Structure and conformational analysis of a bidentate pro-ligand, C₂₁H₃₄N₂S₂, from powder synchrotron diffraction data and solid-state DFTB calculations

The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from ¹H and ¹³C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

S1. Experimental

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S2. Refinement

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Computing details

Molecular graphics: PLATON (Spek, 2003) and DIAMOND 2.1e (Brandenburg, 2001); software used to prepare material for publication: GSAS2CIF (Toby et al., 2003), PLATON (Spek, 2003), and publCIF (Westrip, 2009).

Figures

ethyl 1',2',3',4',4a',5',6',7'-octahydrodispiro[cyclohexane-1,2'- quinazoline-4',1''-cyclohexane]-8'-carbodithioate

Crystal data

C21H34N2S2	F(000) = 824
Mr = 378.64	Dx = 1.236 Mg m^−3
Monoclinic, P21/n	Synchrotron radiation, λ = 0.80098 Å
Hall symbol: -P 2yn	µ = 0.00 mm^−1
a = 21.7356 (4) Å	T = 298 K
b = 10.0565 (2) Å	Particle morphology: thin powder
c = 9.45108 (18) Å	yellow
β = 99.9602 (8)°	cylinder, 40 × 10 mm
V = 2034.72 (7) Å^3	Specimen preparation: Prepared at 298 K
Z = 4

Data collection

High Resolution Diffractometer ID31, ESRF, Grenoble, France.	Specimen mounting: borosilicate glass capillary
Radiation source: synchrotron, Beamline ID31	Data collection mode: transmission
Double crystal Si 111 monochromator	Scan method: step

