Crystal structure and Hirshfeld surface analysis of 6-amino-8-(2,6-di­chloro­phen­yl)-1,3,4,8-tetra­hydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbo­nitrile

Naghiyev, F.N.; Tereshina, T.A.; Khrustalev, V.N.; Akkurt, M.; Rzayev, R.M.; Akobirshoeva, A.A.; Mamedov, İ.G.

doi:10.1107/S2056989021003583

Crystal structure and Hirshfeld surface analysis of 6-amino-8-(2,6-dichlorophenyl)-1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbonitrile

F. N. Naghiyev, T. A. Tereshina, V. N. Khrustalev, M. Akkurt, R. M. Rzayev, A. A. Akobirshoeva and İ.G. Mamedov

In the crystal structure of the title compound, intermolecular N—H

N and C—H

N hydrogen bonds between the molecules lead to sheets extending parallel to the (110) and ( $\overline{1}$ 10) planes.

Keywords: crystal structure; cycloaddition product; 1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrimidine; Hirshfeld surface analysis.

Read article Similar articles

Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989021003583/wm5605sup1.cif Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989021003583/wm5605Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989021003583/wm5605Isup3.cml Supplementary material

CCDC reference: 2075706

checkCIF report

Key indicators

Single-crystal X-ray study
T = 100 K
Mean (C-C) = 0.004 Å
R factor = 0.044
wR factor = 0.090
Data-to-parameter ratio = 27.0

checkCIF/PLATON results

No syntax errors found



Alert level G
PLAT792_ALERT_1_G Model has Chirality at C8          (Polar  SPGR)          R Verify
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          6 Info

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

   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
   0 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


checkCIF publication errors

Alert level A
PUBL024_ALERT_1_A The number of authors is greater than 5.
              Please specify the role of each of the co-authors
              for your paper.

   1 ALERT level A = Data missing that is essential or data in wrong format
   0 ALERT level G = General alerts. Data that may be required is missing

Computing details top

Data collection: APEX3 (Bruker, 2018); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2020).

6-Amino-8-(2,6-dichlorophenyl)-1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbonitrile top

Crystal data top

C₁₆H₁₃Cl₂N₅	F(000) = 712
M_r = 346.21	D_x = 1.421 Mg m⁻³
Monoclinic, Cc	Mo Kα radiation, λ = 0.71073 Å
a = 8.6598 (2) Å	Cell parameters from 4611 reflections
b = 16.0275 (5) Å	θ = 2.5–32.2°
c = 11.6590 (3) Å	µ = 0.41 mm⁻¹
β = 90.7364 (9)°	T = 100 K
V = 1618.08 (8) Å³	Needle, colourless
Z = 4	0.30 × 0.03 × 0.03 mm

Data collection top

Bruker D8 QUEST PHOTON-III CCD diffractometer	4528 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.064
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 32.6°, θ_min = 2.5°
T_min = 0.880, T_max = 0.980	h = −13→13
21346 measured reflections	k = −24→24
5861 independent reflections	l = −17→17

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.044	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.090	w = 1/[σ²(F_o²) + (0.0315P)² + 0.2854P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
5861 reflections	Δρ_max = 0.25 e Å⁻³
217 parameters	Δρ_min = −0.32 e Å⁻³
2 restraints	Absolute structure: Flack x determined using 1774 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013).
Primary atom site location: difference Fourier map	Absolute structure parameter: 0.27 (3)

