Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method
| Autor: | Kazuo Kitaura, Takeshi Nagata, Dmitri G. Fedorov, Shinichiro Nakamura, Hiroya Nakata |
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| Rok vydání: | 2015 |
| Předmět: |
Chemistry
Binding energy Protein Data Bank (RCSB PDB) Hydroxamic Acids Tautomer Chemical reaction Transition state Computer Science Applications Triosephosphate isomerase symbols.namesake Computational chemistry symbols Quantum Theory Physical and Theoretical Chemistry Raman spectroscopy Fragment molecular orbital Triose-Phosphate Isomerase |
| Zdroj: | Journal of Chemical Theory and Computation. 11:3053-3064 |
| ISSN: | 1549-9626 1549-9618 |
| DOI: | 10.1021/acs.jctc.5b00277 |
| Popis: | The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed. |
| Databáze: | OpenAIRE |
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