A dense hydrogen-bonding network and an unusually large packing index in tri­aqua­tris­(2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ato)neodymium(III) trihydrate

The title mononuclear complex, [Nd(C₅H₃N₂O₃)₃(H₂O)₃]·3H₂O, consists of an Nd^III cation, three 2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate ligands and three aqua ligands forming the neutral complex mol­ecule, and three solvent water mol­ecules. The pyrimidine­carboxyl­ate ligands act in a chelating manner, via carboxyl­ate and keto O atoms. The NdO₉ coordination polyhedron is in the form of a distorted monocapped square anti­prism. The availability of numerous hydrogen-bonding donors and acceptors results in a very dense hydrogen-bonding network, the immediate effect of which is an unusually large packing index.

Computing details

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; 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) and PLATON (Spek, 2009).

Triaquatris(2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylato)neodymium(III) trihydrate

Crystal data

[Nd(C5H3N2O3)3(H2O)3]·3H2O	F(000) = 714
Mr = 717.62	Dx = 2.080 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 7791 reflections
a = 6.7298 (4) Å	θ = 2.2–28.0°
b = 11.4266 (7) Å	µ = 2.37 mm^−1
c = 15.2522 (10) Å	T = 297 K
β = 102.292 (1)°	Plates, colourless
V = 1145.99 (12) Å^3	0.30 × 0.24 × 0.02 mm
Z = 2

Data collection

Bruker SMART CCD area-detector diffractometer	4879 independent reflections
Radiation source: fine-focus sealed tube	4662 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
CCD rotation images, thin slices scans	θmax = 28.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS in SAINT-NT; Bruker, 2002)	h = −8→8
Tmin = 0.60, Tmax = 0.86	k = −14→15
9637 measured reflections	l = −20→19