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.48473 (9)	0.76604 (6)	0.16871 (7)	0.0429 (2)
Cl2	0.69787 (9)	0.56058 (4)	0.51124 (7)	0.03080 (17)
N1	0.5635 (3)	0.75406 (14)	0.7250 (2)	0.0199 (5)
H1	0.604 (4)	0.801 (2)	0.709 (3)	0.024*
C2	0.5218 (3)	0.73373 (16)	0.8418 (2)	0.0207 (5)
H2A	0.4154	0.7528	0.8576	0.025*
H2B	0.5934	0.7611	0.8969	0.025*
C3	0.5326 (4)	0.63931 (17)	0.8531 (2)	0.0248 (6)
H3A	0.6392	0.6206	0.8373	0.030*
H3B	0.5064	0.6222	0.9321	0.030*
C4	0.4209 (3)	0.59988 (16)	0.7681 (2)	0.0218 (5)
H4A	0.4471	0.5401	0.7595	0.026*
H4B	0.3151	0.6033	0.7990	0.026*
N5	0.4232 (3)	0.64027 (13)	0.65394 (19)	0.0167 (4)
C6	0.3418 (3)	0.60234 (14)	0.5649 (2)	0.0163 (5)
N6	0.2511 (3)	0.53821 (15)	0.5930 (2)	0.0236 (5)
H6A	0.214 (4)	0.506 (2)	0.541 (3)	0.028*
H6B	0.238 (4)	0.522 (2)	0.661 (3)	0.028*
C7	0.3535 (3)	0.63028 (15)	0.4540 (2)	0.0155 (5)
C8	0.4667 (3)	0.69614 (15)	0.4164 (2)	0.0167 (5)
H8	0.4066	0.7379	0.3704	0.020*
C9	0.5266 (3)	0.74104 (16)	0.5222 (2)	0.0179 (5)
C9A	0.5062 (3)	0.71289 (15)	0.6322 (2)	0.0161 (5)
C10	0.2600 (3)	0.59393 (15)	0.3682 (2)	0.0147 (5)
N10	0.1851 (3)	0.56730 (13)	0.2941 (2)	0.0194 (5)
C11	0.5914 (3)	0.66149 (18)	0.3380 (3)	0.0200 (5)
C12	0.6051 (3)	0.6880 (2)	0.2246 (3)	0.0283 (6)
C13	0.7126 (4)	0.6549 (3)	0.1492 (3)	0.0375 (8)
H13	0.7167	0.6742	0.0723	0.045*
C14	0.8127 (4)	0.5940 (2)	0.1873 (3)	0.0383 (8)
H14	0.8869	0.5715	0.1367	0.046*
C15	0.8058 (3)	0.56565 (19)	0.2989 (3)	0.0314 (7)
H15	0.8746	0.5235	0.3254	0.038*
C16	0.6971 (3)	0.59938 (18)	0.3718 (3)	0.0240 (6)
C17	0.5995 (3)	0.81835 (17)	0.5040 (2)	0.0228 (6)
N17	0.6562 (4)	0.88151 (16)	0.4841 (2)	0.0362 (7)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0391 (4)	0.0681 (6)	0.0215 (4)	−0.0012 (4)	0.0009 (3)	0.0190 (4)
Cl2	0.0305 (4)	0.0267 (3)	0.0353 (4)	0.0081 (3)	0.0050 (3)	0.0077 (3)
N1	0.0294 (12)	0.0147 (10)	0.0156 (11)	−0.0072 (9)	0.0006 (9)	0.0002 (8)
C2	0.0278 (14)	0.0215 (13)	0.0127 (12)	−0.0055 (10)	−0.0012 (10)	−0.0013 (10)
C3	0.0353 (16)	0.0207 (13)	0.0180 (14)	−0.0050 (11)	−0.0071 (12)	0.0033 (10)
C4	0.0328 (14)	0.0189 (12)	0.0136 (13)	−0.0088 (11)	−0.0029 (11)	0.0027 (9)
N5	0.0237 (11)	0.0145 (10)	0.0120 (10)	−0.0050 (8)	0.0000 (8)	0.0003 (7)
C6	0.0200 (12)	0.0127 (10)	0.0161 (12)	−0.0016 (9)	−0.0006 (9)	−0.0018 (9)
N6	0.0354 (13)	0.0211 (11)	0.0142 (11)	−0.0141 (10)	−0.0024 (10)	0.0009 (9)
C7	0.0179 (11)	0.0150 (11)	0.0137 (12)	−0.0006 (9)	0.0007 (9)	−0.0013 (9)
C8	0.0216 (13)	0.0135 (10)	0.0151 (12)	−0.0022 (9)	0.0001 (10)	0.0002 (9)
C9	0.0242 (13)	0.0149 (11)	0.0148 (13)	−0.0040 (9)	0.0029 (10)	−0.0025 (9)
C9A	0.0189 (12)	0.0131 (10)	0.0163 (12)	−0.0025 (9)	0.0001 (9)	−0.0007 (9)
C10	0.0179 (11)	0.0123 (10)	0.0140 (12)	0.0010 (9)	0.0034 (9)	0.0018 (8)
N10	0.0226 (11)	0.0193 (11)	0.0163 (12)	0.0030 (9)	−0.0013 (9)	−0.0016 (8)
C11	0.0220 (12)	0.0199 (11)	0.0181 (12)	−0.0082 (9)	0.0022 (10)	−0.0051 (9)
C12	0.0257 (15)	0.0417 (17)	0.0175 (15)	−0.0130 (13)	0.0008 (11)	−0.0018 (12)
C13	0.0281 (16)	0.067 (2)	0.0179 (15)	−0.0197 (16)	0.0048 (12)	−0.0117 (15)
C14	0.0248 (15)	0.053 (2)	0.038 (2)	−0.0131 (15)	0.0123 (13)	−0.0255 (16)
C15	0.0214 (14)	0.0300 (15)	0.043 (2)	−0.0064 (12)	0.0079 (13)	−0.0150 (14)
C16	0.0228 (14)	0.0229 (13)	0.0264 (15)	−0.0039 (10)	0.0037 (11)	−0.0039 (11)
C17	0.0329 (15)	0.0213 (12)	0.0144 (13)	−0.0073 (11)	0.0054 (11)	−0.0053 (10)
N17	0.064 (2)	0.0259 (12)	0.0189 (13)	−0.0208 (13)	0.0093 (12)	−0.0046 (10)

