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Synthesis and crystal structure of tert-butyl 1-(2-iodo­benzo­yl)cyclo­pent-3-ene-1-carboxyl­ate

aSchool of Biotechnology, Jiangnan University, Lihu Avenue 1800, Wuxi in Jiangsu Province, People's Republic of China
*Correspondence e-mail: ydjszlg@163.com

Edited by M. Weil, Vienna University of Technology, Austria (Received 8 July 2019; accepted 16 August 2019; online 30 August 2019)

1-(2-Iodo­benzo­yl)-cyclo­pent-3-ene-1-carboxyl­ates are novel substrates to construct bi­cyclo­[3.2.1]octa­nes with anti­bacterial and anti­thrombotic activities. In this context, tert-butyl 1-(2-iodo­benzo­yl)-cyclo­pent-3-ene-1-carboxyl­ate, C17H19IO3, was synthesized and structurally characterized. The 2-iodo­benzoyl group is attached to the tertiary C atom of the cyclo­pent-3-ene ring. The dihedral angle between the benzene ring and the mean plane of the envelope-type cyclo­pent-3-ene ring is 26.0 (3)°. In the crystal, pairs of C-H⋯O hydrogen bonds link the mol­ecules to form inversion dimers.

1. Chemical context

1-(2-Iodo­benzo­yl)cyclo­pent-3-ene-1-carboxyl­ates were recently employed as novel substrates to construct bi­cyclo­[3.2.1]octa­nes that are widely found in natural products and bioactive mol­ecules with anti­bacterial and anti­thrombotic activities (Yuan et al., 2019[Yuan, Z. B., Feng, Z. W., Zeng, Y. Y., Zhao, X. B., Lin, A. J. & Yao, H. Q. (2019). Angew. Chem. Int. Ed. 58, 2884-2888.]). Although the authors carried out some control experiments to reveal the reaction mechanism, crystal structures of the substrates have not been reported yet. Moreover, 1-(2-iodo­benzo­yl)cyclo­pent-3-ene is crucial to the reductive Heck reaction and thus may provide more direct information on this reaction mechanism if more detailed structural data are available. Herein, the synthesis and crystal structure of tert-butyl 1-(2-iodo­benzo­yl)cyclo­pent-3-ene-1-carboxyl­ate are reported.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The 2-iodo­benzoyl group is attached to the tertiary C atom (C8) of the cyclo­pent-3-ene ring, with the tert-butyl carboxyl­ate group as the other substituent. The five-membered C8–C12 ring adopts an envelope conformation, with atom C8 as the flap, and with puckering parameters (Cremer & Pople, 1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]) Q = 0.1526 Å and φ = 0.5354°, and pseudo-rotation parameters (Rao et al., 1981[Rao, S. T., Westhof, E. & Sundaralingam, M. (1981). Acta Cryst. A37, 421-425.]) P = 162.5 (1)° and τ(M) = 15.2 (3)°. The deviation of C8 from the mean plane defined by atoms C9–C12 is 0.097 (4) Å. The dihedral angle between the benzene ring and the alkene plane (C9–C12) of the cyclo­pent-3-ene ring is 26.51 (19)°.

[Figure 1]
Figure 1
The mol­ecular structure of title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 20% probability level.

3. Supra­molecular features

In the crystal, mol­ecules are linked by a pair of C—H⋯O hydrogen bonds forming inversion dimers (Table 1[link] and Fig. 2[link]). They stack up the b axis and form layers parallel to the bc plane. There are no other significant inter­molecular inter­actions present in the crystal.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯O3i 0.93 2.48 3.219 (5) 136
Symmetry code: (i) -x+1, -y+1, -z+1.
[Figure 2]
Figure 2
A view along [010] of the crystal packing of the title compound. The inter­molecular C—H⋯O hydrogen bonds are shown as orange dashed lines (Table 1[link]).