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.021	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.047	w = 1/[σ^2(Fo^2) + (0.P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.99	(Δ/σ)max = 0.003
4879 reflections	Δρmax = 1.16 e Å^−3
397 parameters	Δρmin = −0.45 e Å^−3
24 restraints	Absolute structure: Flack (1983), with 2184 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.002 (8)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Nd1	0.67842 (2)	0.748313 (19)	0.793202 (8)	0.01921 (5)
O11	1.0954 (4)	1.2593 (3)	0.73928 (15)	0.0362 (6)
O21	0.9821 (4)	0.8787 (2)	0.78671 (16)	0.0281 (5)
O31	0.8422 (4)	0.82674 (19)	0.93980 (15)	0.0262 (5)
O41	0.9857 (4)	0.9356 (2)	1.05466 (16)	0.0314 (6)
N11	1.0341 (4)	1.2087 (2)	0.87545 (18)	0.0256 (6)
H11	1.0400	1.2802	0.8933	0.031*
C21	1.0620 (5)	1.1843 (3)	0.7910 (2)	0.0257 (7)
N31	1.0518 (4)	1.0674 (2)	0.76917 (18)	0.0245 (6)
H31	1.0803	1.0484	0.7187	0.029*
C41	1.0008 (5)	0.9788 (3)	0.8200 (2)	0.0235 (7)
C51	0.9760 (5)	1.0094 (3)	0.9086 (2)	0.0223 (7)
C61	0.9975 (5)	1.1234 (3)	0.9316 (2)	0.0251 (7)
H61	0.9865	1.1447	0.9893	0.030*
C71	0.9326 (5)	0.9186 (3)	0.9724 (2)	0.0236 (7)
O12	0.7256 (4)	1.1643 (2)	0.4699 (2)	0.0472 (7)
O22	0.5974 (4)	0.8954 (2)	0.66795 (16)	0.0320 (6)
O32	0.7972 (4)	0.68192 (18)	0.66353 (15)	0.0270 (5)
O42	0.7745 (5)	0.6217 (2)	0.52428 (19)	0.0428 (7)
N12	0.7857 (5)	0.9715 (3)	0.4441 (2)	0.0359 (8)
H12	0.8162	0.9873	0.3934	0.043*
C22	0.7277 (5)	1.0615 (3)	0.4929 (3)	0.0334 (8)
N32	0.6712 (5)	1.0252 (3)	0.5698 (2)	0.0315 (7)
H32	0.6325	1.0788	0.6020	0.038*
C42	0.6700 (5)	0.9120 (3)	0.6009 (2)	0.0250 (7)
C52	0.7458 (6)	0.8250 (3)	0.5497 (3)	0.0254 (8)
C62	0.7971 (5)	0.8582 (3)	0.4726 (2)	0.0295 (8)
H62	0.8419	0.8016	0.4375	0.035*
C72	0.7726 (6)	0.6999 (3)	0.5797 (3)	0.0244 (8)
O13	0.5735 (5)	0.1474 (2)	0.7530 (2)	0.0328 (8)
O23	0.5926 (4)	0.5414 (2)	0.75681 (17)	0.0366 (6)
O33	0.5346 (4)	0.65505 (19)	0.90886 (17)	0.0335 (6)
O43	0.4803 (4)	0.54424 (19)	1.01893 (16)	0.0341 (6)
N13	0.5264 (3)	0.2410 (4)	0.87985 (16)	0.0252 (5)
H13	0.5174	0.1758	0.9069	0.030*
C23	0.5580 (4)	0.2385 (4)	0.79405 (19)	0.0234 (6)
