12.5 Effective Fragment Potential Method

12.5.5 Library of Fragments

The effective fragments are rigid and their potentials are generated from a set of ab initio calculations on each unique isolated fragment. The EFP includes: (i) multipoles (produced by the Stone’s Distributed Multipolar Analysis) for Coulomb and polarization terms; (ii) static polarizability tensors centered at localized molecular orbital (LMO) centroids (obtained from coupled-perturbed Hartree-Fock calculations), which are used for calculations of polarization; (iii) dynamic polarizability tensors centered on the LMOs that are generated by time-dependent HF calculations and used for calculations of dispersion; and (iv) the Fock matrix, basis set, and localized orbitals needed for the exchange-repulsion term. Additionally, the EF potential contains coordinates of atoms, coordinates of the points of multi-polar expansion (typically, atoms and bond mid-points), coordinates of the LMO centroids, electrostatic and polarization screening parameters, and atomic labels of the EF atoms.

Q-Chem provides a library of standard fragments with precomputed effective fragment potentials. Currently the library includes common organic solvents, nucleobases, and molecules from S22 and S66 datasets for non-covalent interactions; see Table 12.8. EFP potentials in gamess format are supported by new EFPMAN2 module. They are stored in $QCAUX/fraglib directory.

Table 12.8: Standard fragments available in Q-Chem
acetone ACETONE_L
acetonitrile ACETONITRILE_L
adenine ADENINE_L
ammonia AMMONIA_L
benzene BENZENE_L
carbon tetrachloride CCL4_L
cytosine C1 CYTOSINE_C1_L
cytosine C2a CYTOSINE_C2A_L
cytosine C2b CYTOSINE_C2B_L
cytosine C3a CYTOSINE_C3A_L
cytosine C3b CYTOSINE_C3B_L
dichloromethane DCM_L
dimethyl sulfoxide DMSO_L
guanine enol N7 GUANINE_EN7_L
guanine enol N9 GUANINE_EN9_L
guanine enol N9RN7 GUANINE_EN9RN7_L
guanine keton N7 GUANINE_KN7_L
guanine keton N9 GUANINE_KN9_L
methane METHANE_L
methanol METHANOL_L
phenol PHENOL_L
thymine THYMINE_L
toluene TOLUENE_L
water WATER_L
acetamide, S66, gas phase ACETAMIDE_L
acetamide, S66, H-bonded dimer ACETAMIDE_HB_L
acetic acid, S66, gas phase ACETICAC_L
acetic acid, S66, H-bonded dimer ACETICAC_HB_L
adenine, S22 stack dimer ADENINE_L
adenine, S22 WC dimer ADENINE_WC_L
2-aminopyridine, S22 AMINOPYRIDINE_L
cyclopentane, S66 CPENTANE_L
ethylene ETHENE_L
acetylene ETHYNE_L
formic acid, S22 H-bonded dimer FORMICAC_HB_L
formamide, S22 dimer FORMID_L
hydrogen cyanide HCN_L
indole, S22 INDOLE_L
methylamine, S66 MENH2_L
neopentane, S66 NEOPENTANE_L
O2 O2_L
pentane, S66 PENTANE_L
peptide, S66 PEPTIDE_L
pyrazine PYRAZINE_L
pyridine, S66 PYRIDINE_L
2-pyridoxine, S22 PYRIDOXINE_L
thymine, S22 stack dimer THYMINE_L
thymine, S22 WC dimer THYMINE_WC_L
uracil, S66, gas phase URACIL_L
uracil, S66, H-bonded dimer URACIL_HB_L

Note:  The fragments from Q-Chem fragment library have _L added to their names to distinguish them from user-defined fragments.

The parameters for the standard fragments were computed as follows. The geometries of the solvent molecules were optimized by MP2/cc-pVTZ; geometries of nucleobases were optimized with RI-MP2/cc-pVTZ. Geometries of molecules from S22 and S66 datasets are discussed in Ref. 264. The EFP parameters were obtained in gamess. To generate the electrostatic multipoles and electrostatic screening parameters, analytic DMA procedure was used, with 6-31+G* basis for non-aromatic compounds and 6-31G* for aromatic compounds and nucleobases. The rest of the potential, i.e., static and dynamic polarizability tensors, wave function, Fock matrix, etc., were obtained using 6-311++G(3df,2p) basis set.