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.39, update of August 2018; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for entities containing (1-methyl­cyclo­pent-3-en-1-yl)(phen­yl)methanone yielded 27 hits. Only two of these compounds involve no other substituents at the cyclo­pent-3-ene ring as in the title compound, viz. methyl 4-[(1-methyl­cyclo­pent-3-en-1-yl)carbon­yl]benzoate in the space group Pnma (CSD refcode CIQHAM; Yang et al., 2007[Yang, C., Xia, W., Zhang, X., Li, B. & Gou, B. (2007). Acta Cryst. E63, o4729.]), and 4-benzoyl-4-(meth­oxy­carbon­yl)cyclo­pentene in the space group P21/c, with four independent mol­ecules in the asymmetric unit (CSD refcode KOGSIJ; Jiang et al., 2008[Jiang, X. F., Ma, X. J., Zheng, Z. L. & Ma, S. M. (2008). Chem. Eur. J. 14, 8572-8578.]). In the structures of these two compounds, the folding angles of the cyclo­pent-3-ene ring are 17.00 (13) and 11.91 (12)°, respectively, while in the title compound it is 15.0 (3)°. The benzene ring in each structure is inclined to the alkene plane of the cyclo­pent-3-ene ring by 90.00 (8) and 61.40 (6)°, respectively, while the corresponding dihedral angle in the title compound is 26.51 (19)°. Apparently, different kinds of inter­molecular C—H⋯O hydrogen bonds and the presence or not of weak ππ contacts in the three structures lead to different mol­ecular packing and dihedral angles between the benzene ring and the cyclo­pent-3-ene ring.

5. Synthesis and crystallization

The title compound was prepared according to a general literature protocol (Yuan et al., 2019[Yuan, Z. B., Feng, Z. W., Zeng, Y. Y., Zhao, X. B., Lin, A. J. & Yao, H. Q. (2019). Angew. Chem. Int. Ed. 58, 2884-2888.]). 1H NMR (300 MHz, CDCl3): δ 8.0 (dd, J = 7.9, 1.2 Hz, 1H), 7.4 (dd, J = 7.8, 1.8 Hz, 1H), 7.3 (td, J = 7.5, 1.2 Hz, 1H), 7.1 (td, J = 7.8, 1.8 Hz, 1H), 5.6 (s, 2H), 3.1 (s, 4H), 1.2 (s, 9H). HRMS (ESI) calcd for [C17H19IO3+Na]+ 421.0271, found 421.0272. Crystallization from a 5:1 mixture (v/v) of di­chloro­methane and n-hexane by slow evaporation at room temperature for about 7 d gave block-shaped crystals of the title compound.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms attached to C atoms were included in calculated positions and refined using a riding model: C—H = 0.93-0.97 Å with Uiso(H) = 1.5Ueq(C-meth­yl) and 1.2Ueq(C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula C17H19IO3
Mr 398.22
Crystal system, space group Monoclinic, P21/c
Temperature (K) 299
a, b, c (Å) 9.4977 (2), 9.3635 (2), 19.8978 (4)
β (°) 102.752 (1)
V3) 1725.90 (6)
Z 4
Radiation type Cu Kα
μ (mm−1) 14.64
Crystal size (mm) 0.3 × 0.2 × 0.1
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.262, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections 16056, 3278, 2612
Rint 0.066
(sin θ/λ)max−1) 0.610
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.131, 1.06
No. of reflections 3278
No. of parameters 193
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.61, −1.22
Computer programs: APEX3 and SAINT (Bruker, 2014[Bruker (2014). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Computing details top

