Crystal structure of dimethyl 3,12-dibenzyl-6,10-diphenyl-3,12-diazapentacyclo [6.3.1.02.7.04.11.05.9]-dodecane-7,11-dicarboxylate — acetone (2/1), C40H38N2O2 ⋅ 0.5C3H6O

Ya-Nan Wang; Yan Wu; Ye Tian

doi:10.1515/ncrs-2019-0303

Artikel Open Access

Crystal structure of dimethyl 3,12-dibenzyl-6,10-diphenyl-3,12-diazapentacyclo [6.3.1.0^2.7.0^4.11.0^5.9]-dodecane-7,11-dicarboxylate — acetone (2/1), C₄₀H₃₈N₂O₂ ⋅ 0.5C₃H₆O

Ya-Nan Wang , Yan Wu und Ye Tian

Veröffentlicht/Copyright: 2. August 2019

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Abstract

C₈₃H₈₂N₄O₅, monoclinic, P2₁/c (no. 14), a = 21.705(8) Å, b = 18.455(6) Å, c = 17.774(7) Å, β = 112.216(6)°, V = 6591(4) Å³, Z = 4, R_gt(F) = 0.0647, wR_ref(F²) = 0.1531, T = 128 K.

CCDC no.: 1909229

The asymmetric unit of the title molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:	Colourless prism
Size:	0.36 × 0.22 × 0.20 mm
Wavelength:	Mo Kα radiation (0.71073 Å)
μ:	0.08 mm⁻¹
Diffractometer, scan mode:	Rigaku Saturn 70, ω
θ_max, completeness:	27.9°, >99%
N(hkl)_measured, N(hkl)_unique, R_int:	78677, 15706, 0.075
Criterion for I_obs, N(hkl)_gt:	I_obs > 2 σ(I_obs), 11898
N(param)_refined:	836
Programs:	Rigaku [1], Olex2 [2], SHELX [3], [4]

Table 2:

