Dimethyl 2-[2-(2-amino-6-chloro­purin-9-yl)eth­yl]malonate

In the title compound, C₁₂H₁₄ClN₅O₄, the dihedral angles between the purine plane and two methoxy­carbonyl planes are 15.806 (19) and 68.818 (18)°. Inter­molecular N—H...O and N—H...N hydrogen bonds link mol­ecules into bands along the b axis; they are further aggregated via C—H...O inter­actions into layers parallel to the ab plane.

Key indicators

• Single-crystal X-ray study
• T = 291 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.034
• wR factor = 0.087
• Data-to-parameter ratio = 13.2

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSMU01_ALERT_1_C  The ratio of given/expected absorption coefficient lies
               outside the range 0.99 <> 1.01
            Calculated value of mu =     0.293
            Value of mu given      =     0.290
ABSTM02_ALERT_3_C  The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
            Tmin and Tmax reported:      0.821     0.963
            Tmin(prime) and Tmax expected:      0.943     0.963
            RR(prime) =      0.871
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large .............       0.87
PLAT431_ALERT_2_C Short Inter HL..A Contact  Cl1    ..  O1      ..       3.22 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

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 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: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1998); software used to prepare material for publication: SHELXTL.

Dimethyl 2-[2-(2-amino-6-chloropurin-9-yl)ethyl]malonate

Crystal data

C12H14ClN5O4	Z = 2
Mr = 327.73	F(000) = 340
Triclinic, P1	Dx = 1.516 Mg m^−3
Hall symbol: -p 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.2458 (7) Å	Cell parameters from 2145 reflections
b = 11.1078 (15) Å	θ = 3.0–26.6°
c = 13.1060 (18) Å	µ = 0.29 mm^−1
α = 73.334 (1)°	T = 291 K
β = 88.622 (2)°	Block, colourless
γ = 79.032 (2)°	0.20 × 0.13 × 0.13 mm
V = 717.86 (17) Å^3

Data collection

Bruker SMART CCD detector diffractometer	2654 independent reflections
Radiation source: fine-focus sealed tube	2170 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.015
φ and ω scans	θmax = 25.5°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −6→6
Tmin = 0.821, Tmax = 0.963	k = −13→13
5520 measured reflections	l = −15→15

