(5-Fluoro-2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidin-1-ido-κN¹)(1,4,8,11-tetra­aza­cyclo­tetra­decane-κ⁴N)zinc(II) perchlorate

In the structure of the title complex, [Zn(C₄H₂FN₂O₂)(C₁₀H₂₄N₄)]ClO₄, the zinc(II) ion forms coordination bonds with the four nitro­gen atoms of cyclam (1,4,8,11-tetra­aza­cyclo­tetra­decane or [14]aneN4) as well as with the nitro­gen atom of a deprotonated 5-fluoro­uracil ion (FU⁻). Cyclam adopts a trans-I type conformation within this structure. The coordination structure of the zinc(II) ion is a square pyramid with a distorted base plane formed by the four nitro­gen atoms of the cyclam. FU⁻ engages in inter­molecular hydrogen bonding with neighboring FU⁻ mol­ecules and with the cyclam mol­ecule.

Key indicators

Structure: I

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.064
• wR factor = 0.179
• Data-to-parameter ratio = 13.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT213_ALERT_2_C Atom C3              has ADP max/min Ratio .....        3.1 prolat
PLAT244_ALERT_4_C Low    'Solvent' Ueq as Compared to Neighbors of        Cl1 Check
PLAT250_ALERT_2_C Large U3/U1 Ratio for <U(i,j)> Tensor(Resd    1)        2.3 Note
PLAT341_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00663 Ang.
PLAT420_ALERT_2_C D-H Bond Without Acceptor  N2       --H2       .     Please Check
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      3.108 Check
PLAT971_ALERT_2_C Check Calcd Resid. Dens.  0.97Ang From Zn1             1.58 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.77Ang From N1      .      -0.52 eA-3
PLAT977_ALERT_2_C Check Negative Difference Density on H4        .      -0.35 eA-3

Alert level G
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          5 Report
              H1    H2    H3    H4    H6
PLAT063_ALERT_4_G Crystal Size Possibly too Large for Beam Size ..       0.91 mm
PLAT072_ALERT_2_G SHELXL First  Parameter in WGHT  Unusually Large       0.11 Report
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N6       ..O2       .        167 Degree
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N1       ..O1       .        133 Degree
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N3       ..O2       .        126 Degree
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N3       ..O5       .        138 Degree
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N4       ..O5       .        161 Degree
PLAT484_ALERT_4_G Round D-H..A Angle Rep for N4       ..O6       .        136 Degree
PLAT794_ALERT_5_G Tentative Bond Valency for Zn1       (II)      .       1.78 Info
PLAT802_ALERT_4_G CIF Input Record(s) with more than 80 Characters          4 Info
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         13 Note
PLAT941_ALERT_3_G Average HKL Measurement Multiplicity ...........        4.8 Low
PLAT961_ALERT_5_G Dataset Contains no Negative Intensities .......     Please Check
PLAT969_ALERT_5_G The 'Henn et al.' R-Factor-gap value ...........       4.24 Note
              Predicted wR2: Based on SigI   2  4.21 or SHELX Weight 16.76       
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          2 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   9 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  16 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   8 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
  10 ALERT type 4 Improvement, methodology, query or suggestion
   4 ALERT type 5 Informative message, check

---

Computing details

(5-Fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-1-ido-κN¹)(1,4,8,11-tetraazacyclotetradecane-κ⁴N)zinc(II) perchlorate

Crystal data

[Zn(C4H2FN2O2)(C10H24N4)]ClO4	F(000) = 1024
Mr = 494.23	Dx = 1.665 Mg m^−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54184 Å
a = 9.8065 (2) Å	Cell parameters from 13648 reflections
b = 12.5029 (3) Å	θ = 2.7–68.1°
c = 16.1592 (3) Å	µ = 3.48 mm^−1
β = 95.599 (2)°	T = 100 K
V = 1971.82 (7) Å^3	Block, colourless
Z = 4	0.91 × 0.64 × 0.55 mm

Data collection

Rigaku XtaLAB Synergy-i diffractometer	3587 independent reflections
Radiation source: microfocus sealed X-ray tube, PhotonJet-i	3489 reflections with I > 2σ(I)
Multi-layer mirror optics monochromator	Rint = 0.092
Detector resolution: 10.0 pixels mm^-1	θmax = 68.2°, θmin = 4.5°
ω scans	h = −11→11
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2022)	k = −14→14
Tmin = 0.465, Tmax = 1.000	l = −19→19
17193 measured reflections

Refinement

Refinement on F^2	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.064	H-atom parameters constrained
wR(F^2) = 0.179	w = 1/[σ^2(Fo^2) + (0.1099P)^2 + 4.5604P] where P = (Fo^2 + 2Fc^2)/3
S = 1.11	(Δ/σ)max = 0.002
3587 reflections	Δρmax = 1.60 e Å^−3
262 parameters	Δρmin = −1.36 e Å^−3
0 restraints

Special details

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.

