The title lignin model compound, C
16H
18O
6, resides on a twofold axis parallel with the
b axis, with the mid-point of the internal C-C(-
x + 1,
y, -
z +
) bond located on the twofold axis. The
exo angles between the methoxy groups and the benzene rings deviate significantly from the expected value of 120° [125.15 (7) and 114.27 (6)°]. A 12-coordinated 3-modal three-dimensional net with a new topology was identified on the synthon level. A comparison of the flexibility of related
o,
o'-disubstituted biphenyl derivatives and biphenyl is presented, with the angles between the ring planes in substituted biphenyls found to be in the range 40-70°.
Supporting information
CCDC reference: 810024
Compound (I) was prepared according to the method of Adler & Hernestam
(1955)
[m.p. 458–459 K (Adler & Hernestam reported m.p. 460–463 K under quick
heating)]. Crystals of (I) were obtained by recrystallisation from which
solvent?
H atoms were refined isotropically and their positions were constrained to
ideal geometry using an appropriate riding model, with C—H = 0.95–0.99 Å.
For methyl groups, O—C—H angles (109.5°) were kept fixed, while the
torsion angle was allowed to refine with the starting positions based on the
circular Fourier synthesis averaged using the local three-fold axis. For the
hydroxyl groups, the O—H distances (0.84 Å) and C—O—H angles (109.5°)
were kept fixed, while the torsion angles were allowed to refine with the
starting positions based on the circular Fourier synthesis. The highest
positive peaks in the residual electron-density map with absolute values
higher than that of the minimum peak, -0.22 e Å-3, ranging from 0.23 to
0.55 e Å-3, are located in the middle of the bonds and represent the σ
electrons.
Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003) and SADABS (Sheldrick, 2003); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2010); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
5,5'-Bis(hydroxymethyl)-3,3'-dimethoxy-2,2'-biphenyldiol
top
Crystal data top
C16H18O6 | Dx = 1.440 Mg m−3 |
Mr = 306.30 | Melting point: 458 K |
Orthorhombic, Pbcn | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2n 2ab | Cell parameters from 8263 reflections |
a = 12.4911 (6) Å | θ = 5.8–66.1° |
b = 8.5100 (4) Å | µ = 0.11 mm−1 |
c = 13.2883 (7) Å | T = 153 K |
V = 1412.54 (12) Å3 | Prism, colourless |
Z = 4 | 0.35 × 0.20 × 0.15 mm |
F(000) = 648 | |
Data collection top
Siemens SMART CCD area-detector diffractometer | 2621 independent reflections |
Radiation source: fine-focus sealed tube | 2150 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
Detector resolution: 120 pixels mm-1 | θmax = 33.1°, θmin = 2.9° |
ω scans | h = −19→18 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −12→12 |
Tmin = 0.594, Tmax = 0.984 | l = −19→20 |
23325 measured reflections | |