Geometric parameters (Å, º) top

Cl1—C12	1.749 (4)	N6—H6B	0.85 (4)
Cl2—C16	1.741 (3)	C7—C10	1.406 (4)
N1—C9A	1.355 (3)	C7—C8	1.509 (3)
N1—C2	1.451 (3)	C8—C9	1.514 (4)
N1—H1	0.85 (3)	C8—C11	1.529 (4)
C2—C3	1.522 (4)	C8—H8	1.0000
C2—H2A	0.9900	C9—C9A	1.373 (4)
C2—H2B	0.9900	C9—C17	1.408 (4)
C3—C4	1.514 (4)	C10—N10	1.155 (3)
C3—H3A	0.9900	C11—C12	1.395 (4)
C3—H3B	0.9900	C11—C16	1.405 (4)
C4—N5	1.481 (3)	C12—C13	1.392 (4)
C4—H4A	0.9900	C13—C14	1.375 (5)
C4—H4B	0.9900	C13—H13	0.9500
N5—C6	1.387 (3)	C14—C15	1.380 (5)
N5—C9A	1.393 (3)	C14—H14	0.9500
C6—N6	1.337 (3)	C15—C16	1.385 (4)
C6—C7	1.373 (4)	C15—H15	0.9500
N6—H6A	0.85 (4)	C17—N17	1.150 (3)

C9A—N1—C2	123.1 (2)	C7—C8—C9	108.2 (2)
C9A—N1—H1	114 (2)	C7—C8—C11	112.7 (2)
C2—N1—H1	121 (2)	C9—C8—C11	115.0 (2)
N1—C2—C3	106.8 (2)	C7—C8—H8	106.8
N1—C2—H2A	110.4	C9—C8—H8	106.8
C3—C2—H2A	110.4	C11—C8—H8	106.8
N1—C2—H2B	110.4	C9A—C9—C17	119.5 (2)
C3—C2—H2B	110.4	C9A—C9—C8	123.9 (2)
H2A—C2—H2B	108.6	C17—C9—C8	116.4 (2)
C4—C3—C2	108.7 (2)	N1—C9A—C9	122.4 (2)
C4—C3—H3A	110.0	N1—C9A—N5	116.5 (2)
C2—C3—H3A	110.0	C9—C9A—N5	121.1 (2)
C4—C3—H3B	110.0	N10—C10—C7	176.6 (3)
C2—C3—H3B	110.0	C12—C11—C16	114.7 (3)
H3A—C3—H3B	108.3	C12—C11—C8	121.7 (3)
N5—C4—C3	113.0 (2)	C16—C11—C8	123.5 (3)
N5—C4—H4A	109.0	C13—C12—C11	123.2 (3)
C3—C4—H4A	109.0	C13—C12—Cl1	115.9 (3)
N5—C4—H4B	109.0	C11—C12—Cl1	120.8 (2)
C3—C4—H4B	109.0	C14—C13—C12	119.3 (3)
H4A—C4—H4B	107.8	C14—C13—H13	120.3
C6—N5—C9A	119.3 (2)	C12—C13—H13	120.3
C6—N5—C4	117.9 (2)	C13—C14—C15	120.2 (3)
C9A—N5—C4	122.8 (2)	C13—C14—H14	119.9
N6—C6—C7	122.1 (2)	C15—C14—H14	119.9
N6—C6—N5	116.6 (2)	C14—C15—C16	119.2 (3)
C7—C6—N5	121.2 (2)	C14—C15—H15	120.4
C6—N6—H6A	120 (2)	C16—C15—H15	120.4
C6—N6—H6B	124 (2)	C15—C16—C11	123.3 (3)
H6A—N6—H6B	115 (3)	C15—C16—Cl2	116.0 (3)
C6—C7—C10	119.1 (2)	C11—C16—Cl2	120.6 (2)
C6—C7—C8	123.9 (2)	N17—C17—C9	176.9 (3)
C10—C7—C8	117.0 (2)

