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Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

https://doi.org/10.1039/d0cp02119a
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Molecular polarizabilities calculated with a modified dipole interaction
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Electron correlation and solvation effects. I. Basic formulation and preliminary attempt to include the electron correlation in the quantum mechanical polarizable continuum model so as to study solvation phenomena
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Molecular Properties through Polarizable Embedding
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Enhanced sampling techniques in molecular dynamics simulations of biological systems
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QM/MM studies of enzymes
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Nonadiabatic molecular dynamics with solvent effects: A LR-TDDFT QM/MM study of ruthenium (II) tris (bipyridine) in water
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The Multiple Roles of the Protein in the Photoactivation of Orange Carotenoid Protein
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The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems
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QM/MM methods for free energies and photochemistry
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New developments in force fields for biomolecular simulations
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An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
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An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
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Quantum Chemical Studies of Light Harvesting
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Ab Initio Nonadiabatic Quantum Molecular Dynamics
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Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics
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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
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Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems
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Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
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General Linear Scaling Implementation of Polarizable Embedding Schemes
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CPPE: An Open-Source C++ and Python Library for Polarizable Embedding
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Ab Initio Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable Graphical-Processing-Unit-Accelerated Exciton Framework
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Fragmentation Methods: A Route to Accurate Calculations on Large Systems
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Vertical Electronic Excitations in Solution with the EOM-CCSD Method Combined with a Polarizable Explicit/Implicit Solvent Model
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Polarizable Force Fields: History, Test Cases, and Prospects
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Ultrafast Deactivation of an Excited Cytosine−Guanine Base Pair in DNA
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Photosynthetic Light-Harvesting Is Tuned by the Heterogeneous Polarizable Environment of the Protein
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Conical Intersections in Solution: A QM/MM Study Using Floating Occupation Semiempirical Configuration Interaction Wave Functions
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Infrared Spectrum of p-Benzoquinone in Water Obtained from a QM/MM Hybrid Molecular Dynamics Simulation
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Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
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Ab Initio Molecular Dynamics Computation of the Infrared Spectrum of Aqueous Uracil
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How Solvent Controls Electronic Energy Transfer and Light Harvesting
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Solvent-Induced Frequency Shifts: Configuration Interaction Singles Combined with the Effective Fragment Potential Method
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Nonadiabatic Excited-State Dynamics with Hybrid ab Initio Quantum-Mechanical/Molecular-Mechanical Methods: Solvation of the Pentadieniminium Cation in Apolar Media
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Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies
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Current Status of the AMOEBA Polarizable Force Field
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Molecular and Atomic Polarizabilities: Thole's Model Revisited
