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The title compound, C18H22N2O2S, is of inter­est with respect to anti­bacterial and anti­cancer activity and it has shown good trypanocidal activity. The mol­ecular packing lacks classical hydrogen bonds, being mediated only by weak van der Waals forces.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807019964/cf2100sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807019964/cf2100Isup2.hkl
Contains datablock I

CCDC reference: 601660

Key indicators

  • Single-crystal X-ray study
  • T = 297 K
  • Mean [sigma](C-C) = 0.005 Å
  • Disorder in main residue
  • R factor = 0.052
  • wR factor = 0.135
  • Data-to-parameter ratio = 9.5

checkCIF/PLATON results

No syntax errors found



Alert level B PLAT220_ALERT_2_B Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.63 Ratio
Alert level C PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.79 Ratio PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C17 PLAT245_ALERT_2_C U(iso) H17B Smaller than U(eq) C18B by ... 0.03 AngSq PLAT301_ALERT_3_C Main Residue Disorder ......................... 4.00 Perc. PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 5
Alert level G REFLT03_ALERT_4_G WARNING: Large fraction of Friedel related reflns may be needed to determine absolute structure From the CIF: _diffrn_reflns_theta_max 67.13 From the CIF: _reflns_number_total 2034 Count of symmetry unique reflns 1764 Completeness (_total/calc) 115.31% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 270 Fraction of Friedel pairs measured 0.153 Are heavy atom types Z>Si present yes
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

In continuation of our solid-state studies of bioactive thioxopyrimidine, we performed the crystallographic characterization of the title 4-thioxopyrimidine (I), which exhibited a lowered antifungal but enhanced trypanocidal activities compared to related compounds (Cunha et al., 2007).

The molecule of (I) is depicted in Fig. 1. This derivative differs from those of Parts 1 and 2 by a substituent on the ring atom N1, where (I) has a butyl group instead of a hydroxyethyl group. The conformation of compound (I) is defined by steric effects. The pyrimidine ring is planar with an r.m.s. deviation of 0.022 Å. With reference to this plane, the phenyl ring is rotated by 65.0 (1)°, approaching a gauche conformation. The torsion angles C4—C5—C14—O15 and C20—C19—N1—C6 are -99.3 (4)° and -92.9 (3)°, respectively. Bond lengths are within the expected ranges with the exception of the C2–C7 and C5–C14 bonds which are elongated by an average of 0.035 Å from the formal single bond distance.

It is interesting to note that the crystal packing of compound (I) is maintained by van der Waals forces only; it does not form dimers involving CO···π-ring interactions as observed in the previous derivatives. It is supposed that the steric inaccessibility due to the long butyl substituent group prevents the pyrimidine ring stacking. The packing is shown in Fig. 2.

Related literature top

For the synthesis, see: Cunha et al. (2007). A butyl group on atom N1 in this structure replaces a hydroxyethyl group in the derivatives described in the preceding papers (Sabino, Lariucci et al., 2007; Sabino, Vencato et al., 2007). Owing to the different chemical nature of the butyl group, the title compound does not pack in the same manner and lacks the intermolecular hydrogen-bond contacts observed in the previous derivatives.

Experimental top

Compound (I) (m.p. 447.6–448.6 K) was prepared according to a known procedure (Cunha et al., 2007). Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution in CHCl3 at room temperature.

Refinement top

All H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H distances in the range 0.93–0.97 Å, and with Uiso(H) = 1.5Ueq(C) for methyl H atoms and Uiso(H) = 1.2Ueq(C) for other atoms. The C18 methyl atom were modelled as a disordered group over two sites with refined occupancies 0.80 (2) and 0.20 (2), and refined with equal displacement parameter constraints. In consequence, the bond length C17–C18 was poorly determined. The whole carboxylate group is possibly disordered by a rotation around the C5–C14 σ-bond, but this could not be modelled reliably.

Structure description top

In continuation of our solid-state studies of bioactive thioxopyrimidine, we performed the crystallographic characterization of the title 4-thioxopyrimidine (I), which exhibited a lowered antifungal but enhanced trypanocidal activities compared to related compounds (Cunha et al., 2007).

