US EPA

4274041 

Journal Article 

Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases 

Zhang, C; Bell, D; Harger, M; Ren, P 

2017 

Yes 

Journal of Chemical Theory and Computation
ISSN: 1549-9618
EISSN: 1549-9626 

13 

2 

666-678 

English 

28030769 

10.1021/acs.jctc.6b00918 

WOS:000394924000025 

Aromatic molecules with π electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the π electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobases and 12 aromatic molecules. The permanent electrostatic energy is expressed as atomic multipole interactions between atom pairs, and many-body polarization is accounted for by mutually induced atomic dipoles. We have systematically investigated aromatic ring stacking and aromatic-water interactions for nucleobases and aromatic molecules, as well as base-base hydrogen-bonding pair interactions, all at various distances and orientations. van der Waals parameters were determined by comparison to the quantum mechanical interaction energy of these dimers and fine-tuned using condensed phase simulation. By comparing to quantum mechanical calculations, we show that the resulting classical potential is able to accurately describe molecular polarizability, molecular vibrational frequency, and dimer interaction energy of these aromatic systems. Condensed phase properties, including hydration free energy, liquid density, and heat of vaporization, are also in good overall agreement with experimental values. The structures of benzene liquid phase and benzene-water solution were also investigated by simulation and compared with experimental and PDB structure derived statistical results.