3-Benzyl-6-benzyl-amino-1-methyl-5-nitro-1,2,3,4-tetra-hydro-pyrimidine.

In the title compound, C(19)H(22)N(4)O(2), the tetra-hydro-pyrimidine ring adopts an envelope conformation (with the N atom connected to the benzyl group representing the flap). This benzyl group occupies a quasi-axial position. The two benzyl groups lie over the tetra-hydro-pyridimidine ring. The amino group is a hydrogen-bond donor to the nitro group.

Related literature

For the biological activity of tetra­hydro­pyrimidine derivatives, see: Atwal et al. (1991 ▶); Jauk et al. (2000 ▶); Messer et al. (1997 ▶). For the synthesis of the title compound, see: Chanda et al. (2004 ▶). For conformational anlysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C19H22N4O2

M = 338.41

Trigonal,

a = 29.2634 (12) Å

c = 10.4916 (8) Å

V = 7780.8 (7) Å3

Z = 18

Mo Kα radiation

μ = 0.09 mm−1

T = 292 K

0.28 × 0.23 × 0.19 mm

Data collection

Oxford Diffraction Xcalibur diffractometer with an Eos (Nova) detector

Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009 ▶) T min = 0.979, T max = 0.983

28183 measured reflections

3973 independent reflections

2683 reflections with I > 2σ(I)

R int = 0.044

Standard reflections: 0

Refinement

R[F 2 > 2σ(F 2)] = 0.067

wR(F 2) = 0.160

S = 1.08

3973 reflections

227 parameters

H-atom parameters constrained

Δρmax = 0.27 e Å−3

Δρmin = −0.24 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶).

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681000348X/ng2723sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681000348X/ng2723Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C19H22N4O2	Dx = 1.300 Mg m−3
Mr = 338.41	Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3	Cell parameters from 28183 reflections
Hall symbol: -R 3	θ = 1.4–28.0°
a = 29.2634 (12) Å	µ = 0.09 mm−1
c = 10.4916 (8) Å	T = 292 K
V = 7780.8 (7) Å3	Rectangle, yellow
Z = 18	0.28 × 0.23 × 0.19 mm
F(000) = 3240

Oxford Diffraction Xcalibur diffractometer with an Eos (Nova) detector	3973 independent reflections
Radiation source: Enhance (Mo) X-ray Source	2683 reflections with I > 2σ(I)
graphite	Rint = 0.044
ω scans	θmax = 28.0°, θmin = 1.4°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)	h = −38→38
Tmin = 0.979, Tmax = 0.983	k = −38→38
28183 measured reflections	l = −13→13

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.067	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.160	H-atom parameters constrained
S = 1.08	w = 1/[σ2(Fo2) + (0.0687P)2 + 3.8739P] where P = (Fo2 + 2Fc2)/3
3973 reflections	(Δ/σ)max < 0.001
227 parameters	Δρmax = 0.27 e Å−3
0 restraints	Δρmin = −0.24 e Å−3

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.

