Crystal structure of 4,5-bis-phenyl-8a-phenyl-3,4,4a,5,6,8a-hexahydro-1H,8H-pyrimido[4.5-d]pyrimidine-2,7-dione

Article abstract of DOI:10.1007/s10947-010-0123-y

Single crystal X-ray diffraction is used to determine the crystal structure of 4,5-bis-phenyl-8a-phenyl-3,4,4a,5,6,8a-hexahydro-lH,8H-pyrimido[4.5-d]pyrimidine-2,7-dione and identify its conformation characteristics.

Full text of DOI:10.1007/s10947-010-0123-y

Journal of Structural Chemistry. Vol. 51, No. 5, pp. 1001-1004, 2010
Original Russian Text Copyright © 2010 by M. M. Kurbanova, A. V. Kurbanov, A. B. Novruzova, V. N. Khrustalev, and A. M. Magerramov
CRYSTAL STRUCTURE OF 4,5-BIS-PHENYL-8a-
PHENYL-3,4,4a,5,6,8a-HEXAHYDRO-1H,8H-
PYRIMIDO[4.5-d]PYRIMIDINE-2,7-DIONE
M. M. Kurbanova,1 A. V. Kurbanov,1 A. B. Novruzova,1
V. N. Khrustalev,2 and A. M. Magerramov1
UDC 547.854
Single crystal X-ray diffraction is used to determine the crystal structure of 4,5-bis-phenyl-8ꢀ-phenyl-
3,4,4ꢀ,5,6,8ꢀ-hexahydro-1ꢁ,8ꢁ-pyrimido[4.5-d]pyrimidine-2,7-dione and identify its conformation
characteristics.
Keywords: crystal structure, 4,5-bis-phenyl-8ꢀ-phenyl-3,4,4ꢀ,5,6,8ꢀ-hexahydro-1ꢁ,8ꢁ-pyrimido[4.5-
d]pyrimidine-2,7-dione.
Multicomponent reactions are known to become an ever-developing method to produce new biologically active
compounds and pharmaceuticals. With the participation of three or more compounds, they form a new product containing the
main structural parts of all precursors.
Taking into consideration the above, we set ourselves a goal to continue the studies on Biginelli reaction
modification using aromatic ketones. We chose acetophenone [1] as the aromatic ketone for the investigation. Condensation
of benzaldehyde, acetophenone, and carbamide in isopropyl alcohol in the presence of concentrated HCl resulted in the
formation of 4,5-bis-phenyl-8ꢀ-phenyl-3,4,4ꢀ,5,6,8ꢀ-hexahydro-1ꢁ,8ꢁ-pyrimido[4.5-d]pyrimidine-2,7-dione (I).
This paper describes the single crystal XRD analysis of 4,5-bis-phenyl-8ꢀ-phenyl-3,4,4ꢀ,5,6,8ꢀ-hexahydro-1ꢁ,8ꢁ-
pyrimido[4.5-d]pyrimidine-2,7-dione (I).
Experimental. The synthesis of compound I is described in the work [1]. The crystal for XRD was obtained by
double crystallization of compound I from ethanol. XRD of compound I was performed on a Bruker SMART APEX II CCD
diffractometer (T = 296 K, ꢀMoKꢁ radiation, graphite monochromator, ꢂ- and ꢃ-scanning, 2ꢄmax = 56ꢅ).
The crystals of the monohydrate of compound I (C24H22N4O24H2O, Mr = 416.47) were white; Tm = 165-167ꢅC,
cubic, 0.30ꢆ0.30ꢆ0.30 mm, monoclinic: a = 11.2789(12) Å, b = 17.4774(19) Å, c = 10.5751(11) Å, ꢇ = 94.719(2)ꢅ, V =
2077.6(4) Å3, P21/c space group, Z = 4, dx = 1.332 g/cm3, ꢈ = 0.090 mm–1. We measured the intensities of 23,736 reflections
1Baku State University, Baku, Azerbaijan; mkurbanova72@mail.ru. 2A. N. Nesmeyanov Institute of Organoelement
Compounds, Russian Academy of Sciences, Moscow, Russia. Translated from Zhurnal Strukturnoi Khimii, Vol. 51, No. 5,
pp. 1031-1033, September-October, 2010. Original article submitted November 13, 2009; revision December 22, 2009.
