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Charge Transport in DNA - Insights from Simulations
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AParametrizedModel toSimulateCT inDNA Table7.2: Obtainedwavenumbers for thefluctuationof IPdue to internaldynamicsof thenucleobases adenine andguanine anddue to environmental dynamics Adenine Guanine Environment 1866.7,1860.0,1823.3, 1900.0,1883.3,1833.3, 883.3,796.7,733.3,620.0,450.0, obtained 1790.0,1770.0,1756.7, 1810.0,1783.3,1756.7, 376.7,323.3,220.0,176.7,132.7, wavenumbers 1653.3,1583.3,1540.0, 1670.0,1630.0,1560.0, 103.3,61.7,41.7,30.0,20.7, [cm−1] 1380.0,1310.0,1246.7, 1433.3,1376.7,1243.3, 14.7,9.7,8.7,4.7,4.0, 1126.7,1076.7,943.3, 1156.7,1076.7,1026.7, 3.0,1.6,0.7,0.3, IP(t)=∑ n An ·cos ( t ·2π Tn ) +E0 (7.5) Tn is theperiodandAn is the correspondingamplitudeof theoscillation. While theTn are obtainedwith the Fourier transformation, the An have to be ob- tained fromotherdata. Theamplitudeshave tobefitted to reproduce thestandard deviations of the IP inMD simulations accurately. To this end, additional simu- lations of 20 ns with the IP calculated every 2 ps were performed to obtain the statistics of the IP time series. Two types of simulationswereperformed toobtain different amplitudes for the internal andexternalfluctuations. Toobtain theamplitudesof the internalfluctuations, simulationswithnoQM/MM coupling were performed. This way, the IP will fluctuate only as a result of the internalmodes of vibration of thenucleobases. Table 7.3 (left) shows the statistics of the IPof adeninenucleobases inapolyAsequence,whennoQM/MMcoupling is applied. Now, the sumof cosine functionswas set up including only the internal fluctua- tionswiththecorrespondingperiods. Thesumofcosinefunctionswasthenshifted bya constantE0 to yield the samemeanvalues as obtained fromMDsimulations. And, the amplitudes An were chosen in a way that an overall magnitude of the fluctuations is achieved,whichmatches the value obtained fromMDsimulations withoutQM/MMcoupling, i.e. 0.1 eV. To obtain the amplitudes for the environmental fluctuations, simulations with QM/MM coupling were performed. Again, the obtained time series of IP were analyzed formeanvalues and standarddeviations. Themeanvalues showed that 94
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Charge Transport in DNA Insights from Simulations
Titel
Charge Transport in DNA
Untertitel
Insights from Simulations
Autor
Mario Wolter
Verlag
KIT Scientific Publishing
Datum
2013
Sprache
englisch
Lizenz
CC BY-SA 3.0
ISBN
978-3-7315-0082-7
Abmessungen
17.0 x 24.0 cm
Seiten
156
Schlagwörter
Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
Kategorien
Naturwissenschaften Chemie

Inhaltsverzeichnis

  1. Zusammenfassung 1
  2. Summary 3
  3. 1 Introduction 5
  4. 2 TheoreticalBackground 11
    1. 2.1 MolecularMechanics 11
    2. 2.2 MolecularDynamicsSimulation 13
      1. 2.2.1 Solving theEquationsofMotion 14
      2. 2.2.2 ThermodynamicEnsembles 15
    3. 2.3 QuantumChemistry 18
      1. 2.3.1 DensityFunctionalTheory 18
      2. 2.3.2 ApproximativeDFT–Density-FunctionalTight-Binding 21
    4. 2.4 DynamicsofExcessCharge inDNA 24
      1. 2.4.1 TheMulti-ScaleFramework 25
      2. 2.4.2 TheFragmentOrbitalApproach 26
    5. 2.5 ChargeTransport inDNA 29
      1. 2.5.1 Landauer–BüttikerFramework 29
    6. 2.6 ChargeTransfer inDNA 32
      1. 2.6.1 Basics ofChargeTransfer 32
      2. 2.6.2 Non-adiabaticPropagationSchemes 34
  5. 3 SimulationSetup 39
    1. 3.1 TheDNAMolecule 39
      1. 3.1.1 InvestigatedDNASequences 42
    2. 3.2 MDSimulationofDNA 44
    3. 3.3 DNAunderMechanical Stress 45
    4. 3.4 MicrohydratedDNA 46
  6. 4 DNAUnderExperimentalConditions 49
    1. 4.1 FreeMDSimulations 50
    2. 4.2 TheStructuralChangesofDNAuponStretching 51
    3. 4.3 IrreversibilityofDNAStretching inSimulations 56
    4. 4.4 Effects ofLowHydration 58
    5. 4.5 Effects ofDecreased IonContent 62
    6. 4.6 Effect ofWater and Ionson theStretchingProfileofDNA 64
    7. 4.7 Conclusion 67
  7. 5 ChargeTransport inStretchedDNA 69
    1. 5.1 InvestigatedSequences andStructures 69
    2. 5.2 ChargeTransportCalculations 71
    3. 5.3 SequenceDependentChargeTransport 73
    4. 5.4 DetailedStructuralDifferences 74
    5. 5.5 Conclusion 76
  8. 6 ChargeTransport inMicrohydratedDNA 79
    1. 6.1 InvestigatedSequences andStructures 79
    2. 6.2 ChargeTransferParameters 80
    3. 6.3 ChargeTransportCalculations 84
    4. 6.4 DirectDynamicsofChargeTransfer 86
    5. 6.5 Conclusion 87
  9. 7 AParametrizedModel toSimulateCT inDNA 89
    1. 7.1 Creating theElectronicCouplings 90
    2. 7.2 Modeling the IonizationPotentials 93
    3. 7.3 TestingwithChargeTransportCalculations 97
    4. 7.4 ChargeTransferExtensions 98
    5. 7.5 TestingwithChargeTransferMethods 102
    6. 7.6 Conclusion 103
  10. 8 Conclusion 105
  11. Appendix 111
  12. A DNAUnderExperimentalConditions 111
    1. A.1 TheStructuralChangesofDNAuponStretching 111
    2. A.2 Effect ofLowHydrationandDecreased IonContent 112
    3. A.3 StretchingofMicrohydratedDNA 116
  13. B CTinMicrohydratedDNA 117
    1. B.1 HelicalParameters -CompleteOverview 117
    2. B.2 ElectronicCouplings 118
    3. B.3 IonizationPotentials 119
    4. B.4 ESP InducedbyDifferentGroupsofAtoms 122
    5. B.5 DistanceofChargedAtomGroups fromtheHelicalAxis 123
  14. List ofPublications 137
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Charge Transport in DNA