1,7-Bis(1,3-dimethyl­uracil-6-yl)-1,4,7,10-tetra­azacyclo­dodecane acetonitrile disolvate at 100 K

The title compound [systematic name: 1,1',3,3'-tetra­methyl-1,1',2,2',3,3',4,4'-octa­hydro-6,6-(1,4,7,10-tetra­azacyclo­dodec­ane-1,7-di­yl)dipyrimidine-2,2',4,4'-tetra­one acetonitrile disolvate], C₂₀H₃₂N₈O₄·2CH₃CN, an N-uracil-substituted cyclen derivative, is located on a crystallographic twofold rotation axis running through the center of the 12-membered ring and adopts a [3333] quadrangular conformation with C atoms occupying the corners.

Key indicators

• Single-crystal X-ray study
• T = 90 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.035
• wR factor = 0.094
• Data-to-parameter ratio = 17.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT410_ALERT_2_C Short Intra H...H Contact  H1A    ..  H8      ..       1.93 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       N2     -   H2N    ...          ?

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: APEX2 (Bruker–Nonius, 2004); cell refinement: APEX2; data reduction: SAINT-Plus (Bruker–Nonius, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003) and ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXL97 and PLATON.

1,1',3,3'-tetramethyl-1,1',2,2',3,3',4,4'-octahydro-6,6-(1,4,7,10- tetraazacyclododecane-1,7-diyl)dipyrimidine-2,2',4,4'-tetraone acetonitrile disolvate

Crystal data

C20H32N8O4·2C2H3N	F(000) = 1136
Mr = 530.64	Dx = 1.345 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 3832 reflections
a = 24.2718 (18) Å	θ = 2.8–28.6°
b = 7.5477 (6) Å	µ = 0.10 mm^−1
c = 14.3193 (11) Å	T = 100 K
β = 92.451 (1)°	Block, colourless
V = 2620.8 (3) Å^3	0.40 × 0.40 × 0.25 mm
Z = 4

Data collection

Bruker APEX-II CCD diffractometer	3096 independent reflections
Radiation source: fine-focus sealed tube	2681 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.015
Detector resolution: 8.366 pixels mm^-1	θmax = 28.7°, θmin = 1.7°
φ and ω scans	h = −31→32
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −10→8
Tmin = 0.963, Tmax = 0.977	l = −13→19
7243 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.094	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0465P)^2 + 1.6563P] where P = (Fo^2 + 2Fc^2)/3
3096 reflections	(Δ/σ)max = 0.001
179 parameters	Δρmax = 0.28 e Å^−3
1 restraint	Δρmin = −0.21 e Å^−3

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.

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 (Ų)