Data collection: APEX3 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

tert-Butyl 1-(2-iodobenzoyl)-cyclopent-3-ene-1-carboxylate top
Crystal data top
C17H19IO3F(000) = 792
Mr = 398.22Dx = 1.533 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
a = 9.4977 (2) ÅCell parameters from 5961 reflections
b = 9.3635 (2) Åθ = 4.6–69.9°
c = 19.8978 (4) ŵ = 14.64 mm1
β = 102.752 (1)°T = 299 K
V = 1725.90 (6) Å3Block, colourless
Z = 40.3 × 0.2 × 0.1 mm
Data collection top
Bruker APEXII CCD
diffractometer
2612 reflections with I > 2σ(I)
φ and ω scansRint = 0.066
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
θmax = 70.1°, θmin = 4.6°
Tmin = 0.262, Tmax = 0.753h = 1011
16056 measured reflectionsk = 1111
3278 independent reflectionsl = 2422
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.131H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0548P)2 + 2.0895P]
where P = (Fo2 + 2Fc2)/3
3278 reflections(Δ/σ)max < 0.001
193 parametersΔρmax = 0.61 e Å3
0 restraintsΔρmin = 1.22 e Å3
Special details top

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.22879 (4)0.41049 (5)0.17053 (2)0.0858 (2)
O10.1852 (4)0.6510 (4)0.28314 (19)0.0681 (9)
C10.3928 (4)0.5060 (4)0.3155 (2)0.0425 (8)
O20.2177 (3)0.3021 (3)0.37481 (14)0.0444 (6)
C20.5151 (4)0.5150 (5)0.3679 (2)0.0489 (9)
H20.5099860.5624490.4083730.059*
O30.3190 (4)0.3762 (3)0.48200 (17)0.0596 (8)
C30.6447 (5)0.4554 (6)0.3617 (3)0.0581 (12)
H30.7260780.4638180.3973920.07*
C40.6522 (5)0.3836 (6)0.3024 (3)0.0647 (13)
H40.7388760.342430.2980790.078*
C70.2544 (4)0.5741 (4)0.3257 (2)0.0442 (9)
C60.4034 (5)0.4366 (5)0.2548 (2)0.0496 (10)
C50.5325 (5)0.3725 (6)0.2497 (3)0.0613 (12)
H50.5377680.3215760.210150.074*
C80.2122 (4)0.5470 (4)0.3950 (2)0.0407 (8)
C90.0444 (4)0.5578 (5)0.3866 (3)0.0528 (11)
H9A0.0004470.6018730.3429830.063*
H9B0.0021670.4641740.3890890.063*
C100.0274 (5)0.6489 (5)0.4456 (3)0.0600 (12)
H100.0602860.6631860.4580920.072*
C110.1492 (6)0.7068 (5)0.4781 (3)0.0612 (12)
H110.1568170.7667260.5159510.073*
C120.2749 (5)0.6666 (5)0.4479 (2)0.0506 (10)
H12A0.3544220.6307680.4831330.061*
H12B0.3079660.7474730.4251310.061*
C130.2590 (4)0.4002 (4)0.4236 (2)0.0397 (8)
C140.2441 (5)0.1481 (5)0.3876 (3)0.0530 (10)
C150.1631 (9)0.0987 (6)0.4407 (4)0.091 (2)
H15A0.0708190.1451760.4328020.137*
H15B0.2176240.1224190.4859730.137*
H15C0.1494920.0028290.4372330.137*
C160.1791 (7)0.0833 (6)0.3183 (3)0.0763 (16)