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Ab Initio Multiple Spawning: Photochemistry from First Principles Quantum Molecular Dynamics
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Modeling Solvent Effects on Electronic Excited States
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Conical intersection dynamics of the primary photoisomerization event in vision
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Mixed quantum–classical dynamics
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Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase
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Conical intersection dynamics in solution: The chromophore of Green Fluorescent Protein
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Non covalent interactions in RNA and DNA base pairs: a quantum-mechanical study of the coupling between solvent and electronic density
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Adenine deactivation in DNA resolved at the CASPT2//CASSCF/AMBER level
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Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin
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Computing vibrational spectra from ab initio molecular dynamics
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Modeling environment effects on spectroscopies through QM/classical models
inferredcites →https://doi.org/10.1039/c6cp03834dopenalex-snapshot
Excited states in large molecular systems through polarizable embedding
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Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model
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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
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Performance of TDDFT with and without spin-flip in trajectory surface hopping dynamics: cis – trans azobenzene photoisomerization
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The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach
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The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation
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Excitation energy transfer in condensed media
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Quantum corrections to classical time-correlation functions: Hydrogen bonding and anharmonic floppy modes
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Fast evaluation of polarizable forces
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Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution
inferred← citeshttps://doi.org/10.1021/acsphyschemau.3c00080openalex-snapshot
A Vision for the Future of Multiscale Modeling
inferred← citeshttps://doi.org/10.1021/jacs.3c12700openalex-snapshot
Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine
inferred← citeshttps://doi.org/10.1021/jacs.5c17299openalex-snapshot
Exciton Delocalization Promotes Far-Red Absorption in a Tetrameric Chlorophyll a Light-Harvesting Complex from Trachydiscus minutus
inferred← citeshttps://doi.org/10.1021/jacs.6c07143openalex-snapshot
Molecular Mechanism of the Catalytic Radical Termination in Fatty Acid Photodecarboxylase
inferred← citeshttps://doi.org/10.1021/jacsau.4c00853openalex-snapshot
Protein-Driven Electron-Transfer Process in a Fatty Acid Photodecarboxylase
inferred← citeshttps://doi.org/10.1021/jacsau.6c00568openalex-snapshot
Energy Transfer Pathways in Plant Photosystem I from First-Principles Modeling
inferred← citeshttps://doi.org/10.1038/s41467-022-30308-5openalex-snapshot
Exciton transport in molecular organic semiconductors boosted by transient quantum delocalization
inferred← citeshttps://doi.org/10.1039/9781839169342-00024openalex-snapshot
Quantum-derived embedding schemes for local excitations
inferred← citeshttps://doi.org/10.1039/d0cp04027dopenalex-snapshot
Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems
inferred← citeshttps://doi.org/10.1039/d0cp05907bopenalex-snapshot
Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives
inferred← citeshttps://doi.org/10.1039/d0cp06070dopenalex-snapshot
Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome
inferred← citeshttps://doi.org/10.1039/d1sc00071copenalex-snapshot
Uncovering the interactions driving carotenoid binding in light-harvesting complexes
inferred← citeshttps://doi.org/10.1039/d1sc00186hopenalex-snapshot
The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation
inferred← citeshttps://doi.org/10.1039/d1sc03000kopenalex-snapshot
From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain
inferred← citeshttps://doi.org/10.1039/d2cc07079kopenalex-snapshot
Continuum vs. atomistic approaches to computational spectroscopy of solvated systems
inferred← citeshttps://doi.org/10.1039/d2cp00227bopenalex-snapshot
Probing aqueous ions with non-local Auger relaxation
inferred← citeshttps://doi.org/10.1039/d2cp04512eopenalex-snapshot
Linear response properties of solvated systems: a computational study
