organic compounds
(4-Chloro-2-fluorophenyl)[1-(2,6-difluorophenyl)but-3-enyl]amine
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bSyngene International Ltd., Biocon Park, Plot No. 2&3, Bommasandra 4th Phase, Jigani Link Road, Bangalore 560 100, India, cDepartment of Printing, Manipal Institute of Technology, Manipal 576 104, India, dDepartment of Chemistry, National Institute of Technology–Karnataka, Surathkal, Mangalore 575 025, India, and eCrystal Materials Research Unit, Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90112, Thailand
*Correspondence e-mail: hkfun@usm.my
In the molecule of the title homoallylic amine, C16H13ClF3N, the dihedral angle between the two benzene rings is 84.63 (4)°. Weak intramolecular N—H⋯F hydrogen bonds generate S(6) and S(5) ring motifs. In the weak intermolecuar N—H⋯F hydrogen bonds link molecules into centrosymmetric dimers which are arranged in molecular sheets parallel to the ac plane.
Related literature
For standard bond lengths, see Allen et al. (1987). For hydrogen-bond motifs, see Bernstein et al. (1995). For background to the bioactivity and applications of homoallylic see: Edwards et al. (1998); Robert (1998); Sabine & Horst (1991); Xie et al. (1989). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536809012896/lh2803sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809012896/lh2803Isup2.hkl
To a mixture of 2,6-difluorobenzaldehyde (0.5 g, 3.5 mmol), 4-chloro-2-fluoro aniline (0.51 g, 3.5 mmol) and allyltributyltin (1.1 g, 3.5 mmol) in acetonitrile (5 ml), trifluoro acetic acid (0.04 g, 0.35 mmol) was added. The reaction mixture was stirred at 299 K under nitrogen atmosphere for 2 h. Completion of the reaction was monitored by TLC. The reaction mixture was then extracted with diethyl ether (3 x 20 ml) and the combined organic layer were concentrated in vacuum and purified by flash
to afford the pure homoallylic amine. The yield was found to be 0.98 g (90% yield). Colorless block-shaped single crystals of the title compound was recrystalized in acetone by slow evaporation of the solvent, M.p 399–400 K.Amine and =CH2 H atoms were located from the difference map and refined isotropically. The remaining H atoms were placed in calculated positions with d(C—H) = 0.93 Å, Uiso = 1.2Ueq(C) for aromatic and 0.98 Å, Uiso = 1.2Ueq(C) for CH. The highest residual electron density peak is located at 0.63 Å from Cl1 and the deepest hole is located at 0.62 Å from Cl1.
Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).C16H13ClF3N | F(000) = 640 |
Mr = 311.72 | Dx = 1.450 Mg m−3 |
Monoclinic, P21/c | Melting point = 399–400 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 10.8980 (1) Å | Cell parameters from 7434 reflections |
b = 14.0073 (2) Å | θ = 2.0–37.5° |
c = 10.1651 (1) Å | µ = 0.29 mm−1 |
β = 113.018 (1)° | T = 100 K |
