DFT-based investigation of the electronic structure of a double-stranded AC B-DNA dim

Rengifo, Emerson; Murillo, G.

doi:10.25100/rc.v16i0.507

Cited by 2 publications

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“…In the present OLCAO calculation, we found the HOMO to originate from the (PO 4 3À -Na + ) complex. Conduction band edge states are often assigned to either cytosine 61,63,65 or an Na + /PO 4 3À antibonding state, 62,64 whereas in our calculation, all lower CB states are anti-bonding states from base pairs. While contributions to the band edges from all these states are present in our PDOS, the strong contribution of the PO 28 where the charge compensations occur with different types of positively charged ions, this influence of the phosphate group on valence band structure and subsequently on the observed band gap and optical absorbance follows reasonably from previous results.…”

Section: Comparison With Previous Literaturementioning

confidence: 68%

“…Previous studies of the electronic structure of duplex DNA list a variety of interpretations for the valence band and conduction band edge assignments from the PDOS with conflicting conclusions. Most commonly the valence band edge is assigned to guanine where present [59][60][61][62][63][64][65] or adenine where guanine is not present. 59,66 However, the HOMO state is highly sensitive to the counterions in the proximity of the PO 4 3À group.…”

Section: Comparison With Previous Literaturementioning

confidence: 99%

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Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence

Schimelman

Dryden

Poudel

et al. 2015

Phys. Chem. Chem. Phys.

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The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

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Section: Comparison With Previous Literaturementioning

confidence: 68%

Section: Comparison With Previous Literaturementioning

confidence: 99%

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence

Schimelman

Dryden

Poudel

et al. 2015

Phys. Chem. Chem. Phys.

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“…Hybrid functional is the most popular functional used in DFT computations and one of the common hybrid functional is B3LYP. Hybrid functional is an effective functional for organic, biochemical and large systems without requiring an excessive amount of computing time, memory and disk space [27]. Basis set is a set of mathematical functions expanded as a linear combination of atomic orbitals to represent molecular orbitals.…”

Section: Methodsmentioning

confidence: 99%

The Effects of Split Valence Basis Sets on Muon Hyperfine Interaction in Guanine Nucleobase and Nucleotide Structures

Zaharim

Sulaiman

Bakar

et al. 2019

MSF

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The DFT cluster method was employed to investigate the electronic structures and muonium hyperfine interactions in guanine nucleobase and nucleotide using three different basis sets. The total energy and Fermi contact values were calculated for muon trapped at carbon '8'. The three basis sets, 6-31G, 6-311G and 6-311G(d,p), were used in tandem with the B3LYP functional. There are significant quantitative differences in the calculated total energy. 6-311G(d,p) produced the lowest total energy as compared to the other basis sets. The lowering of the total energy is due to the increase in the number of basis functions to describe the atomic orbitals, which is consistent with the postulate on basis set completeness. The 6-31G basis set produced the muon Fermi contact value that is the closest to the experimental value. The calculated Fermi contact values for the nucleobase and nucleotide are significantly lowered in going from the double-zeta to the triple-zeta basis set by 5% and 4% respectively. The lowering of the Fermi contact value can be attributed to the extension of the triple-zeta basis set in describing the valence atomic orbitals. The presence of the sugar phosphate group in the nucleotide instead of the methyl group tends to lower the Fermi contact value. Thus, the sugar phosphate group should be taken into consideration when designing a calculation model.

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DFT-based investigation of the electronic structure of a double-stranded AC B-DNA dim

Cited by 2 publications

References 0 publications

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence

The Effects of Split Valence Basis Sets on Muon Hyperfine Interaction in Guanine Nucleobase and Nucleotide Structures

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