Ionic Hydrogen Bonding Between Arginine Side Chain and Nucleic Acid Bases†

doi:10.7503/cjcu20160346

Abstract

Abstract:

The optimal structures of twenty-two hydrogen-bonded complexes composed of one charged arginine side chain molecule and one nucleic acid base in gas phase were obtained at the MP2/6-31+G(d,p) level. The binding energies in gas phase were evaluated at the MP2/aug-cc-pVTZ level including basis set superposition error(BSSE) correction. The optimal structures for these hydrogen-bonded complexes in water solvent were further obtained by using PCM model combined with the MP2/6-31+G(d,p) method. The binding energies in water solvent were evaluated by using PCM model combined with the MP2/aug-cc-pVTZ method. It is found that the ionic hydrogen bonding strength between the arginine side chain and one of the five nucleic acid bases highly correlates to the charge transfer between the two monomers, the electron density at the hydrogen bond critical point, and the second-order stabilization energy. Compared to the neutral hydrogen bond, the ionic hydrogen bond exhibits more significant covalent character. It is also found that the stability of the hydrogen-bonded complexes can be predicted according to the enthalpy change of the protonation reaction of the nucleic acid bases. The more negative the enthalpy change of the protonation reaction, the more stable the hydrogen-bonded complexes.

Key words: Arginine side chain, Nucleic acid base, Ionic hydrogen bond, Binding energy, Enthalpy change of protonation reaction

CLC Number:

O641

TrendMD:

LI Lei,HUANG Cuiying,JIANG Xiaonan,GAO Xichan,WANG Changsheng. Ionic Hydrogen Bonding Between Arginine Side Chain and Nucleic Acid Bases^†[J]. Chem. J. Chinese Universities, 2016, 37(8): 1460.

Figures/Tables 3

References 35

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Complex	Type	R_NH…X/nm	E_b/(kJ·mol^-1)	ΔE⁽²⁾ / (kJ·mol^-1)	ΣΔE⁽²⁾ / (kJ·mol^-1)	ρ_c/a.u.	Σρ_c/a.u.	q_t/e
R1-mU1	N—H…O C	0.1885	-104.27(-39.70)	63.76	109.16	0.0279	0.0522	0.0371
	N—H…O C	0.1936		45.40		0.0243
R1-mU2	N—H…O C	0.1905	-87.49(-37.91)	48.91	85.14	0.0263	0.0498	0.0333
	N—H…O C	0.1947		36.23		0.0234
R2-mU1	N—H…O C	0.1893	-104.01(-40.77)	59.66	111.08	0.0266	0.0522	0.0373
	N—H…O C	0.1925		51.42		0.0256
R2-mU2	N—H…O C	0.1889	-87.45(-39.35)	56.07	90.71	0.0272	0.0501	0.0337
	N—H…O C	0.1959		34.64		0.0229
R1-mT1	N—H…O C	0.1874	-104.93(-42.06)	70.58	117.48	0.0289	0.0538	0.0385
	N—H…O C	0.1927		46.90		0.0249
R1-mT2	N—H…O C	0.1894	-93.51(-39.80)	51.00	89.24	0.0270	0.0512	0.0348
	N—H…O C	0.1935		38.24		0.0241
R2-mT1	N—H…O C	0.1890	-105.23(-43.05)	62.51	123.51	0.0270	0.0539	0.0391
	N—H…O C	0.1911		61.00		0.0269
R2-mT2	N—H…O C	0.1877	-93.51(-41.03)	58.41	94.81	0.0280	0.0515	0.0353
	N—H…O C	0.1948		36.40		0.0235
R1-mC1	N—H…O C	0.1709	-151.08(-62.45)	156.06	245.05	0.0428	0.0729	0.0822
	N—H…N	0.1941		88.99		0.0300
R1-mC2	N—H…O C	0.1892	-144.72(-51.31)	61.46	115.18	0.0288	0.0546	0.0472
	N—H…O C	0.1928		53.72		0.0258
R2-mC1	N—H…O C	0.1700	-152.59(-63.58)	172.05	258.32	0.0443	0.0738	0.0858
	N—H…N	0.1950		86.27		0.0295
R2-mC2	N—H…O C	0.1831	-147.11(-55.19)	96.65	137.11	0.0353	0.0577	0.0555
	N—H…O C	0.1963		40.46		0.0224
R1-mG1	N—H…O C	0.1768	-158.82(-59.90)	123.34	245.55	0.0362	0.0716	0.0776
	N—H…N	0.1861		122.21		0.0354
R1-mG2	N—H…O C	0.2056	-142.93(-46.98)	47.03	74.90	0.0241	0.0436	0.0387
	N—H…O C	0.2171		27.87		0.0195
R2-mG1	N—H…O C	0.1762	-160.96(-61.35)	133.68	249.45	0.0375	0.0713	0.0790
	N—H…N	0.1881		115.77		0.0338
R2-mG2	N—H…O C	0.2017	-144.39(-48.66)	59.54	86.07	0.0263	0.0454	0.0437
	N—H…O C	0.2181		26.53		0.0190
R1-mA1	N—H…N	0.1983	-95.31(-39.73)	69.37	105.90	0.0291	0.0535	0.0515
	N—H…N	0.2058		36.53		0.0244
R1-mA2	N—H…N	0.1944	-91.63(-40.76)	75.02	110.75	0.0310	0.0545	0.0529
	N—H…N	0.2078		35.73		0.0235
R1-mA3	N—H…N	0.1965	-90.04(-42.83)	81.46	105.69	0.0297	0.0507	0.0462
	N—H…N	0.2112		24.23		0.0210
R2-mA1	N—H…N	0.1873	-96.11(-43.43)	116.69	134.39	0.0370	0.0555	0.0587
	N—H…N	0.2197		17.70		0.0185
R2-mA2	N—H…N	0.1885	-91.59(-41.37)	103.68	127.53	0.0353	0.0554	0.0574
	N—H…N	0.2156		23.85		0.0200
R2-mA3	N—H…N	0.1839	-90.25(-43.52)	138.49	140.37	0.0382	0.0493	0.0563
	N—H…N	0.2437		1.88		0.0111