0022-4766/10/5105-1001 © 2010 Springer Science+Business Media, Inc.
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Fig. 1. Molecular structure of the monohydrate of
compound I. The alternative position of the less
occupied disordered molecule is not presented. In the
molecule of I, the figure shows only hydrogen atoms
of the amino groups and those at the asymmetric
carbon atoms. The intermolecular hydrogen bond is
shown by a dashed line.
Fig. 2. Hydrogen bonds and packing of the molecules of compound I in the
crystal (hydrogen bonds are shown by dashed lines).
(5127 independent reflections, Rint = 0.025), for which we introduced a semi-empirical correction using the SADABS
program [2].
The structure of compound I was solved by the direct method and refined by LSM in an anisotropic approximation
for non-hydrogen atoms. The crystal of compound I contains a solvate water molecule disordered over two positions with the
0.7:0.3 population. Hydrogen atoms of the amino groups and solvate water molecule were objectively identified in difference
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TABLE 1. Main Interatomic Distances d (Å) and Bond Angles ꢃ (deg) for the Molecule of I
Bond
d
Bond
d
Bond
d
O(1)–C(2)
O(2)–C(7)
N(1)–C(2)
N(1)–C(8a)
C(2)–N(3)
1.2361(14)
1.2435(14)
1.3492(15)
1.4565(14)
1.3529(17)
N(3)–C(4)
C(4)–C(4a)
C(4a)–C(5)
C(4a)–C(8a)
C(5)–N(6)
1.4481(16)
1.5418(14)
1.5422(15)
1.5414(15)
1.4555(14)
N(6)–C(7)
C(7)–N(8)
N(8)–C(8a)
1.3447(15)
1.3460(14)
1.4639(13)
Angle
Angle
Angle
ꢃ
ꢃ
ꢃ
C(2)–N(1)–C(8a)
N(1)–C(2)–N(3)
C(2)–N(3)–C(4)
N(3)–C(4)–C(4a)
C(4)–C(4a)–C(5)
124.51(10)
117.56(10)
125.98(10)
109.28(9)
112.11(9)
C(4)–C(4a)–C(8a)
C(5)–C(4a)–C(8a)
C(4a)–C(5)–N(6)
C(5)–N(6)–C(7)
N(6)–C(7)–N(8)
111.11(8)
108.38(9)
108.00(9)
123.06(9)
117.54(10)
C(7)–N(8)–C(8a)
N(1)–C(8a)–C(4a)
N(1)–C(8a)–N(8)
C(4a)–C(8a)–N(8)
126.35(9)
107.30(8)
108.46(9)
109.52(8)
TABLE 2. Hydrogen Bond Parameters (d, Å and ꢃ, deg) in the Monohydrate of Compound I*
Parameter
d(D–H)
d(H…A)
d(D…A)
ꢃ(D–H…A)
N(1)–H(1N)…O(3)
N(1)–H(1N)…O(3ꢉ)
N(6)–H(6N)…O(2)#1
N(8)–H(8N)…O(1)#2
O(3)–H(3A)…O(2)#3
O(3ꢉ)–H(3A)…O(2)#3
O(3)–H(3B)…O(1)#2
O(3ꢉ)–H(3B)…O(1)#2
0.91
0.91
0.92
0.90
0.98
0.96
0.95
0.96
1.94
1.75
1.99
2.11
1.83
1.83
1.92
1.92
2.829(2)
2.657(2)
2.902(2)
2.975(2)
2.753(2)
2.756(2)
2.756(2)
2.754(2)
167
178
167
160
155
161
147
144
*D is a proton donor, A is a proton acceptor.