	x	y	z	Uiso*/Ueq
N4	0.29963 (4)	0.25272 (12)	0.12094 (6)	0.0181 (2)
N3	0.39079 (3)	0.36176 (12)	0.12019 (6)	0.01568 (19)
N1	0.41518 (3)	0.64543 (12)	0.17864 (6)	0.01467 (18)
O1	0.36745 (3)	0.09401 (10)	0.05582 (5)	0.02215 (18)
O2	0.23296 (3)	0.40361 (12)	0.19547 (6)	0.0258 (2)
C7	0.28128 (4)	0.39824 (15)	0.17173 (7)	0.0185 (2)
C5	0.37429 (4)	0.51810 (14)	0.16271 (7)	0.0147 (2)
C6	0.35348 (4)	0.22828 (14)	0.09620 (7)	0.0169 (2)
C8	0.32106 (4)	0.53547 (14)	0.18841 (7)	0.0177 (2)
H8	0.3102	0.6416	0.2182	0.021*
C9	0.44958 (4)	0.31204 (14)	0.11741 (8)	0.0184 (2)
H9A	0.4529	0.1827	0.1177	0.028*
H9B	0.4698	0.3609	0.1723	0.028*
H9C	0.4650	0.3596	0.0605	0.028*
C3	0.50213 (4)	0.79054 (14)	0.39084 (7)	0.0167 (2)
H3A	0.4924	0.8640	0.4450	0.020*
H3B	0.5010	0.8677	0.3349	0.020*
C4	0.56046 (4)	0.71941 (14)	0.40740 (7)	0.0160 (2)
H4A	0.5844	0.8163	0.4321	0.019*
H4B	0.5600	0.6254	0.4556	0.019*
C2	0.40629 (4)	0.71464 (14)	0.34698 (7)	0.0170 (2)
H2A	0.3956	0.8104	0.3898	0.020*
H2B	0.3795	0.6169	0.3528	0.020*
C10	0.26077 (5)	0.10981 (16)	0.09590 (8)	0.0237 (2)
H10A	0.2656	0.0739	0.0310	0.036*
H10B	0.2229	0.1518	0.1027	0.036*
H10C	0.2678	0.0082	0.1373	0.036*
N2	0.46109 (4)	0.64988 (12)	0.37745 (6)	0.01675 (19)
C11	0.38060 (5)	0.21778 (15)	0.36567 (8)	0.0245 (3)
C12	0.32866 (5)	0.23268 (18)	0.41266 (10)	0.0309 (3)
H12A	0.3274	0.1431	0.4620	0.046*
H12B	0.2978	0.2140	0.3673	0.046*
H12C	0.3258	0.3510	0.4402	0.046*
N5	0.42142 (5)	0.20622 (16)	0.32977 (8)	0.0365 (3)
C1	0.40185 (4)	0.78498 (14)	0.24683 (7)	0.0160 (2)
H1A	0.3639	0.8286	0.2329	0.019*
H1B	0.4275	0.8859	0.2406	0.019*
H2N	0.4721 (6)	0.5761 (17)	0.3359 (8)	0.028 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N4	0.0185 (4)	0.0171 (5)	0.0186 (4)	−0.0041 (3)	−0.0003 (3)	−0.0010 (3)
N3	0.0163 (4)	0.0140 (4)	0.0168 (4)	0.0006 (3)	0.0014 (3)	−0.0017 (3)
N1	0.0156 (4)	0.0137 (4)	0.0148 (4)	−0.0003 (3)	0.0027 (3)	−0.0016 (3)
O1	0.0279 (4)	0.0157 (4)	0.0229 (4)	−0.0011 (3)	0.0021 (3)	−0.0041 (3)
O2	0.0165 (4)	0.0286 (5)	0.0324 (4)	−0.0029 (3)	0.0038 (3)	−0.0039 (4)
C7	0.0180 (5)	0.0198 (5)	0.0177 (5)	0.0004 (4)	−0.0004 (4)	0.0009 (4)
C5	0.0168 (5)	0.0145 (5)	0.0128 (4)	0.0007 (4)	−0.0007 (4)	0.0003 (4)
C6	0.0217 (5)	0.0155 (5)	0.0133 (5)	−0.0011 (4)	−0.0003 (4)	0.0013 (4)
C8	0.0171 (5)	0.0164 (5)	0.0196 (5)	0.0016 (4)	0.0007 (4)	−0.0023 (4)
C9	0.0169 (5)	0.0161 (5)	0.0225 (5)	0.0022 (4)	0.0036 (4)	−0.0023 (4)
C3	0.0186 (5)	0.0147 (5)	0.0170 (5)	−0.0005 (4)	0.0026 (4)	−0.0016 (4)
C4	0.0177 (5)	0.0154 (5)	0.0151 (5)	−0.0013 (4)	0.0015 (4)	−0.0013 (4)
C2	0.0166 (5)	0.0167 (5)	0.0178 (5)	0.0000 (4)	0.0033 (4)	−0.0025 (4)
C10	0.0243 (6)	0.0218 (6)	0.0248 (6)	−0.0082 (4)	−0.0016 (4)	−0.0013 (4)
N2	0.0167 (4)	0.0152 (4)	0.0184 (4)	0.0000 (3)	0.0012 (3)	−0.0031 (3)
C11	0.0329 (6)	0.0176 (5)	0.0224 (5)	−0.0021 (5)	−0.0043 (5)	0.0017 (4)
C12	0.0257 (6)	0.0277 (7)	0.0390 (7)	0.0021 (5)	−0.0030 (5)	0.0086 (5)
N5	0.0445 (7)	0.0318 (6)	0.0339 (6)	−0.0022 (5)	0.0084 (5)	−0.0011 (5)
C1	0.0161 (5)	0.0140 (5)	0.0179 (5)	0.0010 (4)	0.0018 (4)	−0.0031 (4)

Geometric parameters (Å, º)