Complex	Type	R_NH…X/nm	E_b/(kJ·mol^-1)	ΔE⁽²⁾ / (kJ·mol^-1)	ΣΔE⁽²⁾ / (kJ·mol^-1)	ρ_c/a.u.	Σρ_c/a.u.	q_t/e
R1-mU1	N—H…O C	0.1885	-104.27(-39.70)	63.76	109.16	0.0279	0.0522	0.0371
	N—H…O C	0.1936		45.40		0.0243
R1-mU2	N—H…O C	0.1905	-87.49(-37.91)	48.91	85.14	0.0263	0.0498	0.0333
	N—H…O C	0.1947		36.23		0.0234
R2-mU1	N—H…O C	0.1893	-104.01(-40.77)	59.66	111.08	0.0266	0.0522	0.0373
	N—H…O C	0.1925		51.42		0.0256
R2-mU2	N—H…O C	0.1889	-87.45(-39.35)	56.07	90.71	0.0272	0.0501	0.0337
	N—H…O C	0.1959		34.64		0.0229
R1-mT1	N—H…O C	0.1874	-104.93(-42.06)	70.58	117.48	0.0289	0.0538	0.0385
	N—H…O C	0.1927		46.90		0.0249
R1-mT2	N—H…O C	0.1894	-93.51(-39.80)	51.00	89.24	0.0270	0.0512	0.0348
	N—H…O C	0.1935		38.24		0.0241
R2-mT1	N—H…O C	0.1890	-105.23(-43.05)	62.51	123.51	0.0270	0.0539	0.0391
	N—H…O C	0.1911		61.00		0.0269
R2-mT2	N—H…O C	0.1877	-93.51(-41.03)	58.41	94.81	0.0280	0.0515	0.0353
	N—H…O C	0.1948		36.40		0.0235
R1-mC1	N—H…O C	0.1709	-151.08(-62.45)	156.06	245.05	0.0428	0.0729	0.0822
	N—H…N	0.1941		88.99		0.0300
R1-mC2	N—H…O C	0.1892	-144.72(-51.31)	61.46	115.18	0.0288	0.0546	0.0472
	N—H…O C	0.1928		53.72		0.0258
R2-mC1	N—H…O C	0.1700	-152.59(-63.58)	172.05	258.32	0.0443	0.0738	0.0858
	N—H…N	0.1950		86.27		0.0295
R2-mC2	N—H…O C	0.1831	-147.11(-55.19)	96.65	137.11	0.0353	0.0577	0.0555
	N—H…O C	0.1963		40.46		0.0224
R1-mG1	N—H…O C	0.1768	-158.82(-59.90)	123.34	245.55	0.0362	0.0716	0.0776
	N—H…N	0.1861		122.21		0.0354
R1-mG2	N—H…O C	0.2056	-142.93(-46.98)	47.03	74.90	0.0241	0.0436	0.0387
	N—H…O C	0.2171		27.87		0.0195
R2-mG1	N—H…O C	0.1762	-160.96(-61.35)	133.68	249.45	0.0375	0.0713	0.0790
	N—H…N	0.1881		115.77		0.0338
R2-mG2	N—H…O C	0.2017	-144.39(-48.66)	59.54	86.07	0.0263	0.0454	0.0437
	N—H…O C	0.2181		26.53		0.0190
R1-mA1	N—H…N	0.1983	-95.31(-39.73)	69.37	105.90	0.0291	0.0535	0.0515
	N—H…N	0.2058		36.53		0.0244
R1-mA2	N—H…N	0.1944	-91.63(-40.76)	75.02	110.75	0.0310	0.0545	0.0529
	N—H…N	0.2078		35.73		0.0235
R1-mA3	N—H…N	0.1965	-90.04(-42.83)	81.46	105.69	0.0297	0.0507	0.0462
	N—H…N	0.2112		24.23		0.0210
R2-mA1	N—H…N	0.1873	-96.11(-43.43)	116.69	134.39	0.0370	0.0555	0.0587
	N—H…N	0.2197		17.70		0.0185
R2-mA2	N—H…N	0.1885	-91.59(-41.37)	103.68	127.53	0.0353	0.0554	0.0574
	N—H…N	0.2156		23.85		0.0200
R2-mA3	N—H…N	0.1839	-90.25(-43.52)	138.49	140.37	0.0382	0.0493	0.0563
	N—H…N	0.2437		1.88		0.0111