Note. Symmetric transformations for equivalent atoms: #1 –x, –y, –z+2; #2 x, –y+1/2, z+1/2; #3 x, –y+1/2, z–1/2.
Fourier syntheses and included into the refinement with fixed positions and isotropic thermal parameters (Ueq(H) = 1.5Ueq(O)
and Uiso(H) = 1.2Ueq(N)). The coordinates of other hydrogen atoms were calculated from geometric considerations and
refined by the riding model with thermal parameters (Ueq(H) = 1.5Ueq(C) for the CH3 groups and Ueq(H) = 1.2Ueq(C) for all
the other groups). The final values of the divergence factors were R1 = 0.041 for 4084 independent reflections with I > 2ꢊ(I )
and wR2 = 0.111 for all independent reflections. All calculations were made using the SHELXTL program package [3].
The structure of I has been deposited with the Cambridge Crystallographic Data Centre (No. 732855).
Results and Discussion. The structure and crystal packing of compound I are shown in Figs. 1 and 2; bond lengths
and bond angles in the molecule of I are given in Table 1.
The bicyclic system of the molecule of I is formed by two C(4a)–C(8a) cis-conjugated hexahydropyrimidine rings
(H(4a)–C(4a)–C(8a)–C(21) torsion angle is 48.2ꢅ) (Fig. 1). Both six-membered rings have sofa conformation (the deviation
of C(4a) atoms from the C(8a)N(1)C(2)N(3)C(4) (plane A) and C(5)N(6)C(7)N(8)C(8a) (plane B) central planes are –0.611 Å
and 0.680 Å respectively). It is noteworthy that the O(1) oxygen atom is considerably out of the plane A (the deviation is
0.137 Å), while the O(2) oxygen atom actually lies in the similar plane B (the deviation is less than 0.001 Å). This fact
appears to be explained by a distortion of the planar trigonal configuration of the N(1) nitrogen atom (the sum of bond angles
at the N(1) nitrogen atom is 355.4ꢅ) involved in the formation of an intermolecular hydrogen bond with the solvate water
molecule (see below). The planar trigonal configurations of other N(3), N(6), and N(8) nitrogen atoms are practically not
distorted (the sum of bond angles at N(3), N(6), and N(8) nitrogen atoms are 359.4ꢅ, 360.0ꢅ, and 360.0ꢅ respectively). The
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phenyl substituents at C(4) and C(5) carbon atoms have a pseudoaxial and pseudoequatorial orientations respectively. The
phenyl substituent at the C(8a) carbon atom holds a pseudoaxial position with respect to the N(1)C(2)N(3)C(4)C(4a)C(8a)
pyrimidine ring and a pseudoequatorial position with respect to the C(4a)C(5)N(6)C(7)N(8)C(8a) pyrimidine ring.
Compound I is a diastereomer with four asymmetric centers at C(4), C(4a), C(5), and C(8a) carbon atoms. The
crystal of compound I is a racemate with the relative configuration of the chiral atoms: rac-4R*,4aR*,5R*,8aS*.
In the crystal, molecules of I are packed into corrugated layers parallel to the 0YZ plane by means of hydrogen
bonds both directly with each other and through the solvate water molecule (Fig. 2, Table 2). Note that the >N(3)H amino
group is not involved in hydrogen bonding.
REFERENCES
1. M. M. Kurbanova, Azerbaidzhan. Khim. Zh., No. 1, 183 (2007).
2. G. M. Sheldrick, SADABS, v. 2.03, Bruker Siemens Area Detector Absorption Correction Program, Bruker AXS,
Madison, Wisconsin, USA (2003).
3. G. M. Sheldrick, SHELXTL, v. 6.12, Structure Determination Software Suite, Bruker AXS, Madison, Wisconsin, USA
(2001).
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