Energy-Based Molecular Fragmentation Methods.

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Chemical Reviews

• Publication date

  2015-04-06

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1021/cr500455bPMID 25843427
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Predicting crystal structures of organic compounds.

  2014cited by this paper
• A graphene flake under external electric fields reconstructed from field-perturbed kernels

  2014cited by this paper
• Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates.

  2014cited by this paper
• Generalized Energy-Based Fragmentation CCSD(T)-F12a Method and Application to the Relative Energies of Water Clusters (H2O)20.

  2014cited by this paper
• The combined fragmentation and systematic molecular fragmentation methods.

  2014cited by this paper
• Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts

  2014cited by this paper
• Trouble with the Many-Body Expansion.

  2014cited by this paper
• Aiming for benchmark accuracy with the many-body expansion.

  2014cited by this paper
• Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges.

  2014cited by this paper
• Dimers of Dimers (DOD): A New Fragment-Based Method Applied to Large Water Clusters.

  2014cited by this paper
• Molecular tailoring approach: a route for ab initio treatment of large clusters.

  2014cited by this paper
• Ab initio molecular crystal structures, spectra, and phase diagrams.

  2014cited by this paper
• An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.

  2013cited by this paper
• Molecular dynamics and QM/MM-based 3D interaction analyses of cyclin-E inhibitors

  2013cited by this paper
• Analysis of the Errors in the Electrostatically Embedded Many-Body Expansion of the Energy and the Correlation Energy for Zn and Cd Coordination Complexes with Five and Six Ligands and Use of the Analysis to Develop a Generally Successful Fragmentation Strategy.

  2013cited by this paper
• The generalized energy-based fragmentation approach with an improved fragmentation scheme: benchmark results and illustrative applications.

  2013cited by this paper
• Appraisal of molecular tailoring approach for large clusters.

  2013cited by this paper
• Linear‐scaling self‐consistent field methods for large molecules

  2013cited by this paper
• Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy.

  2013cited by this paper
• High-level ab initio investigations on structures and energetics of N2O clusters.

  2013cited by this paper
• Many-Body Expansion with Overlapping Fragments: Analysis of Two Approaches.

  2013cited by this paper
• Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model.

  2013cited by this paper
• Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions.

  2013cited by this paper
• Protoribosome by quantum kernel energy method

  2013cited by this paper
• Cluster-in-molecule local correlation method for large systems

  2013cited by this paper
• Direct folding simulation of a long helix in explicit water

  2013cited by this paper
• Molecular electrostatic potentials by systematic molecular fragmentation.

  2013cited by this paper
• Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

  2013cited by this paper
• Growing Fragmented Potentials for Gas–Surface Reactions: The Reaction between Hydrogen Atoms and Hydrogen-Terminated Silicon (111)

  2012cited by this paper
• A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory.

  2012cited by this paper
• Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

  2012cited by this paper
• Rapid topography mapping of scalar fields: large molecular clusters.

  2012cited by this paper
• Protein–water hydrogen bonds are stabilized by electrostatic polarization

  2012cited by this paper
• Systematic fragmentation of large molecules by annihilation.

  2012cited by this paper
• The ONIOM method: its foundation and applications to metalloenzymes and photobiology

  2012cited by this paper
• Effect of interprotein polarization on protein–protein binding energy

  2012cited by this paper
• Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

  2012cited by this paper
• Dynamical stability and assembly cooperativity of β-sheet amyloid oligomers--effect of polarization.

  2012cited by this paper
• Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 3. Conformational Sampling and Explicit Solvents Model.

  2012cited by this paper
• Fragmentation methods: a route to accurate calculations on large systems.

  2012cited by this paper
• Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method.

  2012cited by this paper
• Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules.

  2012cited by this paper
• Folding and thermodynamic studies of Trp-cage based on polarized force field

  2012cited by this paper
• The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters.

