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Charge Transport in DNA - Insights from Simulations
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TheoreticalBackground of freedomand solve the equations ofmotion directlywith the barostat incorpo- rated. In this sense, theParrinello–Rahmanbarostat [60,61] is theequivalent to the Nosé–Hoover thermostat. 2.3 QuantumChemistry MMmethods, like shown in the latter chapter, are only able todescribe the struc- ture and dynamic properties of molecules without accounting for their explicit electronic structure. In contrast, quantum chemistry (QC)methods are designed todescribe the electronic structures ofmolecular systems. Here, a short introduc- tion into the basic concepts of theQCmethods, which are applied in the studies of CT in the later parts of thiswork,will be given. The starting pointwill be the density functional theory (DFT).Having summarized theDFT, the approximative density-functional tight-binding (DFTB) (chapter 2.3.2)method is introduced. The latterwill beused in theCTcalculations. 2.3.1 DensityFunctionalTheory DFT is a quantumchemicalmethod todescribe electronic structures of atomsand molecules. In contrast to thewave functionbasedmethods likeHartree–Fock (HF) and post-HF (e.g. perturbation theory or configuration interaction), DFT is based on thecalculationof theelectrondensity. This approachhas twomainadvantages: • The system is no longer described by 3Ncoordinates of thewave function, butonlyby3 coordinatesoverall. • Theelectrondensity isaphysicalobservablewhereas thewave-function (WF) isnot. Theprobabilityoffindinganelectronatapositionrcanbecomputedbyintegrating over all other electrons in the system. ρ(r1)=N ∫ Ψ∗(r1...rN)Ψ(r1...rN)dr2...drN (2.14) 18
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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