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On the Binding Strength Sequence for Nucleic Acid Bases and C(60) with Density Functional and Dispersion-corrected Density Functional Theories: Whether C(60) could protect nucleic acid bases from radiation-induced damage?

ABSTRACT: The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C(60) by investigating adsorptions of NABs and their cations on C(60) fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine(G) > cytosine(C) > adenine (A) > thymine (T); however, M06-2x switches the binding strengths of A and C, and PBE-D eventually results in the following sequence, G>A>T>C, which is the same as the widely accepted hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2x or even the M06-2x method. The binding energy of G@C(60) obtained with the M06-2x/6-311++G(d,p) and the PBE-D/cc-pVDZ is -7.10 and -8.07 kcal/mol, respectively, and the latter is only slightly weaker than that predicted by the MP2/6-31G(d,p) (-8.10kca/mol). Thus, the PDE-D performs better than the M06-2x for the observed NAB@C(60) ?-stacked complexes. To discuss whether C(60) could prevent NABs from radiation-induced damage, ionization potentials of NABs and C(60), and frontier molecular orbitals of the complexes NABs@C(60) and (NABs@C(60))(+) are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C(60) for T and C complexes, while for G and A the hole delocalizes over the entire complex, rather than a localization on the C(60) moiety. The interesting finding might open a new strategy for protecting DNA from radiation-induced damage and offer a new idea for designing C(60)-based antiradiation drugs.

SUBMITTER: Sun W

PROVIDER: S-EPMC3101642 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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On the Binding Strength Sequence for Nucleic Acid Bases and C(60) with Density Functional and Dispersion-corrected Density Functional Theories: Whether C(60) could protect nucleic acid bases from radiation-induced damage?

Sun Wenming W Bu Yuxiang Y Wang Yixuan Y

The journal of physical chemistry. C, Nanomaterials and interfaces 20110301 8

The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C(60) by investigating adsorptions of NABs and their cations on C(60) fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine(G) > cytosine(C) > adenine (A) > thym ...[more]

PMID: 21625361

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Project description:Imidazo[1,2-a]pyrazines are cyclic amidine-type compounds composed of α-amino acid residues. A full structural identification of these molecules constitutes an analytical challenge, especially when imidazo[1,2-a]pyrazines are obtained from physical processes (e.g., sublimation and pyrolysis of amino acids). A valuable source of molecular information can be obtained from absorption spectroscopies and related techniques encompassing the use of metallic substrates. The aim of this study is to provide new knowledge and insights into the noncovalent intermolecular interactions between imidazo[1,2-a]pyrazines and two Ag n (n = 4 and 20) clusters using density functional theory (DFT) methods. Semiempirical DFT dispersion (DFT-D) corrections were addressed using Grimme's dispersion (GD2) and Austin-Petersson-Frisch (APF) functionals in conjunction with the 6-31+G(d,p) + LANL2DZ mixed basis set. These DFT-D methods describe strong interactions; besides, in all cases, the APF dispersion (APF-D) energies of interaction appear to be consistently overestimated. In comparison with B3LYP calculations, the mean values for the difference in the energies of interaction calculated are 2.25 (GD2) and 6.24 (APF-D) kcal mol-1 for Ag4-molecules, and 2.30 (GD2) and 8.53 (APF-D) kcal mol-1 for Ag20-molecules. The effect of applying GD2 and APF-D corrections to the noncovalent complexes is nuanced in the intermolecular distances calculated, mainly in the Ag···N(amidine) bonding, which appears to play the most important role for the adsorptive process. Selective enhancement and considerable red shifts for Raman vibrations suggest strong interactions, whereas a charge redistribution involving the metallic substrate and the absorbate leads to a significant rearrangement of frontier molecular orbitals mainly in the Ag20-molecule complexes. Finally, time-dependent DFT calculations were carried out to access the orbital contributions to each of the transitions observed in the absorption spectrum. The corresponding UV-vis spectra involve transitions in the visible region at around 400 and 550 nm for the Ag4-molecule and the Ag20-molecule complexes, respectively.

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On the Binding Strength Sequence for Nucleic Acid Bases and C(60) with Density Functional and Dispersion-corrected Density Functional Theories: Whether C(60) could protect nucleic acid bases from radiation-induced damage?

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On the Binding Strength Sequence for Nucleic Acid Bases and C(60) with Density Functional and Dispersion-corrected Density Functional Theories: Whether C(60) could protect nucleic acid bases from radiation-induced damage?

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