N33	0.5765 (6)	0.3467 (3)	0.7582 (2)	0.0245 (8)
H33	0.5970	0.3483	0.7044	0.029*
C43	0.5657 (5)	0.4533 (3)	0.7992 (2)	0.0236 (7)
C53	0.5263 (5)	0.4490 (3)	0.8883 (2)	0.0219 (7)
C63	0.5089 (5)	0.3421 (3)	0.9238 (2)	0.0252 (7)
H63	0.4837	0.3378	0.9814	0.030*
C73	0.5127 (5)	0.5568 (3)	0.9421 (2)	0.0218 (7)
O1W	0.4896 (4)	0.92668 (19)	0.82582 (16)	0.0294 (5)
H1WA	0.462 (6)	0.948 (3)	0.8750 (13)	0.035*
H1WB	0.506 (6)	0.9892 (18)	0.798 (2)	0.035*
O2W	0.9973 (4)	0.6349 (2)	0.85270 (18)	0.0380 (6)
H2WA	1.019 (5)	0.5706 (14)	0.8814 (15)	0.046*
H2WB	1.094 (3)	0.6403 (16)	0.8250 (12)	0.046*
O3W	0.3033 (3)	0.7379 (5)	0.71871 (17)	0.0447 (8)
H3WA	0.217 (5)	0.787 (3)	0.726 (3)	0.054*
H3WB	0.264 (6)	0.705 (3)	0.6692 (14)	0.054*
O4W	0.9236 (4)	0.9961 (2)	0.29146 (19)	0.0415 (7)
H4WA	0.959 (5)	0.9296 (17)	0.274 (3)	0.050*
H4WB	1.037 (3)	1.030 (3)	0.312 (3)	0.050*
O5W	0.8260 (4)	0.4919 (3)	0.38267 (18)	0.0407 (6)
H5WA	0.816 (6)	0.531 (4)	0.429 (2)	0.049*
H5WB	0.709 (3)	0.462 (3)	0.364 (2)	0.049*
O6W	0.6925 (5)	0.3735 (3)	0.5876 (2)	0.0530 (8)
H6WA	0.734 (7)	0.322 (2)	0.556 (3)	0.064*
H6WB	0.704 (8)	0.4391 (17)	0.564 (3)	0.064*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Nd1	0.02867 (8)	0.01333 (7)	0.01710 (7)	−0.00035 (10)	0.00821 (5)	−0.00010 (9)
O11	0.0538 (13)	0.0248 (14)	0.0337 (12)	−0.0022 (15)	0.0174 (10)	0.0036 (15)
O21	0.0369 (14)	0.0220 (11)	0.0281 (13)	−0.0071 (10)	0.0131 (11)	−0.0057 (10)
O31	0.0374 (13)	0.0203 (11)	0.0195 (12)	−0.0051 (10)	0.0031 (10)	−0.0004 (9)
O41	0.0452 (16)	0.0299 (14)	0.0171 (14)	−0.0047 (13)	0.0025 (11)	0.0016 (12)
N11	0.0341 (15)	0.0177 (12)	0.0259 (14)	−0.0040 (11)	0.0083 (12)	−0.0024 (10)
C21	0.0263 (17)	0.0234 (17)	0.0268 (18)	0.0007 (14)	0.0040 (14)	0.0013 (14)
N31	0.0348 (15)	0.0203 (13)	0.0211 (14)	0.0000 (12)	0.0121 (12)	−0.0006 (11)
C41	0.0213 (16)	0.0237 (16)	0.0259 (17)	−0.0025 (13)	0.0060 (13)	0.0001 (13)
C51	0.0259 (17)	0.0224 (17)	0.0181 (17)	−0.0016 (14)	0.0037 (14)	0.0003 (13)
C61	0.0285 (18)	0.0273 (18)	0.0186 (17)	−0.0016 (15)	0.0027 (14)	0.0009 (14)
C71	0.0247 (16)	0.0221 (16)	0.0240 (17)	0.0007 (13)	0.0055 (13)	0.0009 (13)