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

Atom	x	y	z	U_iso*/U_eq
O1	0.83340(8)	0.07814(8)	0.84145(8)	0.0489(4)
O2	0.83616(7)	0.42329(8)	0.78612(9)	0.0476(4)
N1	0.82604(7)	0.25998(8)	0.92907(8)	0.0260(3)
N2	0.93538(7)	0.25022(7)	0.82162(8)	0.0248(3)
C1	0.88524(8)	0.21999(9)	0.97755(10)	0.0246(4)
H1	0.878319	0.189663	1.020320	0.029*
C2	0.90629(8)	0.17305(9)	0.91595(10)	0.0256(4)
C3	0.98299(8)	0.17677(9)	0.95528(10)	0.0264(4)
H3	0.995766	0.153947	1.010125	0.032*
C4	0.99111(8)	0.25904(9)	0.97012(10)	0.0254(4)
H4	1.038116	0.273063	1.003186	0.030*
C5	0.94373(8)	0.27536(9)	1.01392(10)	0.0250(4)
H5	0.966221	0.270761	1.074269	0.030*
C6	0.92052(8)	0.35335(9)	0.98744(10)	0.0256(4)
H6	0.961196	0.384565	1.006638	0.031*
C7	0.89999(8)	0.34388(9)	0.89444(10)	0.0249(4)
C8	0.84382(8)	0.28571(9)	0.86202(10)	0.0257(4)
H8	0.804347	0.303947	0.815240	0.031*
C9	0.87916(8)	0.22042(9)	0.83728(10)	0.0250(4)
H9	0.847933	0.192894	0.789667	0.030*
C10	0.96173(8)	0.30204(9)	0.88816(10)	0.0249(4)
H10	0.995009	0.335720	0.880554	0.030*
C11	0.87695(9)	0.09696(10)	0.90460(11)	0.0312(4)
C12	0.90232(11)	0.04489(11)	0.97454(13)	0.0454(5)
H12A	0.877312	−0.000595	0.959731	0.068*
H12B	0.896566	0.065966	1.022073	0.068*
H12C	0.949634	0.035307	0.987467	0.068*
C13	0.88574(9)	0.41475(9)	0.84689(11)	0.0297(4)
C14	0.93541(11)	0.47482(11)	0.87717(12)	0.0430(5)
H14A	0.928320	0.510242	0.833609	0.064*
H14B	0.980508	0.454945	0.894168	0.064*
H14C	0.929903	0.498575	0.923543	0.064*
C15	1.02564(9)	0.14057(9)	0.91537(11)	0.0292(4)
C16	1.00007(10)	0.09486(10)	0.84829(11)	0.0359(4)
H16	0.953421	0.086792	0.824430	0.043*
C17	1.04146(11)	0.06073(11)	0.81546(13)	0.0430(5)
H17	1.022815	0.030133	0.769396	0.052*
C18	1.10931(12)	0.07114(12)	0.84948(13)	0.0482(6)
H18	1.137599	0.047935	0.827133	0.058*
C19	1.13585(11)	0.11601(12)	0.91688(14)	0.0467(5)
H19	1.182567	0.123540	0.940899	0.056*
C20	1.09420(10)	0.14992(11)	0.94925(12)	0.0375(4)
H20	1.113058	0.180176	0.995583	0.045*
C21	0.87174(9)	0.38668(9)	1.02019(10)	0.0278(4)
C22	0.88825(10)	0.38870(10)	1.10415(11)	0.0357(4)
H22	0.930286	0.370748	1.139400	0.043*
C23	0.84435(11)	0.41648(11)	1.13726(12)	0.0438(5)
H23	0.856196	0.415959	1.194476	0.053*
C24	0.78409(11)	0.44462(11)	1.08773(12)	0.0418(5)
H24	0.754003	0.463127	1.110310	0.050*
C25	0.76757(10)	0.44571(10)	1.00408(12)	0.0361(4)
H25	0.726587	0.466399	0.969390	0.043*
C26	0.81068(9)	0.41677(9)	0.97137(11)	0.0309(4)
H26	0.798409	0.417374	0.914092	0.037*
C27	0.76337(9)	0.21954(11)	0.90340(11)	0.0335(4)
H27A	0.765764	0.177610	0.869876	0.040*
H27B	0.726465	0.251161	0.869511	0.040*
