8—H8 120.2 C10—C22—H22F 109.5
C6—C7—C8 119.9 (2) H22A—C22—H22F 56.3
C6—C7—H7 120 H22B—C22—H22F 56.3
C8—C7—H7 120 H22C—C22—H22F 141.1
C10—C12—H12A 109.5 H22D—C22—H22F 109.5
C10—C12—H12B 109.5 H22E—C22—H22F 109.5
H12A—C12—H12B 109.5
O1—C1—C2—O3 0.2 (3) O2—C4—C4A—C5 2.6 (3)
O1—C1—C2—C3 −177.5 (2) O2—C4—C4A—C8A −176.8 (2)
C8A—C1—C2—O3 179.69 (19) C3—C4—C4A—C5 −177.0 (2)
C8A—C1—C2—C3 2.0 (3) C3—C4—C4A—C8A 3.5 (3)
O1—C1—C8A—C4A 175.2 (2) C4—C4A—C5—C6 179.6 (2)
O1—C1—C8A—C8 −3.9 (3) C8A—C4A—C5—C6 −1.0 (3)
C2—C1—C8A—C4A −4.3 (3) C4—C4A—C8A—C1 1.6 (3)
C2—C1—C8A—C8 176.6 (2) C4—C4A—C8A—C8 −179.4 (2)
O3—C2—C3—C4 −174.50 (19) C5—C4A—C8A—C1 −177.9 (2)
O3—C2—C3—C9 0.2 (3) C5—C4A—C8A—C8 1.2 (3)
C1—C2—C3—C4 3.1 (3) C4A—C5—C6—C7 −0.4 (3)
C1—C2—C3—C9 177.8 (2) C5—C6—C7—C8 1.5 (3)
C2—C3—C4—O2 174.5 (2) C6—C7—C8—C8A −1.3 (3)
C2—C3—C4—C4A −5.9 (3) C7—C8—C8A—C1 179.0 (2)
C9—C3—C4—O2 −0.5 (3) C7—C8—C8A—C4A −0.1 (3)
C9—C3—C4—C4A 179.15 (19) C3—C9—C10—C12 −176.6 (2)
C2—C3—C9—C10 50.7 (3) C3—C9—C10—C22 4.9 (4)
C4—C3—C9—C10 −134.6 (2)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O3—H1O3···O1i 0.97 (3) 1.93 (3) 2.770 (2) 143 (3)
C7—H7···O2ii 0.93 2.43 3.339 (3) 164
C22—H22C···O3 0.96 2.21 2.959 (3) 134

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

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989015024755/zs2357sup1.cif

e-72-00188-sup1.cif (22.7KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015024755/zs2357Isup2.hkl

e-72-00188-Isup2.hkl (124.4KB, hkl)

Supporting information file. DOI: 10.1107/S2056989015024755/zs2357Isup3.cml

CCDC reference: 1444109

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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