We present a microiterative adiabatic scheme for quantum mechanical/molecular mechanical (QM/MM) energy minimization that fully optimizes the MM part in each QM macroiteration. This scheme is applicable not only to mechanical embedding but also to electrostatic and polarized embedding. The electrostatic QM/MM interactions in the microiterations are calculated from electrostatic potential charges fitted on the fly to the QM density. Corrections to the energy and gradient expressions ensure that macro- and microiterations are performed on the same energy surface. This results in excellent convergence properties and no loss of accuracy compared to standard optimization. We test our implementation on water clusters and on two enzymes using electrostatic embedding, as well as on a surface example using polarized embedding with a shell model. Our scheme is especially well-suited for systems containing large MM regions, since the computational effort for the optimization is almost independent of the MM system size. The microiterations reduce the number of required QM calculations typically by a factor of 2-10, depending on the system.
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http://dx.doi.org/10.1021/ct600346p | DOI Listing |
J Chem Phys
December 2024
Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
Graph neural network interatomic potentials (GNN-IPs) are gaining significant attention due to their capability of learning from large datasets. Specifically, universal interatomic potentials based on GNN, usually trained with crystalline geometries, often exhibit remarkable extrapolative behavior toward untrained domains, such as surfaces and amorphous configurations. However, the origin of this extrapolation capability is not well understood.
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December 2024
Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
Heparin is a widely used blood anticoagulant and its monitoring in blood is essential during surgery. Unavoidable interference factors such as blood color and luminescence can interfere with the fluorescence visualization of heparin. Herein, we found a ratiometric fluorescence probe consisting of SYBR green and cresyl violet responsive to heparin mainly based on electrostatic interactions.
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School of Technology, University of Campinas - UNICAMP, 13484-332 Limeira, São Paulo, Brazil. Electronic address:
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December 2024
Univ. Bordeaux, CNRS, Bordeaux INP, Institut des Sciences Moléculaires, UMR 5255, F-33400 Talence, France.
The effect of conformational dynamics and solvent interactions on the second-order nonlinear optical (NLO) responses of the open and closed forms of a donor-acceptor Stenhouse adduct (DASA) are investigated by a mixed quantum/classical computational approach, which couples molecular dynamics (MD) simulations and time-dependent density functional theory (TD-DFT) calculations. The latter are further combined with various solvation schemes, including polarizable continuum models, hybrid QM/MM approaches using either non polarizable or polarizable electrostatic embedding, and QM/QM' schemes with explicit treatment of a few molecules of the first solvation shell. The performances of the different solvation models are discussed in the context of comparisons with experimental data obtained from hyper-Rayleigh scattering measurements.
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