Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations

1999 ◽  
Vol 110 (3) ◽  
pp. 1329-1337 ◽  
Author(s):  
Robert H. Wood ◽  
Eric M. Yezdimer ◽  
Shinichi Sakane ◽  
Jose A. Barriocanal ◽  
Douglas J. Doren
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Free Energies ◽  
Mechanical Interaction

RANK-ORDERING THE BINDING AFFINITY FOR FKBP12 AND H1N1 NEURAMINIDASE INHIBITORS IN THE COMBINATION OF A PROTEIN MODEL WITH DENSITY FUNCTIONAL THEORY

2011 ◽  
Vol 10 (04) ◽  
pp. 541-565 ◽  
Author(s):  
GANG HE ◽  
JUYING SHI ◽  
YANTAO CHEN ◽  
YI CHEN ◽  
QIANLING ZHANG ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Interaction Energy ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Mechanical Interaction ◽  
Functional Theory ◽  
Protein Model ◽  
Autodock 4.0 ◽  
Binding Free Energies

The quantum mechanical interaction energies between FKBP12 as well as H1N1 neuraminidase and their inhibitors were directly calculated with an efficient density functional theory by mimicking the whole protein with a protein model composed of the amino acids surrounding the ligands. It was found that the calculated quantum mechanical interaction energies correlate well with the experimental binding free energies with the correlation coefficients of 0.88, 0.86, and the standard deviation of 0.93 and 1.00 kcal/mol, respectively. To compare with force field approach, the binding free energies with the correlation coefficient R = 0.80 and 0.47 were estimated by AutoDock 4.0 programs. It was indicated that the quantum interaction energy shows a better performance in rank-ordering the binding affinity between FKBP12 and H1N1 neuraminidase inhibitors than those of AutoDock 4.0 program. In combination protein model with density functional theory, the estimated quantum interaction energy could be a good predictor or scoring function in structure-based computer-aided drug design. Finally, five new FKBP12 inhibitors were designed based on calculated quantum mechanical interaction energy. In particular, the theoretical K i value of one compound is as low as 0.05 nM, nearly 8-fold more active than FK506.

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

Theoretical study of NO3− interacting with carbon nanotube

Open Physics ◽  
2008 ◽  
Vol 6 (1) ◽  
Author(s):  
Silvete Guerini ◽  
David Azevedo ◽  
Maria Lima ◽  
Ivana Zanella ◽  
Josué Filho
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Quantum Mechanical ◽  
Mechanical Interaction ◽  
Electronic Density ◽  
Functional Theory ◽  
Consistent Field ◽  
The Density Functional Theory ◽  
Self Consistent Field ◽  
Field Form

AbstractThis paper deals with quantum mechanical interaction of no 3− with (5,5) and (8,0) swcnts. To perform this we have made an ab initio calculation based on the density functional theory. In these framework the electronic density plays a central role and it was obtained of a self-consistent field form. It was observed through binding energy that NO3− molecule interacts with each nanotube in a physisorption regime. We propose these swcnts as a potential filter device due to reasonable interaction with NO3− molecule. Besides this type of filter could be reusable, therefore after the filtering, the swcnts could be separated from NO3− molecule.

scholarly journals Quantum mechanical synthon interaction energies

2017 ◽  
Vol 73 (a2) ◽  
pp. C682-C682
Author(s):  
Dylan Jayatilaka ◽  
Samuel Thompson ◽  
Sajesh Thomas ◽  
Peter Spackman ◽  
Mark Spackman
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies
Sign in / Sign up

Export Citation Format

Share Document