Refinement top
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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.116 | H-atom parameters constrained |
S = 1.00 | w = 1/[σ2(Fo2) + (0.0706P)2 + 0.2578P] where P = (Fo2 + 2Fc2)/3 |
2621 reflections | (Δ/σ)max < 0.001 |
112 parameters | Δρmax = 0.55 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
Crystal data top
C16H18O6 | V = 1412.54 (12) Å3 |
Mr = 306.30 | Z = 4 |
Orthorhombic, Pbcn | Mo Kα radiation |
a = 12.4911 (6) Å | µ = 0.11 mm−1 |
b = 8.5100 (4) Å | T = 153 K |
c = 13.2883 (7) Å | 0.35 × 0.20 × 0.15 mm |
Data collection top
Siemens SMART CCD area-detector diffractometer | 2621 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2150 reflections with I > 2σ(I) |
Tmin = 0.594, Tmax = 0.984 | Rint = 0.046 |
23325 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.116 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.55 e Å−3 |
2621 reflections | Δρmin = −0.22 e Å−3 |
112 parameters | |
Special details top
Experimental. Data were collected at 153 K using a Siemens SMART CCD diffractometer equipped
with an LT-2 A cooling device. A full sphere of reciprocal space was scanned by
0.3° steps in ω with a crystal-to-detector distance of 3.97 cm, 15 s per
frame. Preliminary orientation matrix was obtained from the first 100 frames
using SMART (Bruker, 2003). The collected frames were integrated using
the preliminary orientation matrix which was updated every 100 frames. Final
cell parameters were obtained by refinement on the position of 8263 reflections
with I>10σ(I) after integration of all the frames data using SAINT
(Bruker, 2003). |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'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 >
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 | |
O1 | 0.43908 (5) | 0.18771 (8) | 0.39864 (5) | 0.02078 (15) | |
H1 | 0.3963 | 0.1571 | 0.4433 | 0.049 (4)* | |
O2 | 0.22560 (5) | 0.20158 (8) | 0.40800 (5) | 0.02033 (14) | |
O3 | 0.11368 (5) | 0.46466 (7) | 0.07418 (5) | 0.02186 (15) | |
H3 | 0.0634 | 0.5248 | 0.0908 | 0.042 (4)* | |
C1 | 0.44040 (6) | 0.34720 (8) | 0.25099 (5) | 0.01441 (15) | |
C2 | 0.38431 (6) | 0.27141 (9) | 0.32729 (5) | 0.01518 (15) | |
C3 | 0.27174 (6) | 0.28087 (9) | 0.32983 (6) | 0.01550 (15) | |
C4 | 0.21651 (6) | 0.36524 (9) | 0.25701 (6) | 0.01603 (15) | |
H4 | 0.1406 | 0.3718 | 0.2598 | 0.023 (3)* | |
C5 | 0.27235 (6) | 0.44051 (8) | 0.17968 (6) | 0.01514 (15) | |
C6 | 0.38324 (6) | 0.43095 (9) | 0.17766 (6) | 0.01527 (15) | |
H6 | 0.4214 | 0.4824 | 0.1253 | 0.024 (3)* | |
C7 | 0.11152 (7) | 0.20158 (13) | 0.41085 (7) | 0.02543 (19) | |
H7A | 0.0855 | 0.3098 | 0.4171 | 0.037 (4)* | |
H7B | 0.0870 | 0.1399 | 0.4687 | 0.044 (4)* | |
H7C | 0.0836 | 0.1550 | 0.3487 | 0.030 (3)* | |
C8 | 0.21401 (6) | 0.53500 (9) | 0.10103 (6) | 0.01858 (16) | |