  2012cited by this paper
• Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system

  2012cited by this paper
• Facilitating Minima Search for Large Water Clusters at the MP2 Level via Molecular Tailoring.

  2012cited by this paper
• Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation.

  2012cited by this paper
• Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence.

  2012cited by this paper
• Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules.

  2012cited by this paper
• Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix.

  2012cited by this paper
• Acetylene aggregates via cluster-building algorithm and molecular tailoring approach

  2012cited by this paper
• Structures, energetics and vibrational spectra of CO2 clusters through molecular tailoring and cluster building algorithm.

  2012cited by this paper
• An efficient local coupled cluster method for accurate thermochemistry of large systems.

  2011cited by this paper
• The Kernel energy method: Application to graphene and extended aromatics

  2011cited by this paper
• Higher-order correlated calculations based on fragment molecular orbital scheme

  2011cited by this paper
• Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

  2011cited by this paper
• Effect of polarization on the stability of a helix dimer

  2011cited by this paper
• Assessment and Validation of the Electrostatically Embedded Many-Body Expansion for Metal-Ligand Bonding.

  2011cited by this paper
• methods in electronic structure calculations

  2011cited by this paper
• Ab initio lattice dynamics of nonconducting crystals by systematic fragmentation.

  2011cited by this paper
• Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems.

  2011cited by this paper
• Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach.

  2011cited by this paper
• Potential energy surfaces for gas-surface reactions.

  2011cited by this paper
• Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: exact formula and its approximate treatment.

  2011cited by this paper
• “Gold standard” coupled-cluster study of acetylene pentamers and hexamers via molecular tailoring approach

  2011cited by this paper
• Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials.

  2011cited by this paper
• Quantifying the stabilizing energy of the intraprotein hydrogen bond due to local mutation.

  2011cited by this paper
• Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups.

  2011cited by this paper
• Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization.

  2011cited by this paper
• Distributed Multipoles and Energies of Flexible Molecules.

  2011cited by this paper
• Topography of scalar fields: molecular clusters and π-conjugated systems.

  2011cited by this paper
• Structures of neutral and protonated water clusters confined in predesigned hosts: a quantum mechanical/molecular mechanical study.

  2011cited by this paper
• The Kernel Energy Method: Construction of 3 & 4 tuple Kernels from a List of Double Kernel Interactions.

  2010cited by this paper
• Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

  2010cited by this paper
• Ab initio investigation of benzene clusters: molecular tailoring approach.

  2010cited by this paper
• Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules.

  2010cited by this paper
• Predicting Organic Crystal Lattice Energies with Chemical Accuracy

  2010cited by this paper
• Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding.

  2010cited by this paper
• Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift Calculations for Large Molecular Systems

  2010cited by this paper
• Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase.

  2010cited by this paper
• Low-lying structures and stabilities of large water clusters: investigation based on the combination of the AMOEBA potential and generalized energy-based fragmentation approach.

  2010cited by this paper
• An efficient implementation of the generalized energy-based fragmentation approach for general large molecules.

  2010cited by this paper
• Molecular tailoring approach for exploring structures, energetics and properties of clusters

  2010cited by this paper
• Molecular tailoring approach in conjunction with MP2 and Ri‐MP2 codes: A comparison with fragment molecular orbital method

  2010cited by this paper
• Communications: Explicitly correlated second-order Møller-Plesset perturbation method for extended systems.

  2010cited by this paper
• CHARMM: The biomolecular simulation program

  2009cited by this paper
• Ab initio study on (CO2)n clusters via electrostatics- and molecular tailoring-based algorithm

  2009cited by this paper
• Accurately reproducing ab initio electrostatic potentials with multipoles and fragmentation.

  2009cited by this paper
• Kernel energy method applied to vesicular stomatitis virus nucleoprotein

  2009cited by this paper
• Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies.

  2009cited by this paper
• Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach.

  2009cited by this paper
• Electronic polarization is important in stabilizing the native structures of proteins.