The molecule of (I) is depicted in Fig. 1. This derivative differs from those of Parts 1 and 2 by a substituent on the ring atom N1, where (I) has a butyl group instead of a hydroxyethyl group. The conformation of compound (I) is defined by steric effects. The pyrimidine ring is planar with an r.m.s. deviation of 0.022 Å. With reference to this plane, the phenyl ring is rotated by 65.0 (1)°, approaching a gauche conformation. The torsion angles C4—C5—C14—O15 and C20—C19—N1—C6 are -99.3 (4)° and -92.9 (3)°, respectively. Bond lengths are within the expected ranges with the exception of the C2–C7 and C5–C14 bonds which are elongated by an average of 0.035 Å from the formal single bond distance.

It is interesting to note that the crystal packing of compound (I) is maintained by van der Waals forces only; it does not form dimers involving CO···π-ring interactions as observed in the previous derivatives. It is supposed that the steric inaccessibility due to the long butyl substituent group prevents the pyrimidine ring stacking. The packing is shown in Fig. 2.

For the synthesis, see: Cunha et al. (2007). A butyl group on atom N1 in this structure replaces a hydroxyethyl group in the derivatives described in the preceding papers (Sabino, Lariucci et al., 2007; Sabino, Vencato et al., 2007). Owing to the different chemical nature of the butyl group, the title compound does not pack in the same manner and lacks the intermolecular hydrogen-bond contacts observed in the previous derivatives.