O12	0.0586 (18)	0.0351 (14)	0.0540 (19)	0.0037 (13)	0.0255 (15)	0.0199 (13)
O22	0.0412 (14)	0.0300 (13)	0.0293 (13)	0.0092 (11)	0.0178 (11)	0.0081 (10)
O32	0.0446 (14)	0.0206 (11)	0.0186 (12)	0.0045 (10)	0.0129 (10)	0.0015 (9)
O42	0.069 (2)	0.0349 (16)	0.0267 (16)	0.0024 (14)	0.0164 (15)	−0.0085 (12)
N12	0.0427 (19)	0.0390 (18)	0.0299 (18)	0.0001 (15)	0.0167 (15)	0.0103 (14)
C22	0.0308 (19)	0.039 (2)	0.032 (2)	0.0001 (16)	0.0096 (16)	0.0118 (17)
N32	0.0377 (17)	0.0281 (16)	0.0306 (17)	0.0060 (13)	0.0115 (14)	0.0057 (13)
C42	0.0239 (16)	0.0270 (17)	0.0233 (17)	0.0003 (13)	0.0033 (13)	0.0034 (13)
C52	0.0272 (19)	0.029 (2)	0.020 (2)	0.0027 (16)	0.0044 (16)	0.0005 (16)
C62	0.0327 (19)	0.033 (2)	0.0243 (19)	−0.0040 (15)	0.0100 (16)	0.0003 (16)
C72	0.0218 (17)	0.0282 (17)	0.025 (2)	−0.0041 (14)	0.0084 (15)	−0.0011 (15)
O13	0.051 (2)	0.0154 (15)	0.035 (2)	0.0028 (15)	0.0159 (17)	−0.0020 (13)
O23	0.0673 (18)	0.0183 (11)	0.0302 (14)	−0.0073 (12)	0.0235 (13)	−0.0017 (10)
O33	0.0609 (17)	0.0165 (11)	0.0301 (14)	−0.0063 (11)	0.0253 (13)	−0.0023 (9)
O43	0.0618 (17)	0.0189 (11)	0.0268 (13)	−0.0028 (11)	0.0208 (12)	−0.0009 (10)
N13	0.0353 (12)	0.0158 (12)	0.0261 (11)	−0.0023 (16)	0.0104 (9)	0.0012 (16)
C23	0.0270 (13)	0.0170 (17)	0.0276 (14)	0.0017 (18)	0.0087 (11)	0.0041 (19)
N33	0.035 (2)	0.0190 (18)	0.022 (2)	−0.0006 (16)	0.0115 (17)	0.0001 (15)
C43	0.0279 (17)	0.0184 (15)	0.0272 (18)	−0.0016 (13)	0.0114 (14)	−0.0014 (13)
C53	0.0262 (16)	0.0181 (15)	0.0224 (17)	−0.0029 (13)	0.0073 (13)	−0.0015 (13)
C63	0.0306 (18)	0.0230 (16)	0.0243 (17)	0.0000 (14)	0.0108 (14)	−0.0013 (13)
C73	0.0276 (16)	0.0163 (15)	0.0226 (17)	−0.0023 (13)	0.0081 (13)	−0.0001 (13)
O1W	0.0435 (15)	0.0216 (11)	0.0245 (13)	0.0037 (11)	0.0105 (11)	−0.0032 (10)
O2W	0.0509 (17)	0.0316 (14)	0.0332 (16)	0.0172 (12)	0.0128 (13)	0.0087 (11)
O3W	0.0377 (13)	0.041 (2)	0.0510 (15)	−0.0081 (16)	−0.0002 (11)	−0.0173 (19)
O4W	0.0586 (18)	0.0302 (14)	0.0418 (17)	−0.0077 (13)	0.0244 (14)	−0.0016 (12)
O5W	0.0447 (16)	0.0495 (17)	0.0319 (16)	−0.0067 (13)	0.0171 (13)	−0.0105 (12)
O6W	0.062 (2)	0.061 (2)	0.0381 (18)	−0.0034 (18)	0.0178 (15)	−0.0001 (15)

