4-Amino-2,6-di­chloro-5-nitro­pyrimidine

The title compound, C₄H₂Cl₂N₄O₂, is a key intermediate in the synthesis of a purine scaffold, as nucleophilic substitution of the chlorides allows access to a diverse array of potentially biologically active compounds. The mol­ecules exhibit an intramolecular N—H...O hydrogen bond between the ortho amino and nitro substituents. Pairs of mol­ecules associate across a crystallographic centre of symmetry through N—H...N intermolecular hydrogen bonding between the ortho amino group and the ring N atom.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.047
• wR factor = 0.144
• Data-to-parameter ratio = 16.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Check Low    U(eq) as Compared to Neighbors ....         N5
PLAT250_ALERT_2_C Large U3/U1 ratio for average U(i,j) tensor ....       2.32
PLAT430_ALERT_2_C Short Inter D...A Contact  O51    ..  O51      =       2.89 Ang.
PLAT431_ALERT_2_C Short Inter HL..A Contact  Cl2    ..  O52      =       3.06 Ang.

   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

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 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

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Computing details

Data collection: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); cell refinement: MSC/AFC7 Diffractometer Control Software; data reduction: TEXSAN for Windows (Molecular Structure Corporation, 1997-2001); program(s) used to solve structure: TEXSAN for Windows; program(s) used to refine structure: TEXSAN for Windows and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1980-2001) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: TEXSAN for Windows and PLATON.

4-amino-2,6-dichloro-5-nitropyrimidine

Crystal data

C4H2Cl2N4O2	F(000) = 832
Mr = 209.00	Dx = 1.816 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: -C 2yc	Cell parameters from 25 reflections
a = 17.667 (3) Å	θ = 12.6–17.0°
b = 6.708 (2) Å	µ = 0.81 mm^−1
c = 14.425 (3) Å	T = 295 K
β = 116.608 (15)°	Prismatic, colorless
V = 1528.5 (6) Å^3	0.30 × 0.30 × 0.25 mm
Z = 8

Data collection

Rigaku AFC-7R diffractometer	Rint = 0.046
Radiation source: Rigaku rotating anode	θmax = 27.5°, θmin = 2.6°
Graphite monochromator	h = −10→22
ω–2θ scans	k = −8→4
2123 measured reflections	l = −18→16
1766 independent reflections	3 standard reflections every 150 reflections
1290 reflections with I > 2σ(I)	intensity decay: 0.7%

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)] = 0.047	H-atom parameters constrained
wR(F^2) = 0.144	w = 1/[σ^2(Fo^2) + (0.0646P)^2 + 2.5264P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
1766 reflections	Δρmax = 0.57 e Å^−3
110 parameters	Δρmin = −0.40 e Å^−3
0 restraints	Extinction correction: SHELXL97, FC^*=KFC[1+0.001XFC^2Λ^3/SIN(2Θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0046 (10)

Special details

Experimental. The scan width was (1.79 + 0.30tanθ)° with an ω scan speed of 16° per minute (up to 4 scans to achieve I/σ(I) > 10). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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
Cl2	0.33745 (5)	−0.22273 (15)	0.63602 (7)	0.0641 (3)
Cl6	0.09354 (6)	−0.20427 (16)	0.73648 (9)	0.0746 (4)
O51	0.0276 (2)	0.3556 (5)	0.5830 (3)	0.1001 (14)
O52	−0.01950 (16)	0.0785 (5)	0.6049 (3)	0.0844 (11)
N1	0.21172 (16)	−0.1855 (4)	0.6805 (2)	0.0527 (9)
N3	0.23196 (14)	0.0673 (4)	0.57753 (18)	0.0447 (8)
N4	0.14712 (18)	0.3373 (4)	0.5180 (2)	0.0604 (10)
N5	0.03583 (15)	0.1792 (4)	0.6017 (2)	0.0506 (9)
C2	0.24977 (17)	−0.0985 (5)	0.6304 (2)	0.0459 (9)
C4	0.16328 (18)	0.1691 (4)	0.5706 (2)	0.0439 (8)
C5	0.11425 (16)	0.0847 (4)	0.6166 (2)	0.0423 (8)
C6	0.14259 (18)	−0.0922 (5)	0.6713 (2)	0.0467 (9)
H41	0.10460	0.40930	0.51140	0.0720*
H42	0.17940	0.37700	0.49150	0.0720*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl2	0.0595 (5)	0.0763 (6)	0.0708 (6)	0.0302 (4)	0.0420 (4)	0.0178 (4)
Cl6	0.0714 (6)	0.0762 (6)	0.1017 (8)	0.0104 (5)	0.0614 (6)	0.0280 (5)
O51	0.099 (2)	0.080 (2)	0.163 (3)	0.0484 (18)	0.096 (2)	0.050 (2)
O52	0.0528 (14)	0.092 (2)	0.123 (2)	0.0061 (14)	0.0523 (16)	0.0049 (18)
N1	0.0536 (15)	0.0525 (15)	0.0631 (16)	0.0134 (12)	0.0360 (13)	0.0100 (12)
N3	0.0420 (12)	0.0520 (14)	0.0482 (13)	0.0078 (10)	0.0273 (11)	0.0019 (11)
N4	0.0625 (17)	0.0569 (16)	0.081 (2)	0.0158 (13)	0.0492 (16)	0.0172 (14)
N5	0.0427 (13)	0.0639 (17)	0.0521 (14)	0.0101 (12)	0.0273 (11)	0.0022 (12)
C2	0.0420 (14)	0.0546 (17)	0.0464 (15)	0.0100 (12)	0.0246 (12)	0.0004 (13)
C4	0.0438 (14)	0.0485 (16)	0.0441 (14)	0.0047 (12)	0.0238 (12)	0.0007 (12)
C5	0.0375 (13)	0.0496 (15)	0.0451 (14)	0.0041 (11)	0.0233 (12)	−0.0033 (12)
C6	0.0458 (15)	0.0505 (17)	0.0526 (16)	0.0002 (12)	0.0300 (13)	−0.0002 (13)