Computing details top

Data collection: CAD-4-PC (Enraf–Nonius, 1993); cell refinement: CAD-4-PC; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitray radius.
[Figure 2] Fig. 2. Packing diagram of (I).
Ethyl 1-butyl-6-methyl-2-phenyl-4-thioxo-1,4-dihydropyrimidine-5-carboxylate top
Crystal data top
C18H22N2O2SF(000) = 352
Mr = 330.45Dx = 1.208 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54180 Å
Hall symbol: P 2ybCell parameters from 25 reflections
a = 10.9870 (18) Åθ = 12.9–40.6°
b = 7.2840 (14) ŵ = 1.66 mm1
c = 12.5885 (13) ÅT = 297 K
β = 115.591 (9)°Prism, yellow
V = 908.6 (3) Å30.35 × 0.25 × 0.05 mm
Z = 2
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.047
ω/2θ scansθmax = 67.1°, θmin = 3.9°
Absorption correction: ψ scan
(North et al., 1968)
h = 1311
Tmin = 0.594, Tmax = 0.922k = 18
2129 measured reflectionsl = 015
2034 independent reflections2 standard reflections every 120 min
1907 reflections with I > 2σ(I) intensity decay: 2%
Refinement top
Refinement on F2 w = 1/[σ2(Fo2) + (0.1111P)2 + 0.0314P]
where P = (Fo2 + 2Fc2)/3
Least-squares matrix: full(Δ/σ)max < 0.001
R[F2 > 2σ(F2)] = 0.052Δρmax = 0.28 e Å3
wR(F2) = 0.136Δρmin = 0.44 e Å3
S = 1.09Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
2034 reflectionsExtinction coefficient: 0.034 (3)
214 parametersAbsolute structure: Flack (1983), 270 Friedel pairs
1 restraintAbsolute structure parameter: 0.10 (3)
H-atom parameters constrained
Crystal data top
C18H22N2O2SV = 908.6 (3) Å3
Mr = 330.45Z = 2
Monoclinic, P21Cu Kα radiation
a = 10.9870 (18) ŵ = 1.66 mm1
b = 7.2840 (14) ÅT = 297 K
c = 12.5885 (13) Å0.35 × 0.25 × 0.05 mm
β = 115.591 (9)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
1907 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.047
Tmin = 0.594, Tmax = 0.9222 standard reflections every 120 min
2129 measured reflections intensity decay: 2%
2034 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.052H-atom parameters constrained
wR(F2) = 0.136Δρmax = 0.28 e Å3
S = 1.09Δρmin = 0.44 e Å3
2034 reflectionsAbsolute structure: Flack (1983), 270 Friedel pairs
214 parametersAbsolute structure parameter: 0.10 (3)
1 restraint
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
S0.77081 (9)0.15710 (13)0.75355 (7)0.0651 (3)
N10.7310 (2)0.5282 (3)0.46126 (19)0.0458 (5)
C20.7929 (2)0.3596 (4)0.4803 (2)0.0423 (6)
N30.8080 (2)0.2499 (4)0.5663 (2)0.0466 (5)
C40.7614 (3)0.3022 (4)0.6479 (2)0.0463 (6)
C50.7055 (2)0.4821 (4)0.6357 (2)0.0462 (6)
C60.6850 (3)0.5898 (4)0.5420 (2)0.0476 (6)
C70.8475 (2)0.2935 (4)0.3973 (2)0.0435 (6)
C80.7920 (3)0.1380 (5)0.3314 (2)0.0508 (7)
H80.71910.08060.33650.061*
C90.8442 (3)0.0673 (6)0.2581 (3)0.0632 (8)
H90.80660.03780.21420.076*
C100.9521 (3)0.1521 (7)0.2496 (3)0.0665 (9)
H100.98740.10410.20020.08*
C111.0069 (3)0.3070 (7)0.3139 (3)0.0681 (10)
H111.07840.36520.30690.082*
C120.9574 (3)0.3781 (5)0.3895 (3)0.0575 (8)
H120.9970.48140.43460.069*
C130.6183 (4)0.7740 (6)0.5228 (3)0.0734 (10)
H13A0.5420.77650.44710.11*
H13B0.68140.86740.52590.11*
H13C0.58880.79630.58320.11*
C140.6638 (3)0.5473 (5)0.7281 (3)0.0556 (7)
O150.5505 (2)0.5468 (6)0.7192 (2)0.0825 (9)
O160.7694 (2)0.6091 (5)0.82076 (18)0.0664 (7)
C170.7489 (5)0.6655 (11)0.9216 (4)0.1002 (18)
H17A0.68630.76780.90030.12*
H17B0.71030.5650.94740.12*
C18A0.8742 (8)0.719 (3)1.0149 (7)0.154 (6)0.807 (19)
