metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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Tetra­aqua­bis­[(1-carboxyl­ato­methyl-1,3-benzimidazol-3-ium-3-yl)acetato-κO]palladium(II) dihydrate

aCollege of Food and Biological Engineering, Shandong Institute of Light Industry, Jinan 250353, People's Republic of China, bMaize Research Insitute, Shandong Academy of Agricultural Science, Jinan 250100, People's Republic of China, and cDepartment of Clinical Medicine, Medical School, Shandong University, Jinan 250012, People's Republic of China
*Correspondence e-mail: lujianghao001@yahoo.com.cn

(Received 13 April 2008; accepted 28 May 2008; online 7 June 2008)

In the title compound, [Pd(C11H9N2O4)2(H2O)4]·2H2O, the palladium(II) cation lies on an inversion centre and is hexa­coordinated by two carboxyl­ate O atoms from two (1-carboxyl­atomethyl-1,3-benzimidazol-3-ium-3-yl)acetate ligands and four water mol­ecules, with a slightly distorted octa­hedral geometry. O—H⋯O hydrogen bonds link the mol­ecules together.

Related literature

For uses of carboxylic acids in materials science, see: Church & Halvorson (1959[Church, B. S. & Halvorson, H. (1959). Nature (London), 183, 124-125.]). For uses in biological systems, see: Chung et al. (1971[Chung, L., Rajan, K. S., Merdinger, E. & Grecz, N. (1971). Biophys. J. 11, 469-482.]); Okabe & Oya (2000[Okabe, N. & Oya, N. (2000). Acta Cryst. C56, 1416-1417.]); Serre et al. (2005[Serre, C., Marrot, J. & Férey, G. (2005). Inorg. Chem. 44, 654-658.]); Pocker & Fong (1980[Pocker, Y. & Fong, C. T. O. (1980). Biochemistry, 19, 2045-2049.]); Scapin et al. (1997[Scapin, G., Reddy, S. G., Zheng, R. & Blanchard, J. S. (1997). Biochemistry, 36, 15081-15088.]); Kim et al. (2001[Kim, Y., Lee, E. & Jung, D. Y. (2001). Chem. Mater. 13, 2684-2690.]).

[Scheme 1]

Experimental

Crystal data
  • [Pd(C11H9N2O4)2(H2O)4]·2H2O

  • Mr = 680.90

  • Monoclinic, P 21 /n

  • a = 5.4702 (10) Å

  • b = 11.794 (2) Å

  • c = 20.886 (3) Å

  • β = 95.13 (3)°

  • V = 1342.1 (4) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.77 mm−1

  • T = 293 (2) K

  • 0.43 × 0.28 × 0.22 mm

Data collection
  • Bruker APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.733, Tmax = 0.849

  • 7075 measured reflections

  • 2425 independent reflections

  • 1958 reflections with I > 2σ(I)

  • Rint = 0.032

Refinement
  • R[F2 > 2σ(F2)] = 0.028

  • wR(F2) = 0.072

  • S = 1.00

  • 2425 reflections

  • 205 parameters

  • 9 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.24 e Å−3

  • Δρmin = −0.49 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O7—H1W⋯O4i 0.822 (10) 1.985 (14) 2.756 (3) 156 (3)
O7—H2W⋯O5i 0.821 (10) 1.937 (10) 2.747 (3) 169 (3)
Symmetry code: (i) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2004[Bruker (2004). APEX2, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

In recent years, carboxylates have been widely used as polydentate ligands, which can coordinate to transition or rare earth ions yielding complexes with interesting properties that are useful in materials science (Church & Halvorson, 1959; Chung et al., 1971) and in biological systems (Okabe & Oya, 2000; Serre et al., 2005; Pocker & Fong, 1980; Scapin et al., 1997). For example, Kim et al. (2001) focused on the syntheses of transition metal complexes containing benzenecarboxylate and rigid aromatic pyridine ligands in order to study their electronic conductivity and magnetic properties. The importance of transition metal dicarboxylate complexes motivated us to pursue synthetic strategies for these compounds, using sodium 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetate as a polydentate ligand. Here we report the synthesis and X-ray crystal structure analysis of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The palladium(II) cation lies on an inversion center and is hexacoordinated by two carboxylate oxygen atoms from two 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetato ligands and four water molecules, with a slightly distorted octahedral geometry. The Pd—O bond distances are in the range 2.2608 (19)–2.276 (2) Å. The packing involves hydrogen bonds, shown in Table 1 and Figure 2.