	x	y	z	Uiso*/Ueq
N3	0.39006 (6)	0.15310 (6)	0.51966 (16)	0.0398 (4)
H3	0.3600	0.1495	0.5406	0.048*
N2	0.42905 (6)	0.10207 (6)	0.47194 (16)	0.0402 (4)
O2	0.31664 (6)	0.11208 (6)	0.69111 (16)	0.0545 (4)
N4	0.33057 (6)	0.07772 (7)	0.71280 (16)	0.0417 (4)
C2	0.39627 (7)	0.11153 (7)	0.54251 (18)	0.0328 (4)
O1	0.30683 (6)	0.04390 (7)	0.79948 (16)	0.0617 (5)
N1	0.43266 (7)	0.04487 (7)	0.63639 (18)	0.0456 (4)
C4	0.37971 (8)	0.03212 (8)	0.6772 (2)	0.0493 (5)
H4A	0.3766	0.0265	0.7687	0.059*
H4B	0.3538	−0.0004	0.6366	0.059*
C3	0.36820 (7)	0.07530 (7)	0.64406 (19)	0.0364 (4)
C6	0.52871 (8)	0.09734 (8)	0.68224 (19)	0.0410 (5)
C13	0.48157 (8)	0.22891 (7)	0.5254 (2)	0.0431 (5)
C12	0.42799 (8)	0.20390 (8)	0.4635 (2)	0.0449 (5)
H12A	0.4142	0.2278	0.4707	0.054*
H12B	0.4317	0.1989	0.3735	0.054*
C5	0.47407 (8)	0.08550 (9)	0.7173 (2)	0.0489 (5)
H5A	0.4672	0.0739	0.8053	0.059*
H5B	0.4724	0.1177	0.7108	0.059*
C1	0.43797 (9)	0.05758 (9)	0.5043 (2)	0.0484 (5)
H1A	0.4130	0.0266	0.4570	0.058*
H1B	0.4732	0.0666	0.4770	0.058*
C7	0.54609 (9)	0.06237 (9)	0.7111 (2)	0.0515 (5)
H7	0.5228	0.0300	0.7481	0.062*
C14	0.48633 (10)	0.23062 (9)	0.6569 (2)	0.0556 (6)
H14	0.4561	0.2158	0.7070	0.067*
C8	0.59728 (10)	0.07457 (11)	0.6862 (2)	0.0595 (6)
H8	0.6081	0.0504	0.7059	0.071*
C11	0.56396 (10)	0.14432 (9)	0.6243 (2)	0.0561 (6)
H11	0.5529	0.1680	0.6012	0.067*
C9	0.63221 (10)	0.12213 (11)	0.6324 (2)	0.0613 (7)
H9	0.6670	0.1309	0.6180	0.074*
C10	0.61539 (11)	0.15683 (10)	0.5999 (3)	0.0665 (7)
H10	0.6387	0.1888	0.5615	0.080*
C18	0.52736 (10)	0.25208 (9)	0.4537 (3)	0.0607 (7)
H18	0.5255	0.2521	0.3652	0.073*
C17	0.57623 (10)	0.27535 (10)	0.5138 (4)	0.0783 (9)
H17	0.6068	0.2907	0.4650	0.094*
C16	0.57985 (12)	0.27599 (11)	0.6432 (4)	0.0806 (9)
H16	0.6127	0.2915	0.6824	0.097*
C15	0.53505 (12)	0.25380 (11)	0.7148 (3)	0.0744 (8)
H15	0.5374	0.2543	0.8032	0.089*
C19	0.44266 (10)	0.12018 (9)	0.3407 (2)	0.0525 (6)
H19A	0.4158	0.1260	0.3051	0.079*
H19B	0.4452	0.0939	0.2915	0.079*
H19C	0.4759	0.1525	0.3391	0.079*

	U11	U22	U33	U12	U13	U23
N3	0.0340 (8)	0.0380 (9)	0.0488 (10)	0.0191 (7)	0.0041 (7)	0.0058 (7)
N2	0.0425 (9)	0.0402 (9)	0.0393 (9)	0.0217 (8)	0.0041 (7)	−0.0024 (7)
O2	0.0521 (9)	0.0546 (9)	0.0664 (10)	0.0338 (8)	0.0166 (8)	0.0059 (8)
N4	0.0327 (8)	0.0406 (9)	0.0442 (10)	0.0125 (7)	0.0024 (7)	0.0018 (8)
C2	0.0275 (9)	0.0326 (9)	0.0357 (9)	0.0130 (8)	−0.0045 (7)	−0.0036 (8)
O1	0.0496 (9)	0.0641 (10)	0.0609 (10)	0.0205 (8)	0.0212 (8)	0.0233 (8)
N1	0.0432 (10)	0.0437 (10)	0.0553 (11)	0.0258 (8)	−0.0043 (8)	−0.0004 (8)
C4	0.0415 (11)	0.0362 (11)	0.0665 (14)	0.0166 (9)	0.0010 (10)	0.0095 (10)
C3	0.0321 (9)	0.0340 (10)	0.0404 (10)	0.0144 (8)	−0.0007 (8)	0.0014 (8)
C6	0.0437 (11)	0.0414 (11)	0.0397 (10)	0.0226 (9)	−0.0038 (9)	−0.0033 (9)
C13	0.0464 (12)	0.0277 (9)	0.0542 (12)	0.0178 (9)	0.0123 (10)	0.0026 (9)
C12	0.0513 (12)	0.0389 (11)	0.0482 (12)	0.0251 (10)	0.0113 (10)	0.0120 (9)
C5	0.0481 (12)	0.0572 (13)	0.0480 (12)	0.0313 (11)	−0.0037 (10)	−0.0041 (10)
C1	0.0517 (13)	0.0476 (12)	0.0546 (13)	0.0313 (11)	−0.0073 (10)	−0.0140 (10)
C7	0.0521 (13)	0.0479 (13)	0.0568 (13)	0.0267 (11)	0.0049 (11)	0.0094 (10)
C14	0.0532 (14)	0.0462 (13)	0.0585 (14)	0.0182 (11)	0.0079 (11)	−0.0032 (11)
C8	0.0637 (15)	0.0754 (17)	0.0582 (14)	0.0490 (14)	−0.0021 (12)	−0.0021 (12)
C11	0.0643 (15)	0.0424 (12)	0.0629 (15)	0.0277 (12)	0.0019 (12)	0.0040 (11)
C9	0.0448 (13)	0.0787 (18)	0.0564 (15)	0.0279 (13)	0.0064 (11)	−0.0091 (13)
C10	0.0614 (16)	0.0503 (14)	0.0671 (16)	0.0125 (12)	0.0150 (13)	0.0025 (12)
C18	0.0580 (15)	0.0430 (12)	0.0717 (16)	0.0181 (11)	0.0240 (13)	0.0032 (11)
C17	0.0443 (15)	0.0445 (14)	0.128 (3)	0.0089 (12)	0.0279 (16)	−0.0001 (16)
C16	0.0569 (17)	0.0500 (16)	0.121 (3)	0.0163 (13)	−0.0147 (18)	−0.0167 (17)
C15	0.0765 (19)	0.0558 (15)	0.0776 (19)	0.0232 (14)	−0.0147 (16)	−0.0131 (14)
C19	0.0618 (14)	0.0498 (13)	0.0398 (12)	0.0233 (11)	0.0123 (10)	−0.0044 (10)