Refinement. All hydrogen atoms were located by a geometrical calculation, and were not refined.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Zn1	0.29929 (5)	0.24605 (3)	0.66114 (3)	0.0114 (2)
Cl1	0.20118 (9)	0.70678 (7)	0.71977 (6)	0.0210 (3)
F1	0.7396 (2)	0.1048 (2)	0.52427 (16)	0.0335 (6)
O2	0.4045 (3)	0.4332 (2)	0.56678 (17)	0.0222 (6)
O1	0.5241 (3)	0.0863 (2)	0.62077 (19)	0.0260 (6)
N5	0.4640 (3)	0.2604 (2)	0.5961 (2)	0.0137 (7)
O5	0.2791 (3)	0.6245 (2)	0.6828 (2)	0.0318 (7)
N6	0.5912 (3)	0.3668 (3)	0.51134 (19)	0.0185 (7)
H6	0.606066	0.429211	0.488664	0.022*
O3	0.1333 (4)	0.6626 (3)	0.7866 (2)	0.0404 (8)
N3	0.2281 (3)	0.3864 (2)	0.7091 (2)	0.0188 (7)
H3	0.280721	0.445380	0.685020	0.023*
N2	0.1593 (4)	0.2636 (3)	0.5461 (2)	0.0225 (8)
H2	0.210131	0.305494	0.506244	0.027*
N4	0.3982 (3)	0.2264 (3)	0.7856 (2)	0.0226 (7)
H4	0.494546	0.202495	0.781057	0.027*
O6	0.2940 (3)	0.7882 (2)	0.7519 (2)	0.0373 (8)
O4	0.1026 (4)	0.7510 (3)	0.6582 (3)	0.0483 (11)
N1	0.2305 (3)	0.0887 (3)	0.6509 (2)	0.0257 (8)
H1	0.308861	0.047100	0.631959	0.031*
C11	0.5473 (4)	0.1728 (3)	0.5874 (2)	0.0185 (8)
C14	0.4839 (4)	0.3561 (3)	0.5584 (2)	0.0160 (7)
C12	0.6572 (4)	0.1887 (3)	0.5358 (3)	0.0226 (8)
C13	0.6767 (4)	0.2824 (4)	0.4984 (2)	0.0206 (8)
H13	0.748516	0.290368	0.463452	0.025*
C6	0.2659 (4)	0.3903 (3)	0.8005 (3)	0.0266 (9)
H6A	0.194817	0.353807	0.829715	0.032*
H6B	0.271740	0.465610	0.819480	0.032*
C7	0.4033 (4)	0.3354 (4)	0.8208 (3)	0.0294 (10)
H7A	0.476186	0.377144	0.797392	0.035*
H7B	0.425105	0.331652	0.881891	0.035*
C3	0.0264 (4)	0.3177 (4)	0.5502 (3)	0.0283 (10)
H3A	−0.035405	0.270211	0.578256	0.034*
H3B	−0.016100	0.330925	0.492978	0.034*
C5	0.0810 (4)	0.4135 (3)	0.6891 (3)	0.0261 (9)
H5A	0.061496	0.482004	0.716349	0.031*
H5B	0.024268	0.357396	0.712116	0.031*
C2	0.1450 (4)	0.1550 (4)	0.5130 (3)	0.0311 (10)
H2A	0.229626	0.133955	0.488375	0.037*
H2B	0.067678	0.151948	0.468791	0.037*
C8	0.3328 (5)	0.1478 (4)	0.8374 (3)	0.0315 (10)
H8A	0.243074	0.176396	0.850267	0.038*
H8B	0.390688	0.138891	0.890634	0.038*
C1	0.1190 (4)	0.0788 (4)	0.5827 (3)	0.0310 (10)
H1A	0.030078	0.095803	0.603804	0.037*
H1B	0.114871	0.004402	0.561604	0.037*
C4	0.0412 (4)	0.4232 (4)	0.5966 (3)	0.0313 (10)
H4A	0.111204	0.466879	0.572068	0.038*
H4B	−0.046910	0.462195	0.587902	0.038*
C10	0.1970 (5)	0.0352 (3)	0.7273 (3)	0.0311 (10)
H10A	0.174303	−0.040501	0.714531	0.037*