H8A | 0.2011 | 0.6424 | 0.1270 | 0.024 (3)* | |
H8B | 0.2594 | 0.5438 | 0.0402 | 0.033 (3)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0132 (3) | 0.0300 (3) | 0.0191 (3) | 0.0030 (2) | 0.0007 (2) | 0.0088 (2) |
O2 | 0.0135 (3) | 0.0281 (3) | 0.0194 (3) | 0.0005 (2) | 0.00324 (19) | 0.0046 (2) |
O3 | 0.0152 (3) | 0.0246 (3) | 0.0257 (3) | 0.0030 (2) | −0.0071 (2) | −0.0043 (2) |
C1 | 0.0115 (3) | 0.0164 (3) | 0.0153 (3) | 0.0003 (2) | −0.0008 (2) | −0.0010 (2) |
C2 | 0.0126 (3) | 0.0177 (3) | 0.0152 (3) | 0.0017 (2) | −0.0008 (2) | 0.0002 (2) |
C3 | 0.0125 (3) | 0.0180 (3) | 0.0161 (3) | 0.0004 (2) | 0.0012 (2) | −0.0011 (2) |
C4 | 0.0113 (3) | 0.0181 (3) | 0.0187 (3) | 0.0016 (2) | −0.0009 (2) | −0.0017 (3) |
C5 | 0.0141 (3) | 0.0140 (3) | 0.0173 (3) | 0.0013 (2) | −0.0029 (2) | −0.0020 (2) |
C6 | 0.0141 (3) | 0.0160 (3) | 0.0157 (3) | −0.0009 (2) | −0.0014 (2) | −0.0003 (2) |
C7 | 0.0139 (4) | 0.0386 (5) | 0.0238 (4) | −0.0024 (3) | 0.0041 (3) | 0.0031 (3) |
C8 | 0.0166 (3) | 0.0170 (3) | 0.0222 (4) | 0.0008 (3) | −0.0057 (3) | 0.0001 (3) |
Geometric parameters (Å, º) top
O1—C2 | 1.3690 (9) | C4—C5 | 1.3974 (11) |
O1—H1 | 0.8400 | C4—H4 | 0.9500 |
O2—C3 | 1.3662 (9) | C5—C6 | 1.3878 (10) |
O2—C7 | 1.4255 (10) | C5—C8 | 1.5066 (11) |
O3—C8 | 1.4339 (10) | C6—H6 | 0.9500 |
O3—H3 | 0.8400 | C7—H7A | 0.9800 |
C1—C2 | 1.3910 (10) | C7—H7B | 0.9800 |
C1—C6 | 1.4024 (10) | C7—H7C | 0.9800 |
C1—C1i | 1.4893 (14) | C8—H8A | 0.9900 |
C2—C3 | 1.4088 (10) | C8—H8B | 0.9900 |
C3—C4 | 1.3886 (10) | | |
| | | |
C2—O1—H1 | 109.5 | C4—C5—C8 | 120.88 (7) |
C3—O2—C7 | 116.23 (6) | C5—C6—C1 | 121.63 (7) |
C8—O3—H3 | 109.5 | C5—C6—H6 | 119.2 |
C2—C1—C6 | 119.06 (7) | C1—C6—H6 | 119.2 |
C2—C1—C1i | 121.09 (7) | O2—C7—H7A | 109.5 |
C6—C1—C1i | 119.78 (7) | O2—C7—H7B | 109.5 |
O1—C2—C1 | 119.63 (7) | H7A—C7—H7B | 109.5 |
O1—C2—C3 | 120.79 (7) | O2—C7—H7C | 109.5 |
C1—C2—C3 | 119.58 (6) | H7A—C7—H7C | 109.5 |
O2—C3—C4 | 125.15 (7) | H7B—C7—H7C | 109.5 |
O2—C3—C2 | 114.27 (6) | O3—C8—C5 | 111.87 (6) |
C4—C3—C2 | 120.58 (7) | O3—C8—H8A | 109.2 |
C3—C4—C5 | 120.10 (7) | C5—C8—H8A | 109.2 |
C3—C4—H4 | 120.0 | O3—C8—H8B | 109.2 |
C5—C4—H4 | 120.0 | C5—C8—H8B | 109.2 |
C6—C5—C4 | 119.04 (7) | H8A—C8—H8B | 107.9 |
C6—C5—C8 | 120.05 (7) | | |
| | | |
C6—C1—C2—O1 | 179.23 (7) | O2—C3—C4—C5 | −179.31 (7) |
C1i—C1—C2—O1 | −3.80 (10) | C2—C3—C4—C5 | 0.63 (11) |
C6—C1—C2—C3 | −0.37 (10) | C3—C4—C5—C6 | −0.72 (11) |
C1i—C1—C2—C3 | 176.60 (6) | C3—C4—C5—C8 | −178.90 (7) |
C7—O2—C3—C4 | 2.86 (11) | C4—C5—C6—C1 | 0.26 (11) |
C7—O2—C3—C2 | −177.09 (7) | C8—C5—C6—C1 | 178.47 (7) |
O1—C2—C3—O2 | 0.28 (10) | C2—C1—C6—C5 | 0.28 (11) |
C1—C2—C3—O2 | 179.87 (7) | C1i—C1—C6—C5 | −176.73 (6) |
O1—C2—C3—C4 | −179.67 (7) | C6—C5—C8—O3 | 144.81 (7) |
C1—C2—C3—C4 | −0.08 (11) | C4—C5—C8—O3 | −37.02 (10) |
