Ab-initio band structure of polycytidine; internal charge transfer in DNA

Ladik, J.; Suhai, S.

doi:10.1002/qua.560180718

Cited by 4 publications

(7 citation statements)

References 14 publications

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“…Finally, in the case of Z-DNA, we should observe that the stacking energy of G, T (for which also MHF is negative) is more negative than in any of the 16 cases in B-DNA (Table I11 and Band structure calculations using a whole nucleotide as a unit cell [2] have shown that there is a charge transfer (CT) of -0.2 e from the sugar to the nucleotide base. This phenomenon has been found for cytidine, thymidine, and adenylic acid.…”

Section: Stacking Energy Calculationsmentioning

confidence: 93%

“…2). In all the three investigated cases, the valence and conduction bands of the polynucleotide are of "base stack" type, while the band below the valence band and the band above the conduction band are of "sugar-phosphate chain" type.…”

Section: Stacking Energy Calculationsmentioning

confidence: 98%

“…Band structure calculations using a whole nucleotide as a unit cell [2] have shown that there is a charge transfer (CT) of -0.2 e from the sugar to the nucleotide base. This phenomenon has been found for cytidine, thymidine, and adenylic acid.…”

Section: Is Dna-b An Intrinsic Semiconductor?mentioning

confidence: 99%

“…In the last years, substantial progress has been achieved in the quantum mechanical investigation of DNA including the water and ion structure around it [l] and band structure calculations using a whole nucleotide as unit cell [2]. Pilot calculations have been performed to assess the effect of water structure on a nucleotide base stack [3] for the investigation of polynucleotide-polypeptide interactions [4] and for the treatment of aperiodicity in the DNA macromolecule [5].…”

Section: Introductionmentioning

confidence: 99%

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Some new results in the quantum mechanical investigation of DNa

Ladik

Otto

Förner

2009

Int. J. Quantum Chem.

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As a first step in testing the possibility of correlation calculations of extended systems using localized orbitals, localization of the canonical Hartree-Fock orbitals of the four nucleotide bases was performed. The results show an excellent localization of the occupied orbitals and a rather good one for the virtuals (both for the IT-and --orbitals). Interaction energy calculations of the stacked nucleotide bases show a few kcaldmol repulsion at the Hartree-Fock level, but they become attractive (again a few kcaldmol) if dispersion energy computed with the aid of London's formula is added. The internal charge transfer of -0.2 e from sugar to the nucleotide base (C, T, or A) found in largescale ab inirio homopolynucleotide calculations raises the question of whether there are free charge carriers in DNA B. Though in the Hartree-Fock level the answer is negative, one cannot rule out this possibility if, using a high-quality basis set, correlated band structures (using an mproved version of the electronic polaron model) will be computed. Interaction energy calculations between a polyglycine chain in different conformation and polynucleotide chains show a few kcaldmol attraction per base and glycine unit and a very small (a fraction of a kcal/mol) additional attraction due to the dispersion correction.

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Section: Stacking Energy Calculationsmentioning

confidence: 93%

Section: Stacking Energy Calculationsmentioning

confidence: 98%

Section: Is Dna-b An Intrinsic Semiconductor?mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Some new results in the quantum mechanical investigation of DNa

Ladik

Otto

Förner

2009

Int. J. Quantum Chem.

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“…5 It has been shown that the bandstructure of a homopolynucleotide is, to a good approximation, the superposition of the bandstructures of the nucleobase stack (NS) and the sugar-phosphate chain (SPC). 6 This is fortunate because, for the determination of the properties relevant for the electronic conduction, one can focus on the electronic structure of the NS. The bandstructures of paired-base and single-base homostacks have been studied at a variety of semi-empirical, 2,7-14 ab-initio, 6,15-17 and density-functional-theory (DFT) 12,18-20 levels.…”

mentioning

confidence: 99%

Modeling the bandstructures of B-DNA base stacks

Rengifo

Murillo

Arce

2013

Journal of Applied Physics

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A pseudohelical approximation for the calculation of the bandstructures of DNA base homostacks in B conformation is introduced. It consists of choosing a unit cell of only two nucleobases with relative parallel displacement and twist that locally mimic the helical conformation. It is tested employing the extended HÃ¼ckel method with a unique Wolfsberg-Helmholtz parameter. The resulting bandgaps and ionization potential trend agree well with the ones reported in the literature employing the full screw-axis symmetry and higher levels of theory. The electron and hole effective masses extracted from the bandstructures follow the same trends as the experimentally reported mobilities

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Electronic Structure Change in DNA Caused by Base Pair Motions and Its Effect on Charge Transfer in DNA Chains

Liu¹,

Liu²,

Zheng³

et al. 2016

Aust. J. Chem.

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One important aspect of carrier transfer in DNA is its coupling with atomic motions. The collective motion of the base pairs can either improve the charge transfer by enhancing the π stacking between the bases, or trap the carriers due to strong coupling. By utilizing a pseudo-helical base pair stack model, we systematically studied the electronic structure and its dependence to geometry changes that represent the important DNA motions, including the translation, the twist and the torsion of the base pairs. Our calculations reveal that the above motions may significantly change the electron structure and affect their transport properties. In order to improve the transport of carriers in DNA so that it can become a prospective material in future electronics, it is necessary to make large changes to the atomic structure. Our calculations of the electronic structure under large geometry variation, including large base pair stacking deformation and the insertion of phenyl rings in the bases, can provide good guidelines for such structural modifications of DNA.

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Ab-initio band structure of polycytidine; internal charge transfer in DNA

Cited by 4 publications

References 14 publications

Some new results in the quantum mechanical investigation of DNa

Some new results in the quantum mechanical investigation of DNa

Modeling the bandstructures of B-DNA base stacks

Electronic Structure Change in DNA Caused by Base Pair Motions and Its Effect on Charge Transfer in DNA Chains

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