C28	0.74929(8)	0.19294(10)	0.97576(11)	0.0315(4)
C29	0.75237(9)	0.24022(11)	1.03789(11)	0.0346(4)
H29	0.763964	0.289520	1.035183	0.042*
C30	0.73861(10)	0.21604(13)	1.10412(12)	0.0437(5)
H30	0.740384	0.248997	1.145950	0.052*
C31	0.72243(12)	0.14444(15)	1.10922(14)	0.0573(7)
H31	0.713353	0.127787	1.154556	0.069*
C32	0.71956(14)	0.09731(14)	1.04786(15)	0.0643(7)
H32	0.708235	0.047975	1.050974	0.077*
C33	0.73298(11)	0.12101(12)	0.98167(13)	0.0479(5)
H33	0.731017	0.087772	0.940008	0.058*
C34	0.91764(8)	0.28036(10)	0.73964(10)	0.0275(4)
H34A	0.889707	0.324008	0.733890	0.033*
H34B	0.891228	0.244283	0.699020	0.033*
C35	0.97870(9)	0.30022(10)	0.72318(10)	0.0281(4)
C36	0.98383(10)	0.36734(10)	0.68976(11)	0.0356(4)
H36	0.949113	0.401875	0.679212	0.043*
C37	1.03896(11)	0.38415(12)	0.67180(12)	0.0437(5)
H37	1.042089	0.430294	0.649826	0.052*
C38	1.08946(10)	0.33404(13)	0.68574(12)	0.0457(5)
H38	1.126759	0.345202	0.672231	0.055*
C39	1.08531(9)	0.26765(12)	0.71942(11)	0.0396(5)
H39	1.120017	0.233198	0.729310	0.048*
C40	1.03077(9)	0.25094(10)	0.73890(11)	0.0328(4)
H40	1.028907	0.205545	0.763155	0.039*
O3	0.65392(7)	0.57176(7)	0.43642(9)	0.0431(3)
O4	0.64735(7)	0.91998(7)	0.48453(9)	0.0456(4)
N3	0.65963(7)	0.73549(8)	0.58466(8)	0.0245(3)
N4	0.55103(7)	0.74461(8)	0.37595(8)	0.0253(3)
C41	0.64229(8)	0.70994(9)	0.50107(10)	0.0246(4)
H41	0.682027	0.692226	0.490981	0.029*
C42	0.58684(8)	0.65107(9)	0.48170(10)	0.0246(4)
C43	0.56541(8)	0.64128(9)	0.55478(10)	0.0250(4)
H43	0.524489	0.610459	0.534920	0.030*
C44	0.54176(8)	0.71889(9)	0.56022(10)	0.0244(3)
H44	0.519041	0.723080	0.599592	0.029*
C45	0.59969(8)	0.77516(9)	0.57768(10)	0.0238(3)
H45	0.606151	0.805445	0.626752	0.029*
C46	0.57893(8)	0.82209(9)	0.49715(10)	0.0249(4)
C47	0.50218(8)	0.81746(9)	0.46588(10)	0.0255(4)
H47	0.489469	0.839483	0.509367	0.031*
C48	0.49475(8)	0.73500(9)	0.47258(10)	0.0249(4)
H48	0.447804	0.720445	0.461884	0.030*
C49	0.52493(8)	0.69218(9)	0.41789(10)	0.0249(4)
H49	0.492091	0.658186	0.379459	0.030*
C50	0.60650(8)	0.77508(9)	0.44346(10)	0.0243(3)
H50	0.637618	0.802969	0.424828	0.029*
C51	0.60344(9)	0.58011(10)	0.44942(10)	0.0297(4)
C52	0.55537(11)	0.51824(11)	0.43586(13)	0.0451(5)
H52A	0.567599	0.479181	0.406794	0.068*
H52B	0.510233	0.535021	0.403527	0.068*
H52C	0.556957	0.500177	0.488409	0.068*
C53	0.60669(9)	0.89898(10)	0.51165(11)	0.0306(4)
C54	0.58278(10)	0.94893(10)	0.56153(12)	0.0404(5)
H54A	0.595767	0.929504	0.616694	0.061*
H54B	0.534197	0.952983	0.536617	0.061*
H54C	0.602750	0.996914	0.563830	0.061*
C55	0.61247(9)	0.60592(9)	0.63226(10)	0.0277(4)
