Effect of guanine-cytosine base pair orientation and cluster size on ionization energy and charge distribution: A theoretical study

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Abstract

Density functional calculations with B3LYP/aug-cc-pVDZ level of theory suggest that the vertical ionization energy (VIE) is minimum for 0° orientation angle of guanine-cytosine (GC). n (. n=. 2-6) base pairs, and maximum at around 30°, which is close to the natural base orientation angle (36°) in DNA. As the (GC). n cluster size is increased, the VIE value is decreased substantially from n=. 1 to n=. 3 (7.23-5.76. eV) followed by a less dramatic decrease for larger n values. In each cationic (GC). n cluster, the charge distribution among the G bases shows a pattern that depends upon odd or even number of base pairs in the cluster. At a very low temperature, when the orientation angle is frozen to its equilibrium value (around 36°), the CT rate is expected to drop significantly (large VIE value) in comparison with the rates at higher temperatures when small orientation angles are accessible with lower VIE values.

Original languageEnglish (US)
Pages (from-to)67-70
Number of pages4
JournalComputational and Theoretical Chemistry
Volume1047
DOIs
StatePublished - Nov 1 2014

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Ionization potential
guanines
Cytosine
Charge distribution
Guanine
Base Pairing
charge distribution
energy distribution
Theoretical Models
ionization
Temperature
energy
Density functional theory
deoxyribonucleic acid
DNA

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

Cite this

@article{de2335480a794e018a38daaf67cf19e9,
title = "Effect of guanine-cytosine base pair orientation and cluster size on ionization energy and charge distribution: A theoretical study",
abstract = "Density functional calculations with B3LYP/aug-cc-pVDZ level of theory suggest that the vertical ionization energy (VIE) is minimum for 0° orientation angle of guanine-cytosine (GC). n (. n=. 2-6) base pairs, and maximum at around 30°, which is close to the natural base orientation angle (36°) in DNA. As the (GC). n cluster size is increased, the VIE value is decreased substantially from n=. 1 to n=. 3 (7.23-5.76. eV) followed by a less dramatic decrease for larger n values. In each cationic (GC). n cluster, the charge distribution among the G bases shows a pattern that depends upon odd or even number of base pairs in the cluster. At a very low temperature, when the orientation angle is frozen to its equilibrium value (around 36°), the CT rate is expected to drop significantly (large VIE value) in comparison with the rates at higher temperatures when small orientation angles are accessible with lower VIE values.",
author = "Arshad Khan",
year = "2014",
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day = "1",
doi = "10.1016/j.comptc.2014.08.018",
language = "English (US)",
volume = "1047",
pages = "67--70",
journal = "Computational and Theoretical Chemistry",
issn = "2210-271X",
publisher = "Elsevier BV",

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T1 - Effect of guanine-cytosine base pair orientation and cluster size on ionization energy and charge distribution

T2 - A theoretical study

AU - Khan, Arshad

PY - 2014/11/1

Y1 - 2014/11/1

N2 - Density functional calculations with B3LYP/aug-cc-pVDZ level of theory suggest that the vertical ionization energy (VIE) is minimum for 0° orientation angle of guanine-cytosine (GC). n (. n=. 2-6) base pairs, and maximum at around 30°, which is close to the natural base orientation angle (36°) in DNA. As the (GC). n cluster size is increased, the VIE value is decreased substantially from n=. 1 to n=. 3 (7.23-5.76. eV) followed by a less dramatic decrease for larger n values. In each cationic (GC). n cluster, the charge distribution among the G bases shows a pattern that depends upon odd or even number of base pairs in the cluster. At a very low temperature, when the orientation angle is frozen to its equilibrium value (around 36°), the CT rate is expected to drop significantly (large VIE value) in comparison with the rates at higher temperatures when small orientation angles are accessible with lower VIE values.

AB - Density functional calculations with B3LYP/aug-cc-pVDZ level of theory suggest that the vertical ionization energy (VIE) is minimum for 0° orientation angle of guanine-cytosine (GC). n (. n=. 2-6) base pairs, and maximum at around 30°, which is close to the natural base orientation angle (36°) in DNA. As the (GC). n cluster size is increased, the VIE value is decreased substantially from n=. 1 to n=. 3 (7.23-5.76. eV) followed by a less dramatic decrease for larger n values. In each cationic (GC). n cluster, the charge distribution among the G bases shows a pattern that depends upon odd or even number of base pairs in the cluster. At a very low temperature, when the orientation angle is frozen to its equilibrium value (around 36°), the CT rate is expected to drop significantly (large VIE value) in comparison with the rates at higher temperatures when small orientation angles are accessible with lower VIE values.

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