Refinement

Refinement on Inet	Profile function: CW Profile function number 4 with 21 terms Pseudovoigt profile coefficients as parameterized in P. Thompson, D.E. Cox & J.B. Hastings (1987). J. Appl. Cryst.,20,79-83. Asymmetry correction of L.W. Finger, D.E. Cox & A. P. Jephcoat (1994). J. Appl. Cryst.,27,892-900. Microstrain broadening by P.W. Stephens, (1999). J. Appl. Cryst.,32,281-289. #1(GU) = 0.000 #2(GV) = 0.000 #3(GW) = 0.000 #4(GP) = 0.000 #5(LX) = 2.373 #6(ptec) = 0.00 #7(trns) = 0.00 #8(shft) = 0.0000 #9(sfec) = 0.00 #10(S/L) = 0.0030 #11(H/L) = 0.0016 #12(eta) = 0.0000 #13(S400 ) = 6.4E-04 #14(S040 ) = 3.8E-03 #15(S004 ) = 5.5E-03 #16(S220 ) = 6.7E-03 #17(S202 ) = 1.3E-03 #18(S022 ) = 1.2E-02 #19(S301 ) = 0.0E+00 #20(S103 ) = 3.1E-04 #21(S121 ) = 2.7E-03 Peak tails are ignored where the intensity is below 0.0015 times the peak Aniso. broadening axis 0.0 0.0 1.0
Least-squares matrix: full	127 parameters
Rp = 0.044	186 restraints
Rwp = 0.054	1 constraint
Rexp = 0.024	H-atom parameters constrained
R(F^2) = 0.12634	(Δ/σ)max = 0.05
χ^2 = 5.290	Background function: GSAS Background function number 1 with 20 terms. Shifted Chebyshev function of 1st kind 1: 1003.18 2: -242.455 3: 44.5847 4: 55.6979 5: -29.4706 6: -81.1134 7: 127.180 8: -98.3496 9: 20.8256 10: 37.3447 11: -40.7733 12: 13.3524 13: 13.5172 14: -16.2420 15: 32.6866 16: 8.33642 17: -35.1107 18: 7.23691 19: 5.42771 20: 5.20341
15665 data points	Preferred orientation correction: Spherical Harmonic
Excluded region(s): none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S1	0.32712 (15)	0.7025 (3)	0.0351 (4)	0.0556 (7)*
S2	0.45772 (16)	0.6464 (4)	0.1717 (4)	0.0556 (7)*
N1	0.25389 (18)	0.6346 (8)	0.2538 (4)	0.0556 (7)*
N2	0.18148 (16)	0.5883 (5)	0.4136 (4)	0.0556 (7)*
C1	0.18865 (19)	0.6238 (4)	0.2697 (4)	0.0556 (7)*
C2	0.22928 (19)	0.6328 (4)	0.5320 (4)	0.0556 (7)*
C3	0.34955 (17)	0.6326 (3)	0.6171 (3)	0.0556 (7)*
C4	0.40475 (15)	0.5606 (3)	0.5778 (4)	0.0556 (7)*
C5	0.41936 (15)	0.6178 (3)	0.4421 (4)	0.0556 (7)*
C6	0.36432 (19)	0.6389 (9)	0.3248 (5)	0.0556 (7)*
