Partitioning of the Vibrational Free Energy

Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

A many-body expansion of ionization potentials and electron affinities is developed based on a combination of the fragment molecular orbital method and equation-of-motion coupled-cluster (EOM-CC). In addition to site-specific values, obtained as one-body properties, pair and triple corrections are added to account for nonlocal EOM-CC contributions of the molecular environment of a chromophore. The developed method is applied to carboxylic acids, alkyl cations, a protein ubiquitin (Protein Data Bank ID 1UBQ), and a nano ribbon of white graphene elucidating the effect of environment on ionization potential and electron affinity.

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).

Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method

Fast parameterized methods such as density-functional tight-binding (DFTB) facilitate realistic calculations of large molecular systems, which can be accelerated by the fragment molecular orbital (FMO) method. Fragmentation facilitates interaction analyses between functional parts of molecular systems. In addition to DFTB, other parameterized methods combined with FMO are also described. Applications of FMO methods to biochemical and inorganic systems are reviewed.

Polarization energies in the fragment molecular orbital method

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.

The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization

Adsorption and chemical reactions occurring on industrially important ZSM-5 and faujasite zeolite catalysts are investigated with the quantum-mechanical fragment molecular orbital method combined with periodic boundary conditions. Suitable fragmentation patterns are devised and tested providing important case studies of computing real materials with fragmentation methods. A good accuracy is demonstrated in comparison to full calculations, and a good agreement with the available experimental data is obtained. The full production cycle of p-xylene on faujasite zeolite is mapped. The catalytic role of the zeolite in the dehydration reaction, analyzed with the partition analysis, is attributed to the delocalization of the negative charge over the zeolite. On the other hand, an increase of the barrier in the Diels-Alder reaction by the zeolite is attributed to the preferential stabilization of the reactants over the transition state as demonstrated by the guest-zeolite interaction energy.

Free Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method

A decomposition of the free energy is developed in the many-body expansion framework of the fragment molecular orbital (FMO) method combined with umbrella sampling molecular dynamics (MD). In FMO/MD simulations, performed with density-functional tight-binding and periodic boundary conditions, all atoms are treated quantum mechanically. The free energy is computed and decomposed for a series of S_N2 Menshutkin reactions in water. The barrier lowering by the solvent is attributed to the competition between the solvent polarization and the solute-solvent interactions including charge transfer.

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method

For gaining insights into interactions in periodic systems, an analysis is developed based on the fragment molecular orbital method combined with periodic boundary conditions. The adsorption energy is decomposed into guest and surface polarization and deformation energy, guest-surface and guest-guest interactions, and the vibrational free energy. The analysis is applied to the adsorption of guest molecules to Ih (001) ice surface. The cooperativity effects result in a non-linear change in the adsorption energy with coverage due to many-body effects. The role of dispersion is found to be dominant for guests with long hydrophobic tails. A rule is proposed relating the length of the alkyl tail with the formation of the guest layer. The computed binding enthalpies are in good agreement with experimental values. For high coverage, adsorbed molecules can form an ordered layer known as self-assembled monolayer.

Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

A fast quantum-mechanical approach, density-functional tight-binding combined with the fragment molecular orbital method and periodic boundary conditions, is used to optimize atomic coordinates and cell parameters for a set of protein crystals: 1ETL, 5OQZ, 3Q8J, 1CBN, and 2VB1. Good agreement between experimental and calculated structures is obtained for both atomic coordinates and cell parameters. Sterical clashes present in the experimental structures are corrected by simulations. The partition analysis is extended to treat periodic boundary conditions and applied to analyze protein-solvent interactions in crystals.