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Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories
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10.1063/1.3146905
/content/aip/journal/jcp/130/21/10.1063/1.3146905
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/21/10.1063/1.3146905

Figures

Image of FIG. 1.
FIG. 1.

MD snapshot of the Dickerson dodecamer DNA: Backbone (pink), base pairs (green), solvent molecules (red and white lines), and sodium counterions (blue spheres). Also shown are the corresponding HOMOs on each of the base pairs being almost completely localized on the purine bases. DNA backbone, solvent, and sodium counterions comprise the electrostatic environment which is described via QM/MM coupling.

Image of FIG. 2.
FIG. 2.

(a) Transmission of the ideal chain including (b) dynamical effects and the (c) effect of environment for various DNA sequences. Note the broader energy range in (c).

Image of FIG. 3.
FIG. 3.

Time-dependent average over onsite energies obtained from a 100 ps MD simulation of a poly(G) heptamer . Snapshots were recorded every femtosecond.

Image of FIG. 4.
FIG. 4.

Length dependence of for poly(G) and poly(A). Shown are logarithmic transmission values for various DNA length, i.e., number of sites at two constant arbitrary energies which are the average onsite energies and for poly(A) and poly(G), respectively. The data points were fitted by functions of the form where ( is the stacking distance of ) and describes the decay rate of transmission. For poly(G) is and for poly(A) at . However, if an energy gap of 1.5 eV to is present both -values increase to 0.77 and for poly(A) and poly(G), respectively. In both cases the exponential decay of transmission in poly(G) is stronger than in poly(A). The complete curves for the different lengths can also be found in the supplementary material (Ref. 101).

Image of FIG. 5.
FIG. 5.

Comparison of for the MD simulation of a poly(A) heptamer with two statistical models. Top panel: The electronic couplings for the three models are set to 0.05 eV. The average transmission function is calculated for onsite energies from the MD simulation time series (blue); for onsite energies drawn from the respective probability distribution functions on each site (green); and the Anderson model (red) where all onsite energies are randomly drawn from a square-box distribution. Bottom panel: Now the original MD time series of onsite energies is used, the same for the three models, while is calculated for electronic couplings from the original MD time series (blue); for drawn from their respective probability distribution functions (green) and the Anderson model (red), respectively. The used probability distribution functions for and are shown in the supplementary material (Ref. 101).

Image of FIG. 6.
FIG. 6.

Statistical analysis of in a poly(G) heptamer for the 30 ns data with electronic parameters for every picosecond (30 000 DNA conformations). depending on and (top); number of conformations found in a given interval of and (bottom).

Image of FIG. 7.
FIG. 7.

Plot of depending on for fixed values of based on the same data as used in Fig. 6.

Image of FIG. 8.
FIG. 8.

Conformational analysis: The amount of conformations that make up 90% of ; calculation of electronic parameters with QM/MM-environment for every picosecond snapshot along the 30 ns MD simulation; comparison between poly(G) and poly(A) heptamers; the values are sorted beginning with the largest.

Image of FIG. 9.
FIG. 9.

Conformational analysis: The amount of conformations that make up 90% of based on the calculation of electronic parameters with QM/MM environment and in vacuo. Comparison between the homogenous poly(G) heptamer (left) and the central heptamer of the heterogeneous Dickerson sequence (right). The values are sorted beginning with the largest.

Image of FIG. 10.
FIG. 10.

Average transmission for various sets of averaged electronic parameters for poly(A) (top) and poly(GT) (bottom). Both of them obtained from 100 ps MD data with a time step of 1 fs.

Image of FIG. 11.
FIG. 11.

Snapshot of a 3 ps time series for the transmission at for poly(A) (top) and poly(GT) (bottom), respectively, based on the simulation data as used in Fig. 10.

Tables

Generic image for table
Table I.

Electronic couplings for a hole transfer in idealized static A- and B-DNA without QM/MM environment compared to MD averaged values with standard deviations including the QM/MM environment for helical parameters of the idealized A- and B-DNA. See Refs. 99 and 100. All values are in eV.

Generic image for table
Table II.

Maximum current values (at voltage ) for seven DNA heptamers sequences for static B-DNA structures for the average current of the MD structures with and without QM/MM environment. All values are in nanoamperes.

Generic image for table
Table III.

Correlation coefficient of with and .

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/content/aip/journal/jcp/130/21/10.1063/1.3146905
2009-06-04
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/21/10.1063/1.3146905
10.1063/1.3146905
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