Related literature top

For uses of carboxylic acids in materials science, see: Church & Halvorson (1959). For uses in biological systems, see: Chung et al. (1971); Okabe & Oya (2000); Serre et al. (2005); Pocker & Fong (1980); Scapin et al. (1997); Kim et al. (2001).

Experimental top

A mixture of palladium dichloride (0.5 mmol), imidazole (1.0 mmol), sodium 1-carboxymethyl-1,3-benzimidazol-3-ium-3-acetate (0.5 mmol), water (8 ml) and ethanol (8 ml) in a 25 ml Teflon-lined stainless steel autoclave was kept at 413 K for three days. Colorless crystals were obtained after cooling to room temperature with a yield of 27%. Anal. Calc. for C22H30N4O14Pd: C 38.77, H 4.41, N 8.22%; Found: C 38.68, H 4.37, N 8.14%.

Refinement top

The H atoms of the water molecule were located in a difference density map and were refined with distance restraints H···H = 1.38 (2) Å, O—H = 0.88 (2) Å, and with a fixed Uiso of 0.80 Å2. All other H atoms were placed in calculated positions with a C—H bond distance of 0.93 Å and Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2004); data reduction: SAINT-Plus (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atomic numbering scheme and 30% probability displacement ellipsoids. [Symmetry code for unlabelled atoms: 1-x, 2-y, -z.]
[Figure 2] Fig. 2. The packing of (I) with hydrogen bonds shown as dashed lines.
Tetraaquabis[(1-carboxylatomethyl-1,3-benzimidazol-3-ium-3-yl)acetato- κO]palladium(II) dihydrate top
Crystal data top
[Pd(C11H9N2O4)2(H2O)4]·2H2OF(000) = 696
Mr = 680.90Dx = 1.685 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2425 reflections
a = 5.4702 (10) Åθ = 2.0–25.2°
b = 11.794 (2) ŵ = 0.77 mm1
c = 20.886 (3) ÅT = 293 K
β = 95.13 (3)°Block, colorless
V = 1342.1 (4) Å30.43 × 0.28 × 0.22 mm
Z = 2
Data collection top
Bruker APEXII CCD area-detector
diffractometer
2425 independent reflections
Radiation source: fine-focus sealed tube1958 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
ϕ and ω scansθmax = 25.2°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
h = 66
Tmin = 0.733, Tmax = 0.849k = 1314
7075 measured reflectionsl = 2413
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.072H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.042P)2]
where P = (Fo2 + 2Fc2)/3
2425 reflections(Δ/σ)max = 0.005
205 parametersΔρmax = 0.24 e Å3
9 restraintsΔρmin = 0.49 e Å3
Crystal data top
[Pd(C11H9N2O4)2(H2O)4]·2H2OV = 1342.1 (4) Å3
Mr = 680.90Z = 2
Monoclinic, P21/nMo Kα radiation
a = 5.4702 (10) ŵ = 0.77 mm1
b = 11.794 (2) ÅT = 293 K
c = 20.886 (3) Å0.43 × 0.28 × 0.22 mm
β = 95.13 (3)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer
2425 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
1958 reflections with I > 2σ(I)
Tmin = 0.733, Tmax = 0.849Rint = 0.032
7075 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0289 restraints
wR(F2) = 0.072H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.24 e Å3
2425 reflectionsΔρmin = 0.49 e Å3
205 parameters
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.