C9A—N1—C2—C3	46.5 (3)	C17—C9—C9A—N5	174.5 (3)
N1—C2—C3—C4	−60.3 (3)	C8—C9—C9A—N5	−1.8 (4)
C2—C3—C4—N5	43.2 (3)	C6—N5—C9A—N1	170.2 (2)
C3—C4—N5—C6	171.2 (2)	C4—N5—C9A—N1	−11.5 (4)
C3—C4—N5—C9A	−7.1 (4)	C6—N5—C9A—C9	−9.1 (4)
C9A—N5—C6—N6	−173.0 (2)	C4—N5—C9A—C9	169.2 (2)
C4—N5—C6—N6	8.6 (4)	C7—C8—C11—C12	116.4 (3)
C9A—N5—C6—C7	6.4 (4)	C9—C8—C11—C12	−118.9 (3)
C4—N5—C6—C7	−172.0 (2)	C7—C8—C11—C16	−61.5 (3)
N6—C6—C7—C10	4.1 (4)	C9—C8—C11—C16	63.2 (3)
N5—C6—C7—C10	−175.2 (2)	C16—C11—C12—C13	1.1 (4)
N6—C6—C7—C8	−173.2 (2)	C8—C11—C12—C13	−176.9 (3)
N5—C6—C7—C8	7.4 (4)	C16—C11—C12—Cl1	−179.0 (2)
C6—C7—C8—C9	−16.0 (3)	C8—C11—C12—Cl1	3.0 (4)
C10—C7—C8—C9	166.6 (2)	C11—C12—C13—C14	−1.0 (5)
C6—C7—C8—C11	112.3 (3)	Cl1—C12—C13—C14	179.1 (2)
C10—C7—C8—C11	−65.1 (3)	C12—C13—C14—C15	0.5 (5)
C7—C8—C9—C9A	13.2 (3)	C13—C14—C15—C16	−0.2 (5)
C11—C8—C9—C9A	−113.8 (3)	C14—C15—C16—C11	0.4 (4)
C7—C8—C9—C17	−163.2 (2)	C14—C15—C16—Cl2	−179.4 (2)
C11—C8—C9—C17	69.8 (3)	C12—C11—C16—C15	−0.8 (4)
C2—N1—C9A—C9	169.2 (3)	C8—C11—C16—C15	177.2 (3)
C2—N1—C9A—N5	−10.1 (4)	C12—C11—C16—Cl2	179.0 (2)
C17—C9—C9A—N1	−4.7 (4)	C8—C11—C16—Cl2	−3.1 (4)
C8—C9—C9A—N1	179.0 (3)

Hydrogen-bond geometry (Å, º) top

Cg3 is the centroid of the C11–C16 dichlorophenyl ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N10ⁱ	0.85 (3)	2.43 (3)	3.152 (3)	143 (3)
N6—H6A···N17ⁱⁱ	0.85 (4)	2.17 (3)	2.927 (3)	149 (3)
N6—H6B···N10ⁱⁱⁱ	0.85 (4)	2.16 (4)	2.953 (3)	156 (3)
C4—H4B···N17^iv	0.99	2.59	3.440 (4)	144
C2—H2A···Cg3^iv	0.99	2.87	3.653 (3)	136

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

Summary of short interatomic contacts (Å) in the title compound top

Contact	Distance	Symmetry operation
H6B···N10	2.16	x, 1 - y, 1/2 + z
H1···N10	2.43	1/2 + x, 3/2 - y, 1/2 + z
H4B···N17	2.59	-1/2 + x, 3/2 - y, 1/2 + z
H6A···N17	2.16	-1/2 + x, -1/2 + y, z
N10···H15	2.81	-1 + x, y, z
H3B···H13	2.57	x, y, 1 + z

Percentage contributions of interatomic contacts to the Hirshfeld surface for the title compound top

Contact	Percentage contribution
N···H/H···N	28.4
H···H	24.5
C···H/H···C	21.4
Cl···H/H···Cl	16.1
Cl···C/C···Cl	3.3
Cl···Cl	2.5
Cl···N/N···Cl	2.3
C···N/N···C	0.8
C···C	0.6
N···N	0.2

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

Crystal structure and Hirshfeld surface analysis of 6-amino-8-(2,6-di­chloro­phen­yl)-1,3,4,8-tetra­hydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbo­nitrile

Supporting information

Key indicators

checkCIF/PLATON results

Crystal structure and Hirshfeld surface analysis of 6-amino-8-(2,6-dichlorophenyl)-1,3,4,8-tetrahydro-2H-pyrido[1,2-a]pyrimidine-7,9-dicarbonitrile