Geometric parameters (Å, º)

Nd1—O32	2.408 (2)	N32—H32	0.8600
Nd1—O33	2.431 (2)	C42—C52	1.424 (5)
Nd1—O31	2.443 (2)	C52—C62	1.350 (5)
Nd1—O23	2.469 (2)	C52—C72	1.499 (5)
Nd1—O2W	2.506 (2)	C62—H62	0.9300
Nd1—O1W	2.507 (2)	O13—C23	1.230 (5)
Nd1—O22	2.516 (2)	O23—C43	1.231 (4)
Nd1—O21	2.548 (2)	O33—C73	1.253 (4)
Nd1—O3W	2.541 (2)	O43—C73	1.244 (4)
O11—C21	1.218 (4)	N13—C63	1.353 (5)
O21—C41	1.247 (4)	N13—C23	1.370 (4)
O31—C71	1.261 (4)	N13—H13	0.8600
O41—C71	1.244 (4)	C23—N33	1.368 (5)
N11—C61	1.354 (4)	N33—C43	1.378 (4)
N11—C21	1.370 (4)	N33—H33	0.8600
N11—H11	0.8600	C43—C53	1.440 (4)
C21—N31	1.374 (4)	C53—C63	1.352 (4)
N31—C41	1.363 (4)	C53—C73	1.494 (4)
N31—H31	0.8600	C63—H63	0.9300
C41—C51	1.439 (5)	O1W—H1WA	0.846 (10)
C51—C61	1.349 (5)	O1W—H1WB	0.848 (10)
C51—C71	1.494 (4)	O2W—H2WA	0.851 (10)
C61—H61	0.9300	O2W—H2WB	0.850 (9)
O12—C22	1.226 (4)	O3W—H3WA	0.835 (10)
O22—C42	1.238 (4)	O3W—H3WB	0.833 (10)
O32—C72	1.271 (4)	O4W—H4WA	0.855 (10)
O42—C72	1.232 (4)	O4W—H4WB	0.854 (10)
N12—C62	1.362 (5)	O5W—H5WA	0.850 (10)
N12—C22	1.374 (5)	O5W—H5WB	0.849 (10)
N12—H12	0.8600	O6W—H6WA	0.841 (10)
C22—N32	1.372 (5)	O6W—H6WB	0.842 (10)
N32—C42	1.378 (4)
O32—Nd1—O33	135.30 (8)	C42—O22—Nd1	132.0 (2)
O32—Nd1—O31	134.69 (8)	C72—O32—Nd1	141.3 (2)
O33—Nd1—O31	70.64 (8)	C62—N12—C22	122.8 (3)
O32—Nd1—O23	67.44 (8)	C62—N12—H12	118.6
O33—Nd1—O23	68.48 (8)	C22—N12—H12	118.6
O31—Nd1—O23	126.54 (8)	O12—C22—N32	123.1 (4)
O32—Nd1—O2W	74.10 (8)	O12—C22—N12	123.4 (3)
O33—Nd1—O2W	87.31 (9)	N32—C22—N12	113.5 (3)
O31—Nd1—O2W	70.94 (8)	C22—N32—C42	127.0 (3)
O23—Nd1—O2W	74.19 (9)	C22—N32—H32	116.5
O32—Nd1—O1W	133.63 (8)	C42—N32—H32	116.5
O33—Nd1—O1W	85.15 (8)	O22—C42—N32	117.4 (3)
O31—Nd1—O1W	70.68 (8)	O22—C42—C52	126.6 (3)
O23—Nd1—O1W	135.97 (9)	N32—C42—C52	115.9 (3)
O2W—Nd1—O1W	141.23 (9)	C62—C52—C42	118.0 (3)
O32—Nd1—O22	69.09 (7)	C62—C52—C72	119.8 (4)
O33—Nd1—O22	142.03 (8)	C42—C52—C72	122.2 (3)
O31—Nd1—O22	115.63 (8)	C52—C62—N12	122.6 (4)
O23—Nd1—O22	117.81 (8)	C52—C62—H62	118.7
O2W—Nd1—O22	130.63 (9)	N12—C62—H62	118.7
O1W—Nd1—O22	64.56 (8)	O42—C72—O32	123.7 (4)
O32—Nd1—O21	75.11 (8)	O42—C72—C52	120.0 (4)
O33—Nd1—O21	136.97 (8)	O32—C72—C52	116.2 (3)
O31—Nd1—O21	67.16 (8)	C43—O23—Nd1	136.0 (2)
O23—Nd1—O21	134.62 (8)	C73—O33—Nd1	141.8 (2)
O2W—Nd1—O21	71.60 (8)	C63—N13—C23	122.6 (4)
O1W—Nd1—O21	88.68 (8)	C63—N13—H13	118.7
O22—Nd1—O21	68.03 (8)	C23—N13—H13	118.7
O32—Nd1—O3W	95.16 (9)	O13—C23—N33	122.4 (3)
O33—Nd1—O3W	78.04 (10)	O13—C23—N13	123.5 (4)