V = 1428.17 (3) Å3 | Block, colorless |
Z = 4 | 0.50 × 0.39 × 0.27 mm |
Bruker APEXII CCD area-detector diffractometer | 7434 independent reflections |
Radiation source: sealed tube | 6099 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
ϕ and ω scans | θmax = 37.5°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −15→18 |
Tmin = 0.868, Tmax = 0.926 | k = −22→23 |
32850 measured reflections | l = −17→14 |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.119 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.059P)2 + 0.3248P] where P = (Fo2 + 2Fc2)/3 |
7434 reflections | (Δ/σ)max = 0.001 |
202 parameters | Δρmax = 0.63 e Å−3 |
0 restraints | Δρmin = −0.86 e Å−3 |
C16H13ClF3N | V = 1428.17 (3) Å3 |
Mr = 311.72 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.8980 (1) Å | µ = 0.29 mm−1 |
b = 14.0073 (2) Å | T = 100 K |
c = 10.1651 (1) Å | 0.50 × 0.39 × 0.27 mm |
β = 113.018 (1)° |
Bruker APEXII CCD area-detector diffractometer | 7434 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 6099 reflections with I > 2σ(I) |
Tmin = 0.868, Tmax = 0.926 | Rint = 0.025 |
32850 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.119 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.63 e Å−3 |
7434 reflections | Δρmin = −0.86 e Å−3 |
202 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.35924 (3) | 0.625873 (17) | 1.05066 (4) | 0.03621 (8) | |
F1 | 0.89730 (5) | 0.44888 (4) | 0.88286 (5) | 0.02227 (11) | |
F2 | 0.65542 (6) | 0.64050 (4) | 0.48567 (6) | 0.02478 (12) | |
F3 | 0.85689 (7) | 0.60562 (5) | 1.18096 (6) | 0.03051 (13) | |
N1 | 0.84154 (7) | 0.64304 (5) | 0.91602 (7) | 0.01799 (11) | |
C1 | 0.59745 (8) | 0.65594 (6) | 0.83617 (9) | 0.01870 (13) | |
H1A | 0.5873 | 0.6695 | 0.7429 | 0.022* | |
C2 | 0.48485 (9) | 0.65290 (6) | 0.86995 (10) | 0.02241 (15) | |
H2A | 0.4007 | 0.6643 | 0.7996 | 0.027* | |
C3 | 0.49921 (10) | 0.63283 (6) | 1.00871 (11) | 0.02434 (16) | |
C4 | 0.62453 (11) | 0.61733 (6) | 1.11567 (10) | 0.02539 (17) | |
H4A | 0.6347 | 0.6051 | 1.2093 | 0.030* | |
C5 | 0.73310 (9) | 0.62070 (6) | 1.07837 (9) | 0.02114 (14) | |
C6 | 0.72486 (8) | 0.63897 (5) | 0.93977 (8) | 0.01658 (12) | |
C7 | 0.84187 (7) | 0.64023 (5) | 0.77318 (8) | 0.01602 (12) | |
H7A | 0.7900 | 0.6949 | 0.7199 | 0.019* | |
C8 | 0.78026 (7) | 0.55017 (5) | 0.68918 (7) | 0.01418 (11) | |
C9 | 0.69022 (8) | 0.55353 (5) | 0.54747 (8) | 0.01668 (12) | |
C10 | 0.63233 (8) | 0.47417 (6) | 0.46594 (8) | 0.01959 (13) | |
H10A | 0.5721 | 0.4806 | 0.3717 | 0.024* | |
C11 | 0.66630 (9) | 0.38468 (6) | 0.52828 (9) | 0.02012 (14) | |
H11A | 0.6285 | 0.3303 | 0.4754 | 0.024* | |
C12 | 0.75652 (8) | 0.37582 (5) | 0.66927 (9) | 0.01879 (13) | |
H12A | 0.7801 | 0.3161 | 0.7117 | 0.023* | |
C13 | 0.81007 (7) | 0.45824 (5) | 0.74445 (8) | 0.01578 (12) | |
C14 | 0.98669 (8) | 0.65337 (6) | 0.78678 (9) | 0.02065 (14) | |
