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The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle-mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make(More)
We present an application of a molecular-dynamics-based scheme to evaluate the solvent reorganization energy of hole transfer in DNA. The obtained parameters can be used for simulations of hole transfer in DNA by means of Marcus' theory. Also, we perform an analysis of the reorganization energies, including the case of transfer of a delocalized hole.
In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated(More)
We present a new computational strategy to evaluate the charge-transfer (CT) parameters for hole transfer in DNA. On the basis of a fragment-orbital approach, site energies and coupling integrals for a coarse-grained tight-binding description of the electronic structure of DNA are rapidly calculated using the approximative density functional method(More)
Parametrization of the approximative DFT method SCC-DFTB for halogen elements is presented. The new parameter set is intended to describe halogenated organic as well as inorganic molecules, and it is compatible with the established parametrization of SCC-DFTB for carbon, hydrogen, oxygen, and nitrogen. The performance of the parameter set is tested on a(More)
Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the(More)
Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions. We addressed this(More)
We present an extension to the recent 3OB parametrization of the Density Functional Tight Binding Model DFTB31,2 for biological and organic systems. Parameters for the halogens F, Cl, Br, and I have been developed for use in covalently bound systems and benchmarked on a test set of 106 molecules (the ‘OrgX’ set), using bonding distances, bonding angles,(More)
Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study(More)
We investigated the intercalation of an antitumor drug ellipticine into four adenine-thymine (AT) rich DNA duplexes with the focus on the configurational entropy, by means of molecular dynamics (MD) simulations. Two possible binding orientations of ellipticine in a DNA double helix were studied, and the orientation with the pyrrole nitrogen exposed into a(More)