2-Methyl-7-oxo-5,6,7,8-tetra­hydro­pyrimido­[4,5-d]­pyrimidin-3-ium chloride, a product of the thermal decomposition of nimustine hydro­chloride (ACNU)

The title compound, C₇H₉N₄O⁺·Cl⁻, was obtained as a product of the thermal decomposition of nimustine hydro­chloride (ACNU). In the crystal structure, intermolecular N—H...O hydrogen bonds link the cations into centrosymmetric dimers, which are further connected by N—H...Cl and C—H...Cl hydrogen bonding to form two-dimensional networks.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.010 Å
• R factor = 0.038
• wR factor = 0.086
• Data-to-parameter ratio = 6.8

checkCIF/PLATON results

No syntax errors found



Alert level A
THETM01_ALERT_3_A  The value of sine(theta_max)/wavelength is less than 0.550
            Calculated sin(theta_max)/wavelength =    0.4805

Author Response: Due to the poor crystal quality and small crystal size the diffraction was observed only up to \Q~max~ = 20\% on the CAD-4 diffractometer (see also contact letter).

PLAT023_ALERT_3_A Resolution (too) Low [sin(th)/Lambda < 0.6].....      19.97 Deg.

Author Response: see above (and contact letter).

PLAT027_ALERT_3_A _diffrn_reflns_theta_full (too) Low ............      19.97 Deg.

Author Response: see above (and contact letter).

Alert level B
REFNR01_ALERT_3_B  Ratio of reflections to parameters is < 8 for a
            centrosymmetric structure
            sine(theta)/lambda                0.4805
            Proportion of unique data used    1.0000
            Ratio reflections to parameters   6.8417
PLAT088_ALERT_3_B Poor Data / Parameter Ratio ....................       6.84

Alert level C
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...         10

   3 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   1 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
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 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: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Branderburg, 1998) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

2-Methyl-7-oxo-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-3-ium chloride

Crystal data

C7H9N4O^+·Cl^−	Z = 2
Mr = 200.63	F(000) = 208
Triclinic, P1	Dx = 1.520 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 4.877 (3) Å	Cell parameters from 25 reflections
b = 8.104 (6) Å	θ = 5.3–8.6°
c = 11.832 (7) Å	µ = 0.40 mm^−1
α = 105.60 (7)°	T = 298 K
β = 91.87 (7)°	Prism, colorless
γ = 102.17 (7)°	0.15 × 0.06 × 0.05 mm
V = 438.3 (5) Å^3

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.098
Radiation source: fine-focus sealed tube	θmax = 20.0°, θmin = 1.8°
Graphite monochromator	h = −4→4
ω scans	k = −7→7
1639 measured reflections	l = −11→11
821 independent reflections	1 standard reflections every 120 min
421 reflections with I > 2σ(I)	intensity decay: 2%

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)] = 0.038	H-atom parameters constrained
wR(F^2) = 0.086	w = 1/[σ^2(Fo^2) + (0.0243P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.97	(Δ/σ)max = 0.002
821 reflections	Δρmax = 0.24 e Å^−3
120 parameters	Δρmin = −0.20 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: 0.004 (1)