H14A | 1.0232 | 0.7107 | 0.8416 | 0.025* | |
H14B | 1.0396 | 0.5996 | 0.8389 | 0.025* | |
C15 | 0.99758 (9) | 0.66087 (6) | 0.64501 (10) | 0.02264 (15) | |
H15A | 0.9501 | 0.7093 | 0.5836 | 0.027* | |
C16 | 1.06994 (12) | 0.60355 (8) | 0.60087 (13) | 0.0329 (2) | |
H1N1 | 0.9099 (16) | 0.6141 (10) | 0.9828 (17) | 0.033 (4)* | |
H16B | 1.1209 (16) | 0.5526 (12) | 0.6600 (17) | 0.041 (4)* | |
H16A | 1.0756 (18) | 0.6098 (12) | 0.513 (2) | 0.049 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.04381 (15) | 0.02600 (11) | 0.05793 (18) | −0.00690 (9) | 0.04060 (14) | −0.00647 (10) |
F1 | 0.0223 (2) | 0.0231 (2) | 0.0163 (2) | 0.00354 (17) | 0.00191 (17) | 0.00387 (17) |
F2 | 0.0323 (3) | 0.0181 (2) | 0.0175 (2) | 0.00117 (18) | 0.0027 (2) | 0.00436 (17) |
F3 | 0.0343 (3) | 0.0376 (3) | 0.0167 (2) | 0.0065 (2) | 0.0068 (2) | 0.0050 (2) |
N1 | 0.0171 (3) | 0.0222 (3) | 0.0138 (2) | 0.0005 (2) | 0.0051 (2) | −0.0018 (2) |
C1 | 0.0189 (3) | 0.0205 (3) | 0.0177 (3) | −0.0013 (2) | 0.0083 (2) | −0.0033 (2) |
C2 | 0.0216 (4) | 0.0214 (3) | 0.0271 (4) | −0.0026 (3) | 0.0127 (3) | −0.0062 (3) |
C3 | 0.0312 (4) | 0.0177 (3) | 0.0338 (4) | −0.0045 (3) | 0.0233 (4) | −0.0050 (3) |
C4 | 0.0398 (5) | 0.0197 (3) | 0.0243 (4) | −0.0011 (3) | 0.0208 (4) | 0.0002 (3) |
C5 | 0.0286 (4) | 0.0187 (3) | 0.0172 (3) | 0.0009 (3) | 0.0101 (3) | 0.0003 (2) |
C6 | 0.0199 (3) | 0.0149 (3) | 0.0159 (3) | −0.0008 (2) | 0.0080 (2) | −0.0023 (2) |
C7 | 0.0162 (3) | 0.0165 (3) | 0.0151 (3) | −0.0012 (2) | 0.0059 (2) | −0.0011 (2) |
C8 | 0.0144 (3) | 0.0153 (3) | 0.0132 (3) | 0.0001 (2) | 0.0057 (2) | 0.0001 (2) |
C9 | 0.0193 (3) | 0.0159 (3) | 0.0141 (3) | 0.0004 (2) | 0.0057 (2) | 0.0012 (2) |
C10 | 0.0214 (3) | 0.0205 (3) | 0.0148 (3) | −0.0019 (2) | 0.0049 (2) | −0.0024 (2) |
C11 | 0.0224 (3) | 0.0178 (3) | 0.0206 (3) | −0.0028 (2) | 0.0089 (3) | −0.0038 (2) |
C12 | 0.0209 (3) | 0.0155 (3) | 0.0213 (3) | 0.0006 (2) | 0.0096 (3) | 0.0007 (2) |
C13 | 0.0148 (3) | 0.0177 (3) | 0.0146 (3) | 0.0016 (2) | 0.0054 (2) | 0.0019 (2) |
C14 | 0.0166 (3) | 0.0239 (3) | 0.0214 (3) | −0.0038 (2) | 0.0075 (3) | −0.0009 (3) |
C15 | 0.0211 (3) | 0.0241 (3) | 0.0254 (4) | −0.0005 (3) | 0.0120 (3) | 0.0054 (3) |
C16 | 0.0365 (5) | 0.0360 (5) | 0.0357 (5) | 0.0056 (4) | 0.0245 (4) | 0.0063 (4) |
Cl1—C3 | 1.7398 (9) | C7—H7A | 0.9800 |
F1—C13 | 1.3618 (9) | C8—C9 | 1.3910 (10) |
F2—C9 | 1.3550 (9) | C8—C13 | 1.3915 (10) |
F3—C5 | 1.3608 (11) | C9—C10 | 1.3826 (11) |
N1—C6 | 1.3851 (11) | C10—C11 | 1.3879 (11) |
N1—C7 | 1.4539 (10) | C10—H10A | 0.9300 |
N1—H1N1 | 0.886 (16) | C11—C12 | 1.3907 (12) |
C1—C6 | 1.3964 (11) | C11—H11A | 0.9300 |
C1—C2 | 1.3983 (12) | C12—C13 | 1.3816 (11) |
C1—H1A | 0.9300 | C12—H12A | 0.9300 |
C2—C3 | 1.3857 (14) | C14—C15 | 1.4953 (12) |
C2—H2A | 0.9300 | C14—H14A | 0.9700 |
C3—C4 | 1.3904 (15) | C14—H14B | 0.9700 |
