N¹,N³-Di-2-pyridylmalonamide

The title compound, C₁₃H₁₂N₄O₂, consists of two pyridine rings connected by a malonamide chain. The dihedral angle between the two pyridine rings is 88.84 (7)°. The crystal packing is stabilized by N—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C)= 0.003 Å
• R factor = 0.040
• wR factor = 0.105
• Data-to-parameter ratio = 14.8

checkCIF/PLATON results

No syntax errors found




No errors found in this datablock

---

S1. Comment

The title compound, (I), is a derivative of malonamides who were proved to be effective and selective κ optical receptor agonists (Chu et al., 2007). These compounds can coordinate to the alkali metals, alkaline earth metals and transition metals easily (Shoukry et al., 2004,

Yolanda et al., 2002). Simultaneity, they are also the 'green' extraction of quadrivalent actinides and zirconium (Siddall, 1960, Gasparini & Grossi, 1980).

The molecular structure of (I) is shown in Fig. 1. The dihedral angle between two pyridine rings of one molecule is 88.84 (7)°. In (I), the molecules are packed with hydrogen bonds of N—H···O as listed in Table 1 and π-π interactions are not observed between the aromatic pyridine rings.

Related literature

For related literature, see: Chu et al. (2007); Shoukry et al. (2004); Yolanda et al. (2002); Siddall (1960); Gasparini & Grossi (1980); Goujon & Shipman (2002); McArdle (1995).

S2. Experimental

The diethyl malonate (1.69 g 10.6 mmol) was added to a solution of pyridin-2-amine (2.50 g 27 mmol) in xylene (15 ml, 141 mmol) carefully and then the solution was refluxed at 413 K for 8 hrs(Goujon & Shipman, 2002). After cooling to room temperature, the mixture was filtered, the solid crude product was dried at 80 °C and recrystallized from a mixture of toluene and DMF (10: 1) to give colorless crystals, in yield of 31%.

Computing details

Data collection: RAPID-AUTO (Rigaku, 2006); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97-2 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97-2 (Sheldrick, 1997); molecular graphics: ORTEX (McArdle, 1995); software used to prepare material for publication: SHELXL97-2.

Figures

Fig. 1. A view of the molecular structure of (I), with displacement ellipsoids drawn at the 50% probabilty level for non-H atoms.

N¹,N³—Di-2-pyridylmalonamide

Crystal data

C13H12N4O2	F(000) = 536
Mr = 256.27	Dx = 1.412 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71069 Å
Hall symbol: -P2ybc	Cell parameters from 7891 reflections
a = 13.112 (9) Å	θ = 6.0–55.3°
b = 9.412 (5) Å	µ = 0.10 mm^−1
c = 9.799 (5) Å	T = 298 K
β = 94.30 (3)°	Block, colorless
V = 1205.9 (12) Å^3	0.60 × 0.40 × 0.10 mm
Z = 4

