Polarization energies in the fragment molecular orbital method

Abstract

Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density‐functional tight‐binding (DFTB) is developed in the framework of the fragment molecular orbital method. For DFTB, the method is extended into the use of periodic boundary conditions (PBC), for which a new component, a periodic self‐polarization energy, is derived. The couplings of the polarization to other components in the pair interaction energy analysis (PIEDA) are derived for DFT and DFTB, and compared to Hartree–Fock and second‐order Møller‐Plesset perturbation theory (MP2). The effect of the self‐consistent (DFT) and perturbative (MP2) treatment of the electron correlation on the polarization is discussed. The difference in the polarization in the bulk (PBC) and micro (cluster) solvation is elucidated.

Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method

“…20,21 To define polarization energies of fragments, FMO can be used without embedding, 22 employing methyl cap fragments. 23,24 To improve the accuracy of FMO for basis sets with diffuse functions, a point charge embedding (PCE) 25 and an auxiliary polarization (AP) 26 approach using dual basis sets have been proposed. AP provides a way to treat both polarization and a basis set superposition error (BSSE) [27][28][29][30] correction.…”

“…A many‐body expansion, 18,19 is applied in FMO to the energies of fragments or to the electron density of fragments 20,21 . To define polarization energies of fragments, FMO can be used without embedding, 22 employing methyl cap fragments 23,24 …”

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

“…Secondly, it is of interest to compare interactions in molecular mechanics (MM) and QM and discuss the role of polarization [ 28 ] and charge transfer. The polarization of proteins can be critical to ligand binding [ 29 ].…”

System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study

“…The fragment molecular orbital (FMO) method has gained attention as an accurate and fast scoring function to calculate the binding affinity by QM 11–21 . The systems are divided into smaller pieces called fragments, and ab initio calculations are performed for each fragment and their pairs.…”

“…The fragment molecular orbital (FMO) method has gained attention as an accurate and fast scoring function to calculate the binding affinity by QM. [11][12][13][14][15][16][17][18][19][20][21] The systems are divided into smaller pieces called fragments, and ab initio calculations are performed for each fragment and their pairs. As the method is well suitable for parallel computing, one may expect to obtain the QM calculation result in much shorter time.…”