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
xyzUiso*/Ueq
Pd10.50001.00000.00000.02449 (11)
C10.7711 (5)1.0484 (2)0.14648 (12)0.0299 (6)
C20.5544 (5)0.9924 (2)0.17543 (12)0.0326 (6)
H2A0.40651.03540.16310.039*
H2B0.53160.91660.15780.039*
C30.4539 (5)1.0371 (2)0.28620 (12)0.0294 (6)
H30.32371.08580.27450.035*
C40.7676 (4)0.9208 (2)0.28035 (12)0.0279 (6)
C50.9568 (5)0.8536 (2)0.26202 (14)0.0365 (7)
H50.98340.84330.21900.044*
C61.1029 (6)0.8030 (3)0.31070 (17)0.0480 (8)
H61.23460.75860.30060.058*
C71.0587 (6)0.8166 (3)0.37470 (17)0.0540 (9)
H71.15950.77930.40620.065*
C80.8726 (6)0.8828 (3)0.39307 (15)0.0449 (7)
H80.84440.89160.43600.054*
C90.7282 (5)0.9361 (2)0.34427 (12)0.0299 (6)
C110.4355 (5)1.0558 (3)0.40327 (13)0.0369 (7)
H11A0.42760.99550.43460.044*
H11B0.26961.08310.39230.044*
C120.5910 (5)1.1527 (2)0.43369 (13)0.0347 (6)
H1W0.545 (5)0.681 (2)0.2365 (7)0.042*
H2W0.571 (4)0.693 (2)0.1719 (9)0.042*
H3W0.160 (5)1.1619 (14)0.0196 (13)0.042*
H4W0.074 (4)1.078 (2)0.0568 (12)0.042*
H5W0.503 (3)0.7896 (18)0.0589 (13)0.042*
H6W0.270 (3)0.799 (2)0.0290 (13)0.042*
N10.5889 (4)0.98516 (17)0.24523 (11)0.0290 (5)
N20.5306 (4)1.01001 (17)0.34575 (11)0.0301 (5)
O10.1897 (3)1.09974 (17)0.03739 (10)0.0394 (5)
O20.3926 (4)0.83292 (17)0.04423 (10)0.0451 (5)
O30.7682 (3)1.03890 (18)0.08641 (9)0.0384 (5)
O40.9339 (4)1.09448 (18)0.18150 (9)0.0460 (5)
O50.7726 (4)1.1842 (2)0.40763 (11)0.0650 (7)
O60.5172 (3)1.19231 (18)0.48365 (9)0.0439 (5)
O70.4821 (4)0.7010 (2)0.20114 (10)0.0485 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02495 (17)0.02873 (18)0.01952 (16)0.00361 (11)0.00047 (11)0.00121 (11)
C10.0280 (14)0.0368 (15)0.0252 (15)0.0003 (12)0.0035 (11)0.0001 (12)
C20.0323 (15)0.0429 (17)0.0225 (14)0.0058 (12)0.0013 (12)0.0005 (11)
C30.0301 (14)0.0302 (14)0.0285 (15)0.0017 (11)0.0057 (12)0.0005 (11)
C40.0297 (14)0.0259 (14)0.0280 (14)0.0057 (11)0.0025 (11)0.0017 (11)
C50.0348 (15)0.0316 (16)0.0433 (18)0.0014 (12)0.0053 (13)0.0082 (13)
C60.0394 (17)0.0315 (17)0.072 (2)0.0073 (13)0.0003 (16)0.0058 (15)
C70.055 (2)0.042 (2)0.061 (2)0.0064 (16)0.0148 (17)0.0110 (16)
C80.0555 (19)0.0411 (18)0.0369 (17)0.0030 (15)0.0020 (14)0.0067 (13)
C90.0336 (15)0.0261 (15)0.0295 (15)0.0037 (12)0.0007 (11)0.0001 (11)
C110.0397 (16)0.0461 (18)0.0264 (15)0.0038 (14)0.0115 (12)0.0088 (13)
C120.0360 (15)0.0362 (16)0.0322 (16)0.0023 (12)0.0049 (12)0.0056 (12)
N10.0282 (12)0.0365 (14)0.0227 (12)0.0006 (9)0.0046 (9)0.0024 (9)
N20.0342 (13)0.0327 (13)0.0239 (12)0.0027 (9)0.0058 (10)0.0037 (9)
O10.0368 (11)0.0391 (12)0.0445 (13)0.0023 (9)0.0158 (9)0.0021 (9)
O20.0349 (12)0.0429 (13)0.0558 (14)0.0055 (9)0.0058 (10)0.0164 (10)
O30.0353 (11)0.0585 (13)0.0212 (11)0.0095 (9)0.0023 (8)0.0004 (9)
O40.0425 (12)0.0675 (15)0.0279 (11)0.0240 (10)0.0021 (9)0.0049 (9)
O50.0650 (16)0.0750 (17)0.0596 (15)0.0360 (13)0.0314 (13)0.0339 (13)
O60.0475 (13)0.0510 (14)0.0339 (11)0.0038 (9)0.0067 (9)0.0152 (9)
O70.0458 (13)0.0635 (15)0.0366 (13)0.0001 (11)0.0067 (10)0.0083 (11)
Geometric parameters (Å, º) top
Pd1—O12.2608 (19)C6—C71.389 (4)
Pd1—O1i2.2608 (19)C6—H60.930