Geometric parameters (Å, º)

Cl2—C2	1.729 (3)	N3—C4	1.356 (4)
Cl6—C6	1.712 (3)	N4—C4	1.318 (4)
O51—N5	1.208 (4)	N5—C5	1.449 (4)
O52—N5	1.206 (4)	N4—H42	0.8588
N1—C2	1.323 (4)	N4—H41	0.8617
N1—C6	1.325 (5)	C4—C5	1.423 (4)
N3—C2	1.305 (4)	C5—C6	1.388 (4)
Cl2···O52^i	3.063 (4)	N3···N4^iii	3.084 (4)
Cl2···Cl6^ii	3.6462 (18)	N4···Cl2^iii	3.498 (3)
Cl2···N5^ii	3.489 (3)	N4···O51	2.670 (5)
Cl2···C5^ii	3.522 (3)	N4···N5	2.928 (4)
Cl2···C6^ii	3.621 (3)	N4···N3^iii	3.084 (4)
Cl2···N4^iii	3.498 (3)	N5···N4	2.928 (4)
Cl2···C2^iv	3.644 (3)	N5···Cl6	3.108 (3)
Cl6···Cl6^v	3.497 (2)	N5···Cl2^vi	3.489 (3)
Cl6···O52	2.792 (4)	N3···H42^iii	2.2317
Cl6···N5	3.108 (3)	N5···H41	2.6406
Cl6···Cl2^vi	3.6462 (18)	C2···Cl2^iv	3.644 (3)
Cl6···N3^ii	3.412 (3)	C4···O52^viii	3.140 (5)
Cl2···H42^iii	2.8914	C4···N1^vi	3.408 (4)
O51···N4	2.670 (5)	C5···O52^viii	3.069 (5)
O51···O51^vii	2.889 (5)	C5···Cl2^vi	3.522 (3)
O52···Cl6	2.792 (4)	C6···Cl2^vi	3.621 (3)
O52···C5^viii	3.069 (5)	C2···H42^iii	2.9726
O52···Cl2^ix	3.063 (4)	H41···O51	2.0750
O52···C4^viii	3.140 (5)	H41···N5	2.6406
O51···H41^vii	2.6358	H41···O51^vii	2.6358
O51···H41	2.0750	H42···Cl2^iii	2.8914
N1···C4^ii	3.408 (4)	H42···N3^iii	2.2317
N3···Cl6^vi	3.412 (3)	H42···C2^iii	2.9726
C2—N1—C6	114.1 (3)	N1—C2—N3	130.3 (3)
C2—N3—C4	116.5 (3)	N3—C4—N4	115.4 (3)
O51—N5—O52	122.6 (3)	N3—C4—C5	118.5 (2)
O51—N5—C5	118.2 (3)	N4—C4—C5	126.1 (3)
O52—N5—C5	119.1 (3)	C4—C5—C6	117.7 (3)
H41—N4—H42	119.79	N5—C5—C4	119.9 (2)
C4—N4—H41	119.79	N5—C5—C6	122.4 (3)
C4—N4—H42	120.40	Cl6—C6—N1	114.1 (2)
Cl2—C2—N3	114.5 (2)	Cl6—C6—C5	123.0 (3)
Cl2—C2—N1	115.2 (2)	N1—C6—C5	122.8 (3)
C6—N1—C2—Cl2	−177.2 (2)	O52—N5—C5—C4	152.4 (3)
C6—N1—C2—N3	3.2 (5)	O52—N5—C5—C6	−24.9 (4)
C2—N1—C6—Cl6	−179.8 (2)	N3—C4—C5—N5	−173.8 (2)
C2—N1—C6—C5	−2.0 (4)	N3—C4—C5—C6	3.7 (4)
C4—N3—C2—Cl2	179.6 (2)	N4—C4—C5—N5	4.0 (4)
C4—N3—C2—N1	−0.7 (5)	N4—C4—C5—C6	−178.5 (3)
C2—N3—C4—N4	179.2 (3)	N5—C5—C6—N1	176.2 (3)
C2—N3—C4—C5	−2.8 (4)	C4—C5—C6—Cl6	176.4 (2)
O51—N5—C5—C4	−25.1 (4)	C4—C5—C6—N1	−1.2 (4)
O51—N5—C5—C6	157.5 (3)	N5—C5—C6—Cl6	−6.2 (4)

Symmetry codes: (i) x+1/2, y−1/2, z; (ii) −x+1/2, y−1/2, −z+3/2; (iii) −x+1/2, −y+1/2, −z+1; (iv) −x+1/2, −y−1/2, −z+1; (v) −x, y, −z+3/2; (vi) −x+1/2, y+1/2, −z+3/2; (vii) −x, −y+1, −z+1; (viii) −x, −y, −z+1; (ix) x−1/2, y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H41···O51	0.86	2.08	2.670 (5)	126
N4—H42···N3^iii	0.86	2.23	3.084 (4)	172

Symmetry code: (iii) −x+1/2, −y+1/2, −z+1.