Fragmentation methods: A route to accurate calculations on large systems

MS Gordon, DG Fedorov, SR Pruitt… - Chemical …, 2012 - ACS Publications
Theoretical chemists have always strived to perform quantum mechanics (QM) calculations
on larger and larger molecules and molecular systems, as well as condensed phase …

Energy-based molecular fragmentation methods

MA Collins, RPA Bettens - Chemical reviews, 2015 - ACS Publications
1.1 Objectives A major objective of theoretical and computational chemistry is the calculation
of the energy and properties of molecules, so that chemical reactivity and material properties …

Exploring chemistry with the fragment molecular orbital method

DG Fedorov, T Nagata, K Kitaura - Physical Chemistry Chemical …, 2012 - pubs.rsc.org
The fragment molecular orbital (FMO) method makes possible nearly linear scaling
calculations of large molecular systems, such as water clusters, proteins and DNA. In …

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

S Tanaka, Y Mochizuki, Y Komeiji, Y Okiyama… - Physical Chemistry …, 2014 - pubs.rsc.org
Recent developments in the fragment molecular orbital (FMO) method for theoretical
formulation, implementation, and application to nano and biomolecular systems are …

FMODB: The world's first database of quantum mechanical calculations for biomacromolecules based on the fragment molecular orbital method

D Takaya, C Watanabe, S Nagase… - Journal of Chemical …, 2021 - ACS Publications
We developed the world's first web-based public database for the storage, management,
and sharing of fragment molecular orbital (FMO) calculation data sets describing the …

High-precision atomic charge prediction for protein systems using fragment molecular orbital calculation and machine learning

K Kato, T Masuda, C Watanabe… - Journal of Chemical …, 2020 - ACS Publications
Here, we have constructed neural network-based models that predict atomic partial charges
with high accuracy at low computational cost. The models were trained using high-quality …

Machine learning to improve efficiency of non-empirical interaction parameter for dissipative particle dynamics (DPD) simulation

H Doi, S Matsuoka, K Okuwaki, R Hatada… - Japanese Journal of …, 2023 - iopscience.iop.org
We have attempted to use machine learning to streamline the calculation of non-empirical
parameters for use in dissipative particle dynamics simulations. We replaced the calculation …

Enhancement of energy decomposition analysis in fragment molecular orbital calculations

S Matsuoka, K Sakakura, Y Akinaga… - Journal of …, 2024 - Wiley Online Library
Energy decomposition analysis is one of the most attractive features of fragment molecular
orbital (FMO) calculations from the point of view of practical applications. Here we report …

Systematic study of the embedding potential description in the fragment molecular orbital method

DG Fedorov, LV Slipchenko… - The Journal of Physical …, 2010 - ACS Publications
We analyzed the accuracy of the fragment molecular orbital method using various
representations of the embedding potential and extended its applicability to large basis sets …

Fragment molecular orbital calculations with implicit solvent based on the Poisson–Boltzmann equation: implementation and DNA study

Y Okiyama, T Nakano, C Watanabe… - The Journal of …, 2018 - ACS Publications
In this study, an ab initio fragment molecular orbital (FMO) methodology was developed to
evaluate the solvent effects on electrostatic interactions, which make a significant …