Site-preference of Quercetin Hydrogen Bonding to Adenine†

doi:10.7503/cjcu20141136

Abstract

Abstract:

Sixteen stable hydrogen-bonded quercetin-adenine complexes were located at the B3LYP/6-31+G(d,p) level. The binding energies in gas phase were evaluated at the MP2/6-311++G(d,p) level with the basis set superposition error correction. The binding energies in water solvent were obtained at the MP2/6-311++G(d,p) level with PCM model. The calculation results indicate that no matter in gas phase or water solvent, the hydrogen-bonded complexes formed through the quercetin site qu1 are the most stable. The relative stability of the hydrogen-bonded quercetin-adenine complexes and the thymine-adenine Waston-Crick base pair was further explored. The calculation results show that the base pair is more stable in gas phase whereas the hydrogen-bonded quercetin-adenine complexes are more stable in water solvent. Based on the calculation results of the standard Gibbs free energy change, the relative equilibrium concentrations between the hydrogen-bonded quercetin-adenine complexes and the base pair in water solvent were estimated.

Key words: Quercetin, Adenine, Hydrogen-bonded complex, Binding energy, Standard Gibbs free energy change

CLC Number:

O641

TrendMD:

WANG Xiaowen, LI Shuang, JIANG Xiaonan, WANG Changsheng. Site-preference of Quercetin Hydrogen Bonding to Adenine^†[J]. Chem. J. Chinese Universities, 2015, 36(5): 932.

Figures/Tables 5

Fig.1 Structures and binding sites of quercetin(A) and adenine(B)

Fig.2 Optimal structures of twelve hydrogen-bonded quercetin-adenine complexesThe hydrogen bond distances in gas phase and in water solvent are given in the corresponding position and in parentheses, respectively. ΔEb(gas) is the binding energy in gas phase. ΔEb1(water) and ΔEb2(water) are the binding energies in water solvent using the optimal structure in gas phase and the optimal structure in water solvent, respectively. The hydrogen bond distance units are in nm.

Table 1 n→σ* second-order stabilization energies ΔE(2) obtained at the B3LYP/6-31G(d,p) level and the electron densities(ρc) at the hydrogen bond critical points obtained at the B3LYP/6-311+G(d,p) level

Complex	Hydrogen bond	R(Y…H)/nm	ΔE⁽²⁾/(kJ·mol^-1)	∑ΔE⁽²⁾/(kJ·mol^-1)	ρ_c/a.u.	∑ρ_c/a.u.
qu1-a1	N—H…O═C	0.1938	41.21	135.22	0.023	0.059
	O—H…N	0.1850	94.01		0.036
qu1-a2	N—H…O═C	0.1896	52.47	164.14	0.025	0.067
	O—H…N	0.1806	111.67		0.041
qu2-a1	N—H…O	0.2120	27.32	45.73	0.016	0.028
	C—H…N	0.2417	18.41		0.012
qu2-a2	N—H…O	0.2068	33.39	50.42	0.017	0.029
	C—H…N	0.2461	17.03		0.011
qu3-a1	N—H…O	0.2213	19.08	34.87	0.013	0.026
	C—H…O	0.2954	1.23		0.003
	C—H…N	0.2508	14.56		0.010
qu3-a2	N—H…O	0.2113	28.28	40.20	0.016	0.025
	C—H…O	0.3559	0.00		0.000
	C—H…N	0.2579	11.92		0.008
qu4-a1	N—H…O	0.2059	29.87	139.45	0.018	0.059
	C—H…O	0.3166	0.00		0.000
	O—H…N	0.1804	109.58		0.041
qu4-a2	N—H…O	0.2181	15.56	125.26	0.014	0.060
	C—H…O	0.2809	1.17		0.005
	O—H…N	0.1812	108.53		0.041
qu5-a1	O—H…N	0.1859	89.12	122.84	0.035	0.053
	N—H…O	0.2080	33.72		0.018
qu5-a2	O—H…N	0.1838	98.53	131.58	0.038	0.057
	N—H…O	0.2073	33.05		0.018
qu6-a1	N—H…O═C	0.2012	32.59	55.60	0.019	0.033
	O—H…N	0.2290	23.01		0.014
qu6-a2	N—H…O═C	0.1996	36.11	61.42	0.019	0.035
	O—H…N	0.2249	25.31		0.016

Fig.3 Optimal structures of six hydrogen-bonded complexesThe hydrogen bond distances are given in the corresponding position. ΔEb(gas) and ΔEb1(water) are the binding energies in gas phase and in water solvent using the optimal structure in gas phase. ΔrG0(water) is the standard Gibbs free energy change in water solvent using the optimal structure in water solvent. The bond distance units are in nm.

Fig.4 Optimal structures of the hydrogen-bonded quercetin-adenine-thymine and quercetin-deoxyadenosine-deoxythymidine complexesThe hydrogen bond distances are given in the corresponding position. ΔEb(gas) and ΔEb1(water) are the binding energies in gas phase and in water solvent using the optimal structure in gas phase. The bond distance units are in nm.

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