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11.5 Effective Fragment Potential Method

11.5.6 Library of Fragments

(December 20, 2021)

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 11.8. EFP potentials in gamess format are supported by new EFPMAN2 module. They are stored in $QCAUX/fraglib directory.

Table 11.8: 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.  323 Flick J. C. et al.
J. Chem. Theory Comput.
(2012), 8, pp. 2835.
. 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.