Development of a True Transition State Force Field from Quantum Mechanical Calculations

2016 ◽  
Vol 12 (4) ◽  
pp. 1833-1844 ◽  
Author(s):  
Ádám Madarász ◽  
Dénes Berta ◽  
Robert S. Paton
Keyword(s):  
Transition State ◽  
Force Field ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
State Force

scholarly journals Transition State Force Field for the Asymmetric Redox-Relay Heck Reaction

2020 ◽  
Author(s):  
Anthony R. Rosales ◽  
Sean P. Ross ◽  
Paul Helquist ◽  
Per-Ola Norrby ◽  
Matthew S. Sigman ◽  
...  
Keyword(s):  
Transition State ◽  
Force Field ◽  
Heck Reaction ◽  
State Force

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Thomas Hamelryck ◽  
Jan H Jensen
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

scholarly journals Stereoselectivity Predictions for the Pd-Catalyzed 1,4-Conjugate Addition Using Q2MM

2021 ◽  
Author(s):  
Jessica Wahlers ◽  
Michael Maloney ◽  
Farbod Salahi ◽  
Anthony Rosales ◽  
Paul Helquist ◽  
...  
Keyword(s):  
Transition State ◽  
Force Field ◽  
Conjugate Addition ◽  
Virtual Library ◽  
Title Reaction ◽  
State Force

The parameterization of a transition state force field for the title reaction is described. Validation for 82 literature examples leads to a MUE of 1.8 kJ/mol and an R2 of 0.877 between computed and experimental stereoselectivities. The use if the TSFF is demonstrated for a virtual library of 27 ligands and 59 enones. <br>

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Jan H Jensen ◽  
Thomas Hamelryck
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

Energizing Listless Pyrimidines by Pre-Distortion for the General Synthesis of 7-Aza-Indazoles from 2-Hydrazonylpyrimidines via Intramolecular Diels-Alder Reactions

2019 ◽  
Author(s):  
Vincent Le Fouler ◽  
yu Chen ◽  
Vincent Gandon ◽  
Vincent Bizet ◽  
Christophe Salomé ◽  
...  
Keyword(s):  
Transition State ◽  
Medicinal Chemistry ◽  
Functional Group ◽  
Diels Alder ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Mild Conditions ◽  
General Synthesis

<p>Pyrimidines are almost unreactive partners in Diels-Alder cycloadditions with alkenes and alkynes, and usually only reactions under drastic conditions were historically reported. We describe how 2-hydrazonylpyrimidines, easily obtained in two steps from commercially available 2-halopyrimidines can be exceptionally activated by trifluoro acetylation. This allows a Diels-Alder cycloaddition under very mild conditions, leading to a large diversity of <i>aza</i>-indazoles, a ubiquitous scaffold in medicinal chemistry. This reaction is general, scalable and has an excellent functional group tolerance. Quantum mechanical calculations show how the simple <i>N</i>-trifluoromethylation of 2-hydrazonylpyrimidines distorts the substrate into a transition state-like geometry that readily undergoes the intramolecular Diels-Alder cycloaddition. </p>

The acidity of β-phosphoglucomutase monofluoromethylenephosphonate ligands probed by NMR spectroscopy and quantum mechanical methods

2016 ◽  
Vol 94 (11) ◽  
pp. 902-908 ◽  
Author(s):  
Stephanie M. Forget ◽  
Eric A.C. Bushnell ◽  
Russell J. Boyd ◽  
David L. Jakeman
Keyword(s):  
Nmr Spectroscopy ◽  
Transition State ◽  
Quantum Mechanical ◽  
Phosphoryl Transfer ◽  
Quantum Mechanical Calculations ◽  
Transition State Analogues ◽  
Mechanical Methods ◽  
Insight Into ◽  
Computational Quantum

We recently described the binding of 1-β-phosphonomethylene-1-deoxy-d-glucopyranose, (S)-1-β-phosphonofluoromethylene-1-deoxy-D-glucopyranose (βG1CFSP), and (R)-1-β-phosphonofluoromethylene-1-deoxy-d-glucopyranose (βG1CFRP) to the enzyme β-phosphoglucomutase as transition state analogues of phosphoryl transfer through formation of stable MgF3− and AlF4− complexes (Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 12384). Herein, we describe in detail the five-fold difference in acidity (pKa2) for the (S)- and (R)-configured diastereomeric fluorophosphonates through a series of NMR spectroscopy experiments. The differences in acidity were corroborated using computational quantum mechanical calculations to determine structures of lowest energy conformers and provide insight into why the (S) isomer is substantially more acidic.

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