inferred← citeshttps://doi.org/10.1039/d2cp04937fopenalex-snapshot
A method to capture the large relativistic and solvent effects on the UV-vis spectra of photo-activated metal complexes
inferred← citeshttps://doi.org/10.1039/d2dd00102kopenalex-snapshot
Neural network potentials for chemistry: concepts, applications and prospects
inferred← citeshttps://doi.org/10.1039/d2dt02233hopenalex-snapshot
New relativistic quantum chemical methods for understanding light-induced therapeutics
inferred← citeshttps://doi.org/10.1039/d3cp00247kopenalex-snapshot
Surface hopping modeling of charge and energy transfer in active environments
inferred← citeshttps://doi.org/10.1039/d3cp03092jopenalex-snapshot
Intermolecular resonance energy transfer between two lutein pigments in light-harvesting complex II studied by frenkel exciton models
inferred← citeshttps://doi.org/10.1039/d3cp05278hopenalex-snapshot
Energy transfer from two luteins to chlorophylls in light-harvesting complex II study by using exciton models with phase correction
inferred← citeshttps://doi.org/10.1039/d3sc02202aopenalex-snapshot
Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints
inferred← citeshttps://doi.org/10.1039/d3sc02662kopenalex-snapshot
How orange carotenoid protein controls the excited state dynamics of canthaxanthin
inferred← citeshttps://doi.org/10.1039/d5cp03816bopenalex-snapshot
Bridging scales and paradigms: a perspective from atomistic simulation to AI-enhanced modeling of sodium-ion capacitors
inferred← citeshttps://doi.org/10.1039/d5sc04961jopenalex-snapshot
Structural and spectroscopic basis of excitation energy transfer in microbial rhodopsins binding xanthophylls
inferred← citeshttps://doi.org/10.1039/d6sc02180hopenalex-snapshot
Methods for the establishment of enzymatic mechanisms – from QM to ML
inferred← citeshttps://doi.org/10.1063/5.0035165openalex-snapshot
General formulation of polarizable embedding models and of their coupling
inferred← citeshttps://doi.org/10.1063/5.0038196openalex-snapshot
Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy
inferred← citeshttps://doi.org/10.1063/5.0046844openalex-snapshot
An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone
inferred← citeshttps://doi.org/10.1063/5.0064075openalex-snapshot
Hybrid QM/classical models: Methodological advances and new applications
inferred← citeshttps://doi.org/10.1063/5.0079788openalex-snapshot
QM/MM optimization with quantum coupling: Host–guest interactions in a pentacene-doped p-terphenyl crystal
inferred← citeshttps://doi.org/10.1063/5.0083340openalex-snapshot
The ΔSCF method for non-adiabatic dynamics of systems in the liquid phase
inferred← citeshttps://doi.org/10.1063/5.0085855openalex-snapshot
State-averaged CASSCF with polarizable continuum model for studying photoreactions in solvents: Energies, analytical nuclear gradients, and non-adiabatic couplings
inferred← citeshttps://doi.org/10.1063/5.0086275openalex-snapshot
The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol
inferred← citeshttps://doi.org/10.1063/5.0088271openalex-snapshot
Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges
inferred← citeshttps://doi.org/10.1063/5.0118664openalex-snapshot
Assessing the quality of QM/MM approaches to describe vacuo-to-water solvatochromic shifts
inferred← citeshttps://doi.org/10.1063/5.0123698openalex-snapshot
Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1063/5.0131689openalex-snapshot
State averaged CASSCF in AMOEBA polarizable water model for simulating nonadiabatic molecular dynamics with nonequilibrium solvation effects
inferred← citeshttps://doi.org/10.1063/5.0155992openalex-snapshot
PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations
inferred← citeshttps://doi.org/10.1063/5.0159247openalex-snapshot
Machine learning accelerated photodynamics simulations
inferred← citeshttps://doi.org/10.1063/5.0170295openalex-snapshot
First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex
inferred← citeshttps://doi.org/10.1063/5.0182745openalex-snapshot
Taming the third order cumulant approximation to linear optical spectroscopy
inferred← citeshttps://doi.org/10.1063/5.0198251openalex-snapshot
The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics
inferred← citeshttps://doi.org/10.1063/5.0200722openalex-snapshot
Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP
inferred← citeshttps://doi.org/10.1063/5.0203637openalex-snapshot
Static versus dynamically polarizable environments within the many-body GW formalism
inferred← citeshttps://doi.org/10.1063/5.0211053openalex-snapshot
MiMiC: A high-performance framework for multiscale molecular dynamics simulations
inferred← citeshttps://doi.org/10.1063/5.0215036openalex-snapshot
The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications
inferred← citeshttps://doi.org/10.1063/5.0221974openalex-snapshot
Electrostatically embedded symmetry-adapted perturbation theory
inferred← citeshttps://doi.org/10.1063/5.0241573openalex-snapshot