C7	0.3035 (2)	0.6267 (9)	0.3579 (5)	0.0556 (7)*
C8	0.29393 (18)	0.5908 (3)	0.5055 (4)	0.0556 (7)*
C9	0.15551 (17)	0.7531 (3)	0.2148 (3)	0.0556 (7)*
C10	0.08500 (16)	0.7428 (3)	0.2039 (3)	0.0556 (7)*
C11	0.06036 (13)	0.6345 (4)	0.0975 (3)	0.0556 (7)*
C12	0.09052 (16)	0.5051 (3)	0.1495 (3)	0.0556 (7)*
C13	0.16133 (16)	0.5092 (3)	0.1698 (3)	0.0556 (7)*
C14	0.22770 (15)	0.7821 (3)	0.5579 (3)	0.0556 (7)*
C15	0.16609 (15)	0.8265 (3)	0.5969 (3)	0.0556 (7)*
C16	0.15206 (13)	0.7511 (3)	0.7253 (3)	0.0556 (7)*
C17	0.15536 (15)	0.6020 (3)	0.7110 (3)	0.0556 (7)*
C18	0.21347 (15)	0.5534 (3)	0.6592 (4)	0.0556 (7)*
C19	0.3798 (2)	0.6567 (11)	0.1841 (5)	0.0556 (7)*
C20	0.46088 (13)	0.6879 (3)	−0.0107 (4)	0.0556 (7)*
C21	0.47095 (13)	0.8327 (3)	−0.0297 (3)	0.0556 (7)*
H1	0.2617	0.6594	0.1599	0.0681 (9)*
H2	0.142	0.6301	0.4306	0.0681 (9)*
H31	0.3556	0.7303	0.6124	0.0681 (9)*
H32	0.3433	0.6063	0.7154	0.0681 (9)*
H41	0.4414	0.571	0.6558	0.0681 (9)*
H42	0.3945	0.4634	0.5633	0.0681 (9)*
H51	0.4389	0.7062	0.4642	0.0681 (9)*
H52	0.449	0.5567	0.4049	0.0681 (9)*
H81	0.2931	0.4908	0.5099	0.0681 (9)*
H91	0.171	0.8282	0.2819	0.0681 (9)*
H92	0.1647	0.774	0.1172	0.0681 (9)*
H101	0.0653	0.8302	0.1716	0.0681 (9)*
H102	0.0753	0.7209	0.3013	0.0681 (9)*
H111	0.0714	0.6576	0.0026	0.0681 (9)*
H112	0.0145	0.6285	0.0909	0.0681 (9)*
H121	0.0781	0.4814	0.244	0.0681 (9)*
H122	0.0754	0.4345	0.0776	0.0681 (9)*
H131	0.174	0.5226	0.075	0.0681 (9)*
H132	0.1785	0.424	0.2137	0.0681 (9)*
H141	0.2619	0.8073	0.6393	0.0681 (9)*
H142	0.2337	0.8297	0.4693	0.0681 (9)*
H151	0.1683	0.924	0.6203	0.0681 (9)*
H152	0.132	0.8103	0.5139	0.0681 (9)*
H161	0.1832	0.7786	0.812	0.0681 (9)*
H162	0.1091	0.7755	0.7411	0.0681 (9)*
H171	0.1539	0.5612	0.8074	0.0681 (9)*
H172	0.1181	0.5721	0.641	0.0681 (9)*
H181	0.2493	0.5593	0.7419	0.0681 (9)*
H182	0.207	0.4583	0.6297	0.0681 (9)*
H201	0.4961	0.6377	−0.0365	0.0681 (9)*
H202	0.4207	0.6613	−0.072	0.0681 (9)*
H211	0.4736	0.8515	−0.1317	0.0681 (9)*
H212	0.5107	0.8617	0.0336	0.0681 (9)*
H213	0.4353	0.8853	−0.0018	0.0681 (9)*