  2009cited by this paper
• Partition Density Functional Theory

  2009cited by this paper
• Coupled-cluster and many-body perturbation study of energies, structures, and phonon dispersions of solid hydrogen fluoride†

  2009cited by this paper
• Dual-level hierarchical scheme for linear-scaling divide-and-conquer correlation theory†

  2009cited by this paper
• Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization.

  2009cited by this paper
• QM/MM methods for biomolecular systems.

  2009cited by this paper
• NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization.

  2009cited by this paper
• Accurate treatment of nonbonded interactions within systematic molecular fragmentation

  2009cited by this paper
• Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin.

  2008cited by this paper

• A template-based automatic fragmentation algorithm for complex and large systems in the generalized energy-based fragmentation framework.

  2026cites this paper
• An innovative linear-scaling method: integrating divide-and-conquer with fragment molecular approach via nonorthogonal localized orbitals for large systems

  2026cites this paper
• Enhancing Molecular Property Predictions by Learning from Bond Modelling and Interactions

  2026cites this paper
• Modelling phosphate hydration with a polarizable bond-dipole framework: parameter optimization and benchmark testing.

  2025cites this paper
• Tailoring approach for exploring vibrational features of large molecular systems: A short review

  2025cites this paper
• Component-wise AO basis reduction: norm loss, negative contribution normalization, and functional implications.

  2025cites this paper
• Ultrafast Correlation Energy Estimator

  2025cites this paper
• The continuous evolution of biomolecular force fields.

  2025cites this paper
• Efficient High‐Level Quantum Chemical Exploration of Clathrate Hydrates via Fragmentation

  2025cites this paper
• Machine Learning-Based Excited-State Reactive Force Field: A New Approach for Modeling the Photodissociation Dynamics of 2-Fluorothiophenol.

  2025cites this paper
• A perspective marking 20 years of using permutationally invariant polynomials for molecular potentials.

  2025cites this paper
• Quick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry

  2025cites this paper
• Efficient, Hierarchical, and Object-Oriented Electronic Structure Interfaces for Direct Nonadiabatic Dynamics Simulations

  2025cites this paper
• Assisting calculation of vibrational circular dichroism spectra by molecular tailoring approach.

  2025cites this paper
• Toward Reliable Computation of Vibrational Signatures of Complex Molecular Systems/Trendbericht Physikalische Chemie 2025 (3/3)

  2025cites this paper
• The density-based many-body expansion for poly-peptides and proteins.

  2025cites this paper
• CKDTA: A chemical knowledge-enhanced framework for drug-target affinity prediction

  2025cites this paper
• Bayesian Computation in Deep Learning

  2025cites this paper
• “Gold-Standard” Δ‑Machine Learned Transferable Potential for Linear Alkanes

  2025cites this paper
• Efficient Simulation of Raman Optical Activity Spectra via Molecular Tailoring Approach

  2025cites this paper
• Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

  2025cites this paper
• Theoretical Predictions of Spectral Properties of Multilayer Boron Nitride Introduced by Point Defects

  2025cites this paper
• Electrostatically embedded grid-adapted many-body analysis (EE-GAMA): A charge embedded fragment-based quantum chemistry method for accurate modelling of neutral and charged molecular clusters

  2025cites this paper
• Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates.

  2024cites this paper
• From a simple push–pull dye to a broad-band absorbing and photoconducting material by assembly with CuBr

  2024cites this paper
• Size‐consistency and orbital‐invariance issues revealed by VQE‐UCCSD calculations with the FMO scheme

  2024cites this paper
• Unveiling fructose and glucose binding to human serum albumin: fluorescence measurements and docking, molecular dynamics and quantum biochemistry computations

  2024cites this paper
• Reformulation of All ONIOM-Type Molecular Fragmentation Approaches and Many-Body Theories Using Graph-Theory-Based Projection Operators: Applications to Dynamics, Molecular Potential Surfaces, Machine Learning, and Quantum Computing.