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.087	H-atom parameters constrained
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0354P)^2 + 0.2243P] where P = (Fo^2 + 2Fc^2)/3
2654 reflections	(Δ/σ)max < 0.001
201 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.16 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
Cl1	0.04375 (10)	1.20201 (5)	0.26804 (4)	0.05175 (16)
O1	0.2630 (3)	0.44351 (13)	0.11911 (11)	0.0509 (3)
O2	0.4535 (3)	0.43747 (14)	0.27221 (12)	0.0572 (4)
O3	−0.1448 (3)	0.73801 (13)	0.07302 (11)	0.0558 (4)
O4	0.2142 (3)	0.75120 (14)	0.15395 (12)	0.0619 (4)
N1	−0.2262 (3)	0.78852 (14)	0.32370 (12)	0.0392 (3)
N2	−0.2913 (3)	0.99687 (15)	0.22712 (12)	0.0430 (4)
N3	0.1211 (3)	0.78325 (14)	0.44523 (11)	0.0380 (3)
N4	0.2392 (3)	0.99116 (14)	0.41315 (11)	0.0365 (3)
N5	0.4439 (3)	0.81730 (15)	0.54447 (12)	0.0462 (4)
H5A	0.4693	0.7376	0.5800	0.055*
H5B	0.5356	0.8669	0.5593	0.055*
C1	−0.3621 (3)	0.88667 (18)	0.24310 (14)	0.0429 (4)
H1	−0.4947	0.8753	0.2030	0.051*
C2	−0.0520 (3)	0.84183 (17)	0.36495 (13)	0.0353 (4)
C3	0.2605 (3)	0.86436 (17)	0.46577 (13)	0.0358 (4)
C4	0.0646 (3)	1.04109 (16)	0.33410 (13)	0.0366 (4)
C5	−0.0940 (3)	0.97003 (16)	0.30443 (13)	0.0356 (4)
C6	−0.2531 (4)	0.65413 (18)	0.35867 (16)	0.0460 (5)
H6A	−0.4026	0.6444	0.3217	0.055*
H6B	−0.2857	0.6305	0.4343	0.055*
C7	−0.0144 (4)	0.56313 (18)	0.33831 (15)	0.0449 (4)
H7A	−0.0248	0.4768	0.3802	0.054*
H7B	0.1384	0.5846	0.3636	0.054*
C8	0.0223 (3)	0.56423 (17)	0.22197 (14)	0.0409 (4)
H8	−0.1255	0.5361	0.1977	0.049*
C9	0.2710 (4)	0.47412 (17)	0.20979 (15)	0.0429 (4)
C10	0.0445 (4)	0.69538 (18)	0.14704 (15)	0.0423 (4)
C11	0.4920 (4)	0.3588 (2)	0.09725 (19)	0.0594 (6)
H11A	0.6410	0.3980	0.0946	0.089*
H11B	0.4668	0.3435	0.0301	0.089*
H11C	0.5191	0.2790	0.1527	0.089*
C12	−0.1434 (6)	0.8616 (2)	−0.00429 (18)	0.0745 (7)
H12A	−0.1570	0.9262	0.0320	0.112*
H12B	−0.2879	0.8823	−0.0539	0.112*
H12C	0.0157	0.8579	−0.0420	0.112*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0601 (3)	0.0401 (3)	0.0535 (3)	−0.0167 (2)	−0.0042 (2)	−0.0059 (2)
O1	0.0523 (8)	0.0494 (8)	0.0504 (8)	−0.0040 (6)	−0.0032 (6)	−0.0167 (6)
O2	0.0492 (8)	0.0556 (9)	0.0666 (9)	−0.0034 (7)	−0.0162 (7)	−0.0203 (7)
O3	0.0685 (9)	0.0467 (8)	0.0495 (8)	−0.0110 (7)	−0.0164 (7)	−0.0079 (6)
O4	0.0592 (9)	0.0565 (9)	0.0740 (10)	−0.0297 (7)	−0.0022 (8)	−0.0126 (8)
N1	0.0365 (8)	0.0432 (8)	0.0440 (8)	−0.0154 (7)	0.0004 (6)	−0.0168 (7)
N2	0.0385 (8)	0.0493 (9)	0.0425 (9)	−0.0081 (7)	−0.0045 (7)	−0.0151 (7)
N3	0.0408 (8)	0.0404 (8)	0.0365 (8)	−0.0133 (7)	−0.0009 (6)	−0.0131 (7)
N4	0.0369 (8)	0.0411 (8)	0.0358 (8)	−0.0132 (6)	0.0022 (6)	−0.0141 (7)
N5	0.0495 (9)	0.0471 (9)	0.0426 (9)	−0.0160 (7)	−0.0113 (7)	−0.0085 (7)
C1	0.0361 (10)	0.0538 (12)	0.0430 (10)	−0.0102 (9)	−0.0040 (8)	−0.0192 (9)
C2	0.0353 (9)	0.0421 (10)	0.0352 (9)	−0.0144 (8)	0.0041 (7)	−0.0174 (8)
C3	0.0360 (9)	0.0429 (10)	0.0327 (9)	−0.0116 (8)	0.0030 (7)	−0.0148 (8)
C4	0.0389 (9)	0.0379 (10)	0.0360 (9)	−0.0108 (8)	0.0064 (7)	−0.0135 (8)
C5	0.0351 (9)	0.0387 (10)	0.0355 (9)	−0.0079 (7)	0.0005 (7)	−0.0141 (8)
C6	0.0473 (11)	0.0488 (11)	0.0499 (11)	−0.0236 (9)	0.0054 (9)	−0.0177 (9)
C7	0.0501 (11)	0.0418 (10)	0.0453 (10)	−0.0179 (9)	−0.0015 (8)	−0.0103 (8)
C8	0.0387 (10)	0.0388 (10)	0.0493 (11)	−0.0137 (8)	−0.0045 (8)	−0.0147 (8)
C9	0.0446 (11)	0.0338 (10)	0.0506 (11)	−0.0142 (8)	−0.0032 (9)	−0.0079 (8)
C10	0.0448 (10)	0.0419 (10)	0.0444 (10)	−0.0103 (9)	0.0009 (8)	−0.0177 (9)
C11	0.0575 (13)	0.0533 (13)	0.0683 (14)	−0.0043 (10)	0.0051 (11)	−0.0230 (11)
C12	0.113 (2)	0.0506 (13)	0.0519 (13)	−0.0117 (13)	−0.0094 (13)	−0.0039 (11)

Geometric parameters (Å, º)

