Web-Books
im Austria-Forum
Austria-Forum
Web-Books
Naturwissenschaften
Chemie
Charge Transport in DNA - Insights from Simulations
Seite - 32 -
  • Benutzer
  • Version
    • Vollversion
    • Textversion
  • Sprache
    • Deutsch
    • English - Englisch

Seite - 32 - in Charge Transport in DNA - Insights from Simulations

Bild der Seite - 32 -

Bild der Seite - 32 - in Charge Transport in DNA - Insights from Simulations

Text der Seite - 32 -

TheoreticalBackground 2.6 ChargeTransfer inDNA In this chapter, a short introduction into the basics of charge transfer and the needed parameters is given. Then, two advanced methods for the propagation of thewave-functionof the excess chargewill be summarized. This represents the rather chemical point of view of a charge transfer process, where the charge re- sides on onemolecule, or part of themolecule, and then is transferred to another molecule. Two of these non-adiabatic methods were implemented in our frame- workandrecentlypublished[72,73]. 2.6.1 BasicsofChargeTransfer The classical way to the CT in complexmolecular systems isMarcus’ theory [71, 85] and its extensions [86–90] Here, a rate of transfer between a donor and an acceptor for the non-adiabatic case can be calculated from several charge transfer parameters. kDA= |VDA|2 h¯ √ π λkBT exp [ −(ΔG 0+λ)2 4λkBT ] (2.36) Theseparameters are: • the electronic coupling (EC) |VDA|2 between thedonorand theacceptor • the reaction free energyΔGof theCTprocess • and the reorganizationenergy (RE)λ All three can be obtained using various computationalmethods. The static elec- tronic couplings can be calculated with highly accurate quantum chemical (QC) methods likeCAS-PT2.Moreefficientmethodshave tobeused tocalculate thedy- namicelectroniccouplings in thecourseofanMDsimulation. Inourapproach, the dynamicECareobtainedusingtheDFTB2method(seesection2.3.2 fordetails)and a fragment orbital approach[91]. ΔG andλ are thermodynamic quantities, so that their computationcanbedonebysamplingof theconfigurationspace, e.g. freeen- ergy calculations. TheRE is the energyneeded to reorient themolecules and their environmenttotheconformationcorrespondingtothefinalstateof theCTreaction. 32
zurück zum  Buch Charge Transport in DNA - Insights from Simulations"
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
Web-Books
Bibliothek
Datenschutz
Impressum
Austria-Forum
Austria-Forum
Web-Books
Charge Transport in DNA