Journal ArticleDOI
A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
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In this article, a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes is presented. But it is not suitable for the simulation of proteins.Abstract:
We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be...read more
Citations
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Journal ArticleDOI
QM/MM Methods for Biomolecular Systems
Hans Martin Senn,Walter Thiel +1 more
TL;DR: To model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region and an MM treatment for the surroundings, enabling the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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QM/MM: what have we learned, where are we, and where do we go from here?
TL;DR: A review of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages, can be found in this article.
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The ONIOM Method and Its Applications
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TL;DR: This paper presents a meta-analyses of the proton-probes of Na6(CO3)(SO4)2, Na2SO4, and Na2CO3 of the response of the H2O/O2 “spatially aggregating substance,” which has the potential to alter the structure of the molecule and provide clues to the “building blocks” of DNA.
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Quantum mechanical methods for enzyme kinetics
Jiali Gao,Donald G. Truhlar +1 more
TL;DR: This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model.
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A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
TL;DR: In this article, a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car-Parrinello mixed quantum mechanics/molecular mechanics (QM/MM) method is presented.
References
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Journal ArticleDOI
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