Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

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

(2018) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The many-body expansion combined with neural networks

(2017) Kun Yao et al.   JOURNAL OF CHEMICAL PHYSICS

Group molecular orbital approach to solve the Huzinaga subsystem self-consistent-field equations

(2017) Tomomi Shimazaki et al.   JOURNAL OF CHEMICAL PHYSICS

Many-body expansion of the Fock matrix in the fragment molecular orbital method

(2017) Dmitri G. Fedorov et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Calculation of Electronic Structure Using O(N) Density Functional Theory

(2017) Ayako Nakata et al.   Journal of Chemical Theory and Computation

Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding

(2017) Yoshio Nishimoto et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method

(2017) Inaki Morao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fragment Molecular Orbital Based Parametrization Procedure for Mesoscopic Structure Prediction of Polymeric Materials

(2017) Koji Okuwaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale Simulations on Charge Transport in Covalent Organic Frameworks Including Dynamics of Transfer Integrals from the FMO-DFTB/LCMO Approach

(2017) Hirotaka Kitoh-Nishioka et al.   Journal of Physical Chemistry C

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

(2017) Dmitri G. Fedorov   Wiley Interdisciplinary Reviews-Computational Molecular Science

Generalized energy-based fragmentation approach for modeling condensed phase systems

(2017) Tao Fang et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Quantum Embedding Theories

(2016) Qiming Sun et al.   ACCOUNTS OF CHEMICAL RESEARCH

Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method

(2016) Hiroya Nakata et al.   JOURNAL OF CHEMICAL PHYSICS

Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

(2016) Nityananda Sahu et al.   JOURNAL OF CHEMICAL PHYSICS

Calculation of the static and dynamical correlation energy of pseudo-one-dimensional beryllium systems via a many-body expansion

(2016) D. Koch et al.   JOURNAL OF CHEMICAL PHYSICS

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations

(2016) Christian F. A. Negre et al.   Journal of Chemical Theory and Computation

Analytic Gradients for the Effective Fragment Molecular Orbital Method

(2016) Colleen Bertoni et al.   Journal of Chemical Theory and Computation

Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method

(2016) Spencer R. Pruitt et al.   Journal of Chemical Theory and Computation

Pair–Pair Approximation to the Generalized Many-Body Expansion: An Alternative to the Four-Body Expansion for ab Initio Prediction of Protein Energetics via Molecular Fragmentation

(2016) Jie Liu et al.   Journal of Chemical Theory and Computation

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation

(2016) Hiroaki Nishizawa et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems

(2016) Ben Nebgen et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Extension of the Effective Fragment Potential Method to Macromolecules

(2016) Pradeep Kumar Gurunathan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

(2016) Juan R. Perilla et al.   Journal of Physical Chemistry Letters

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

(2016) Yoshio Nishimoto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins

(2016) Jinfeng Liu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Third-order density-functional tight-binding combined with the fragment molecular orbital method

(2015) Yoshio Nishimoto et al.   CHEMICAL PHYSICS LETTERS

Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field

(2015) Alexey V. Akimov et al.   CHEMICAL REVIEWS

Time-dependent density-functional tight-binding method with the third-order expansion of electron density

(2015)   JOURNAL OF CHEMICAL PHYSICS

Evaluation of Energy Gradients and Infrared Vibrational Spectra through Molecules-in-Molecules Fragment-Based Approach

(2015) K. V. Jovan Jose et al.   Journal of Chemical Theory and Computation

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method

(2015) Yoshio Nishimoto et al.   Journal of Physical Chemistry Letters

Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems

(2015) Juan Torras   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Use of Many-Body Expansions and Geometry Optimizations in Fragment-Based Methods

(2014) Dmitri G. Fedorov et al.   ACCOUNTS OF CHEMICAL RESEARCH

Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method

(2014) Yoshio Nishimoto et al.   Journal of Chemical Theory and Computation

Water 26-mers Drawn from Bulk Simulations: Benchmark Binding Energies for Unprecedentedly Large Water Clusters and Assessment of the Electrostatically Embedded Three-Body and Pairwise Additive Approximations

(2014) Joachim Friedrich et al.   Journal of Physical Chemistry Letters

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

(2014) Shigenori Tanaka et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Hiroya Nakata et al.   THEORETICAL CHEMISTRY ACCOUNTS

Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations

(2013) Yoshio Okiyama et al.   CHEMICAL PHYSICS LETTERS

GAMESS As a Free Quantum-Mechanical Platform for Drug Research

(2013) Yuri Alexeev et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Determination of a Density Functional Tight Binding Model with an Extended Basis Set and Three-Body Repulsion for Carbon Under Extreme Pressures and Temperatures

(2013) Nir Goldman et al.   Journal of Physical Chemistry C

Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

(2013) Luke Roskop et al.   MOLECULAR PHYSICS

Density functional tight binding: application to organic and biological molecules

(2013) Michael Gaus et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Subsystem density-functional theory

(2013) Christoph R. Jacob et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Edge-stress-induced spontaneous twisting of graphene nanoribbons

(2012) Ashwin Ramasubramaniam et al.   JOURNAL OF APPLIED PHYSICS

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation

(2012) György G. Ferenczy   JOURNAL OF COMPUTATIONAL CHEMISTRY

Intrinsic Edge Asymmetry in Narrow Zigzag Hexagonal Heteroatomic Nanoribbons Causes their Subtle Uniform Curvature

(2012) Pavel V. Avramov et al.   Journal of Physical Chemistry Letters

An elongation method for large systems toward bio-systems

(2012) Yuriko Aoki et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Exploring chemistry with the fragment molecular orbital method

(2012) Dmitri G. Fedorov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

(2012) Casper Steinmann et al.   PLoS One

Density-functional tight binding-an approximate density-functional theory method

(2012) Gotthard Seifert et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

(2011) Takeshi Nagata et al.   JOURNAL OF CHEMICAL PHYSICS

Fully analytic energy gradient in the fragment molecular orbital method

(2011) Kurt Brorsen et al.   JOURNAL OF CHEMICAL PHYSICS

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Efficient and Accurate Methods for the Geometry Optimization of Water Clusters: Application of Analytic Gradients for the Two-Body:Many-Body QM:QM Fragmentation Method to (H2O)n,n= 3–10

(2011) Desiree M. Bates et al.   Journal of Chemical Theory and Computation

Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics

(2011) Ivan S. Ufimtsev et al.   Journal of Physical Chemistry Letters

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

(2011) Michael P Mazanetz et al.   Journal of Cheminformatics

Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method

(2010) Takeshi Nagata et al.   CHEMICAL PHYSICS LETTERS

Ligand Affinities Estimated by Quantum Chemical Calculations

(2010) Pär Söderhjelm et al.   Journal of Chemical Theory and Computation

Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method†

(2010) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Role of the Key Mutation in the Selective Binding of Avian and Human Influenza Hemagglutinin to Sialosides Revealed by Quantum-Mechanical Calculations

(2010) Toshihiko Sawada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

“White Graphenes”: Boron Nitride Nanoribbons via Boron Nitride Nanotube Unwrapping

(2010) Haibo Zeng et al.   NANO LETTERS

Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method

(2009) Dmitri G. Fedorov et al.   CHEMICAL PHYSICS LETTERS

Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method

(2009) Takeshi Nagata et al.   CHEMICAL PHYSICS LETTERS

Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)

(2009) Yuto Komeiji et al.   CHEMICAL PHYSICS LETTERS

Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules

(2009) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Density-functional based tight-binding: an approximate DFT method

(2009) Augusto F. Oliveira et al.   JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY

Calculation of strong and weak interactions in TDA1 and RangDP52 by the kernel energy method

(2009) L. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of the PM6 method to modeling proteins

(2008) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Atypical Quantum Confinement Effect in Silicon Nanowires

(2008) Pavel B. Sorokin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment Molecular Orbital Method

(2008) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Theoretical Analysis of the Intermolecular Interaction Effects on the Excitation Energy of Organic Pigments: Solid State Quinacridone

(2008) Hiroo Fukunaga et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Efficient Calculation of Charge-Transfer Matrix Elements for Hole Transfer in DNA

(2008) Tomáš Kubař et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density functional study of⟨110⟩-oriented thin silicon nanowires

(2008) Pavel B. Sorokin et al.   PHYSICAL REVIEW B