Comparison of Molecular Mechanics, Semi-Empirical Quantum Mechanical, and Density Functional Theory Methods for Scoring Protein–Ligand Interactions

2013 ◽  
Vol 117 (27) ◽  
pp. 8075-8084 ◽  
Author(s):  
Nusret Duygu Yilmazer ◽  
Martin Korth
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanics ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Functional Theory ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Semi Empirical

Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data

2015 ◽  
Vol 14 (01) ◽  
pp. 1540001 ◽  
Author(s):  
Nusret Duygu Yilmazer ◽  
Pascal Heitel ◽  
Tobias Schwabe ◽  
Martin Korth
Keyword(s):  
Density Functional ◽  
Difficult Problem ◽  
Model Systems ◽  
Quantum Mechanical ◽  
Test Cases ◽  
Functional Theory ◽  
Protein Ligand Interactions ◽  
Mechanical Methods ◽  
Ligand Interactions ◽  
High Level

The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.

METAL ATOM ENDOHEDRALLY DOPED C20 CAGE STRUCTURE: (X@C20; X =Ni, Fe, Co)

2005 ◽  
Vol 16 (10) ◽  
pp. 1553-1560 ◽  
Author(s):  
ŞAKIR ERKOÇ
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanics ◽  
Metal Atom ◽  
Density Functional ◽  
Neutral Systems ◽  
Cage Structure ◽  
Functional Theory ◽  
Semi Empirical ◽  
C20 Cage

The C 20 cage structure ( X @ C 20; X =Fe , Co , Ni ) endohedrally doped with a metal atom has been investigated theoretically by performing molecular-mechanics optimizations, and semi-empirical PM3 level and density functional theory B3LYP/6-31G* level calculations within UHF formalism. Calculations have been performed with different spin configurations for the neutral systems.

Modelling the Structure and Properties of Aluminophosphonates

2002 ◽  
Vol 726 ◽  
Author(s):  
Paramjit Grewal ◽  
Paul A Wright ◽  
Mark Edgar ◽  
Julian D Gale ◽  
Paul A Cox
Keyword(s):  
Density Functional Theory ◽  
Ambient Temperature ◽  
Density Functional ◽  
Quantum Mechanical ◽  
Structure And Properties ◽  
Functional Theory ◽  
Rapid Rotation ◽  
Barrier Heights ◽  
Electronic Distribution ◽  
Semi Empirical

AbstractSeveral aluminophosphonate materials have been investigated using both semi-empirical quantum mechanical and Density Functional Theory (DFT) methodologies. The optimised structures obtained are in excellent agreement with experimental results. Important information on the electronic distribution in these structures is obtained, allowing charge distributions to be determined and H2O-framework interactions to be probed. The barriers to rotation for the organic groups in three structures have been investigated. Results for –(CH3) groups in AlMePO-α and AlMePO-β, yield barrier heights that are consistent with rapid rotation at ambient temperature, whereas the barrier height obtained for –(C6H5) in AlBzPO-I suggests that the framework will significantly hinder rotation. The use of modelling to help elucidate the structure of a novel compound, AlMePO-2, and to probe the structure and stability of a hypothetical aluminium ethyl phosphonate, AlEtPO, are also illustrated.

scholarly journals STRUCTURAL AND ELECTRONIC PROPERTIES OF BRIDGED BITHIOPHENE S-OXIDES (BTO) WITH S, S=O, O, SiH2 and BH2 BRIDGE: SEMI-EMPIRICAL AND AB INITIO STUDY

2010 ◽  
Vol 18 (18) ◽  
pp. 1-10
Author(s):  
Banjo Semire ◽  
Isaiah Ajibade Adejoro ◽  
Olusegun Ayobami Odunola
Keyword(s):  
Density Functional Theory ◽  
Thermodynamic Properties ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Study ◽  
Empirical Methods ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Semi Empirical ◽  
Good Agreement

In this paper, we theoretically studied the geometries, stabilities, electronic and thermodynamic properties of bridged bithiophene S-oxide (BTO-X) derivates (with X = BH2, SiH2, S, S=O, and O) by using semi-empirical methods, ab-initio, and Density functional theory. The geometries and thermodynamic parameters calculated by PM3 were in good agreement with that of B3LYP/6-31G(d). The bandgap calculated by B3LYP/6-31G(d) ranged from 3.94eV (BTO-O)-3.16eV (BTO-BH2). The absorption λmax calculated suing B3LYP/6-31G(d) shifted to longer wavelength with X=BH2, SiH2, and S=O due to enhancement of π-conjugated system whereas, BTO-S and BTO-O shifted to shorter wavelengths as compared to dimmer thiophene S-oxide (2TO).

scholarly journals Analysis of the structural and electronic properties of 1-(5-Hydroxymethyl - 4 –[ 5 – (5-oxo-5-piperidin-1-yl-penta- 1,3dienyl)-benzo[1,3]dioxol-2-yl] -tetrahydro-furan-2-yl)-5- methyl-1H-pyrimidine-2,4dione molecule

2018 ◽  
Vol 33 (1) ◽  
pp. 71
Author(s):  
Ali Hashem Essa ◽  
A. F. Jalbout
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Ground State ◽  
Density Functional ◽  
Molecular Orbital Calculations ◽  
Active Molecule ◽  
Dft Methods ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Semi Empirical

The structural and electronic properties of 1-(5-Hydroxymethyl - 4 –[ 5 – (5-oxo-5-piperidin- 1 -yl-penta- 1,3 -dienyl)-benzo [1,3] dioxol- 2 -yl]- tetrahydro -furan-2 -yl)-5-methy l-1Hpyrimidine-2,4dione (AHE) molecule have been investigated theoretically by performing density functional theory (DFT), and semi empirical molecular orbital calculations. The geometry of the molecule is optimized at the level of Austin Model 1 (AM1), and the electronic properties and relative energies of the molecules have been calculated by density functional theory in the ground state. The resultant dipole moment of the AHE molecule is about 2.6 and 2.3 Debyes by AM1 and DFT methods respectively, This property of AHE makes it an active molecule with its environment, that is AHE molecule may interacts with its environment strongly in solution.

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