Pd1—O32.2687 (19)C7—C81.364 (5)
Pd1—O3i2.2687 (19)C7—H70.930
Pd1—O2i2.276 (2)C8—C91.383 (4)
Pd1—O22.276 (2)C8—H80.930
C1—O41.227 (3)C9—N21.392 (3)
C1—O31.258 (3)C11—N21.455 (3)
C1—C21.529 (4)C11—C121.528 (4)
C2—N11.456 (3)C11—H11A0.970
C2—H2A0.970C11—H11B0.970
C2—H2B0.970C12—O51.232 (3)
C3—N21.316 (4)C12—O61.243 (3)
C3—N11.329 (3)O1—H3W0.832 (10)
C3—H30.930O1—H4W0.823 (10)
C4—C91.383 (3)O2—H5W0.828 (10)
C4—C51.384 (4)O2—H6W0.824 (10)
C4—N11.394 (3)O7—H1W0.822 (10)
C5—C61.373 (4)O7—H2W0.821 (10)
C5—H50.930
O1—Pd1—O1i180.00 (9)C5—C6—H6119.2
O1—Pd1—O394.14 (7)C7—C6—H6119.2
O1i—Pd1—O385.86 (8)C8—C7—C6122.4 (3)
O1—Pd1—O3i85.86 (8)C8—C7—H7118.8
O1i—Pd1—O3i94.14 (7)C6—C7—H7118.8
O3—Pd1—O3i180.0C7—C8—C9116.3 (3)
O1—Pd1—O2i85.34 (7)C7—C8—H8121.8
O1i—Pd1—O2i94.66 (7)C9—C8—H8121.8
O3—Pd1—O2i88.61 (7)C8—C9—C4121.6 (3)
O3i—Pd1—O2i91.39 (7)C8—C9—N2131.4 (3)
O1—Pd1—O294.66 (7)C4—C9—N2106.9 (2)
O1i—Pd1—O285.34 (7)N2—C11—C12113.2 (2)
O3—Pd1—O291.39 (7)N2—C11—H11A108.9
O3i—Pd1—O288.61 (7)C12—C11—H11A108.9
O2i—Pd1—O2180.00 (10)N2—C11—H11B108.9
O4—C1—O3125.3 (2)C12—C11—H11B108.9
O4—C1—C2120.2 (2)H11A—C11—H11B107.7
O3—C1—C2114.5 (2)O5—C12—O6126.3 (3)
N1—C2—C1112.7 (2)O5—C12—C11118.9 (2)
N1—C2—H2A109.1O6—C12—C11114.8 (2)
C1—C2—H2A109.1C3—N1—C4108.4 (2)
N1—C2—H2B109.1C3—N1—C2126.0 (2)
C1—C2—H2B109.1C4—N1—C2125.5 (2)
H2A—C2—H2B107.8C3—N2—C9108.3 (2)
N2—C3—N1110.3 (2)C3—N2—C11125.6 (2)
N2—C3—H3124.8C9—N2—C11125.9 (2)
N1—C3—H3124.8Pd1—O1—H3W115.2 (18)
C9—C4—C5121.8 (2)Pd1—O1—H4W130.4 (18)
C9—C4—N1106.0 (2)H3W—O1—H4W111 (2)
C5—C4—N1132.3 (2)Pd1—O2—H5W118.6 (19)
C6—C5—C4116.4 (3)Pd1—O2—H6W120.1 (19)
C6—C5—H5121.8H5W—O2—H6W112 (2)
C4—C5—H5121.8C1—O3—Pd1139.53 (17)
C5—C6—C7121.5 (3)H1W—O7—H2W114 (2)
Symmetry code: (i) x+1, y+2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H1W···O4ii0.82 (1)1.99 (1)2.756 (3)156 (3)
O7—H2W···O5ii0.82 (1)1.94 (1)2.747 (3)169 (3)
Symmetry code: (ii) x+3/2, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formula[Pd(C11H9N2O4)2(H2O)4]·2H2O
Mr680.90
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)5.4702 (10), 11.794 (2), 20.886 (3)
β (°) 95.13 (3)
V3)1342.1 (4)
Z2
Radiation typeMo Kα
µ (mm1)0.77
Crystal size (mm)0.43 × 0.28 × 0.22
Data collection
DiffractometerBruker APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2004)
Tmin, Tmax0.733, 0.849
No. of measured, independent and
observed [I > 2σ(I)] reflections
7075, 2425, 1958
Rint0.032
(sin θ/λ)max1)0.599
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.028, 0.072, 1.00
No. of reflections2425
No. of parameters205
No. of restraints9
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.24, 0.49

Computer programs: APEX2 (Bruker, 2004), SAINT-Plus (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O7—H1W···O4i0.822 (10)1.985 (14)2.756 (3)156 (3)
O7—H2W···O5i0.821 (10)1.937 (10)2.747 (3)169 (3)
Symmetry code: (i) x+3/2, y1/2, z+1/2.
 

Acknowledgements

This work was supported by the Natural Science Foundation of Shandong Province (grant No. Y2007D39).

References

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