C56	0.67411(9)	0.57733(10)	0.64108(11)	0.0341(4)
H56	0.689647	0.582585	0.598070	0.041*
C57	0.71314(11)	0.54150(12)	0.71101(12)	0.0443(5)
H57	0.754774	0.521723	0.715392	0.053*
C58	0.69177(12)	0.53432(13)	0.77474(13)	0.0534(6)
H58	0.718557	0.509573	0.822884	0.064*
C59	0.63129(13)	0.56333(14)	0.76796(13)	0.0564(6)
H59	0.616669	0.559263	0.811863	0.068*
C60	0.59192(10)	0.59835(11)	0.69719(11)	0.0388(5)
H60	0.550111	0.617578	0.692854	0.047*
C61	0.45950(9)	0.85474(9)	0.38755(10)	0.0289(4)
C62	0.39038(9)	0.85148(10)	0.36358(12)	0.0365(4)
H62	0.371639	0.824366	0.395118	0.044*
C63	0.34874(11)	0.88726(12)	0.29438(13)	0.0480(6)
H63	0.301852	0.884102	0.278791	0.058*
C64	0.37504(12)	0.92758(12)	0.24784(12)	0.0484(6)
H64	0.346501	0.952143	0.200528	0.058*
C65	0.44300(11)	0.93156(11)	0.27105(12)	0.0430(5)
H65	0.461474	0.959151	0.239573	0.052*
C66	0.48494(10)	0.89553(10)	0.34024(11)	0.0353(4)
H66	0.531770	0.898879	0.355378	0.042*
C67	0.72193(8)	0.77715(10)	0.61489(10)	0.0298(4)
H67A	0.720790	0.814484	0.574387	0.036*
H67B	0.759805	0.744341	0.621949	0.036*
C68	0.73209(8)	0.81316(10)	0.69461(11)	0.0304(4)
C69	0.73147(9)	0.77331(11)	0.76097(11)	0.0364(4)
H69	0.725526	0.722267	0.756656	0.044*
C70	0.73953(10)	0.80813(14)	0.83337(12)	0.0475(6)
H70	0.738408	0.780825	0.878140	0.057*
C71	0.74922(10)	0.88262(15)	0.84077(14)	0.0533(6)
H71	0.754988	0.906136	0.890530	0.064*
C72	0.75041(10)	0.92209(13)	0.77584(15)	0.0516(6)
H72	0.757326	0.972983	0.780728	0.062*
C73	0.74151(9)	0.88761(11)	0.70311(13)	0.0388(5)
H73	0.741872	0.915427	0.658309	0.047*
C74	0.57028(9)	0.71452(10)	0.31124(10)	0.0281(4)
H74A	0.600641	0.672938	0.333010	0.034*
H74B	0.594580	0.751865	0.293399	0.034*
C75	0.51083(9)	0.69005(10)	0.23974(10)	0.0281(4)
C76	0.50720(11)	0.62060(11)	0.20859(12)	0.0416(5)
H76	0.542323	0.587324	0.234101	0.050*
C77	0.45307(13)	0.59901(14)	0.14077(13)	0.0558(6)
H77	0.450726	0.550953	0.120705	0.067*
C78	0.40271(12)	0.64751(16)	0.10263(13)	0.0578(7)
H78	0.365912	0.633181	0.055561	0.069*
C79	0.40561(10)	0.71685(14)	0.13262(12)	0.0476(6)
H79	0.370978	0.750321	0.105872	0.057*
C80	0.45876(9)	0.73785(11)	0.20151(11)	0.0355(4)
H80	0.459724	0.785210	0.222876	0.043*
O5	0.91123(10)	0.59322(12)	0.99920(13)	0.0843(7)
C81	0.86986(14)	0.61444(19)	1.10067(17)	0.0806(9)
H81A	0.908945	0.586870	1.135085	0.121*
H81B	0.829597	0.592599	1.103369	0.121*
H81C	0.873764	0.664661	1.119847	0.121*
C82	0.86578(12)	0.61325(12)	1.01616(14)	0.0499(6)
C83	0.80240(19)	0.6403(2)	0.9553(2)	0.1148(14)
H83A	0.796538	0.691313	0.966245	0.172*
H83B	0.765361	0.611769	0.958425	0.172*
H83C	0.803303	0.635640	0.900760	0.172*

