Symmetry-adapted perturbation theory potentials for DNA bases

Deoxyribonucleic acid (DNA) is considered as the fundamental structure of life and it contains the all genetic information of known living beings and some viruses. Therefore, DNA is the one of the most important and heavily inspected biological molecule. The diversity it can produce, however, rests upon the combination of the four different molecules; adenine, cytosine, thymine, and guanine. These DNA bases are stabilized by non-bonded interactions, especially with hydrogen bonding and stacking. This unique structure gives the DNA the ability to form triplexes, quadruplexes and many other complex structures. These DNA bases can also be embedded on metal surfaces and the resulting metal-DNA complexes can be used for many special purposes such as biochip sensors, organic semiconductors, and organic photovoltaic tools. In this study, we developed a new force field specialized for adenine, thymine and adenine-thymine oligomers. For this purpose, the first step of this study will be to compare the performances of various ab initio methods for calculating the interaction energies. MP2, SCS-MP2, SCS-MI-MP2, B3LYP-D and DFT-SAPT (PBE0AC and LPBE0AC) was used to calculate Potential Energy Curves(PEC) with Dunning's aug-cc-pVXZ (aVXZ) base sets (X = D, T and in some cases Q) to find the most accurate and computationally cheap method. After this step, acquired results compared with the CCSD(T), which is considered as the most accurate but computationally expensive method. The best resultant method will be used to calculate the potential energy surfaces (PES) and used as an alternative to CCSD(T). As a next step, the resulting interaction forces fitted to an analytical function to develop force fields. Then, the model function was used to perform a global search to find the local and global minima of adenine, thymine and adenine-thymine dimers, trimers, and tetramers by using the one of the most successful and robust global optimization algorithm, Simulated Annealing. Our structure optimizations showed us that the new potential is able to reproduce the 2-D filament structures and some new non-planar adenine, thymine and adenine-thymine clusters. For the final step, we compared the well-known AMBER with our generated force field, for all considered systems. Although AMBER force field generally agrees with ab initio methods and proposed model, it can fail to produce the correct interaction energies for certain cases while proposed model potential performs better. Therefore, we suggest our proposed force field is suitable to perform molecular dynamics simulations of much larger DNA systems.