H16A0.0799780.1122540.3040440.114*
H16B0.1842210.0188890.3216270.114*
H16C0.2316210.1154160.2850770.114*
C170.4050 (6)0.1218 (6)0.4074 (4)0.0851 (19)
H17A0.4504570.1652240.3739230.128*
H17B0.4232460.0208490.4088840.128*
H17C0.4435610.162550.4519080.128*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0721 (3)0.1182 (4)0.0569 (2)0.0009 (2)0.00751 (17)0.0218 (2)
O10.0613 (19)0.078 (2)0.065 (2)0.0208 (17)0.0140 (17)0.0253 (18)
C10.0403 (19)0.045 (2)0.042 (2)0.0023 (16)0.0093 (16)0.0044 (17)
O20.0465 (14)0.0380 (14)0.0462 (15)0.0051 (11)0.0046 (12)0.0032 (12)
C20.041 (2)0.059 (3)0.046 (2)0.0017 (18)0.0091 (17)0.002 (2)
O30.074 (2)0.0489 (17)0.0468 (18)0.0025 (14)0.0058 (15)0.0017 (14)
C30.036 (2)0.079 (3)0.058 (3)0.002 (2)0.0082 (19)0.004 (2)
C40.046 (2)0.083 (4)0.068 (3)0.010 (2)0.019 (2)0.002 (3)
C70.040 (2)0.046 (2)0.045 (2)0.0018 (17)0.0072 (17)0.0028 (18)
C60.045 (2)0.058 (3)0.043 (2)0.0054 (18)0.0062 (17)0.0026 (19)
C50.067 (3)0.069 (3)0.053 (3)0.003 (2)0.024 (2)0.010 (2)
C80.0350 (18)0.043 (2)0.045 (2)0.0019 (15)0.0090 (15)0.0025 (17)
C90.0351 (19)0.063 (3)0.062 (3)0.0045 (18)0.0126 (18)0.005 (2)
C100.059 (3)0.061 (3)0.066 (3)0.020 (2)0.028 (2)0.014 (2)
C110.084 (3)0.044 (2)0.062 (3)0.012 (2)0.029 (3)0.001 (2)
C120.057 (2)0.043 (2)0.053 (2)0.0029 (18)0.015 (2)0.0033 (19)
C130.0361 (18)0.042 (2)0.041 (2)0.0002 (15)0.0096 (16)0.0013 (16)
C140.057 (2)0.035 (2)0.068 (3)0.0008 (18)0.016 (2)0.004 (2)
C150.143 (6)0.051 (3)0.096 (5)0.019 (3)0.061 (5)0.000 (3)
C160.087 (4)0.057 (3)0.082 (4)0.007 (3)0.013 (3)0.024 (3)
C170.067 (3)0.063 (3)0.117 (5)0.021 (3)0.002 (3)0.008 (3)
Geometric parameters (Å, º) top
I1—C62.096 (4)C9—H9A0.97
O1—C71.193 (5)C9—H9B0.97
C1—C21.382 (6)C10—C111.312 (8)
C1—C61.395 (6)C10—H100.93
C1—C71.514 (5)C11—C121.497 (6)
O2—C131.331 (5)C11—H110.93
O2—C141.476 (5)C12—H12A0.97
C2—C31.382 (6)C12—H12B0.97
C2—H20.93C14—C161.508 (8)
O3—C131.197 (5)C14—C151.511 (8)
C3—C41.373 (7)C14—C171.512 (7)
C3—H30.93C15—H15A0.96
C4—C51.371 (7)C15—H15B0.96
C4—H40.93C15—H15C0.96
C7—C81.540 (6)C16—H16A0.96
C6—C51.389 (7)C16—H16B0.96
C5—H50.93C16—H16C0.96
C8—C131.516 (5)C17—H17A0.96
C8—C121.561 (6)C17—H17B0.96
C8—C91.568 (5)C17—H17C0.96
C9—C101.489 (7)
C2—C1—C6118.2 (4)C10—C11—C12113.1 (4)
C2—C1—C7118.9 (4)C10—C11—H11123.4
C6—C1—C7122.9 (4)C12—C11—H11123.4
C13—O2—C14122.5 (3)C11—C12—C8103.4 (4)
C1—C2—C3121.7 (4)C11—C12—H12A111.1