H10B	0.114558	0.069387	0.746486	0.037*
C9	0.3108 (5)	0.0393 (4)	0.7964 (3)	0.0370 (11)
H9A	0.396983	0.017282	0.774066	0.044*
H9B	0.291247	−0.013409	0.839419	0.044*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Zn1	0.0045 (3)	0.0164 (3)	0.0130 (3)	−0.00001 (15)	−0.0012 (2)	0.00062 (16)
Cl1	0.0161 (5)	0.0239 (5)	0.0228 (5)	−0.0025 (3)	0.0017 (4)	−0.0047 (3)
F1	0.0190 (12)	0.0423 (15)	0.0409 (15)	0.0160 (11)	0.0114 (11)	0.0067 (12)
O2	0.0159 (13)	0.0226 (13)	0.0293 (15)	0.0014 (11)	0.0087 (11)	0.0055 (11)
O1	0.0149 (13)	0.0264 (14)	0.0370 (16)	0.0072 (11)	0.0043 (12)	0.0098 (12)
N5	0.0052 (14)	0.0212 (16)	0.0141 (16)	0.0008 (11)	−0.0025 (12)	0.0044 (11)
O5	0.0373 (17)	0.0244 (15)	0.0364 (17)	0.0027 (13)	0.0177 (14)	−0.0023 (13)
N6	0.0085 (14)	0.0293 (17)	0.0175 (16)	−0.0018 (12)	−0.0002 (12)	0.0070 (13)
O3	0.046 (2)	0.0431 (19)	0.0362 (18)	−0.0070 (16)	0.0235 (16)	−0.0082 (15)
N3	0.0142 (15)	0.0187 (15)	0.0235 (17)	−0.0018 (12)	0.0027 (12)	0.0001 (13)
N2	0.0134 (17)	0.039 (2)	0.0148 (17)	−0.0011 (14)	−0.0029 (13)	0.0009 (14)
N4	0.0096 (16)	0.0353 (18)	0.0227 (18)	0.0010 (14)	0.0001 (13)	0.0054 (15)
O6	0.0218 (16)	0.0215 (15)	0.067 (2)	−0.0057 (13)	−0.0039 (15)	−0.0077 (15)
O4	0.035 (2)	0.077 (3)	0.032 (2)	0.0136 (17)	−0.0048 (17)	−0.0084 (16)
N1	0.0142 (16)	0.0202 (16)	0.044 (2)	−0.0012 (13)	0.0062 (14)	−0.0012 (15)
C11	0.0074 (16)	0.030 (2)	0.0176 (18)	0.0036 (15)	−0.0030 (14)	0.0009 (15)
C14	0.0086 (16)	0.0249 (18)	0.0137 (17)	−0.0042 (14)	−0.0033 (13)	0.0017 (14)
C12	0.0103 (17)	0.032 (2)	0.025 (2)	0.0058 (16)	−0.0006 (15)	0.0011 (17)
C13	0.0057 (17)	0.038 (2)	0.0181 (19)	0.0009 (16)	−0.0005 (14)	0.0044 (17)
C6	0.024 (2)	0.027 (2)	0.029 (2)	−0.0044 (17)	0.0063 (17)	−0.0105 (17)
C7	0.019 (2)	0.048 (3)	0.020 (2)	−0.0122 (19)	−0.0057 (16)	−0.0106 (19)
C3	0.0088 (17)	0.050 (3)	0.025 (2)	0.0003 (18)	−0.0067 (15)	0.0113 (19)
C5	0.0123 (18)	0.0234 (19)	0.044 (2)	0.0036 (15)	0.0084 (17)	−0.0005 (18)
C2	0.0163 (19)	0.055 (3)	0.021 (2)	−0.0066 (19)	−0.0030 (16)	−0.012 (2)
C8	0.029 (2)	0.052 (3)	0.0137 (19)	0.005 (2)	−0.0008 (16)	0.0146 (19)
C1	0.020 (2)	0.030 (2)	0.044 (3)	−0.0044 (17)	0.0064 (18)	−0.0156 (19)
C4	0.0132 (19)	0.032 (2)	0.048 (3)	0.0081 (17)	0.0009 (18)	0.013 (2)
C10	0.025 (2)	0.0191 (19)	0.051 (3)	−0.0006 (16)	0.012 (2)	0.0098 (18)
C9	0.034 (2)	0.032 (2)	0.049 (3)	0.0103 (19)	0.018 (2)	0.020 (2)

