Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26940
Abstract: Fragment molecular orbital (FMO) method is a powerful computational tool for structure‐based drug design, in which protein–ligand interactions can be described by the inter‐fragment interaction energy (IFIE) and its pair interaction energy decomposition analysis (PIEDA).… read more here.
Keywords: interaction energy; fragment molecular; energy; protein ligand ... See more keywords
A quantum chemical study of the interactions of uracil as a constituent of ribonucleic acid (RNA) with thiazolidinedione and rhodanine bioactive molecules: an insight into energetic and structural features
Sign Up to like & getrecommendations! Published in 2017 at "Structural Chemistry"
DOI: 10.1007/s11224-017-1062-4
Abstract: In this study, the biologically active configurations composed of Thiazolidinedione–Uracil (TU) and Rhodanine–Uracil (RU) have been fully investigated from the energetic and structural points of view, employing B3LYP and M062X functionals in combination with the… read more here.
Keywords: energetic structural; energy; study; interaction energy ... See more keywords
Molecular dynamics simulation of cross-linked epoxy resin and its interaction energy with graphene under two typical force fields
Sign Up to like & getrecommendations! Published in 2018 at "Computational Materials Science"
DOI: 10.1016/j.commatsci.2017.11.007
Abstract: Abstract A model of cross-linked epoxy system composed of bisphenol-A resin, 2,3,6-tetrahydro-3-methylphthalic anhydride curing agent, and 2,4,6-tris(dimethylaminomethyl)phenol accelerator was established and molecular dynamics simulations were performed to calculate the properties of the epoxy and its… read more here.
Keywords: resin; graphene; interaction energy; cross ... See more keywords
Particle–bubble interaction energies for particles with physical and chemical heterogeneities
Sign Up to like & getrecommendations! Published in 2020 at "Minerals Engineering"
DOI: 10.1016/j.mineng.2020.106472
Abstract: Abstract The interaction between a particle and bubble in a liquid medium is important in processes such as mineral flotation or paper deinking. The sum of van der Waals, electrostatic, and hydrophobic interaction energies can… read more here.
Keywords: particle bubble; bubble interaction; interaction energy; particle ... See more keywords
Interaction energy of pyrrole and pyridine with 1-ethyl-3-methylimidazolium ethyl sulphate
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Molecular Liquids"
DOI: 10.1016/j.molliq.2017.01.082
Abstract: Abstract In this work, the fundamental nature of the interaction between pyrrole and pyridine with 1-ethyl-3-methylimidazolium ethylsulphate ([EMIM][EtSO 4 ]) was investigated using DFT theory and was confirmed with the sigma profile analysis via Co… read more here.
Keywords: ethyl; pyridine; interaction energy; pyrrole pyridine ... See more keywords
Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.2c01184
Abstract: Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM… read more here.
Keywords: interaction; effect; energy; region ... See more keywords
How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.8b00892
Abstract: The Argonaute-2 protein is part of the RNA-induced silencing complex (RISC) and anchors the guide strand of the small interfering RNA (siRNA). The 3'-end of the RNA contains two unpaired nucleotides (3'-overhang) that interact with… read more here.
Keywords: molecular interaction; energy profiling; paz; guide strand ... See more keywords
Method to Compute the Interaction Energy of a Molecule in Ground and Excited States with a Discrete Environment: The Case of Uracil in Water
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.4c01375
Abstract: In this work, we present a method that is able to compute the interaction energy of a system of interest, in the ground or excited state, with an arbitrary number of water molecules representing the… read more here.
Keywords: environment; energy; ground excited; water ... See more keywords
Interaction energy flow paths analysis of PMSG-based wind power integrated systems during LVRT and its parameter adjustment strategy
Sign Up to like & getrecommendations! Published in 2024 at "Scientific Reports"
DOI: 10.1038/s41598-024-62507-z
Abstract: To solve the problem of oscillation instability in permanent magnetic synchronous generator (PMSG)-based wind power connected systems during low-voltage ride through (LVRT) process, a parameter adjustment strategy based on interaction energy path optimization is proposed… read more here.
Keywords: interaction energy; adjustment strategy; energy;
Understanding the ML black box with simple descriptors to predict cluster–adsorbate interaction energy
Sign Up to like & getrecommendations! Published in 2020 at "New Journal of Chemistry"
DOI: 10.1039/d0nj00633e
Abstract: Density functional theory (DFT) is currently one of the most accurate and yet practical theories used to gain insight into the properties of materials. Although successful, the computational cost required is still the main hurdle… read more here.
Keywords: interaction energy; cluster adsorbate; descriptors predict; interaction ... See more keywords
Theory and simulations of light-induced self-assembly in colloids with quantum chemistry derived empirical potentials.
Sign Up to like & getrecommendations! Published in 2024 at "Soft matter"
DOI: 10.1039/d4sm00459k
Abstract: Light-induced self-assembly (LISA) is a non-invasive method for tuning material properties. Photoresponsive ligands coated on the surfaces of nanoparticles are often used to achieve LISA. We report simulation studies for a photoresponsive ligand, azobenzene dithiol… read more here.
Keywords: chemistry; energy; interaction energy; ligand ... See more keywords