H18A0.87070.70031.0890.231*0.807 (19)
H18B0.89080.84611.00630.231*0.807 (19)
H18C0.94550.64581.01220.231*0.807 (19)
C18B0.843 (4)0.569 (11)1.019 (3)0.154 (6)0.193 (19)
H18D0.84990.6251.09030.231*0.193 (19)
H18E0.930.5731.01740.231*0.193 (19)
H18F0.8150.44391.01570.231*0.193 (19)
C190.7021 (3)0.6331 (5)0.3526 (2)0.0546 (7)
H19A0.7780.62130.33290.066*
H19B0.69280.7620.3670.066*
C200.5751 (3)0.5694 (5)0.2488 (2)0.0565 (7)
H20A0.49820.58360.26680.068*
H20B0.58320.44040.23380.068*
C210.5532 (4)0.6817 (7)0.1401 (2)0.0729 (10)
H21A0.550.81080.15760.087*
H21B0.62970.66380.12190.087*
C220.4257 (5)0.6321 (9)0.0332 (3)0.0909 (13)
H22A0.41740.70790.0320.136*
H22B0.34930.65140.04990.136*
H22C0.42930.50540.01370.136*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S0.0847 (5)0.0628 (5)0.0606 (4)0.0110 (4)0.0435 (4)0.0122 (4)
N10.0506 (11)0.0397 (12)0.0433 (11)0.0013 (10)0.0166 (9)0.0012 (10)
C20.0426 (11)0.0394 (14)0.0428 (12)0.0002 (10)0.0163 (10)0.0022 (11)
N30.0534 (11)0.0428 (13)0.0476 (11)0.0064 (11)0.0255 (9)0.0035 (11)
C40.0426 (12)0.0493 (15)0.0463 (13)0.0003 (12)0.0186 (10)0.0024 (13)
C50.0388 (11)0.0492 (16)0.0475 (13)0.0005 (11)0.0157 (9)0.0088 (12)
C60.0448 (12)0.0441 (14)0.0470 (13)0.0032 (11)0.0134 (10)0.0076 (12)
C70.0437 (12)0.0437 (14)0.0441 (12)0.0013 (11)0.0200 (9)0.0026 (12)
C80.0529 (13)0.0488 (17)0.0592 (14)0.0056 (13)0.0322 (11)0.0033 (14)
C90.0650 (16)0.070 (2)0.0627 (17)0.0080 (16)0.0350 (14)0.0179 (18)
C100.0630 (16)0.087 (3)0.0629 (16)0.008 (2)0.0401 (13)0.002 (2)
C110.0493 (14)0.088 (3)0.078 (2)0.0044 (17)0.0380 (14)0.005 (2)
C120.0467 (13)0.0606 (18)0.0642 (17)0.0108 (13)0.0230 (12)0.0040 (16)
C130.086 (2)0.057 (2)0.068 (2)0.026 (2)0.0248 (17)0.0021 (18)
C140.0483 (13)0.0607 (19)0.0589 (15)0.0017 (14)0.0243 (11)0.0098 (15)
O150.0518 (11)0.118 (3)0.0857 (15)0.0043 (14)0.0368 (10)0.0215 (18)
O160.0597 (11)0.0851 (18)0.0565 (11)0.0044 (12)0.0269 (9)0.0261 (12)
C170.096 (3)0.136 (5)0.077 (2)0.001 (3)0.044 (2)0.045 (3)
C18A0.100 (5)0.269 (19)0.080 (3)0.018 (7)0.027 (3)0.099 (8)
C18B0.100 (5)0.269 (19)0.080 (3)0.018 (7)0.027 (3)0.099 (8)
C190.0628 (15)0.0433 (16)0.0532 (14)0.0017 (13)0.0208 (12)0.0074 (14)
C200.0618 (15)0.0568 (18)0.0475 (14)0.0066 (15)0.0204 (11)0.0068 (15)
C210.085 (2)0.080 (3)0.0484 (15)0.003 (2)0.0241 (14)0.0064 (18)
C220.109 (3)0.093 (3)0.0504 (16)0.009 (3)0.0157 (17)0.003 (2)
Geometric parameters (Å, º) top
S—C41.666 (3)C14—O151.201 (3)
N1—C21.374 (4)C14—O161.319 (4)
N1—C61.390 (4)O16—C171.442 (4)
N1—C191.477 (4)C17—C18B1.40 (6)
C2—N31.297 (4)C17—C18A1.424 (10)
C2—C71.492 (4)C17—H17A0.97
N3—C41.385 (3)C17—H17B0.97
C4—C51.427 (4)C18A—H18A0.96
C5—C61.353 (4)C18A—H18B0.96
C5—C141.499 (4)C18A—H18C0.96
C6—C131.498 (5)C18B—H18D0.96
C7—C81.381 (4)C18B—H18E0.96
C7—C121.396 (4)C18B—H18F0.96
C8—C91.380 (4)C19—C201.515 (4)
C8—H80.93C19—H19A0.97
C9—C101.382 (5)C19—H19B0.97
C9—H90.93C20—C211.522 (4)
C10—C111.367 (7)C20—H20A0.97
C10—H100.93C20—H20B0.97
C11—C121.384 (5)C21—C221.508 (5)
C11—H110.93C21—H21A0.97
C12—H120.93C21—H21B0.97
C13—H13A0.96C22—H22A0.96
C13—H13B0.96C22—H22B0.96
C13—H13C0.96C22—H22C0.96
C2—N1—C6118.0 (2)C18B—C17—O16106.8 (16)
C2—N1—C19121.1 (2)C18A—C17—O16109.9 (4)
C6—N1—C19120.6 (2)C18B—C17—H17A142.5
N3—C2—N1124.9 (2)C18A—C17—H17A109.7
N3—C2—C7116.1 (2)O16—C17—H17A109.7
