ArticleJournal of chemical theory and computation2012
Electronic Absorption Spectra from MM and
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- The UV-Visible Absorption Spectra of Coumarin and Nile Red in Aqueous Solution: A Polarizable QM/MM Study.Molecules (Basel, Switzerland) · 2025Article
- Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach.The journal of physical chemistry. B · 2025Article
- In silico study of active delivery of a photodynamic therapy drug targeting the folate receptor.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2025Article
- Direct All-Atom Nonadiabatic Semiclassical Simulations for Electronic Absorption Spectroscopy of Organic Photovoltaic Non-Fullerene Acceptor in Solution.The journal of physical chemistry letters · 2025Article
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM.Journal of chemical theory and computation · 2025Article
- Effect of Leaving Centrosymmetric Character on Spectral Properties in Mono-, Bi-, and Triphotonic Absorption Spectroscopies.ACS omega · 2024Article
- Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies.Molecules (Basel, Switzerland) · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- The Role of Aqueous Solvation on the Intersystem Crossing of Nitrophenols.Journal of chemical theory and computation · 2024Article
- Embedding Nonrigid Solutes in an Averaged Environment: A Case Study on Rhodopsins.Journal of chemical theory and computation · 2023Article
- Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening.Journal of chemical theory and computation · 2023Article
- An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning.Molecules (Basel, Switzerland) · 2023Article
- Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis.Journal of chemical information and modeling · 2023Article
- Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution.ACS physical chemistry Au · 2023Review
- Spectroscopic and QM/MM studies of the Cu(I) binding site of the plant ethylene receptor ETR1.Biophysical journal · 2022Article
- Excited-State Barrier ControlsThe journal of physical chemistry letters · 2022Article
- Transition-Based Constrained DFT for the Robust and Reliable Treatment of Excitations in Supramolecular Systems.Journal of chemical theory and computation · 2022Article
- Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.Journal of chemical theory and computation · 2022Article
- Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent.Journal of chemical theory and computation · 2022Article
- Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs.Frontiers in chemistry · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.