C4—C5 | 1.3773 (13) | C15—C16 | 1.3208 (14) |
C4—H4A | 0.9300 | C15—H15A | 0.9300 |
C5—C6 | 1.3999 (11) | C16—H16B | 0.958 (17) |
C7—C8 | 1.5242 (10) | C16—H16A | 0.924 (19) |
C7—C14 | 1.5406 (11) | ||
C6—N1—C7 | 122.26 (7) | C13—C8—C7 | 123.88 (6) |
C6—N1—H1N1 | 113.7 (10) | F2—C9—C10 | 117.74 (7) |
C7—N1—H1N1 | 115.1 (10) | F2—C9—C8 | 117.83 (6) |
C6—C1—C2 | 121.26 (8) | C10—C9—C8 | 124.42 (7) |
C6—C1—H1A | 119.4 | C9—C10—C11 | 118.34 (7) |
C2—C1—H1A | 119.4 | C9—C10—H10A | 120.8 |
C3—C2—C1 | 119.70 (9) | C11—C10—H10A | 120.8 |
C3—C2—H2A | 120.2 | C10—C11—C12 | 120.40 (7) |
C1—C2—H2A | 120.2 | C10—C11—H11A | 119.8 |
C2—C3—C4 | 120.87 (8) | C12—C11—H11A | 119.8 |
C2—C3—Cl1 | 120.00 (8) | C13—C12—C11 | 118.10 (7) |
C4—C3—Cl1 | 119.13 (7) | C13—C12—H12A | 120.9 |
C5—C4—C3 | 117.80 (8) | C11—C12—H12A | 120.9 |
C5—C4—H4A | 121.1 | F1—C13—C12 | 117.66 (7) |
C3—C4—H4A | 121.1 | F1—C13—C8 | 117.69 (7) |
F3—C5—C4 | 118.99 (8) | C12—C13—C8 | 124.64 (7) |
F3—C5—C6 | 116.99 (8) | C15—C14—C7 | 112.74 (7) |
C4—C5—C6 | 124.01 (8) | C15—C14—H14A | 109.0 |
N1—C6—C1 | 124.85 (7) | C7—C14—H14A | 109.0 |
N1—C6—C5 | 118.75 (7) | C15—C14—H14B | 109.0 |
C1—C6—C5 | 116.34 (8) | C7—C14—H14B | 109.0 |
N1—C7—C8 | 114.16 (6) | H14A—C14—H14B | 107.8 |
N1—C7—C14 | 108.04 (6) | C16—C15—C14 | 124.58 (9) |
C8—C7—C14 | 111.13 (6) | C16—C15—H15A | 117.7 |
N1—C7—H7A | 107.8 | C14—C15—H15A | 117.7 |
C8—C7—H7A | 107.8 | C15—C16—H16B | 121.1 (10) |
C14—C7—H7A | 107.8 | C15—C16—H16A | 123.1 (11) |
C9—C8—C13 | 114.10 (6) | H16B—C16—H16A | 115.8 (14) |
C9—C8—C7 | 122.01 (6) | ||
C6—C1—C2—C3 | 0.07 (12) | N1—C7—C8—C13 | −47.16 (10) |
C1—C2—C3—C4 | 1.19 (12) | C14—C7—C8—C13 | 75.34 (9) |
C1—C2—C3—Cl1 | −178.34 (6) | C13—C8—C9—F2 | 179.74 (7) |
C2—C3—C4—C5 | −1.30 (12) | C7—C8—C9—F2 | −1.57 (11) |
Cl1—C3—C4—C5 | 178.24 (6) | C13—C8—C9—C10 | 0.69 (11) |
C3—C4—C5—F3 | −179.88 (7) | C7—C8—C9—C10 | 179.38 (7) |
C3—C4—C5—C6 | 0.17 (13) | F2—C9—C10—C11 | −179.51 (8) |
C7—N1—C6—C1 | −16.99 (11) | C8—C9—C10—C11 | −0.46 (13) |
C7—N1—C6—C5 | 165.95 (7) | C9—C10—C11—C12 | −0.06 (13) |
C2—C1—C6—N1 | −178.25 (7) | C10—C11—C12—C13 | 0.28 (12) |
C2—C1—C6—C5 | −1.12 (11) | C11—C12—C13—F1 | 179.36 (7) |
F3—C5—C6—N1 | −1.62 (11) | C11—C12—C13—C8 | −0.01 (12) |
C4—C5—C6—N1 | 178.32 (8) | C9—C8—C13—F1 | −179.82 (6) |
F3—C5—C6—C1 | −178.93 (7) | C7—C8—C13—F1 | 1.51 (11) |
C4—C5—C6—C1 | 1.02 (12) | C9—C8—C13—C12 | −0.44 (11) |
C6—N1—C7—C8 | −59.79 (9) | C7—C8—C13—C12 | −179.11 (7) |
C6—N1—C7—C14 | 176.04 (7) | N1—C7—C14—C15 | −174.60 (7) |
N1—C7—C8—C9 | 134.28 (7) | C8—C7—C14—C15 | 59.43 (9) |
C14—C7—C8—C9 | −103.22 (8) | C7—C14—C15—C16 | −122.17 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···F1 | 0.886 (17) | 2.510 (14) | 2.8354 (9) | 102.4 (11) |
N1—H1N1···F3 | 0.886 (17) | 2.306 (17) | 2.6839 (9) | 105.7 (14) |
