On the Dimers Stability of Allicin and Its Derivatives Interacting with AT, GC, and DNA Bridge: DFT Study

Table 1

Complexes of the investigated and interacting structures: positions, distances, Wiberg bond index, and binding energies.

Investigated structure	Interacting structure		Δ, kJ/mol (between 3 structures in the group)	The largest Wiberg bond index between atoms of the interacting and investigated structures		Distance between 2 atoms of the interacting and investigated structures, Å		Mulliken/NBO charges on S of the interacting structure		HOMO-LUMO gap, eV	Binding energy between structures, kJ/mol
	Structure	Position		Atoms	Wiberg bond index	S-O atoms	S-N atoms	1	2
G-C base pair	Allicin	1	0.00	S⋯H	0.011	3.71	3.57	0.52/1.12	−0.18/−0.08	4.08	−31.745
		2	10.81	H⋯O	0.003	4.22	4.06	0.48/1.08	−0.11/−0.01	3.97	−20.936
		3	16.95	S⋯H	0.015	4.67	3.63	0.49/1.1	−0.14/−0.05	3.89	−14.798
	(E)-Ajoene	1	0.00	O⋯H	0.005	7.42	5.28	0.01/0.15	−0.05/0.08	3.37	−26.219
		2	6.64	S⋯N	0.003	4.71	3.67	−0.01/0.14	−0.1/0.05	4.09	−19.582
		3	15.53	S⋯H	0.011	5.89	3.72	0.0/0.15	−0.08/0.06	3.95	−10.691
	(Z)-Ajoene	1	0.00	H⋯O	0.005	4.09	3.78	−0.03/0.11	−0.09/0.07	4.29	−37.682
		2	3.24	S⋯H	0.008	4.32	3.70	−0.1/0.04	−0.07/0.08	4.20	−34.442
		3	3.24	S⋯H	0.008	4.32	3.70	−0.1/0.04	−0.07/0.08	4.20	−34.442
	Amz121	1	54.28	S⋯N	0.516	3.47	2.02	0.62/1.34	—	3.24	−235.715
		2	52.73	S⋯N	0.476	3.52	2.08	0.62/1.35	—	2.96	−237.257
		3	0.00	S⋯O	0.48	1.89	3.62	0.66/1.44	—	3.76	−289.991
	Bmz73	1	1.82	S⋯N	0.912	3.51	1.74	0.03/0.37	—	3.67	−402.415
		2	9.60	S⋯N	0.827	3.42	1.81	0.09/0.09	—	4.25	−394.636
		3	0.00	S⋯O	0.736	1.74	3.91	0.17/0.17	—	4.38	−404.239
A-T base pair	Allicin	1	0.00	O⋯N	0.008	5.22	4.01	0.49/1.09	−0.12/−0.02	4.38	−28.319
		2	4.71	H⋯N	0.005	9.80	4.47	0.49/1.08	−0.11/−0.02	4.35	−23.613
		3	6.84	O⋯H	0.007	4.45	5.29	0.49/1.08	−0.13/−0.03	4.49	−21.477
	(E)-Ajoene	1	13.02	S⋯H	0.002	4.38	5.79	−0.01/0.14	−0.07/0.07	4.75	−8.553
		2	1.74	S⋯H	0.003	4.65	4.67	0.01/0.15	−0.08/0.07	4.74	−19.825
		3	0.00	H⋯N	0.006	4.79	4.31	0.01/0.15	−0.08/0.07	4.64	−21.570
	(Z)-Ajoene	1	11.38	S⋯N	0.006	5.60	3.71	−0.04/0.1	−0.08/0.07	4.52	−11.422
		2	9.22	S⋯H	0.015	3.93	5.44	−0.05/0.09	−0.07/0.88	4.53	−13.582
		3	0.00	S⋯H	0.005	4.35	3.87	−0.02/0.13	−0.06/0.08	4.54	−22.800
	Amz121	1	33.94	S⋯O	0.638	1.76	2.82	0.69/1.49	—	5.21	−280.671
		2	63.11	S⋯O	0.592	1.78	3.83	0.64/1.46	—	4.76	−251.506
		3	0.00	S⋯O	0.625	2.90	1.76	0.64/1.46	—	4.94	−314.616
	Bmz73	1	0.00	S⋯N	0.857	3.61	1.75	0.07/0.42	—	4.30	−433.700
		2	38.94	S⋯O	0.754	1.73	2.83	0.15/0.51	—	4.92	−394.761
		3	58.58	S⋯O	0.771	1.73	3.59	0.14/0.5	—	4.60	−375.121
Bridge of the base pairs	Allicin	1	25.74	C⋯O	0.01	4.40	—	0.46/1.07	−0.1/−0.01	3.66	−42.874
		2	0.00	C⋯O	0.005	3.74	—	0.51/1.12	−0.17/−0.06	4.79	−68.611
		3	25.81	C⋯O	0.007	4.40	—	0.46/1.07	−0.11/−0.02	4.08	−42.798
	(E)-Ajoene	1	0.00	H⋯O	0.015	3.67	—	−0.05/0.11	−0.08/0.06	4.36	−85.815
		2	39.24	C⋯O	0.008	4.26	—	0.01/0.16	−0.08/0.07	3.65	−46.573
		3	1.55	H⋯O	0.028	3.85	—	−0.09/0.07	−0.1/0.05	4.49	−84.262
	(Z)-Ajoene	1	0.00	H⋯O	0.009	4.12	—	−0.08/0.07	−0.11/0.05	4.40	−72.999
		2	1.77	H⋯O	0.008	4.14	—	0.07/0.08	−0.1/0.05	4.45	−71.225
		3	8.29	H⋯O	0.014	3.99	—	−0.06/0.09	−0.12/−0.05	4.40	−64.708
	Amz121	1	1.97	S⋯O	0.641	1.73	—	0.63/1.47	—	6.17	−684.153
		2	2.73	S⋯O	0.651	1.73	—	0.63/1.47	—	6.24	−683.398
		3	0.00	S⋯O	0.642	1.73	—	0.65/1.47	—	5.90	−686.124
	Bmz73	1	128.01	S⋯O	0.787	1.71	—	0.16/0.52	—	5.42	−673.970
		2	0.00	S⋯O	0.795	1.71	—	0.13/0.5	—	5.43	−801.977
		3	7.92	S⋯O	0.783	1.71	—	0.13/0.51	—	5.28	−794.061

Increase of the P-O bond distance in the bridge of the base pairs: the length is 2.18 Å and Wiberg bond index is 0.15.