Geometric parameters (Å, º)

S1—C19	1.717 (6)	C3—H32	1.0000
S2—C19	1.721 (6)	C4—H41	0.9900
S2—C20	1.787 (5)	C4—H42	1.0100
N1—C1	1.456 (6)	C5—H51	0.9900
N1—C7	1.330 (6)	C5—H52	1.0000
N2—C1	1.440 (5)	C8—H81	1.0100
N2—C2	1.459 (5)	C9—H91	1.0100
N1—H1	0.9600	C9—H92	1.0000
N2—H2	0.9900	C10—H101	1.0000
C1—C13	1.542 (5)	C10—H102	1.0000
C1—C9	1.533 (5)	C11—H111	1.0000
C2—C8	1.529 (6)	C11—H112	0.9900
C2—C14	1.523 (5)	C12—H121	1.0100
C2—C18	1.531 (5)	C12—H122	1.0000
C3—C4	1.502 (5)	C13—H131	0.9900
C3—C8	1.520 (5)	C13—H132	1.0000
C4—C5	1.489 (5)	C14—H141	1.0100
C5—C6	1.499 (6)	C14—H142	0.9900
C6—C19	1.438 (7)	C15—H151	1.0000
C6—C7	1.416 (6)	C15—H152	0.9900
C7—C8	1.490 (6)	C16—H161	1.0100
C9—C10	1.522 (5)	C16—H162	1.0000
C10—C11	1.516 (4)	C17—H171	1.0000
C11—C12	1.501 (4)	C17—H172	1.0000
C12—C13	1.518 (5)	C18—H181	1.0100
C14—C15	1.516 (5)	C18—H182	1.0000
C15—C16	1.506 (4)	C20—H201	0.9800
C16—C17	1.508 (4)	C20—H202	1.0000
C17—C18	1.513 (5)	C21—H211	0.9900
C20—C21	1.488 (4)	C21—H212	1.0100
C3—H31	0.9900	C21—H213	1.0100
C19—S2—C20	104.7 (3)	C7—C8—H81	107.00
C1—N1—C7	126.8 (4)	C1—C9—H91	110.00
C1—N2—C2	118.0 (4)	C1—C9—H92	109.00
C1—N1—H1	116.00	C10—C9—H91	108.00
C7—N1—H1	117.00	C10—C9—H92	108.00
C1—N2—H2	107.00	H91—C9—H92	109.00
C2—N2—H2	105.00	C9—C10—H101	109.00
N2—C1—C13	107.4 (3)	C9—C10—H102	109.00
C9—C1—C13	108.6 (3)	C11—C10—H101	110.00
N1—C1—C13	105.8 (4)	C11—C10—H102	110.00
N1—C1—N2	112.5 (3)	H101—C10—H102	109.00
N1—C1—C9	108.1 (4)	C10—C11—H111	109.00
N2—C1—C9	114.1 (3)	C10—C11—H112	109.00
N2—C2—C8	110.0 (3)	C12—C11—H111	110.00
C14—C2—C18	111.9 (3)	C12—C11—H112	110.00
C8—C2—C18	108.8 (3)	H111—C11—H112	111.00
N2—C2—C14	113.1 (3)	C11—C12—H121	109.00
N2—C2—C18	102.4 (3)	C11—C12—H122	109.00
C8—C2—C14	110.2 (3)	C13—C12—H121	108.00
C4—C3—C8	105.6 (3)	C13—C12—H122	108.00
C3—C4—C5	109.0 (3)	H121—C12—H122	109.00
C4—C5—C6	115.5 (3)	C1—C13—H131	108.00
C5—C6—C7	118.7 (4)	C1—C13—H132	108.00
C5—C6—C19	114.7 (4)	C12—C13—H131	109.00
C7—C6—C19	126.3 (4)	C12—C13—H132	109.00
N1—C7—C6	120.0 (4)	H131—C13—H132	111.00
C6—C7—C8	121.0 (4)	C2—C14—H141	110.00
N1—C7—C8	118.7 (4)	C2—C14—H142	109.00
C2—C8—C3	117.0 (3)	C15—C14—H141	108.00
C2—C8—C7	111.6 (3)	C15—C14—H142	108.00
C3—C8—C7	111.1 (3)	H141—C14—H142	110.00
C1—C9—C10	112.0 (3)	C14—C15—H151	109.00
C9—C10—C11	109.3 (2)	C14—C15—H152	109.00
C10—C11—C12	108.8 (2)	C16—C15—H151	109.00
C11—C12—C13	113.2 (3)	C16—C15—H152	109.00
C1—C13—C12	111.9 (3)	H151—C15—H152	110.00
C2—C14—C15	112.0 (3)	C15—C16—H161	108.00
C14—C15—C16	111.0 (2)	C15—C16—H162	109.00
C15—C16—C17	114.1 (2)	C17—C16—H161	108.00
C16—C17—C18	113.9 (3)	C17—C16—H162	108.00
C2—C18—C17	113.5 (3)	H161—C16—H162	109.00
S1—C19—C6	124.2 (4)	C16—C17—H171	108.00
S2—C19—C6	116.5 (4)	C16—C17—H172	108.00
S1—C19—S2	119.0 (3)	C18—C17—H171	109.00
S2—C20—C21	112.1 (3)	C18—C17—H172	108.00
C4—C3—H31	110.00	H171—C17—H172	109.00
C4—C3—H32	110.00	C2—C18—H181	109.00
C8—C3—H31	110.00	C2—C18—H182	109.00
C8—C3—H32	111.00	C17—C18—H181	108.00
H31—C3—H32	110.00	C17—C18—H182	108.00
C3—C4—H41	110.00	H181—C18—H182	109.00
C3—C4—H42	110.00	S2—C20—H201	106.00
C5—C4—H41	110.00	S2—C20—H202	109.00
C5—C4—H42	109.00	C21—C20—H201	110.00
H41—C4—H42	109.00	C21—C20—H202	109.00
C4—C5—H51	108.00	H201—C20—H202	111.00
C4—C5—H52	108.00	C20—C21—H211	110.00
C6—C5—H51	107.00	C20—C21—H212	110.00
C6—C5—H52	108.00	C20—C21—H213	110.00
H51—C5—H52	110.00	H211—C21—H212	110.00
C2—C8—H81	104.00	H211—C21—H213	109.00
C3—C8—H81	105.00	H212—C21—H213	108.00
C7—C6—C19—S1	14.9 (15)	C20—S2—C19—C6	−174.8 (7)
C20—S2—C19—S1	−1.0 (8)	C19—S2—C20—C21	91.3 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···S1	0.96	2.040	2.900 (5)	147
C5—H52···S2	1.00	2.420	2.837 (5)	104
C20—H202···S1	1.00	2.460	3.016 (4)	115