N3—C2	1.338 (2)	C5—H5A	0.9700
N3—C12	1.463 (2)	C5—H5B	0.9700
N3—H3	0.8600	C1—H1A	0.9700
N2—C2	1.346 (2)	C1—H1B	0.9700
N2—C19	1.458 (3)	C7—C8	1.380 (3)
N2—C1	1.490 (3)	C7—H7	0.9300
O2—O2	0.000 (5)	C14—C15	1.376 (4)
O2—N4	1.280 (2)	C14—H14	0.9300
N4—O1	1.265 (2)	C8—C9	1.370 (4)
N4—O2	1.280 (2)	C8—H8	0.9300
N4—C3	1.347 (3)	C11—C10	1.383 (4)
C2—C3	1.436 (3)	C11—H11	0.9300
N1—C1	1.423 (3)	C9—C10	1.374 (4)
N1—C4	1.465 (3)	C9—H9	0.9300
N1—C5	1.470 (3)	C10—H10	0.9300
C4—C3	1.502 (3)	C18—C17	1.390 (4)
C4—H4A	0.9700	C18—H18	0.9300
C4—H4B	0.9700	C17—C16	1.361 (5)
C6—C11	1.381 (3)	C17—H17	0.9300
C6—C7	1.385 (3)	C16—C15	1.362 (4)
C6—C5	1.502 (3)	C16—H16	0.9300
C13—C18	1.383 (3)	C15—H15	0.9300
C13—C14	1.386 (3)	C19—H19A	0.9600
C13—C12	1.506 (3)	C19—H19B	0.9600
C12—H12A	0.9700	C19—H19C	0.9600
C12—H12B	0.9700
C2—N3—C12	128.11 (16)	C6—C5—H5B	108.9
C2—N3—H3	115.9	H5A—C5—H5B	107.7
C12—N3—H3	115.9	N1—C1—N2	113.99 (17)
C2—N2—C19	122.57 (17)	N1—C1—H1A	108.8
C2—N2—C1	120.59 (17)	N2—C1—H1A	108.8
C19—N2—C1	113.44 (16)	N1—C1—H1B	108.8
O2—O2—N4	0(10)	N2—C1—H1B	108.8
O1—N4—O2	118.41 (17)	H1A—C1—H1B	107.6
O1—N4—O2	118.41 (17)	C8—C7—C6	121.3 (2)
O2—N4—O2	0.00 (19)	C8—C7—H7	119.4
O1—N4—C3	119.16 (17)	C6—C7—H7	119.4
O2—N4—C3	122.39 (17)	C15—C14—C13	121.2 (2)
O2—N4—C3	122.39 (17)	C15—C14—H14	119.4
N3—C2—N2	121.55 (17)	C13—C14—H14	119.4
N3—C2—C3	121.09 (17)	C9—C8—C7	120.2 (2)
N2—C2—C3	117.36 (17)	C9—C8—H8	119.9
C1—N1—C4	108.36 (17)	C7—C8—H8	119.9
C1—N1—C5	114.36 (17)	C6—C11—C10	121.1 (2)
C4—N1—C5	112.11 (17)	C6—C11—H11	119.4
N1—C4—C3	111.80 (17)	C10—C11—H11	119.4
N1—C4—H4A	109.3	C8—C9—C10	119.5 (2)
C3—C4—H4A	109.3	C8—C9—H9	120.3
N1—C4—H4B	109.3	C10—C9—H9	120.3
C3—C4—H4B	109.3	C9—C10—C11	120.2 (2)
H4A—C4—H4B	107.9	C9—C10—H10	119.9
N4—C3—C2	122.62 (17)	C11—C10—H10	119.9
N4—C3—C4	116.93 (17)	C13—C18—C17	120.1 (3)
C2—C3—C4	120.45 (17)	C13—C18—H18	120.0
C11—C6—C7	117.7 (2)	C17—C18—H18	120.0
C11—C6—C5	121.1 (2)	C16—C17—C18	120.9 (3)
C7—C6—C5	121.2 (2)	C16—C17—H17	119.6
