Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides

作者：Zhang, Lei; Li, Wei^*; Fang, Tao; Li, Shuhua

来源：Theoretical Chemistry Accounts, 2016, 135(2): 34.

DOI：10.1007/s00214-015-1799-z

• Ab initio molecular dynamics
• Fragment-based approach
• Noncovalent interactions
• Conformational dynamics
• Unsolvated polypeptides

Ab inito molecular dynamics (AIMD) based on the generalized energy-based fragmentation (GEBF) approach is employed for the ultrafast conformational dynamics of two unsolvated polypeptides, -helical acetyl(ala) and a subunit of DNA polymerase . In the GEBF approach, the energies and energy gradients of subsystems are obtained with M06-2X functionals, which can describe intramolecular noncovalent interaction. The results are compared with those obtained from the simulations based on AMBER99 and CHARMM22 force fields, and semiempirical density-functional tight-binding (DFTB) and DFTB with empirical dispersion correction (DFTB-D) methods. Our results show that the GEBF-M06-2X simulations may provide reasonable results for the conformational changes of the two unsolvated polypeptides due to the description of intramolecular noncovalent interactions. The AMBER99, CHARMM22, DFTB, and DFTB-D simulations give quite different results. The GEBF-M06-2X-based AIMD simulations are expected to be applied to the fast or ultrafast conformational dynamics of large unsolvated polypeptides and to be employed for improving the empirical force fields.

• 出版日期2016-1-25
• 单位南京大学