A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules

Abstract

A common feature of traditional tight-binding (TB) methods is the non-self-consistent solution of the eigenvalue problem of a Hamiltonian operator, represented in a minimal basis set. These TB schemes have been applied mostly to solid state systems, containing atoms with similar electronegativities. Recently self-consistent TB schemes have been developed which now allow the treatment of systems where a redistribution of charges, and the related detailed charge balance between the atoms, become important as e.g. in biological systems. We discuss the application of such a method, a self-consistent charge density-functional based TB scheme (SCC-DFTB), to biological model compounds. We present recent extensions of the method: (i) The combination of the tight binding scheme with an empirical force field, that makes large scale simulations with several thousand atoms possible. (ii) An extension which allows a quantitative description of weak-bonding interactions in biological systems. The latter include an improved description of hydrogen bonding achieved by extending the basis set and improved molecular stacking interactions achieved by incorporating the dispersion contributions empirically. In applying the method, we present benchmarks for conformational energies, geometries and frequencies of small peptides and compare with ab initio and semiempirical quantum chemistry data. These developments provide a fast and reliable method, which can handle large scale quantum molecular dynamic simulations in biological systems.

Greatly enhanced adsorption of platinum on periodic graphene nanobuds: A first-principles study

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An atomistic-continuum Cosserat rod model of carbon nanotubes

“…The atomistic simulations in the present work are performed using a density-functional-based tight-binding (DFTB) method (Elstner et al, 1998(Elstner et al, , 2000Frauenheim et al, 2002) maintaining self-consistency in electronic charges (SCC). This semi-empirical method is best viewed as an approximation to DFT, and is parameterized based on LDA-DFT calculations.…”

“…This semi-empirical method is best viewed as an approximation to DFT, and is parameterized based on LDA-DFT calculations. It has been tested and shown to reproduce, quite accurately, the mechanical properties of brittle materials such as diamond, CNTs, and graphene, as predicted by DFT, while being on the order of 100 times faster than DFT based on first-principles (Elstner et al, 1998(Elstner et al, , 2000Frauenheim et al, 2002).…”

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