N4—C6	1.3810 (14)	C3—H3B	0.9900
N4—C7	1.4005 (14)	C4—N1^i	1.4973 (13)
N4—C10	1.4673 (14)	C4—H4A	0.9900
N3—C6	1.3879 (13)	C4—H4B	0.9900
N3—C5	1.3944 (13)	C2—N2	1.4659 (13)
N3—C9	1.4777 (13)	C2—C1	1.5287 (14)
N1—C5	1.3934 (13)	C2—H2A	0.9900
N1—C1	1.4814 (13)	C2—H2B	0.9900
N1—C4^i	1.4972 (13)	C10—H10A	0.9800
O1—C6	1.2219 (13)	C10—H10B	0.9800
O2—C7	1.2356 (13)	C10—H10C	0.9800
C7—C8	1.4291 (15)	N2—H2N	0.865 (9)
C5—C8	1.3647 (14)	C11—N5	1.1389 (17)
C8—H8	0.9500	C11—C12	1.4584 (18)
C9—H9A	0.9800	C12—H12A	0.9800
C9—H9B	0.9800	C12—H12B	0.9800
C9—H9C	0.9800	C12—H12C	0.9800
C3—N2	1.4627 (13)	C1—H1A	0.9900
C3—C4	1.5232 (14)	C1—H1B	0.9900
C3—H3A	0.9900
C6—N4—C7	124.30 (9)	N1^i—C4—H4A	108.8
C6—N4—C10	116.40 (9)	C3—C4—H4A	108.8
C7—N4—C10	119.21 (9)	N1^i—C4—H4B	108.8
C6—N3—C5	121.73 (9)	C3—C4—H4B	108.8
C6—N3—C9	115.44 (8)	H4A—C4—H4B	107.7
C5—N3—C9	121.48 (8)	N2—C2—C1	114.94 (8)
C5—N1—C1	115.10 (8)	N2—C2—H2A	108.5
C5—N1—C4^i	115.21 (8)	C1—C2—H2A	108.5
C1—N1—C4^i	112.48 (8)	N2—C2—H2B	108.5
O2—C7—N4	119.69 (10)	C1—C2—H2B	108.5
O2—C7—C8	124.94 (10)	H2A—C2—H2B	107.5
N4—C7—C8	115.31 (9)	N4—C10—H10A	109.5
C8—C5—N1	124.44 (9)	N4—C10—H10B	109.5
C8—C5—N3	119.46 (9)	H10A—C10—H10B	109.5
N1—C5—N3	116.07 (9)	N4—C10—H10C	109.5
O1—C6—N4	121.13 (10)	H10A—C10—H10C	109.5
O1—C6—N3	121.86 (10)	H10B—C10—H10C	109.5
N4—C6—N3	117.01 (9)	C3—N2—C2	113.65 (8)
C5—C8—C7	121.74 (10)	C3—N2—H2N	109.2 (10)
C5—C8—H8	119.1	C2—N2—H2N	108.2 (10)
C7—C8—H8	119.1	N5—C11—C12	179.35 (13)
N3—C9—H9A	109.5	C11—C12—H12A	109.5
N3—C9—H9B	109.5	C11—C12—H12B	109.5
H9A—C9—H9B	109.5	H12A—C12—H12B	109.5
N3—C9—H9C	109.5	C11—C12—H12C	109.5
H9A—C9—H9C	109.5	H12A—C12—H12C	109.5
H9B—C9—H9C	109.5	H12B—C12—H12C	109.5
N2—C3—C4	112.82 (9)	N1—C1—C2	111.27 (8)
N2—C3—H3A	109.0	N1—C1—H1A	109.4
C4—C3—H3A	109.0	C2—C1—H1A	109.4
N2—C3—H3B	109.0	N1—C1—H1B	109.4
C4—C3—H3B	109.0	C2—C1—H1B	109.4
H3A—C3—H3B	107.8	H1A—C1—H1B	108.0
N1^i—C4—C3	113.60 (8)
C6—N4—C7—O2	−175.70 (10)	C5—N3—C6—O1	177.24 (9)
C10—N4—C7—O2	0.68 (15)	C9—N3—C6—O1	−15.82 (14)
C6—N4—C7—C8	6.99 (15)	C5—N3—C6—N4	−3.46 (14)
C10—N4—C7—C8	−176.63 (9)	C9—N3—C6—N4	163.47 (9)
C1—N1—C5—C8	14.84 (14)	N1—C5—C8—C7	−178.70 (9)
C4^i—N1—C5—C8	−118.57 (11)	N3—C5—C8—C7	−0.90 (15)
C1—N1—C5—N3	−163.03 (8)	O2—C7—C8—C5	177.94 (10)
C4^i—N1—C5—N3	63.56 (11)	N4—C7—C8—C5	−4.92 (15)
C6—N3—C5—C8	5.35 (14)	N2—C3—C4—N1^i	73.27 (11)
C9—N3—C5—C8	−160.80 (9)	C4—C3—N2—C2	−170.94 (8)
C6—N3—C5—N1	−176.67 (8)	C1—C2—N2—C3	70.45 (11)
C9—N3—C5—N1	17.18 (13)	C5—N1—C1—C2	74.99 (11)
C7—N4—C6—O1	176.32 (10)	C4^i—N1—C1—C2	−150.35 (8)
C10—N4—C6—O1	−0.15 (15)	N2—C2—C1—N1	60.59 (11)
C7—N4—C6—N3	−2.98 (15)	C1—N1—C4^i—C3^i	70.80 (10)
C10—N4—C6—N3	−179.45 (9)

Symmetry code: (i) −x+1, y, −z+1/2.