N1—C2—C7119.0 (2)C18B—C17—H17B66.2
C2—N3—C4119.7 (2)C18A—C17—H17B109.7
N3—C4—C5116.9 (3)O16—C17—H17B109.7
N3—C4—S120.2 (2)H17A—C17—H17B108.2
C5—C4—S122.9 (2)C17—C18A—H18A109.5
C6—C5—C4121.9 (2)C17—C18A—H18B109.5
C6—C5—C14120.1 (3)H18A—C18A—H18B109.5
C4—C5—C14118.0 (3)C17—C18A—H18C109.5
C5—C6—N1118.3 (3)H18A—C18A—H18C109.5
C5—C6—C13123.1 (3)H18B—C18A—H18C109.5
N1—C6—C13118.6 (3)C17—C18B—H18D109.5
C8—C7—C12119.4 (3)C17—C18B—H18E109.5
C8—C7—C2118.6 (2)H18D—C18B—H18E109.5
C12—C7—C2121.9 (3)C17—C18B—H18F109.5
C9—C8—C7120.3 (3)H18D—C18B—H18F109.5
C9—C8—H8119.8H18E—C18B—H18F109.5
C7—C8—H8119.8N1—C19—C20112.9 (3)
C8—C9—C10120.2 (4)N1—C19—H19A109
C8—C9—H9119.9C20—C19—H19A109
C10—C9—H9119.9N1—C19—H19B109
C11—C10—C9119.7 (3)C20—C19—H19B109
C11—C10—H10120.1H19A—C19—H19B107.8
C9—C10—H10120.1C19—C20—C21109.8 (3)
C10—C11—C12120.9 (3)C19—C20—H20A109.7
C10—C11—H11119.6C21—C20—H20A109.7
C12—C11—H11119.6C19—C20—H20B109.7
C11—C12—C7119.4 (3)C21—C20—H20B109.7
C11—C12—H12120.3H20A—C20—H20B108.2
C7—C12—H12120.3C22—C21—C20113.5 (4)
C6—C13—H13A109.5C22—C21—H21A108.9
C6—C13—H13B109.5C20—C21—H21A108.9
H13A—C13—H13B109.5C22—C21—H21B108.9
C6—C13—H13C109.5C20—C21—H21B108.9
H13A—C13—H13C109.5H21A—C21—H21B107.7
H13B—C13—H13C109.5C21—C22—H22A109.5
O15—C14—O16124.3 (3)C21—C22—H22B109.5
O15—C14—C5125.3 (3)H22A—C22—H22B109.5
O16—C14—C5110.3 (2)C21—C22—H22C109.5
C14—O16—C17117.6 (3)H22A—C22—H22C109.5
C18B—C17—C18A48 (3)H22B—C22—H22C109.5
C6—N1—C2—N32.4 (4)N3—C2—C7—C12112.8 (3)
C19—N1—C2—N3171.8 (3)N1—C2—C7—C1267.4 (4)
C6—N1—C2—C7177.8 (2)C12—C7—C8—C90.3 (5)
C19—N1—C2—C78.0 (3)C2—C7—C8—C9176.8 (3)
N1—C2—N3—C40.9 (4)C7—C8—C9—C100.3 (5)
C7—C2—N3—C4179.3 (2)C8—C9—C10—C110.2 (6)
C2—N3—C4—C53.6 (3)C9—C10—C11—C121.3 (6)
C2—N3—C4—S175.89 (19)C10—C11—C12—C71.9 (6)
N3—C4—C5—C67.1 (4)C8—C7—C12—C111.4 (5)
S—C4—C5—C6172.4 (2)C2—C7—C12—C11177.7 (3)
N3—C4—C5—C14175.5 (2)C6—C5—C14—O1578.1 (5)
S—C4—C5—C145.0 (3)C4—C5—C14—O1599.3 (4)
C4—C5—C6—N15.7 (4)C6—C5—C14—O16100.7 (3)
C14—C5—C6—N1176.9 (2)C4—C5—C14—O1681.8 (4)
C4—C5—C6—C13175.9 (3)O15—C14—O16—C175.4 (7)
C14—C5—C6—C131.5 (4)C5—C14—O16—C17175.8 (4)
C2—N1—C6—C51.0 (4)C14—O16—C17—C18B126 (3)
C19—N1—C6—C5175.2 (2)C14—O16—C17—C18A177.0 (9)
C2—N1—C6—C13179.5 (3)C2—N1—C19—C2081.1 (3)
C19—N1—C6—C136.3 (4)C6—N1—C19—C2092.9 (3)
N3—C2—C7—C863.6 (3)N1—C19—C20—C21179.2 (3)
N1—C2—C7—C8116.2 (3)C19—C20—C21—C22177.8 (4)

Experimental details

Crystal data
Chemical formulaC18H22N2O2S
Mr330.45
Crystal system, space groupMonoclinic, P21
Temperature (K)297
a, b, c (Å)10.9870 (18), 7.2840 (14), 12.5885 (13)
β (°) 115.591 (9)
V3)908.6 (3)
Z2
Radiation typeCu Kα
µ (mm1)1.66
Crystal size (mm)0.35 × 0.25 × 0.05
Data collection
DiffractometerEnraf–Nonius CAD-4
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.594, 0.922
No. of measured, independent and
observed [I > 2σ(I)] reflections
2129, 2034, 1907
Rint0.047
(sin θ/λ)max1)0.598
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.136, 1.09
No. of reflections2034
No. of parameters214
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.28, 0.44
Absolute structureFlack (1983), 270 Friedel pairs
Absolute structure parameter0.10 (3)

Computer programs: CAD-4-PC (Enraf–Nonius, 1993), CAD-4-PC, XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), WinGX (Farrugia, 1999).

 

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