N1—H1N1···F1i | 0.886 (17) | 2.194 (17) | 3.0639 (9) | 167.1 (16) |
C7—H7A···F2 | 0.98 | 2.38 | 2.8330 (10) | 107 |
Symmetry code: (i) −x+2, −y+1, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C16H13ClF3N |
Mr | 311.72 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 10.8980 (1), 14.0073 (2), 10.1651 (1) |
β (°) | 113.018 (1) |
V (Å3) | 1428.17 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.29 |
Crystal size (mm) | 0.50 × 0.39 × 0.27 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.868, 0.926 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 32850, 7434, 6099 |
Rint | 0.025 |
(sin θ/λ)max (Å−1) | 0.856 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.119, 1.04 |
No. of reflections | 7434 |
No. of parameters | 202 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.63, −0.86 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···F1 | 0.886 (17) | 2.510 (14) | 2.8354 (9) | 102.4 (11) |
N1—H1N1···F3 | 0.886 (17) | 2.306 (17) | 2.6839 (9) | 105.7 (14) |
N1—H1N1···F1i | 0.886 (17) | 2.194 (17) | 3.0639 (9) | 167.1 (16) |
C7—H7A···F2 | 0.98 | 2.38 | 2.8330 (10) | 107 |
Symmetry code: (i) −x+2, −y+1, −z+2. |
Acknowledgements
AMI is grateful to the Head of the Department of Chemistry and the Director, NITK, Surathkal, India, for providing research facilities. SR thanks Dr Gautam Das, Syngene International Limited, Bangalore, India, for allocation of research resources. The authors also thank Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.
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Homoallylic amines are valuable intermediates in organic synthesis and as starting materials in the preparation of biologically active substances, resolving agents and chiral auxillaries for asymmetric synthesis (Sabine & Horst, 1991) and synthesis of β-amino acids (Xie et al., 1989), β-lactams (Edwards et al., 1998) and HIV-proteaseinhibitors (Robert, 1998). Prompted by these observations, we have synthesized the title compound and its crystal structure is presented herein.
In the molecular structure of the title homoallylic amine (I) (Fig. 1), angle between the mean planes of the benzene rings is 84.63 (4)°. The orientation of the but-3-enyl substituent group [C7/C14–C16] with respect to the 2,6-difluoro-phenyl ring is reflected in the torsion angle C8–C7–C14–C15 = 59.43 (9)° which indicates a (+)-syn-clinal conformation. The torsion angle C7–C14–C15–C16 = -122.17 (11)°. The bond distances in (I) have normal values (Allen et al., 1987).
In the structure, intramolecular N1—H1N1···F1 and N1—H1N1···F3 hydrogen bonds generate S(6) and S(5) ring motifs, respectively (Bernstein et al., 1995) (Table 1). In the crystal structure, weak N—H···F hydrogen bonds (Table 1, Fig. 2) link molecules into centrosymmetric dimers and these dimers are arranged into molecular sheets parallel to the ac plane.