C1—C2—H2119.2C8—C12—H12A111.1
C3—C2—H2119.2C11—C12—H12B111.1
C4—C3—C2119.4 (4)C8—C12—H12B111.1
C4—C3—H3120.3H12A—C12—H12B109.1
C2—C3—H3120.3O3—C13—O2125.3 (4)
C5—C4—C3120.2 (4)O3—C13—C8124.9 (4)
C5—C4—H4119.9O2—C13—C8109.7 (3)
C3—C4—H4119.9O2—C14—C16102.5 (4)
O1—C7—C1121.2 (4)O2—C14—C15109.0 (4)
O1—C7—C8121.5 (4)C16—C14—C15110.4 (5)
C1—C7—C8117.1 (3)O2—C14—C17109.1 (4)
C5—C6—C1119.9 (4)C16—C14—C17111.1 (5)
C5—C6—I1116.5 (3)C15—C14—C17114.1 (6)
C1—C6—I1123.4 (3)C14—C15—H15A109.5
C4—C5—C6120.5 (4)C14—C15—H15B109.5
C4—C5—H5119.8H15A—C15—H15B109.5
C6—C5—H5119.8C14—C15—H15C109.5
C13—C8—C7111.9 (3)H15A—C15—H15C109.5
C13—C8—C12111.1 (3)H15B—C15—H15C109.5
C7—C8—C12110.5 (3)C14—C16—H16A109.5
C13—C8—C9107.8 (3)C14—C16—H16B109.5
C7—C8—C9110.7 (3)H16A—C16—H16B109.5
C12—C8—C9104.7 (3)C14—C16—H16C109.5
C10—C9—C8103.7 (4)H16A—C16—H16C109.5
C10—C9—H9A111.0H16B—C16—H16C109.5
C8—C9—H9A111.0C14—C17—H17A109.5
C10—C9—H9B111.0C14—C17—H17B109.5
C8—C9—H9B111.0H17A—C17—H17B109.5
H9A—C9—H9B109.0C14—C17—H17C109.5
C11—C10—C9112.8 (4)H17A—C17—H17C109.5
C11—C10—H10123.6H17B—C17—H17C109.5
C9—C10—H10123.6
C6—C1—C2—C31.1 (7)C13—C8—C9—C10104.1 (4)
C7—C1—C2—C3179.9 (4)C7—C8—C9—C10133.3 (4)
C1—C2—C3—C40.9 (7)C12—C8—C9—C1014.3 (5)
C2—C3—C4—C50.6 (8)C8—C9—C10—C119.5 (5)
C2—C1—C7—O1130.7 (5)C9—C10—C11—C120.2 (6)
C6—C1—C7—O148.0 (6)C10—C11—C12—C89.2 (5)
C2—C1—C7—C845.7 (5)C13—C8—C12—C11101.9 (4)
C6—C1—C7—C8135.7 (4)C7—C8—C12—C11133.3 (4)
C2—C1—C6—C53.4 (6)C9—C8—C12—C1114.1 (4)
C7—C1—C6—C5177.9 (4)C14—O2—C13—O30.9 (6)
C2—C1—C6—I1179.2 (3)C14—O2—C13—C8178.2 (3)
C7—C1—C6—I12.2 (6)C7—C8—C13—O3133.6 (4)
C3—C4—C5—C61.7 (8)C12—C8—C13—O39.6 (5)
C1—C6—C5—C43.7 (7)C9—C8—C13—O3104.5 (5)
I1—C6—C5—C4179.8 (4)C7—C8—C13—O249.1 (4)
O1—C7—C8—C13150.6 (4)C12—C8—C13—O2173.1 (3)
C1—C7—C8—C1333.0 (5)C9—C8—C13—O272.8 (4)
O1—C7—C8—C1285.0 (5)C13—O2—C14—C16180.0 (4)
C1—C7—C8—C1291.3 (4)C13—O2—C14—C1563.0 (6)
O1—C7—C8—C930.4 (6)C13—O2—C14—C1762.2 (6)
C1—C7—C8—C9153.2 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O3i0.932.483.219 (5)136
Symmetry code: (i) x+1, y+1, z+1.
 

Acknowledgements

Generous financial support from the National Natural Science Foundation of China (21602084) is greatly acknowledged.

Funding information

Funding for this research was provided by: National Natural Science Foundation of China (grant No. 21602084).

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