In silico approaches and challenges for quantum chemical calculations on macromolecules

Massa, Lou; Fahimi, Peyman; Castanedo, Lázaro A.M.; Matta, Chérif F.

doi:10.1016/b978-0-323-90995-2.00013-8

Cited by 1 publication

(2 citation statements)

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“…To reduce the high scaling of QM calculations, many fragment-based approaches have been proposed. [1][2][3][4][5][6][7][8][9][10] There are three main points of difference between them: (a) whether caps (hydrogen 11 or peptide 9 ) are used to terminate bonds between fragments, (b) whether an embedding potential 9 is used or not, 11 and (c) whether the energies of fragments are added directly 6 or the energy is computed from the combined total electron density. 5 The fragment molecular orbital (FMO) method [12][13][14][15][16] can be used for a variety of QM approaches, including Hartree-Fock (HF) 12 and second-order Møller-Plesset perturbation theory (MP2).…”

Section: Introductionmentioning

confidence: 99%

“…To reduce the high scaling of QM calculations, many fragment‐based approaches have been proposed 1–10 . There are three main points of difference between them: (a) whether caps (hydrogen 11 or peptide 9 ) are used to terminate bonds between fragments, (b) whether an embedding potential 9 is used or not, 11 and (c) whether the energies of fragments are added directly 6 or the energy is computed from the combined total electron density 5 …”

Section: Introductionmentioning

confidence: 99%

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

Fedorov

2024

J Comput Chem

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An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated.

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