Theoretical Studies on the Effect of Amino Acid Side Chains on Hydrogen Bonding for G:C in Aqueous Solution†

doi:10.7503/cjcu20160270

Abstract

Abstract:

Quantum chemical method was employed to study the hydrogen bond interaction between the amino acid side chain(AASC) analogues and G, C bases, as well as GC base pair in gas and aqueous solution. B3LYP/6-31+G(d,p) was carried out to optimize the complex structures. Moreover, MP2/aug-cc-pVDZ was performed to calculate the energies, natural bond orbital(NBO) charges and second order stabilization energies of these complexes. It demonstrates that hydrogen bond interaction between AASC analogues and bases or base pair can be dramatically weakened in aqueous solution, compared with in gas. For the complexes of AASC analogues with positive charge along with the base or base pair, the difference of their hydrogen bond energies between in gas and aqueous solution is 50.63—146.48 kJ/mol, whereas 0.17—24.94 kJ/mol for neutral AASC analogues. The value of charge transfer is proportional to the hydrogen bonding energy, the more the charge transfer, the more stable the complex. The second-order stabilization energies are inverse proportional to the hydrogen bonds, and the second-order stabilization energies of gas divide ones of aqueous solution is approximately to the value of charge transfer in two phases. It is explicitly shown that aqueous solution has an extremely large impact on hydrogen bonding in these systems.

Key words: Amino acid side chain, Guanine, Cytosine, Hydrogen bond, Natural bond orbital(NBO) charge

CLC Number:

O641

TrendMD:

ZHAO Jian, DU Jing, LIU Shuo, YANG Zhongzhi, ZHAO Dongxia, LIU Cui. Theoretical Studies on the Effect of Amino Acid Side Chains on Hydrogen Bonding for G:C in Aqueous Solution^†[J]. Chem. J. Chinese Universities, 2016, 37(9): 1686.

Figures/Tables 6

Fig.1 Sites of hydrogen bonds of guanine(G), cytosine(C), G:C and amino acid side chain The sites of hydrogen bonds are labeled by number.

Fig.2 Snapshot of the first and second regions of hydrogen bond

Table 1 Geometry structure of complexes in gas and aqueous solution within region 1

Hydrogen bond	Length of HB/nm		Angle of HB/(°)
Hydrogen bond	Gas	Aqueous	Gas	Aqueous
N—H…N	0.178—0.220	0.182—0.268	142.4—178.9	120.4—179.8
N—H…O	0.166—0.204	0.177—0.218	137.2—179.1	126.6—179.8
O—H…N	0.168—0.213	0.168—0.237	148.1—155.7	145.8—158.6
O—H…O	0.186	0.187	149.2	151.1

Table 2 Bond length of hydrogen bond of G:C in gas and aqueous solution within region 2

Complex	d[N—H…O(upper)]/nm		d[N—H…N(middle)]/nm		d[N—H…O(lower)]/nm
Complex	Gas	Aqueous	Gas	Aqueous	Gas	Aqueous
G:C	0.1764	0.1873	0.1923	0.1926	0.1901	0.1837
GC1:Arg1	0.1928	0.1909	0.1903	0.1919	0.1791	0.1815
GC1:Arg2	0.1928	0.1903	0.1900	0.1918	0.1790	0.1817
GC1:Arg3	0.1924	0.1891	0.1913	0.1922	0.1793	0.1819
GC1:Arg4	0.1918	0.1892	0.1915	0.1925	0.1796	0.1821
GC1:Asn/Gln2	0.1832	0.1886	0.1938	0.1927	0.1879	0.1828
GC1:Lys1	0.1949	0.1902	0.1902	0.1919	0.1761	0.1811
GC2:Asn/Gln1	0.1768	0.1863	0.1937	0.1938	0.1929	0.1869
GC2:Ser/Thr1	0.1776	0.1876	0.1923	0.1924	0.1901	0.1838
GC3:Asn/Gln1	0.1815	0.1861	0.1915	0.1925	0.1859	0.1842
GC4:Asn/Gln1	0.1729	0.1883	0.1973	0.1951	0.2009	0.1850
GC5:Arg1	0.1902	0.1880	0.1914	0.1918	0.1817	0.1827
GC5:Arg2	0.1886	0.1878	0.1893	0.1917	0.1799	0.1828
GC6:Arg1	0.1839	0.1881	0.1872	0.1917	0.1751	0.1809
GC6:Arg2	0.1840	0.1882	0.1871	0.1916	0.1753	0.1808

Fig.3 Hydrogen bond energies of complexes (A) EHB1 of the complexes in gas and aqueous solution. (B) EHB2 of G:C of complexes in gas and aqueous solution. a. G1:Arg1; b. G1:Arg2; c. G1:Lys1; d. G3:Asn/Glu1; e. C1:Arg1; f. C1:Arg2; g. C3:Arg1; h. C3:Arg2; i. GC1:Arg1; j. GC1:Arg2; k. GC1:Arg3; l. GC1:Arg4; m. GC1:Lys1; n. GC5:Arg1; o. GC5:Arg2; p. GC6:Arg1; q. GC6:Arg2; r. G1:Asn/Gln2; s. G2:Asn/Gln1; t. G2:Ser/Thr1; u. G4:Asn/Gln1; v. G4:Asn/thr1; w. C2:Ser/Thr1; x. C2:Asn/Gln1; y. GC1:Asn/Gln2; z. GC2:Asn/Gln1; a1. GC2:Ser/Thr1; a2. GC3:Asn/Gln1; a3. GC4:Asn/Gln1. (B) a. G:C; b. GC1:Arg1; c. GC1:Arg2; d. GC1:Arg3; e. GC1:Arg4; f. GC1:Lys1; g. GC5:Arg1; h. GC5:Arg2; i. GC6:Arg1; j. GC6:Arg2; k. GC1:Asn/Gln2; l. GC2:Asn/Gln1; m. GC2:Ser/Thr1; n. GC3:Asn/Gln1; o. GC4:Asn/Gln1.

Fig.4 Atomic charges of hydrogen bonds of GC1:Arg1(A) and GC2:Ser/Thr1(B) complexes in aqueous solution Value in parenthesis denotes the atomic charges(e) of forming the triple-body complexes; values without parenthesis are those of G, C and AASC.

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