The Electronic Property Differences between dA::dG and dA::dGoxo. A Theoretical Approach
Abstract
1. Introduction
2. Results and Discussion
2.1. Nucleoside Pair (NP) Structure and Its Electronic Properties
2.2. Electronic Properties of Isolated Nucleoside Pairs
2.3. Molecular Orbital Analysis of dA::dGoxo and dA:dG Pairs
3. Materials and Methods
4. Conclusions
Supplementary Materials
Funding
Conflicts of Interest
References
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System | HB Length [Å] | HB Energy | d1[Å] | d2[Å] | λR[°] | λY[°] | λ3[°] | ||
---|---|---|---|---|---|---|---|---|---|
HB1 | HB2 | HB3 | |||||||
dC:::dG | 2.89 | 2.94 | 2.84 | −17.55 | 10.77 | 9.00 | 52.98 | 51.94 | −6.01 |
dC:::dGoxo | 2.87 | 2.91 | 2.83 | −18.27 | 10.71 | 8.99 | 52.41 | 54.48 | −6.69 |
dA:dG | 2.91 | 4.03 | −4.09 | 12.57 | 10.27 | 43.10 | 30.76 | −8.77 | |
dA::dGoxo | 2.91 | 2.83 | −11.67 | 10.76 | 8.87 | 53.89 | 43.97 | −5.35 | |
Reference Parameters of ds-DNA [29] | |||||||||
T::dA | 3.05 | 2.96 | 10.7 | 54.5 | 54.5 | ||||
dC:::dG | 2.87 | 3.00 | 3.00 | 10.8 | 54.2 | 54.5 |
System | Electronic Properties in [eV] | |||||||
---|---|---|---|---|---|---|---|---|
VIPNE-PCM | VIPEQ-PCM | AIP | VEANE-PCM | VEAEQ-PCM | AEA* | VEAENE/EQ-PCM | VEDENE/EQ-PCM | |
dC:::dG | 6.12 | 6.12 | 5.77 | 1.51 | 1.51 | 2.00 | 2.58/2.57 | 5.44/5.43 |
dC:::dGoxo | 6.01 | 6.01 | 5.63 | 1.53 | 1.53 | 2.02 | 2.61/2.61 | 5.26/5.26 |
dA:dG | 6.45 | 6.44 | 6.03 | 0.99 | 1.00 | 1.28 | 1.61/1.60 | 5.71/5.71 |
dA::dGoxo | 6.00 | 6.00 | 5.26 | 1.10 | 1.10 | 1.57 | 2.55/2.55 | 4.55/4.55 |
SER 1 | NER 1 | SER 2 | NER 2 | SER 3 | NER 3 | SER 4 | NER 4 | |
dC:::dG | 0.00 | 0.35 | 0.00 | 0.34 | 0.00 | 0.49 | 0.00 | 0.58 |
dC:::dGoxo | 0.00 | 0.37 | 0.00 | 0.37 | 0.00 | 0.49 | 0.00 | 0.59 |
dA:dG | 0.01 | 0.42 | 0.01 | 0.31 | 0.01 | 0.29 | 0.00 | 0.32 |
dA::dGoxo | 0.00 | 0.73 | 0.00 | 0.71 | 0.00 | 0.47 | 0.00 | 0.98 |
Nucleoside Pair | ||||||||
dC:::dG | dC:::dGoxo | dA:dG | dA::dGoxo | |||||
dC | dG | dC | dGoxo | dA | dG | dA | dGoxo | |
Form | Charge distribution [a.u] | |||||||
Neutral | 0.16 | −0.16 | 0.18 | −0.18 | −0.11 | 0.11 | 0.04 | −0.04 |
VCEQ-PCM | 0.20 | 0.80 | 0.21 | 0.79 | −0.09 | 1.09 | 0.08 | 0.92 |
AC | 0.29 | 0.71 | 0.29 | 0.71 | 0.07 | 0.93 | 0.65 | 0.35 |
VAEQ-PCM | −0.77 | −0.23 | −0.76 | −0.24 | −1.09 | 0.09 | −0.91 | −0.09 |
AA | −0.68 | −0.32 | −0.66 | −0.34 | −1.07 | 0.07 | −0.90 | −0.10 |
VNCEQ-PCM | 0.25 | −0.25 | 0.25 | −0.25 | −0.09 | 0.09 | 0.59 | −0.59 |
VNAEQ-PCM | 0.26 | −0.26 | 0.28 | −0.28 | −0.08 | 0.08 | 0.08 | −0.08 |
Form | Spin Distribution [a.u] | |||||||
VCEQ-PCM | 0.00 | 1.00 | 0.20 | 0.80 | 0.00 | 1.00 | 0.00 | 1.00 |
AC | 0.00 | 1.00 | 0.29 | 0.71 | 0.00 | 1.00 | 0.00 | 1.00 |
VAEQ-PCM | 0.98 | 0.02 | 0.99 | 0.01 | 0.99 | 0.01 | 0.99 | 0.01 |
AA | 0.99 | 0.01 | 0.99 | 0.01 | 1.00 | 0.00 | 1.00 | 0.00 |
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Karwowski, B.T. The Electronic Property Differences between dA::dG and dA::dGoxo. A Theoretical Approach. Molecules 2020, 25, 3828. https://doi.org/10.3390/molecules25173828
Karwowski BT. The Electronic Property Differences between dA::dG and dA::dGoxo. A Theoretical Approach. Molecules. 2020; 25(17):3828. https://doi.org/10.3390/molecules25173828
Chicago/Turabian StyleKarwowski, Boleslaw T. 2020. "The Electronic Property Differences between dA::dG and dA::dGoxo. A Theoretical Approach" Molecules 25, no. 17: 3828. https://doi.org/10.3390/molecules25173828
APA StyleKarwowski, B. T. (2020). The Electronic Property Differences between dA::dG and dA::dGoxo. A Theoretical Approach. Molecules, 25(17), 3828. https://doi.org/10.3390/molecules25173828