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

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

Divide-and-Conquer-Type Density-Functional Tight-Binding Molecular Dynamics Simulations of Proton Diffusion in a Bulk Water System

(2016) Hiromi Nakai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Coherent quantum transport in disordered systems: A unified polaron treatment of hopping and band-like transport

(2015) Chee Kong Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

(2015) Hiroya Nakata 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

Efficient vibrational analysis for unrestricted Hartree–Fock based on the fragment molecular orbital method

(2014) Hiroya Nakata et al.   CHEMICAL PHYSICS LETTERS

Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges

(2014) Michael A. Collins   JOURNAL OF CHEMICAL PHYSICS

Critical interpretation of CH– and OH– stretching regions for infrared spectra of methanol clusters (CH3OH)n (n = 2–5) using self-consistent-charge density functional tight-binding molecular dynamics simulations

(2014) Yoshifumi Nishimura et al.   JOURNAL OF CHEMICAL PHYSICS

Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein

(2014) Steffen Wolf et al.   JOURNAL OF CHEMICAL PHYSICS

Simulations of Raman Spectra Using the Fragment Molecular Orbital Method

(2014) Hiroya Nakata et al.   Journal of Chemical Theory and Computation

Hybrid MPI-OpenMP Parallelism in the ONETEP Linear-Scaling Electronic Structure Code: Application to the Delamination of Cellulose Nanofibrils

(2014) Karl A. Wilkinson et al.   Journal of Chemical Theory and Computation

Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST

(2014) Ayako Nakata et al.   Journal of Chemical Theory and Computation

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

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

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

(2014) Kurt R. Brorsen 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

Accurate First Principles Model Potentials for Intermolecular Interactions

(2013) Mark S. Gordon et al.   Annual Review of Physical Chemistry

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

(2013) Yoshio Okiyama et al.   CHEMICAL PHYSICS LETTERS

An effective energy gradient expression for divide-and-conquer second-order Møller–Plesset perturbation theory

(2013) Masato Kobayashi et al.   JOURNAL OF CHEMICAL PHYSICS

N-body:Many-body QM:QM vibrational frequencies: Application to small hydrogen-bonded clusters

(2013) J. Coleman Howard et al.   JOURNAL OF CHEMICAL PHYSICS

Analytic second derivatives of the energy in the fragment molecular orbital method

(2013) Hiroya Nakata et al.   JOURNAL OF CHEMICAL PHYSICS

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

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory

(2013) Karin Kiewisch et al.   Journal of Chemical Theory and Computation

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

(2013) Luke Roskop et al.   MOLECULAR PHYSICS

Parametrization and Benchmark of DFTB3 for Organic Molecules

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

Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence

(2012) Andrea Frank et al.   Journal of Chemical Theory and Computation

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

Exploring chemistry with the fragment molecular orbital method

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

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

(2012) Casper Steinmann et al.   PLoS One

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

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

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

Structure and Dynamics of the 1-Hydroxyethyl-4-amino-1,2,4-triazolium Nitrate High-Energy Ionic Liquid System

(2011) Philip J. Carlson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dramatic Reduction of IR Vibrational Cross Sections of Molecules Encapsulated in Carbon Nanotubes

(2011) Dmitry V. Kazachkin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Convergence in the Evolution of Nanodiamond Raman Spectra with Particle Size: A Theoretical Investigation

(2010) Wunfan Li et al.   ACS Nano

Divide and Conquer Hartree−Fock Calculations on Proteins

(2010) Xiao He et al.   Journal of Chemical Theory and Computation

Ligand Affinities Estimated by Quantum Chemical Calculations

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

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

QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

(2010) YAN TONG et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

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

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

Density-functional tight-binding for beginners

(2009) Pekka Koskinen et al.   COMPUTATIONAL MATERIALS SCIENCE

Comparison of geometric, electronic, and vibrational properties for all pentagon/hexagon-bearing isomers of fullerenes C38, C40, and C42

(2009) Edyta Małolepsza et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Enabling ab initio Hessian and frequency calculations of large molecules

(2008) Anuja P. Rahalkar et al.   JOURNAL OF CHEMICAL PHYSICS

Application of the PM6 method to modeling proteins

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

Geometry Optimizations and Vibrational Spectra of Large Molecules from a Generalized Energy-Based Fragmentation Approach

(2008) Weijie Hua et al.   JOURNAL OF PHYSICAL CHEMISTRY A