Symmetry code: (i) −x+1, y, −z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O2 | 0.84 | 2.22 | 2.6720 (9) | 114 |
O1—H1···O3ii | 0.84 | 2.03 | 2.7489 (8) | 144 |
O3—H3···O1iii | 0.84 | 2.09 | 2.9138 (9) | 168 |
Symmetry codes: (ii) −x+1/2, −y+1/2, z+1/2; (iii) x−1/2, y+1/2, −z+1/2. |
Experimental details
Crystal data |
Chemical formula | C16H18O6 |
Mr | 306.30 |
Crystal system, space group | Orthorhombic, Pbcn |
Temperature (K) | 153 |
a, b, c (Å) | 12.4911 (6), 8.5100 (4), 13.2883 (7) |
V (Å3) | 1412.54 (12) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.35 × 0.20 × 0.15 |
|
Data collection |
Diffractometer | Siemens SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.594, 0.984 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23325, 2621, 2150 |
Rint | 0.046 |
(sin θ/λ)max (Å−1) | 0.768 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.116, 1.00 |
No. of reflections | 2621 |
No. of parameters | 112 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.55, −0.22 |
Selected geometric parameters (Å, º) topO1—C2 | 1.3690 (9) | O3—C8 | 1.4339 (10) |
O2—C7 | 1.4255 (10) | C1—C1i | 1.4893 (14) |
| | | |
C2—C1—C1i | 121.09 (7) | O2—C3—C4 | 125.15 (7) |
C6—C1—C1i | 119.78 (7) | O2—C3—C2 | 114.27 (6) |
O1—C2—C1 | 119.63 (7) | C6—C5—C4 | 119.04 (7) |
O1—C2—C3 | 120.79 (7) | C6—C5—C8 | 120.05 (7) |
Symmetry code: (i) −x+1, y, −z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O2 | 0.84 | 2.22 | 2.6720 (9) | 114 |
O1—H1···O3ii | 0.84 | 2.03 | 2.7489 (8) | 144 |
O3—H3···O1iii | 0.84 | 2.09 | 2.9138 (9) | 168 |
Symmetry codes: (ii) −x+1/2, −y+1/2, z+1/2; (iii) x−1/2, y+1/2, −z+1/2. |
Torsion angles C(O)—C—C—C(O) [C2—C1—C1i—C2i in (I)] and
C(H)—C—C—C(H) [C6—C11—C1i—C6i in (I)] (°), and angle A
between the aromatic rings (°), for (I) and related compounds topCompound (CSD code) | Reference | Remark | C(O)-C-C-C(O) | C(H)-C-C-C(H) | A |
(I) | a | BP | 114.43 (8) | 108.33 (8) | 68.88 (2) |
AJAPUW | a | BP | 53.96 | 47.95 | 51.52 |
CIPXII | b | BP | 49.04 | 41.98 | 44.86 |
MEBMIP | c | BP | -55.18 | -49.49 | 52.77 |
MEBMOV | c | BP | -46.49 | -41.09 | 43.81 |
TECQOH | d | BP | 62.10 | 63.16 | 62.12 |
TECQOH | d | BP | -61.73 | -61.22 | 61.47 |
NUTSUQ | e | BP | -51.39 | -45.75 | 48.65 |
MAYFEX | f | NP | 65.86 | 64.45 | 65.11 |
TUGVUM | g | NP | -53.41 | -48.04 | 50.87 |
NOZZUX | h | NP | -63.35 | -57.09 | 60.15 |
NOZZUX | h | NP | -115.39 | -115.34 | 65.09 |
NOZZOR | h | NP | -62.85 | -56.41 | 59.42 |
ZIZDIV | i | NP | 120.70 | 119.49 | 59.83 |
ZIZDOB | i | NP | 128.82 | 125.23 | 53.10 |
ZIZDOB | i | NP | -123.74 | -120.36 | 59.10 |
BP = biphenolic, NP = non-phenolic
References: (a) this work; (b) Wang et al. (1983); (c) Bocelli
et al. (1999);
(d) Xi et al. (1996); (e) Byrne et al. (1998);
(f) Roblin et al. (2000);
(g) Karhunen et al. (1996); (h) Ferreira et al.