Data collection

Rigaku model???? imaging plate system diffractometer	1970 reflections with I > 2σ(I)
Radiation source: Rigaku rotating anode generator	Rint = 0.033
Graphite Monochromator monochromator	θmax = 27.5°, θmin = 3.0°
Detector resolution: 10 pixels mm^-1	h = −17→16
imaging plate scans	k = −12→12
11080 measured reflections	l = −11→12
2732 independent 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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.105	Only H-atom displacement parameters refined
S = 1.02	w = 1/[σ^2(Fo^2) + (0.0497P)^2 + 0.1727P] where P = (Fo^2 + 2Fc^2)/3
2732 reflections	(Δ/σ)max < 0.001
184 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.19 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
N1	0.60032 (11)	0.40681 (15)	0.35915 (12)	0.0532 (4)
N2	0.74584 (9)	0.28807 (13)	0.31452 (11)	0.0404 (3)
H1	0.7615	0.2972	0.4009	0.064 (5)*
N3	1.04889 (9)	0.27078 (11)	0.17253 (12)	0.0373 (3)
H2	1.0310	0.3543	0.1972	0.053 (5)*
N4	1.15370 (10)	0.39584 (13)	0.04360 (14)	0.0498 (3)
O1	0.80805 (8)	0.20945 (12)	0.11820 (9)	0.0506 (3)
O2	1.01988 (9)	0.03660 (10)	0.20936 (11)	0.0504 (3)
C1	0.64675 (11)	0.33103 (15)	0.26822 (13)	0.0374 (3)
C2	0.60119 (12)	0.29727 (19)	0.14094 (15)	0.0509 (4)
H3	0.6353	0.2426	0.0797	0.064 (5)*
C3	0.50414 (14)	0.3465 (2)	0.10707 (17)	0.0628 (5)
H4	0.4720	0.3263	0.0214	0.087 (7)*
C4	0.45468 (14)	0.4249 (2)	0.19851 (18)	0.0647 (5)
H5	0.3888	0.4589	0.1773	0.079 (6)*
C5	0.50561 (15)	0.4517 (2)	0.32254 (18)	0.0657 (5)
H6	0.4721	0.5047	0.3856	0.074 (6)*
C6	0.81999 (11)	0.23400 (13)	0.24058 (13)	0.0340 (3)
C7	0.91980 (11)	0.20588 (14)	0.32271 (13)	0.0351 (3)
H7	0.9103	0.1313	0.3889	0.047 (4)*
H8	0.9416	0.2911	0.3724	0.046 (4)*
C8	1.00105 (11)	0.16180 (13)	0.23043 (13)	0.0351 (3)
C9	1.12351 (11)	0.26680 (14)	0.07794 (13)	0.0360 (3)
C10	1.16187 (13)	0.14448 (16)	0.02381 (16)	0.0499 (4)
H9	1.1396	0.0554	0.0500	0.069 (5)*
C11	1.23391 (14)	0.15810 (18)	−0.06999 (18)	0.0564 (4)
H10	1.2614	0.0774	−0.1079	0.075 (6)*
C12	1.26539 (13)	0.28983 (18)	−0.10785 (16)	0.0509 (4)
H11	1.3139	0.3008	−0.1716	0.066 (5)*
C13	1.22311 (13)	0.40432 (18)	−0.04889 (17)	0.0545 (4)
H12	1.2439	0.4942	−0.0747	0.071 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0513 (8)	0.0685 (9)	0.0401 (6)	0.0177 (7)	0.0053 (6)	−0.0027 (6)
N2	0.0355 (7)	0.0557 (7)	0.0300 (5)	0.0019 (5)	0.0025 (5)	−0.0042 (5)
N3	0.0372 (7)	0.0301 (5)	0.0457 (6)	−0.0003 (5)	0.0106 (5)	−0.0011 (5)
N4	0.0505 (8)	0.0397 (6)	0.0617 (8)	−0.0026 (6)	0.0205 (6)	0.0044 (6)
O1	0.0454 (7)	0.0736 (7)	0.0329 (5)	0.0052 (5)	0.0033 (4)	−0.0088 (5)
O2	0.0584 (7)	0.0315 (5)	0.0642 (7)	−0.0004 (4)	0.0233 (5)	0.0000 (5)
C1	0.0351 (8)	0.0425 (7)	0.0353 (6)	−0.0021 (6)	0.0067 (5)	0.0041 (6)
C2	0.0391 (9)	0.0707 (10)	0.0429 (8)	−0.0039 (7)	0.0036 (6)	−0.0112 (8)
C3	0.0421 (10)	0.0954 (14)	0.0496 (9)	−0.0013 (9)	−0.0055 (7)	−0.0036 (9)
C4	0.0448 (10)	0.0911 (13)	0.0574 (10)	0.0175 (9)	−0.0003 (8)	0.0093 (9)
C5	0.0582 (12)	0.0862 (13)	0.0532 (9)	0.0296 (10)	0.0072 (8)	−0.0011 (9)
C6	0.0356 (8)	0.0339 (6)	0.0329 (6)	−0.0047 (5)	0.0055 (5)	0.0012 (5)
C7	0.0363 (8)	0.0352 (7)	0.0339 (6)	−0.0017 (5)	0.0036 (5)	0.0021 (6)
C8	0.0356 (7)	0.0324 (6)	0.0370 (6)	−0.0011 (5)	0.0019 (5)	0.0011 (6)
C9	0.0302 (7)	0.0384 (7)	0.0395 (7)	−0.0014 (5)	0.0024 (5)	0.0016 (6)
C10	0.0503 (10)	0.0404 (8)	0.0611 (9)	0.0011 (7)	0.0188 (7)	−0.0017 (7)
C11	0.0516 (11)	0.0566 (10)	0.0635 (10)	0.0053 (8)	0.0198 (8)	−0.0086 (8)
C12	0.0369 (9)	0.0689 (10)	0.0482 (8)	−0.0027 (7)	0.0120 (7)	0.0027 (8)
C13	0.0508 (10)	0.0520 (9)	0.0628 (10)	−0.0056 (7)	0.0184 (8)	0.0095 (8)