C18—C13—C14	117.9 (2)	C18—C17—H17	119.6
C18—C13—C12	121.5 (2)	C17—C16—C15	119.6 (3)
C14—C13—C12	120.56 (19)	C17—C16—H16	120.2
N3—C12—C13	113.37 (16)	C15—C16—H16	120.2
N3—C12—H12A	108.9	C16—C15—C14	120.3 (3)
C13—C12—H12A	108.9	C16—C15—H15	119.8
N3—C12—H12B	108.9	C14—C15—H15	119.8
C13—C12—H12B	108.9	N2—C19—H19A	109.5
H12A—C12—H12B	107.7	N2—C19—H19B	109.5
N1—C5—C6	113.41 (17)	H19A—C19—H19B	109.5
N1—C5—H5A	108.9	N2—C19—H19C	109.5
C6—C5—H5A	108.9	H19A—C19—H19C	109.5
N1—C5—H5B	108.9	H19B—C19—H19C	109.5
O2—O2—N4—O1	0.0 (2)	C1—N1—C5—C6	−59.3 (2)
O2—O2—N4—C3	0.0 (3)	C4—N1—C5—C6	176.85 (17)
C12—N3—C2—N2	−28.0 (3)	C11—C6—C5—N1	108.5 (2)
C12—N3—C2—C3	151.8 (2)	C7—C6—C5—N1	−73.9 (3)
C19—N2—C2—N3	−26.1 (3)	C4—N1—C1—N2	57.6 (2)
C1—N2—C2—N3	176.02 (17)	C5—N1—C1—N2	−68.2 (2)
C19—N2—C2—C3	154.08 (18)	C2—N2—C1—N1	−29.4 (3)
C1—N2—C2—C3	−3.7 (3)	C19—N2—C1—N1	170.85 (18)
C1—N1—C4—C3	−53.7 (2)	C11—C6—C7—C8	1.8 (3)
C5—N1—C4—C3	73.4 (2)	C5—C6—C7—C8	−176.0 (2)
O1—N4—C3—C2	178.79 (18)	C18—C13—C14—C15	−1.1 (3)
O2—N4—C3—C2	1.1 (3)	C12—C13—C14—C15	−179.4 (2)
O2—N4—C3—C2	1.1 (3)	C6—C7—C8—C9	0.3 (4)
O1—N4—C3—C4	−0.6 (3)	C7—C6—C11—C10	−2.2 (4)
O2—N4—C3—C4	−178.39 (18)	C5—C6—C11—C10	175.5 (2)
O2—N4—C3—C4	−178.39 (18)	C7—C8—C9—C10	−2.0 (4)
N3—C2—C3—N4	6.9 (3)	C8—C9—C10—C11	1.5 (4)
N2—C2—C3—N4	−173.30 (17)	C6—C11—C10—C9	0.6 (4)
N3—C2—C3—C4	−173.65 (18)	C14—C13—C18—C17	1.1 (3)
N2—C2—C3—C4	6.1 (3)	C12—C13—C18—C17	179.3 (2)
N1—C4—C3—N4	−157.21 (18)	C13—C18—C17—C16	−0.4 (4)
N1—C4—C3—C2	23.3 (3)	C18—C17—C16—C15	−0.3 (4)
C2—N3—C12—C13	−50.2 (3)	C17—C16—C15—C14	0.3 (4)
C18—C13—C12—N3	136.4 (2)	C13—C14—C15—C16	0.5 (4)
C14—C13—C12—N3	−45.4 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O2	0.86	1.98	2.591 (2)	127
N3—H3···O2i	0.86	2.50	3.056 (2)	123
N3—H3···N4	0.86	2.57	2.857 (2)	101
C12—H12A···O2i	0.97	2.54	3.184 (3)	124
C19—H19B···O1ii	0.96	2.40	3.232 (3)	145

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯O2	0.86	1.98	2.591 (2)	127