(1998); (i) Brunow et al.
(1995). For the Cambridge Structural Database (CSD), see: Allen
(2002). |
The title compound, (I), is a lignin model compound representative of a type of biphenyl structure in lignins (Ralph et al., 2004). A perspective drawing and the atom-numbering of (I) are shown in Fig. 1 and selected geometric parameters are given in Table 1. The molecule is located with the midpoint of the C1—C1i bond [symmetry code: (i) -x + 1, y, -z + 1/2] on a twofold axis parallel with the b axis. A striking deformation in (I) is the deviation of the O2—C3—C2 and O2—C3—C4 angles from 120° (Table 1). Such deformation was observed earlier by, for example, Lundquist et al. (1987) and Gallagher et al. (2001). There is an intramolecular hydrogen bond between the methoxy group and the adjacent hydroxy group (Fig. 1, Table 2). There are also two strong intermolecular hydrogen bonds of O—H···O type present in the crystal structure of (I); geometric details of these hydrogen bonds are given in Table 2. On the first-level graph-set, as defined by Bernstein et al. (1995) and Grell et al. (1999), an S(5) string is formed by the intramolecular hydrogen bond, while both intermolecular hydrogen bonds form C(8) and C(9) chains. On the second-level graph-set, R44(8) rings are formed by the two intermolecular hydrogen bonds (Fig. 2).
Due to the symmetry of the molecule of (I) and the arrangement in the unit cell, an infinite three-dimensional framework is built, with a body-centred cubic (b.c.u.) topology, using the nomenclature of the Reticular Chemistry Structural Resource (RCSR) database (O'Keeffe et al., 2008). We contracted the molecular residues to synthons, defined by O1, C11 (the midpoint of the C1—C1i bond), C5 and O3, and a 12-coordinated 3-modal three-dimensional net with a new topology was identified using the program TOPOS (Blatov et al., 2000; Blatov & Shevchenko, 2010). This new topology, denoted vla1, has a point (Schläfli) symbol for the net of (123)(4;122)2. This means that each synthon is connected with 11 other synthons through symmetry-related molecules (Fig. 3).
The crystal structures of a number of lignin model compounds of the biphenyl type have previously been reported in the literature (Brunow et al., 1995; Karhunen et al., 1996; Xi et al., 1996; Ferreira et al., 1998; Roblin et al., 2000). Compound (I) is phenolic and only one structurally related compound with phenolic groups has been examined previously, namely 5,5'-bis[(2-hydroxy-3-methoxy-5-methylphenyl)methyl]-3,3'-dimethoxy-2,2'-biphenyldiol (Xi et al., 1996). In these two compounds there are hydrogen bonds between the hydroxy groups and methoxy groups. In biphenyls o,o'-disubstituted with hydroxy groups lacking adjacent methoxy groups (Bedford et al., 2003; Wang et al., 1983; Bocelli et al., 1999; Xi et al., 1996; Byrne et al., 1998), hydrogen bonds are formed between the hydroxy groups.
The angle between the aromatic rings is flexible in the structures of o,o'-disubstituted biphenyl derivatives. For (I) it is 68.88 (2)°. In Table 3, the angles between the aromatic rings and selected torsion angles are presented for a series of such compounds. The non-derivatized biphenyl molecule is planar in crystals at room temperature, but libration around the long axis of the molecule suggests a statistically centrosymmetric arrangement (Charbonneau & Delugeard, 1977). At 41 K, crystals of biphenyl undergo a structural phase transition to an intermediate phase called phase II, and at 21 K another phase III is formed. Surprisingly, Cailleau et al. (1979) found the angle between the phenyl rings to be 10.2° for crystals of phase III, which was later correctly attributed to the existence of a modulated structure by Baudour & Sanquer (1983). In crystal structures where biphenyl is cocrystallized with other molecules or complexes as a solvent, the angle between the phenyl rings is dependent on the type and strength of the interactions, with a maximum of 50.8° for a dichromium complex (Van Order et al., 1987).