Derivatives of the approximated electrostatic potentials in unrestricted Hartree–Fock based on the fragment molecular orbital method and an application to polymer radicals

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

“…To describe systems with radical character in GAMESS-US, one can use restricted open-shell (RO) and unrestricted (U) methods, ROHF, 113,114 UHF, [115][116][117] UDFT, 118 ROMP2, 113 UMP2, 119 and ROCC. 113 Multiple open-shell fragments may be specified allowing for treating complex systems with multiple open-shell centers, which can be of interest to spintronics.…”

“…All applications of FMO can be roughly divided into three groups, nanomaterials, processes in explicit solvent (water), and biochemical applications. FMO was applied to optimize the geometry of a polymer, 116 a silicon nanowire, 68 a boron nitride ring with the diameter of 105 nm, 69 and a slab of fullerite surface 87 with the size of 74.4 × 74.4 × 1.4 nm 3 . The binding of guest molecules to faujesite zeolite, 53 mesoporous silica nanoparticles 70 and hydroxyapatite surface 71 was studied with FMO.…”

Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics

“…The fragment molecular orbital method (FMO) 25−29 is a fragmentation approach in which the electronic states of fragments and their pairs are determined in the electrostatic embedding of the whole system and the total properties are computed from those of fragments, their pairs, and, optionally, trimers or even tetramers. 30 FMO has been successfully applied to a large number of various molecular systems such as organic polymers, 31 sugars, 32 DNA, 33 proteins, 34 molecular clusters and crystals, 35 and inorganic materials. 36 Recently, molecular dynamics simulations (MD) using FMO are becoming accessible.…”

Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution

“…However, there is a complication in the application of it to fragments connected by covalent bonds (for example, in proteins). In this case the interaction energy can be large, because of the treatment of fragment boundaries (for fragments connected by C–C bonds, the interaction energy is about −15 hartree) . If one is interested in energy differences (as below in protein–ligand binding) then in the relative sense the above components can be used even for covalently connected fragments, but if one considers absolute values, then the analysis above can be applied, but in order to make it more useful, one more step is necessary.…”