Geometric parameters (Å, º)

N1—C1	1.325 (2)	C3—H4	0.9300
N1—C5	1.335 (2)	C4—C5	1.366 (3)
N2—C6	1.355 (2)	C4—H5	0.9300
N2—C1	1.403 (2)	C5—H6	0.9300
N2—H1	0.8600	C6—C7	1.508 (2)
N3—C8	1.349 (2)	C7—C8	1.506 (2)
N3—C9	1.398 (2)	C7—H7	0.9700
N3—H2	0.8600	C7—H8	0.9700
N4—C9	1.329 (2)	C9—C10	1.378 (2)
N4—C13	1.334 (2)	C10—C11	1.372 (2)
O1—C6	1.220 (2)	C10—H9	0.9300
O2—C8	1.225 (2)	C11—C12	1.367 (2)
C1—C2	1.379 (2)	C11—H10	0.9300
C2—C3	1.372 (3)	C12—C13	1.360 (2)
C2—H3	0.9300	C12—H11	0.9300
C3—C4	1.362 (3)	C13—H12	0.9300
C1—N1—C5	117.06 (14)	N2—C6—C7	114.18 (12)
C6—N2—C1	128.29 (12)	C6—C7—C8	110.65 (11)
C6—N2—H1	115.9	C6—C7—H7	109.5
C1—N2—H1	115.9	C8—C7—H7	109.5
C8—N3—C9	128.98 (11)	C6—C7—H8	109.5
C8—N3—H2	115.5	C8—C7—H8	109.5
C9—N3—H2	115.5	H7—C7—H8	108.1
C9—N4—C13	117.27 (13)	O2—C8—N3	123.68 (13)
N1—C1—C2	122.87 (14)	O2—C8—C7	121.79 (12)
N1—C1—N2	113.50 (12)	N3—C8—C7	114.52 (11)
C2—C1—N2	123.63 (13)	N4—C9—C10	122.81 (14)
C3—C2—C1	118.17 (15)	N4—C9—N3	112.34 (12)
C3—C2—H3	120.9	C10—C9—N3	124.84 (12)
C1—C2—H3	120.9	C11—C10—C9	117.97 (14)
C4—C3—C2	120.18 (16)	C11—C10—H9	121.0
C4—C3—H4	119.9	C9—C10—H9	121.0
C2—C3—H4	119.9	C12—C11—C10	120.23 (15)
C5—C4—C3	117.41 (17)	C12—C11—H10	119.9
C5—C4—H5	121.3	C10—C11—H10	119.9
C3—C4—H5	121.3	C11—C12—C13	117.54 (15)
N1—C5—C4	124.30 (16)	C11—C12—H11	121.2
N1—C5—H6	117.8	C13—C12—H11	121.2
C4—C5—H6	117.8	N4—C13—C12	124.17 (15)
O1—C6—N2	123.55 (13)	N4—C13—H12	117.9
O1—C6—C7	122.27 (13)	C12—C13—H12	117.9
C5—N1—C1—C2	−0.5 (2)	C9—N3—C8—O2	2.3 (2)
C5—N1—C1—N2	179.97 (15)	C9—N3—C8—C7	−176.65 (13)
C6—N2—C1—N1	−166.38 (13)	C6—C7—C8—O2	−95.13 (15)
C6—N2—C1—C2	14.1 (2)	C6—C7—C8—N3	83.80 (14)
N1—C1—C2—C3	1.0 (2)	C13—N4—C9—C10	1.0 (2)
N2—C1—C2—C3	−179.50 (15)	C13—N4—C9—N3	−178.39 (14)
C1—C2—C3—C4	−0.8 (3)	C8—N3—C9—N4	−179.77 (14)
C2—C3—C4—C5	0.2 (3)	C8—N3—C9—C10	0.9 (2)
C1—N1—C5—C4	−0.2 (3)	N4—C9—C10—C11	−0.3 (2)
C3—C4—C5—N1	0.4 (3)	N3—C9—C10—C11	178.94 (15)
C1—N2—C6—O1	−3.0 (2)	C9—C10—C11—C12	−0.3 (3)
C1—N2—C6—C7	177.10 (12)	C10—C11—C12—C13	0.3 (3)
O1—C6—C7—C8	6.48 (18)	C9—N4—C13—C12	−1.0 (3)
N2—C6—C7—C8	−173.63 (11)	C11—C12—C13—N4	0.4 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1···O1^i	0.86	2.17	3.026 (2)	172
N3—H2···O2^ii	0.86	2.08	2.9272 (19)	169

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