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
Cl	0.4633 (4)	0.6821 (2)	0.39839 (15)	0.0554 (7)
O1	0.5386 (9)	−0.1181 (5)	0.1028 (4)	0.0493 (14)
N1	0.2644 (12)	0.0843 (7)	0.1167 (4)	0.0413 (15)
H1	0.3018	0.0920	0.0475	0.050*
N3	0.3026 (11)	−0.0475 (6)	0.2658 (5)	0.0509 (16)
H3	0.3863	−0.1102	0.2969	0.061*
N6	−0.1909 (11)	0.4086 (7)	0.2915 (5)	0.0454 (15)
H6	−0.2867	0.4809	0.3278	0.055*
N8	0.0333 (12)	0.3059 (7)	0.1247 (4)	0.0448 (16)
C2	0.3741 (15)	−0.0368 (10)	0.1595 (7)	0.0454 (19)
C4	0.1017 (15)	0.0335 (9)	0.3350 (6)	0.052 (2)
H4A	0.1803	0.0830	0.4165	0.062*
H4B	−0.0687	−0.0550	0.3324	0.062*
C5	−0.1187 (14)	0.2930 (9)	0.3446 (6)	0.0460 (19)
H5	−0.1713	0.2932	0.4195	0.055*
C7	−0.1173 (13)	0.4137 (8)	0.1839 (6)	0.0393 (19)
C9	0.1028 (14)	0.1908 (9)	0.1770 (6)	0.0373 (18)
C10	0.0306 (13)	0.1768 (8)	0.2882 (6)	0.0395 (19)
C11	−0.2161 (15)	0.5387 (8)	0.1295 (6)	0.060 (2)
H11A	−0.3120	0.4759	0.0530	0.090*
H11B	−0.0573	0.6266	0.1219	0.090*
H11C	−0.3429	0.5943	0.1785	0.090*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl	0.0672 (14)	0.0606 (13)	0.0491 (12)	0.0273 (11)	0.0235 (9)	0.0213 (9)
O1	0.060 (3)	0.060 (3)	0.038 (3)	0.032 (3)	0.020 (3)	0.014 (3)
N1	0.060 (4)	0.049 (4)	0.023 (3)	0.021 (3)	0.014 (3)	0.016 (3)
N3	0.063 (4)	0.063 (4)	0.041 (4)	0.030 (3)	0.025 (3)	0.024 (3)
N6	0.052 (4)	0.047 (4)	0.041 (4)	0.025 (3)	0.021 (3)	0.006 (3)
N8	0.061 (4)	0.042 (3)	0.041 (4)	0.026 (3)	0.013 (3)	0.017 (3)
C2	0.049 (5)	0.055 (5)	0.035 (5)	0.009 (4)	0.009 (4)	0.019 (4)
C4	0.059 (6)	0.060 (5)	0.047 (5)	0.022 (5)	0.018 (4)	0.024 (4)
C5	0.040 (5)	0.055 (5)	0.046 (5)	0.002 (4)	0.007 (4)	0.027 (5)
C7	0.042 (5)	0.039 (5)	0.043 (6)	0.014 (4)	0.011 (4)	0.017 (4)
C9	0.033 (5)	0.039 (4)	0.036 (5)	0.015 (4)	0.021 (4)	−0.003 (4)
C10	0.034 (5)	0.052 (5)	0.032 (5)	0.012 (4)	0.015 (4)	0.009 (4)
C11	0.074 (6)	0.062 (5)	0.058 (5)	0.030 (5)	0.021 (4)	0.028 (4)

Geometric parameters (Å, º)

O1—C2	1.244 (7)	N8—C9	1.341 (8)
N1—C9	1.367 (7)	C4—C10	1.510 (8)
N1—C2	1.406 (7)	C4—H4A	0.97
N1—H1	0.86	C4—H4B	0.97
N3—C2	1.336 (7)	C5—C10	1.359 (8)
N3—C4	1.448 (7)	C5—H5	0.93
N3—H3	0.86	C7—C11	1.487 (7)
N6—C7	1.343 (7)	C9—C10	1.400 (8)
N6—C5	1.356 (7)	C11—H11A	0.96
N6—H6	0.86	C11—H11B	0.96
N8—C7	1.329 (7)	C11—H11C	0.96
C9—N1—C2	124.8 (6)	N6—C5—C10	119.8 (6)
C9—N1—H1	117.6	N6—C5—H5	120.1
C2—N1—H1	117.6	C10—C5—H5	120.1
C2—N3—C4	128.1 (6)	N8—C7—N6	121.2 (6)
C2—N3—H3	116.0	N8—C7—C11	120.1 (6)
C4—N3—H3	116.0	N6—C7—C11	118.7 (6)
C7—N6—C5	122.0 (5)	N8—C9—N1	116.0 (6)
C7—N6—H6	119.0	N8—C9—C10	125.2 (6)
C5—N6—H6	119.0	N1—C9—C10	118.8 (7)
C7—N8—C9	116.7 (5)	C5—C10—C9	115.1 (6)
O1—C2—N3	124.2 (7)	C5—C10—C4	124.1 (7)
O1—C2—N1	120.5 (7)	C9—C10—C4	120.8 (6)
N3—C2—N1	115.2 (6)	C7—C11—H11A	109.5
N3—C4—C10	110.6 (5)	C7—C11—H11B	109.5
N3—C4—H4A	109.5	H11A—C11—H11B	109.5
C10—C4—H4A	109.5	C7—C11—H11C	109.5
N3—C4—H4B	109.5	H11A—C11—H11C	109.5
C10—C4—H4B	109.5	H11B—C11—H11C	109.5
H4A—C4—H4B	108.1

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.86	2.01	2.859 (6)	170
N3—H3···Cl^ii	0.86	2.40	3.221 (6)	161
N6—H6···Cl^iii	0.86	2.24	3.092 (6)	172
C5—H5···Cl^iv	0.93	2.61	3.501 (7)	161

Symmetry codes: (i) −x+1, −y, −z; (ii) x, y−1, z; (iii) x−1, y, z; (iv) −x, −y+1, −z+1.