Decoherence and vibrational energy relaxation of the electronically excited PtPOP complex in solution
inferred← citeshttps://doi.org/10.1063/5.0310192openalex-snapshot
Vertical excitation energies of embedded systems: The vertical excitation model (VEM) within polarizable QM/MM
inferred← citeshttps://doi.org/10.1063/5.0331913openalex-snapshot
Polarizable embeddings and quantum chemistry: Concepts, progress, and open challenges
inferred← citeshttps://doi.org/10.1080/00268976.2022.2089605openalex-snapshot
A ΔSCF model for excited states within a polarisable embedding
inferred← citeshttps://doi.org/10.1080/17460441.2022.2114451openalex-snapshot
Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern
inferred← citeshttps://doi.org/10.1080/23746149.2026.2660655openalex-snapshot
Multiscale modeling approaches in biomolecular physics
inferred← citeshttps://doi.org/10.1088/1361-648x/ac6f3copenalex-snapshot
A fast method for electronic couplings in embedded multichromophoric systems
inferred← citeshttps://doi.org/10.1088/2516-1075/ac8c73openalex-snapshot
Insights into the stability of engineered mini-proteins from their dynamic electronic properties
inferred← citeshttps://doi.org/10.1088/2632-2153/ae47b9openalex-snapshot
Design, assessment, and application of machine learning potential energy surfaces
inferred← citeshttps://doi.org/10.1103/nxs1-rhqxopenalex-snapshot
Quantum dynamics of dissipative polarizable media
inferred← citeshttps://doi.org/10.1111/nph.70562openalex-snapshot
Structural determinants for red‐shifted absorption in higher‐plants Photosystem I
inferred← citeshttps://doi.org/10.1111/php.13922openalex-snapshot
Reconciling TD‐DFT and CASPT2 electronic structure methods for describing the photophysics of DNA
inferred← citeshttps://doi.org/10.1139/cjc-2022-0243openalex-snapshot
Massively parallel fragment-based quantum chemistry for large molecular systems: the serestipy software
inferred← citeshttps://doi.org/10.1146/annurev-biophys-111622-091140openalex-snapshot
Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines
inferred← citeshttps://doi.org/10.1146/annurev-physchem-090419-051350openalex-snapshot
Vibronic and Environmental Effects in Simulations of Optical Spectroscopy
inferred← citeshttps://doi.org/10.1146/annurev-physchem-090419-104031openalex-snapshot
Multiscale Models for Light-Driven Processes
inferred← citeshttps://doi.org/10.1360/tb-2020-1321openalex-snapshot
QM/MM study of the enzymatic catalysis
inferred← citeshttps://doi.org/10.1515/pac-2025-0500openalex-snapshot
The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes
inferred← citeshttps://doi.org/10.1515/pac-2025-0517openalex-snapshot
A quantum chemical perspective of photoactivated biological functions
inferred← citeshttps://doi.org/10.2142/biophysico.bppb-v20.s007openalex-snapshot
Induction effects on the absorption maxima of photoreceptor proteins
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-hrbpxopenalex-snapshot
Quantum chemical simulation of transient absorption spectroscopy in the CP29 light-harvesting complex
inferred← citeshttps://doi.org/10.26434/chemrxiv.13368692openalex-snapshot
Quantifying the Long-Range Coupling of Electronic Properties in Proteins with Ab Initio Molecular Dynamics
inferred← citeshttps://doi.org/10.26434/chemrxiv.13368692.v1openalex-snapshot
Quantifying the Long-Range Coupling of Electronic Properties in Proteins with Ab Initio Molecular Dynamics
inferred← citeshttps://doi.org/10.3390/ijms22179272openalex-snapshot
Towards Quantum-Chemical Modeling of the Activity of Anesthetic Compounds
inferred← citeshttps://doi.org/10.3390/molecules29184378openalex-snapshot
Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies
inferred← citeshttps://doi.org/10.3390/molecules30244675openalex-snapshot
The UV-Visible Absorption Spectra of Coumarin and Nile Red in Aqueous Solution: A Polarizable QM/MM Study
inferred← citeshttps://doi.org/10.48550/arxiv.2010.14723openalex-snapshot
Development and Application of QM/MM Methods with Advanced Polarizable Potentials
inferred← citeshttps://doi.org/10.70322/sbe.2025.10017openalex-snapshot
Enzyme-Mediated Carbon Dioxide Fixation: Catalytic Mechanisms and Computational Insights
inferred← citeshttps://doi.org/10.70675/4585a058z6335z4b9az92a8zca19f33f93a3openalex-snapshot
Modeling the dynamics and properties of key DNA lesions intermediates in realistic environments
inferred← citeshttps://doi.org/10.70675/a216143czaf99z456az891az42809552f7e8openalex-snapshot
Analytic second derivatives of QM/MM energy : theoretical study of vibrations in cryptochrome
inferred← citeshttps://doi.org/10.70675/b88702d8ze6b2z480cza673zea22e509f810openalex-snapshot
Computational modeling of photoactive materials and heterointerfaces for solar energy conversion
inferred← citeshttps://doi.org/10.70675/fadeed66z0253z4df9za915zdee544d0a6aaopenalex-snapshot
Development of efficient multiscale methods and extrapolation techniques for multiphysics molecular chemistry
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