  2024cites this paper
• An efficient and flexible approach for local distortion: distortion distribution analysis enabled by fragmentation

  2024cites this paper
• On Multilevel Energy-Based Fragmentation Methods

  2024cites this paper
• Development of a machine learning finite-range nonlocal density functional.

  2024cites this paper
• AROFRAG─A Systematic Approach for Fragmentation of Aromatic Molecules.

  2024cites this paper
• The Quality of Embedding Charges Is Critical for Convergence of Many-Body Expansions When BSSE Is Absent.

  2024cites this paper
• Delocalization error poisons the density-functional many-body expansion

  2024cites this paper
• Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

  2024cites this paper
• Intermolecular interaction energies with AROFRAG–A systematic approach for fragmentation of aromatic molecules

  2024cites this paper
• SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning

  2024cites this paper
• Automatic molecular fragmentation by evolutionary optimisation

  2024cites this paper
• Cluster-in-Cluster Approach for Computing MP2-Level Vibrational Infrared Spectra of Large Molecular Clusters.

  2024cites this paper
• Photoluminescent Cu(I) Assemblies with High‐Temperature Solid‐State Transitions as a New Class of Thermic History Tracers

  2024cites this paper
• FragPT2: Multifragment Wave Function Embedding with Perturbative Interactions

  2024cites this paper
• Conformational analysis of lipid membrane mimetics modified with Aβ42 peptide by Raman spectroscopy and computer simulations

  2024cites this paper
• Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method.

  2024cites this paper
• Protein–Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions

  2024cites this paper
• Time-Dependent Multilevel Density Functional Theory.

  2024cites this paper
• DFT-Based Permutationally Invariant Polynomial Potentials Capture the Twists and Turns of C14H30

  2024cites this paper
• State-of-the-art local correlation methods enable affordable gold standard quantum chemistry for up to hundreds of atoms

  2024cites this paper
• Excitonic Configuration Interaction: Going Beyond the Frenkel Exciton Model

  2024cites this paper
• Excited-State Polarizabilities: A Combined Density Functional Theory and Information-Theoretic Approach Study

  2023cites this paper
• Porting Fragmentation Methods to Graphical Processing Units Using an OpenMP Application Programming Interface: Offloading the Fock Build for Low Angular Momentum Functions.

  2023cites this paper
• RASCBEC: Raman spectroscopy calculation via born effective charge

  2023cites this paper
• Integrated Multiscale Multilevel Approach to Open Shell Molecular Systems

  2023cites this paper
• Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions.

  2023cites this paper
• Divide-and-Conquer Linear-Scaling Quantum Chemical Computations.

  2023cites this paper
• Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach.

  2023cites this paper
• Constructing Potential Energy Surface With Correlated Theory For Dipeptides Using Molecular Tailoring Approach.

  2023cites this paper
• Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems.

  2023cites this paper
• Accurate and efficient prediction of vibrational circular dichroism spectra of condensed-phase systems with the generalized energy-based fragmentation method

  2023cites this paper
• Many-body expansion for light nuclear systems

  2023cites this paper
• Efficient Machine Learning Force Field for Large-Scale Molecular Simulations of Organic Systems

  2023cites this paper
• Deep learning for complex chemical systems

  2023cites this paper
• Editorial: Fragment-based electronic structure methods for solids

  2023cites this paper
• Capturing Weak Interactions in Surface Adsorbate Systems at Coupled Cluster Accuracy: A Graph-Theoretic Molecular Fragmentation Approach Improved through Machine Learning.

  2023cites this paper
• Linear-Scaling Local Natural Orbital CCSD(T) Approach for Open-Shell Systems: Algorithms, Benchmarks, and Large-Scale Applications

  2023cites this paper
• REAlgo: Rapid and efficient algorithm for estimating MP2/CCSD energy gradients for large molecular clusters.