Geometric parameters (Å, º)

Zn1—N5	2.019 (3)	C11—C12	1.438 (5)
Zn1—N3	2.067 (3)	C12—C13	1.340 (6)
Zn1—N2	2.211 (3)	C13—H13	0.9500
Zn1—N4	2.159 (4)	C6—H6A	0.9900
Zn1—N1	2.082 (3)	C6—H6B	0.9900
Cl1—O5	1.445 (3)	C6—C7	1.520 (6)
Cl1—O3	1.433 (3)	C7—H7A	0.9900
Cl1—O6	1.429 (3)	C7—H7B	0.9900
Cl1—O4	1.429 (4)	C3—H3A	0.9900
F1—C12	1.348 (5)	C3—H3B	0.9900
O2—C14	1.255 (5)	C3—C4	1.517 (7)
O1—C11	1.240 (5)	C5—H5A	0.9900
N5—C11	1.381 (5)	C5—H5B	0.9900
N5—C14	1.365 (5)	C5—C4	1.513 (7)
N6—H6	0.8800	C2—H2A	0.9900
N6—C14	1.363 (5)	C2—H2B	0.9900
N6—C13	1.377 (5)	C2—C1	1.517 (7)
N3—H3	1.0000	C8—H8A	0.9900
N3—C6	1.489 (5)	C8—H8B	0.9900
N3—C5	1.486 (5)	C8—C9	1.516 (7)
N2—H2	1.0000	C1—H1A	0.9900
N2—C3	1.476 (5)	C1—H1B	0.9900
N2—C2	1.462 (6)	C4—H4A	0.9900
N4—H4	1.0000	C4—H4B	0.9900
N4—C7	1.476 (6)	C10—H10A	0.9900
N4—C8	1.478 (6)	C10—H10B	0.9900
N1—H1	1.0000	C10—C9	1.501 (7)
N1—C1	1.479 (6)	C9—H9A	0.9900
N1—C10	1.469 (6)	C9—H9B	0.9900
N5—Zn1—N3	115.88 (13)	N3—C6—H6B	109.8
N5—Zn1—N2	90.91 (13)	N3—C6—C7	109.2 (3)
N5—Zn1—N4	100.68 (13)	H6A—C6—H6B	108.3
N5—Zn1—N1	108.17 (13)	C7—C6—H6A	109.8
N3—Zn1—N2	91.50 (13)	C7—C6—H6B	109.8
N3—Zn1—N4	83.40 (14)	N4—C7—C6	109.8 (3)
N3—Zn1—N1	135.54 (13)	N4—C7—H7A	109.7
N4—Zn1—N2	168.41 (14)	N4—C7—H7B	109.7
N1—Zn1—N2	81.80 (14)	C6—C7—H7A	109.7
N1—Zn1—N4	94.55 (15)	C6—C7—H7B	109.7
O3—Cl1—O5	109.9 (2)	H7A—C7—H7B	108.2
O6—Cl1—O5	108.3 (2)	N2—C3—H3A	109.2
O6—Cl1—O3	109.1 (2)	N2—C3—H3B	109.2
O6—Cl1—O4	109.9 (2)	N2—C3—C4	112.2 (3)
O4—Cl1—O5	109.6 (2)	H3A—C3—H3B	107.9
O4—Cl1—O3	110.0 (2)	C4—C3—H3A	109.2
C11—N5—Zn1	119.6 (2)	C4—C3—H3B	109.2
C14—N5—Zn1	117.8 (2)	N3—C5—H5A	109.1
C14—N5—C11	122.5 (3)	N3—C5—H5B	109.1
C14—N6—H6	119.2	N3—C5—C4	112.6 (3)
C14—N6—C13	121.6 (3)	H5A—C5—H5B	107.8
C13—N6—H6	119.2	C4—C5—H5A	109.1
Zn1—N3—H3	105.9	C4—C5—H5B	109.1
C6—N3—Zn1	109.8 (2)	N2—C2—H2A	109.8
C6—N3—H3	105.9	N2—C2—H2B	109.8
C5—N3—Zn1	117.9 (2)	N2—C2—C1	109.2 (3)
C5—N3—H3	105.9	H2A—C2—H2B	108.3
C5—N3—C6	110.5 (3)	C1—C2—H2A	109.8
Zn1—N2—H2	106.6	C1—C2—H2B	109.8
C3—N2—Zn1	119.1 (3)	N4—C8—H8A	108.9
C3—N2—H2	106.6	N4—C8—H8B	108.9
C2—N2—Zn1	104.2 (3)	N4—C8—C9	113.5 (4)
C2—N2—H2	106.6	H8A—C8—H8B	107.7
C2—N2—C3	112.9 (3)	C9—C8—H8A	108.9