Cl1—C4	1.7318 (18)	C1—H1	0.9300
O1—C9	1.330 (2)	C2—C5	1.395 (2)
O1—C11	1.456 (2)	C4—C5	1.381 (2)
O2—C9	1.204 (2)	C6—C7	1.523 (3)
O3—C10	1.325 (2)	C6—H6A	0.9700
O3—C12	1.455 (3)	C6—H6B	0.9700
O4—C10	1.196 (2)	C7—C8	1.529 (3)
N1—C2	1.375 (2)	C7—H7A	0.9700
N1—C1	1.376 (2)	C7—H7B	0.9700
N1—C6	1.464 (2)	C8—C9	1.521 (3)
N2—C1	1.305 (2)	C8—C10	1.529 (3)
N2—C5	1.395 (2)	C8—H8	0.9800
N3—C2	1.336 (2)	C11—H11A	0.9600
N3—C3	1.348 (2)	C11—H11B	0.9600
N4—C4	1.320 (2)	C11—H11C	0.9600
N4—C3	1.363 (2)	C12—H12A	0.9600
N5—C3	1.345 (2)	C12—H12B	0.9600
N5—H5A	0.8600	C12—H12C	0.9600
N5—H5B	0.8600
C9—O1—C11	116.19 (15)	H6A—C6—H6B	107.8
C10—O3—C12	116.88 (17)	C6—C7—C8	115.31 (16)
C2—N1—C1	105.66 (14)	C6—C7—H7A	108.4
C2—N1—C6	126.09 (15)	C8—C7—H7A	108.4
C1—N1—C6	128.23 (15)	C6—C7—H7B	108.4
C1—N2—C5	102.85 (15)	C8—C7—H7B	108.4
C2—N3—C3	111.92 (14)	H7A—C7—H7B	107.5
C4—N4—C3	117.49 (14)	C9—C8—C7	111.09 (15)
C3—N5—H5A	120.0	C9—C8—C10	105.60 (14)
C3—N5—H5B	120.0	C7—C8—C10	113.75 (15)
H5A—N5—H5B	120.0	C9—C8—H8	108.8
N2—C1—N1	115.03 (15)	C7—C8—H8	108.8
N2—C1—H1	122.5	C10—C8—H8	108.8
N1—C1—H1	122.5	O2—C9—O1	124.28 (18)
N3—C2—N1	127.40 (16)	O2—C9—C8	124.91 (18)
N3—C2—C5	127.45 (15)	O1—C9—C8	110.79 (15)
N1—C2—C5	105.15 (15)	O4—C10—O3	124.52 (18)
N5—C3—N3	118.04 (16)	O4—C10—C8	123.92 (17)
N5—C3—N4	115.35 (15)	O3—C10—C8	111.55 (15)
N3—C3—N4	126.61 (15)	O1—C11—H11A	109.5
N4—C4—C5	122.47 (16)	O1—C11—H11B	109.5
N4—C4—Cl1	116.46 (13)	H11A—C11—H11B	109.5
C5—C4—Cl1	121.07 (13)	O1—C11—H11C	109.5
C4—C5—N2	134.64 (16)	H11A—C11—H11C	109.5
C4—C5—C2	114.06 (15)	H11B—C11—H11C	109.5
N2—C5—C2	111.30 (15)	O3—C12—H12A	109.5
N1—C6—C7	113.17 (15)	O3—C12—H12B	109.5
N1—C6—H6A	108.9	H12A—C12—H12B	109.5
C7—C6—H6A	108.9	O3—C12—H12C	109.5
N1—C6—H6B	108.9	H12A—C12—H12C	109.5
C7—C6—H6B	108.9	H12B—C12—H12C	109.5
C5—N2—C1—N1	−0.8 (2)	N3—C2—C5—C4	−0.4 (3)
C2—N1—C1—N2	1.0 (2)	N1—C2—C5—C4	179.93 (14)
C6—N1—C1—N2	−177.90 (16)	N3—C2—C5—N2	179.90 (16)
C3—N3—C2—N1	−179.53 (16)	N1—C2—C5—N2	0.27 (19)
C3—N3—C2—C5	0.9 (2)	C2—N1—C6—C7	−64.9 (2)
C1—N1—C2—N3	179.68 (17)	C1—N1—C6—C7	113.8 (2)
C6—N1—C2—N3	−1.4 (3)	N1—C6—C7—C8	−74.0 (2)
C1—N1—C2—C5	−0.69 (18)	C6—C7—C8—C9	177.81 (14)
C6—N1—C2—C5	178.21 (15)	C6—C7—C8—C10	58.8 (2)
C2—N3—C3—N5	−179.47 (15)	C11—O1—C9—O2	0.8 (3)
C2—N3—C3—N4	−0.8 (2)	C11—O1—C9—C8	179.19 (15)
C4—N4—C3—N5	178.93 (15)	C7—C8—C9—O2	−21.5 (2)
C4—N4—C3—N3	0.3 (2)	C10—C8—C9—O2	102.3 (2)
C3—N4—C4—C5	0.3 (2)	C7—C8—C9—O1	160.08 (15)
C3—N4—C4—Cl1	−179.49 (12)	C10—C8—C9—O1	−76.14 (17)
N4—C4—C5—N2	179.31 (18)	C12—O3—C10—O4	−0.2 (3)
Cl1—C4—C5—N2	−0.9 (3)	C12—O3—C10—C8	−179.25 (17)
N4—C4—C5—C2	−0.3 (2)	C9—C8—C10—O4	−59.9 (2)
Cl1—C4—C5—C2	179.57 (12)	C7—C8—C10—O4	62.2 (2)
C1—N2—C5—C4	−179.3 (2)	C9—C8—C10—O3	119.12 (16)
C1—N2—C5—C2	0.29 (19)	C7—C8—C10—O3	−118.79 (17)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5B···N4^i	0.86	2.25	3.109 (2)	176
N5—H5A···O2^ii	0.86	2.30	3.107 (2)	157
C1—H1···O4^iii	0.93	2.45	3.313 (2)	154

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