  2023cites this paper
• Graph-|Q⟩⟨C|: A Quantum Algorithm with Reduced Quantum Circuit Depth for Electronic Structure.

  2023cites this paper
• Cluster-in-Molecule Local Correlation Method for Dispersion Interactions in Large Systems and Periodic Systems.

  2023cites this paper
• Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations

  2023cites this paper
• Many-Body-Expansion Based on Variational Quantum Eigensolver and Deflation for Dynamical Correlation.

  2023cites this paper
• Competition between Solvent···Solvent and Solvent···Solute Interactions in the Microhydration of the Tetrafluoroborate Anion, BF4-(H2O)n=1,2,3,4.

  2023cites this paper
• Accurate and Efficient Prediction of Post-Hartree-Fock Polarizabilities of Condensed-Phase Systems.

  2023cites this paper
• Fragment-based approach for the efficient calculation of the refractive index of metal-organic frameworks.

  2023cites this paper
• Approaching Coupled Cluster Accuracy with Density Functional Theory Using the Generalized Connectivity-Based Hierarchy.

  2023cites this paper
• Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.

  2023cites this paper
• Toward an extreme-scale electronic structure system.

  2023cites this paper
• Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

  2023cites this paper
• A simple and consistent quantum‐chemical fragmentation scheme for proteins that includes two‐body contributions

  2023cites this paper
• Another Torture Track for Quantum Chemistry: Reinvestigation of the Benzaldehyde Amidation by Nitrogen‐Atom Transfer from Platinum(II) and Palladium(II) Metallonitrenes

  2023cites this paper
• Calculating 13C NMR chemical shifts of large molecules using the eXtended ONIOM method at high accuracy with a low cost

  2023cites this paper
• Coupled-Cluster Density-Based Many-Body Expansion

  2023cites this paper
• A Quantum Chemistry Approach of Breast Cancer Drugs Bound to Human Serum Albumin

  2022cites this paper
• Fragmentation and transferability in Hirshfeld atom refinement

  2022cites this paper
• Predicting properties of periodic systems from cluster data: A case study of liquid water.

  2022cites this paper
• Electronic Correlation Contribution to the Intermolecular Interaction Energy from Symmetrized Systematic Molecular Fragmentation Model

  2022cites this paper
• Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy‐based fragmentation method

  2022cites this paper
• The Seamless Connection of Local and Collective Excited States in Subsystem Time-Dependent Density Functional Theory.

  2022cites this paper
• MTASpec software for calculating the vibrational IR and Raman spectra of large molecules at ab initio level

  2022cites this paper
• Decomposition of the interaction energy of several flavonoids with Escherichia coli DNA Gyr using the SAPT (DFT) method: The relation between the interaction energy components, ligand structure, and biological activity.

  2022cites this paper
• Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials.

  2022cites this paper
• An Embedded Fragment Method for Molecules in Strong Magnetic Fields

  2022cites this paper
• Optimal clustering for quantum refinement of biomolecular structures: Q|R#4

  2022cites this paper
• Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods

  2022cites this paper
• Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems

  2022cites this paper
• Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning.

  2022cites this paper
• Graph-Theoretic Molecular Fragmentation for Potential Surfaces Leads Naturally to a Tensor Network Form and Allows Accurate and Efficient Quantum Nuclear Dynamics.

  2022cites this paper
• Linear-Scaling Systematic Molecular Fragmentation Approach for Perturbation Theory and Coupled-Cluster Methods

  2022cites this paper
• Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry.

  2022cites this paper
• General, Rigorous Approach for the Treatment of Interfragment Covalent Bonds.

  2022cites this paper
• Combined fragment-based machine learning force field with classical force field and its application in the NMR calculations of macromolecules in solutions.

  2022cites this paper
• Δ-Machine Learned Potential Energy Surfaces and Force Fields.

  2022cites this paper