Zn1—N4—H4	107.9	C9—C8—H8B	108.9
C7—N4—Zn1	104.5 (3)	N1—C1—C2	109.6 (3)
C7—N4—H4	107.9	N1—C1—H1A	109.7
C7—N4—C8	113.3 (3)	N1—C1—H1B	109.7
C8—N4—Zn1	115.0 (3)	C2—C1—H1A	109.7
C8—N4—H4	107.9	C2—C1—H1B	109.7
Zn1—N1—H1	105.2	H1A—C1—H1B	108.2
C1—N1—Zn1	110.4 (3)	C3—C4—H4A	108.5
C1—N1—H1	105.2	C3—C4—H4B	108.5
C10—N1—Zn1	117.4 (3)	C5—C4—C3	115.0 (4)
C10—N1—H1	105.2	C5—C4—H4A	108.5
C10—N1—C1	112.2 (3)	C5—C4—H4B	108.5
O1—C11—N5	120.7 (3)	H4A—C4—H4B	107.5
O1—C11—C12	123.6 (4)	N1—C10—H10A	108.9
N5—C11—C12	115.7 (4)	N1—C10—H10B	108.9
O2—C14—N5	120.5 (3)	N1—C10—C9	113.5 (4)
O2—C14—N6	120.3 (3)	H10A—C10—H10B	107.7
N6—C14—N5	119.1 (3)	C9—C10—H10A	108.9
F1—C12—C11	117.7 (4)	C9—C10—H10B	108.9
C13—C12—F1	120.2 (4)	C8—C9—H9A	108.6
C13—C12—C11	122.0 (4)	C8—C9—H9B	108.6
N6—C13—H13	120.5	C10—C9—C8	114.8 (4)
C12—C13—N6	119.0 (4)	C10—C9—H9A	108.6
C12—C13—H13	120.5	C10—C9—H9B	108.6
N3—C6—H6A	109.8	H9A—C9—H9B	107.6
Zn1—N5—C11—O1	−1.8 (5)	N2—C2—C1—N1	−55.9 (4)
Zn1—N5—C11—C12	176.4 (3)	N4—C8—C9—C10	−73.7 (5)
Zn1—N5—C14—O2	2.3 (5)	N1—C10—C9—C8	73.2 (5)
Zn1—N5—C14—N6	−177.4 (2)	C11—N5—C14—O2	178.8 (3)
Zn1—N3—C6—C7	33.7 (4)	C11—N5—C14—N6	−1.0 (5)
Zn1—N3—C5—C4	−59.2 (4)	C11—C12—C13—N6	1.7 (6)
Zn1—N2—C3—C4	48.6 (4)	C14—N5—C11—O1	−178.2 (3)
Zn1—N2—C2—C1	46.3 (4)	C14—N5—C11—C12	0.0 (5)
Zn1—N4—C7—C6	44.9 (4)	C14—N6—C13—C12	−2.8 (6)
Zn1—N4—C8—C9	52.6 (4)	C13—N6—C14—O2	−177.4 (3)
Zn1—N1—C1—C2	34.4 (4)	C13—N6—C14—N5	2.4 (5)
Zn1—N1—C10—C9	−53.3 (4)	C6—N3—C5—C4	173.4 (3)
F1—C12—C13—N6	−180.0 (3)	C7—N4—C8—C9	172.6 (4)
O1—C11—C12—F1	−0.6 (6)	C3—N2—C2—C1	−84.4 (4)
O1—C11—C12—C13	177.7 (4)	C5—N3—C6—C7	165.5 (3)
N5—C11—C12—F1	−178.7 (3)	C2—N2—C3—C4	171.2 (4)
N5—C11—C12—C13	−0.4 (6)	C8—N4—C7—C6	−80.9 (4)
N3—C6—C7—N4	−54.1 (4)	C1—N1—C10—C9	177.2 (4)
N3—C5—C4—C3	75.5 (4)	C10—N1—C1—C2	167.4 (3)
N2—C3—C4—C5	−69.3 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N6—H6···O2^i	0.88	1.94	2.803 (4)	167
N1—H1···O1	1.00	2.19	2.966 (4)	133
N3—H3···O2	1.00	2.37	3.066 (4)	126
N3—H3···O5	1.00	2.24	3.055 (4)	138
N4—H4···O5^ii	1.00	2.44	3.403 (5)	161
N4—H4···O6^ii	1.00	2.44	3.229 (5)	136

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, y−1/2, −z+3/2.