Page - 45 - in Charge Transport in DNA - Insights from Simulations

3.3DNAunderMechanicalStress number of water molecules, depending upon the length of DNA, were replaced with sodiumcounterions toneutralize thenegatively chargedDNAbackbones. ClassicalMDsimulationswereperformedwith theparm99/BSC0 force-field,[111– 113] and theparameterizationbyÅqvistwasapplied todescribe theNa+ counter- ions.[114] The topologieswere createdwithAmberTools[115] andconverted to the Gromacs formatwithAmbconv.[116]All simulationswereperformedwith a time step of 2 fs with LINCS[117] to constrain the bonds involving hydrogen to their reference lengths. Pilot calculations,performedonnucleobases in thegasphaseas well as ona solvatedoligonucleotides, showed that these constraints affect neither the ionization potentials of the nucleobases nor the electronic couplings between them. The Lennard-Jones interactionswere cut off at 1 nm, and the electrostatics were treatedwith theparticle–meshEwaldmethod [52]. The prepared systems were equilibrated in a multi-step procedure. First of all, a steepest-descentsminimizationwas performed for 100 steps to removepossible badcontacts. Subsequently, the initialvelocities forallatomswererandomlydrawn from a Maxwell–Boltzmann distribution at 10K. The water was heated up first in an NVT simulation of 20 ps length. Here the DNA was weakly coupled to a bath at 10Kand the solvent coupled to a separate bath at 300K. The Berendsen thermostat was used for this purpose.[57] After that, anotherNVT simulation of 20ps lengthwasused tobring the entire system to 300K,with a singleheat bath. Finally, anNPT simulation at 300Kand 1barwasperformedover the interval of 0.5ns. TheNosé–Hoover extended-ensemble thermostatwith a characteristic time of 0.5pswas used to keep the temperature of 300K.[58, 59] InNPT simulations, the Parrinello–Rahman barostatwith characteristic time of 0.5ps and a reference pressure of 1 barwas used.[60] The consecutive production simulationswere run with the same parameters as the last equilibration step. The Gromacs package (versions4.0and4.5)[118,119]wasused for all simulations. 3.3 DNAunderMechanicalStress EachDNAspecieswas stretchedbypulling its3’-ends inoppositedirections. This setupwas inspiredbytheexperimentswhere the3’-endsofdsDNAwerecontacted to the electrodes. To do so, an additional force along the z-axis of the simulation 45