O31—Nd1—O3W	129.65 (10)	N33—C23—N13	114.1 (4)
O23—Nd1—O3W	72.06 (15)	C23—N33—C43	126.8 (3)
O2W—Nd1—O3W	146.14 (14)	C23—N33—H33	116.6
O1W—Nd1—O3W	68.26 (14)	C43—N33—H33	116.6
O22—Nd1—O3W	69.98 (12)	O23—C43—N33	117.2 (3)
O21—Nd1—O3W	137.62 (12)	O23—C43—C53	126.9 (3)
C41—O21—Nd1	122.2 (2)	N33—C43—C53	115.9 (3)
C71—O31—Nd1	138.8 (2)	C63—C53—C43	117.3 (3)
C61—N11—C21	121.9 (3)	C63—C53—C73	120.2 (3)
C61—N11—H11	119.0	C43—C53—C73	122.5 (3)
C21—N11—H11	119.0	N13—C63—C53	123.3 (3)
O11—C21—N11	123.1 (3)	N13—C63—H63	118.4
O11—C21—N31	122.3 (3)	C53—C63—H63	118.4
N11—C21—N31	114.5 (3)	O43—C73—O33	122.9 (3)
C41—N31—C21	126.1 (3)	O43—C73—C53	117.8 (3)
C41—N31—H31	116.9	O33—C73—C53	119.3 (3)
C21—N31—H31	116.9	Nd1—O1W—H1WA	129 (2)
O21—C41—N31	117.7 (3)	Nd1—O1W—H1WB	118 (2)
O21—C41—C51	125.7 (3)	H1WA—O1W—H1WB	106.0 (16)
N31—C41—C51	116.6 (3)	Nd1—O2W—H2WA	132 (2)
C61—C51—C41	116.9 (3)	Nd1—O2W—H2WB	118.0 (14)
C61—C51—C71	121.7 (3)	H2WA—O2W—H2WB	104.8 (15)
C41—C51—C71	121.4 (3)	Nd1—O3W—H3WA	124 (3)
C51—C61—N11	123.6 (3)	Nd1—O3W—H3WB	121 (3)
C51—C61—H61	118.2	H3WA—O3W—H3WB	109.0 (17)
N11—C61—H61	118.2	H4WA—O4W—H4WB	103.3 (16)
O41—C71—O31	122.6 (3)	H5WA—O5W—H5WB	105.3 (16)
O41—C71—C51	119.6 (3)	H6WA—O6W—H6WB	108.0 (17)
O31—C71—C51	117.8 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1WA···O43^i	0.85 (3)	1.93 (3)	2.692 (3)	150 (4)
O1W—H1WB···O13^ii	0.85 (2)	2.02 (2)	2.860 (3)	170 (3)
O2W—H2WA···O41^iii	0.85 (2)	1.83 (2)	2.670 (3)	169 (3)
O2W—H2WB···O4W^iv	0.85 (2)	2.41 (2)	2.852 (4)	113 (2)
O3W—H3WA···O21^v	0.83 (4)	2.25 (4)	3.048 (4)	160 (4)
O3W—H3WB···O12^vi	0.84 (2)	2.19 (2)	2.964 (4)	155 (3)
O4W—H4WA···O11	0.86 (2)	1.98 (2)	2.745 (4)	148 (3)
O4W—H4WB···O32^vii	0.85 (3)	2.05 (3)	2.822 (3)	149 (3)
O5W—H5WA···O42	0.85 (4)	1.85 (4)	2.703 (4)	175 (4)
O5W—H5WB···O22^vi	0.85 (2)	2.15 (2)	2.999 (4)	173 (2)
O6W—H6WA···O12^viii	0.85 (4)	2.22 (3)	3.026 (4)	159 (4)
O6W—H6WB···O42	0.84 (3)	2.25 (3)	3.083 (4)	170 (4)
N11—H11···O41^ix	0.86	1.97	2.817 (3)	170
N31—H31···O5W^vii	0.86	1.90	2.756 (4)	171
N12—H12···O4W	0.86	1.85	2.698 (4)	168
N32—H32···O13^ii	0.86	2.54	3.312 (4)	150
N13—H13···O43^x	0.86	1.88	2.733 (5)	172
N33—H33···O6W	0.86	2.04	2.888 (4)	169
C61—H61···O2W^ix	0.93	2.39	3.285 (4)	161

Symmetry codes: (i) −x+1, y+1/2, −z+2; (ii) x, y+1, z; (iii) −x+2, y−1/2, −z+2; (iv) −x+2, y−1/2, −z+1; (v) x−1, y, z; (vi) −x+1, y−1/2, −z+1; (vii) −x+2, y+1/2, −z+1; (viii) x, y−1, z; (ix) −x+2, y+1/2, −z+2; (x) −x+1, y−1/2, −z+2.