Source of material

The title compound was synthesized by 1-(1-benzyl-4-phenyl-1,4-dihydropyridin-3-yl)ethan-1-one under irradiation of UV-light in methanol/THF solution. After approximately one week. By thin-layer chromatography, the residue was purified using ethyl acetate-petroleum ether (1:5 v/v). After concentration in vacuo colorless solids were collected and dried, and recrystallized from acetone. After one week colorless crystals of the title compound were obtained.

Experimental details

The diazatetrakishomocubanes hydrogen atom as well as those at acetone were refined freely. Fixed U_iso at 1.2 times were set for all C(H) groups, and 1.5 times for all C(H,H,H) groups. The hydrogen atoms attached to carbon were placed on calculated positions with the help of the Olex2 program [2].

Comment

The structural similarity of the C₂-symmetric tetrakishomocubanes compound to the 3,9-diazatetraasteranes gives rises to great interest in these compounds in particular as potential inhibitors of C₂-symmetric HIV-1 protease [5]. X-ray crystallography analyses reveal that the title compound contains 3,12-diazatetrakishomocubanes.

The asymmetric unit – containing two diazatetrakishomocubanes (systematic name: dimethyl 1,9-dibenzyl-4,6-diphenylhexahydro-3H-2,7,3,5-(epimethanetriylimi-nomethanetriyl)cyclopenta[b]pyridine-3,7(2H)-dicarboxylate) and one acetone molecule – of the title structure is shown in the figure. Crystal structure analysis revealed that the piperidinyl rings are in chair conformation, the apexes (prows) being the N2 and C3 atoms. In contrast to the previously observed head-to-tail 1,4-dihydropyridine dimers with centrosymmetric cage structures of 3,9-diazatetraasteranes or their C₂-symmetric, syn-dimeric intermediates, the linkage of the two 1,4-dihydropyridine rings in the compound is not in a head-to-tail arrangement of 180° to each other, but form an angle of only 90°. Stereochemically the compound is the product of common enantiometric forms. It can formally be considered as resulting from the attack of one dihydropyridine molecule on the far side of the dihydropyridine ring of the second molecule (i.e., the side that does not face the aryl moiety). Steric reasons are responsible for the axial arrangement of the phenyl rings in this case [5].

Because of the Csp² nature of the substituent at C3, the orientation of the cyclohexyl ring around the C3—C15 bond is characterized by the following torsion angles: C2—C3—C15—C16: −8.5°, C4—C3—C15—C16: −129.57°. On the other hand, the torsion angle N1—C27—C28—C29 is 50.4°.

The geometric parameters of the second crystallographically independent molecule are very similar to the one discuss before.

Acknowledgements

This work was financially supported by the CAMS Innovation Fund for Medical Sciences(CIFMS)2016-I2M-3-010.

References

1. Rigaku/MSC. CrystalClear. Rigaku/MSC Inc., The Woodlands, TX, USA (2006).Suche in Google Scholar

2. Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H.: OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42 (2009) 339–341.10.1107/S0021889808042726Suche in Google Scholar

3. Sheldrick, G. M.: SHELXT-integrated space-group and crystal-structure determination. Acta Crystallogr. A71 (2015) 3–8.10.1107/S2053273314026370Suche in Google Scholar

4. Sheldrick, G. M.: Crystal structure refinement with SHELXL. Acta Crystallogr. C71 (2015) 3–8.10.1107/S2053229614024218Suche in Google Scholar

5. Hilgeroth, A.; Baumeister, U.: The first functionalized 6,12-diazatetrakishomocubanes. Angew. Chem. Int. Ed. 39 (2000) 576–578.10.1002/(SICI)1521-3773(20000204)39:3<576::AID-ANIE576>3.0.CO;2-GSuche in Google Scholar

Received: 2019-04-27

Accepted: 2019-06-21

Published Online: 2019-08-02

Published in Print: 2019-11-26

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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Crystal structure of dimethyl 3,12-dibenzyl-6,10-diphenyl-3,12-diazapentacyclo [6.3.1.02.7.04.11.05.9]-dodecane-7,11-dicarboxylate — acetone (2/1), C40H38N2O2 ⋅ 0.5C3H6O

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Crystal structure of dimethyl 3,12-dibenzyl-6,10-diphenyl-3,12-diazapentacyclo [6.3.1.0^2.7.0^4.11.0^5.9]-dodecane-7,11-dicarboxylate — acetone (2/1), C₄₀H₃₈N₂O₂ ⋅ 0.5C₃H₆O