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7.2Modeling the IonizationPotentials
Table7.3: Statistics of the IP of adenine nucleobases in a polyA oligomer. Left: Sim-
ulation without QM/MM coupling; only internal modes of vibration con-
tribute to the fluctuations. Right: Simulation with QM/MM coupling to
the environment; fluctuations of solvent and DNA backbone contribute to
thefluctuations of IP.
invacuo
nucleobase mean± std. dev. [eV]
A1 5.354± 0.099
A2 5.356± 0.090
A3 5.357± 0.101
A4 5.357± 0.095
A5 5.357± 0.095
A6 5.359± 0.096 QM/MM
nucleobase mean± std. dev. [eV]
A1 5.565± 0.304
A2 5.572± 0.303
A3 5.563± 0.301
A4 5.554± 0.302
A5 5.549± 0.304
A6 5.551± 0.305
an additional shift of IP had to be introduced to account for the environmental
effect. Then theamplitudesAn of thecosine functionsof theenvironmentalfluctu-
ationswerefitted in combinationwith theamplitudes for the internalfluctuations,
obtainedpreviously, so that the largerfluctuations of about 0.3 eVobserved in the
QM/MMenvironment are reproduced.
Additionally, the amplitudes of the cosine functions that correspond to the nine
lowest environmentalfluctuationswere scaleddownbya factorof0.6. These slow
fluctuations correspond to movements of the whole molecular system, therefore
theyhavevery longperiodsand rather lowamplitudes.
TheMDsimulationsperformed toobtain the time series of IPwere conductedus-
ing anon-polarizable forcefield. In such simulations, the electric field inducedby
the environment is overestimated by 26-34%[80], thereforeQM/MMinteractions
have to be scaled down by a factor of 1.5 for charge transfer calculations[73]. To
model this scaling,MDsimulationswith andwithout this scaling factorwereper-
formedand theCTparameters recorded. The time serieswere analyzed formean
values and standard deviations. A new set of amplitudes for the environmental
fluctuationswas introduced to reproduce these scaledfluctuations.
95
Charge Transport in DNA
Insights from Simulations
- Title
- Charge Transport in DNA
- Subtitle
- Insights from Simulations
- Author
- Mario Wolter
- Publisher
- KIT Scientific Publishing
- Date
- 2013
- Language
- English
- License
- CC BY-SA 3.0
- ISBN
- 978-3-7315-0082-7
- Size
- 17.0 x 24.0 cm
- Pages
- 156
- Keywords
- Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
- Categories
- Naturwissenschaften Chemie
Table of contents
- Zusammenfassung 1
- Summary 3
- 1 Introduction 5
- 2 TheoreticalBackground 11
- 3 SimulationSetup 39
- 4 DNAUnderExperimentalConditions 49
- 5 ChargeTransport inStretchedDNA 69
- 6 ChargeTransport inMicrohydratedDNA 79
- 7 AParametrizedModel toSimulateCT inDNA 89
- 8 Conclusion 105
- Appendix 111
- A DNAUnderExperimentalConditions 111
- B CTinMicrohydratedDNA 117
- List ofPublications 137