Mechanism Studies on Adsorption of DNA Bases and Base Pair-Zn2+ mplexes for CO2, N2 and H2†

doi:10.7503/cjcu20140137

Abstract

Abstract:

As an intriguing material building block for microporous metal-organic framework(MOF) materials, DNA base(pair) holds usually rigid-ring structures, multiple metal coordination sites, biological compatibility, and molecular recognition as well as self-assembling characteristics that could ultimately translate into interesting material properties. In the present paper, guanine G, cytosine C, adenine A, thymine T, and their pairs GC/AT as well as their Zn²⁺ complexes were selected as models to study their potential behavior of building block to adsorb mixed small molecules H₂, N₂, CO₂ by employing M062X/6-31+G^* method. The interaction modes and strengths as well as potential binding sites were predicted. These results reveal that CO₂ prefers H-bonding to the amino hydrogen(s) or/and imino hydrogen(s) of these bases(pairs), whereas both H₂ and N₂ prefer being adsorbed over the base ring with a π-stacking interaction mode. A comparison for the binding energies of these different small molecules shows that AT is the more potential building block of MOF material than GC and AA, and will adsorb these small molecules hierarchically according to the following order: H₂ < N₂ < CO₂. The result offers theoretical predictions and direction for the experimental synthesis of such MOF materials built by these different base-pair building blocks.

Key words: Base pair-Zn2+ complex, M062X method, Adsorption, Hydrogen bond, Small molecule, Metal-organic framework(MOF) material

CLC Number:

O641

TrendMD:

SHI Shuai, HUANG Ximing, AI Hongqi. Mechanism Studies on Adsorption of DNA Bases and Base Pair-Zn²⁺ mplexes for CO₂, N₂ and $H 2 †$ [J]. Chem. J. Chinese Universities, 2014, 35(7): 1492.

Figures/Tables 6

References 23

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Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
C-H₂1	-5.9	0.014	G-H₂1	-6.6	0.014	GC-H₂1	-6.4	0.014
C-H₂2	-5.5	0.014	G-H₂2	-6.4	0.014	GC-H₂2	-6.2	0.014
C-H₂3	-5.4	0.014	G-H₂3	-6.3	0.014	GC-H₂3	-6.0	0.014
C-H₂4	-4.8	0.015	G-H₂4	-6.2	0.014	GC-H₂4	-5.6	0.022
C-H₂5	-2.5	0.015	G-H₂5	-6.2	0.014
			G-H₂6	-5.8	0.014
			G-H₂7	-2.7	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
C-H₂1	-5.9	0.014	G-H₂1	-6.6	0.014	GC-H₂1	-6.4	0.014
C-H₂2	-5.5	0.014	G-H₂2	-6.4	0.014	GC-H₂2	-6.2	0.014
C-H₂3	-5.4	0.014	G-H₂3	-6.3	0.014	GC-H₂3	-6.0	0.014
C-H₂4	-4.8	0.015	G-H₂4	-6.2	0.014	GC-H₂4	-5.6	0.022
C-H₂5	-2.5	0.015	G-H₂5	-6.2	0.014
			G-H₂6	-5.8	0.014
			G-H₂7	-2.7	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
A-H₂1	-6.1	0.014	T-H₂1	-5.5	0.014	AT-H₂1	-5.4	0.014
A-H₂2	-6.1	0.014	T-H₂2	-5.5	0.014	AT-H₂2	-4.6	0.014
A-H₂3	-6.0	0.014	T-H₂3	-5.3	0.014	AT-H₂3	-4.6	0.014
A-H₂4	-5.8	0.014	T-H₂4	-1.5	0.014	AT-H₂4	-3.6	0.014
A-H₂5	-5.6	0.014
A-H₂6	-5.6	0.014
A-H₂7	-4.2	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
A-H₂1	-6.1	0.014	T-H₂1	-5.5	0.014	AT-H₂1	-5.4	0.014
A-H₂2	-6.1	0.014	T-H₂2	-5.5	0.014	AT-H₂2	-4.6	0.014
A-H₂3	-6.0	0.014	T-H₂3	-5.3	0.014	AT-H₂3	-4.6	0.014
A-H₂4	-5.8	0.014	T-H₂4	-1.5	0.014	AT-H₂4	-3.6	0.014
A-H₂5	-5.6	0.014
A-H₂6	-5.6	0.014
A-H₂7	-4.2	0.014

Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm	Complex	ΔE₁/(kJ·mol^-1)	Δr_d/nm
AAA-Zn²⁺-H₂1	-6.6	0.014	AAT-Zn²⁺-H₂1	-6.6	0.014	GGC-Zn²⁺-H₂1	-8.6	0.014
AAA-Zn²⁺-H₂2	-6.2	0.014	AAT-Zn²⁺-H₂2	-6.5	0.014	GGC-Zn²⁺-H₂2	-8.6	0.014
AAA-Zn²⁺-H₂3	-6.0	0.014	AAT-Zn²⁺-H₂3	-6.4	0.014	GGC-Zn²⁺-H₂3	-6.8	0.014
AAA-Zn²⁺-H₂4	-5.6	0.014	AAT-Zn²⁺-H₂4	-6.4	0.014	GGC-Zn²⁺-H₂4	-6.2	0.014
AAA-Zn²⁺-H₂5	-2.8	0.014	AAT-Zn²⁺-H₂5	-5.9	0.014	GGC-Zn²⁺-H₂5	-5.9	0.014
			AAT-Zn²⁺-H₂6	-2.0	0.014	GGC-Zn²⁺-H₂6	-4.7	0.014
						GGC-Zn²⁺-H₂7	-3.9	0.014

Mechanism Studies on Adsorption of DNA Bases and Base Pair-Zn²⁺ mplexes for CO₂, N₂ and $H 2 †$

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