scholarly journals Docking with combined use of a force field and a quantum-chemical method

2019 ◽  
Vol 65 (2) ◽  
pp. 80-85 ◽  
Author(s):  
A.V. Sulimov ◽  
D.K. Kutov ◽  
I.S. Ilin ◽  
V.B. Sulimov
Keyword(s):  
Force Field ◽  
Quantum Chemical ◽  
Continuum Model ◽  
Chemical Method ◽  
Second Step ◽  
Quantum Chemical Method ◽  
Ligand Complex ◽  
Combined Use ◽  
Solvent Model ◽  
Wide Range

The paper presents the results concerning the application of docking programs FLM to combined use of the MMFF94 force field and the semiempirical quantum-chemical method PM7 in the docking procedure. At the first step of this procedure a fairly wide range of low-energy minima of the protein-ligand complex is found in the frame of the MMFF94 force field using the FLM program. The energies of all these minima are recalculated using the PM7 method and the COSMO solvent continuum model at the second step. On the basis of these calculations the deepest minimum of the protein-ligand energy, calculated by the PM7 method with COSMO solvent, is determined, which gives the position of the ligand closest to its position in the crystal of the protein-ligand complex. It is shown that the first step of the combined procedure is performed more quickly and more efficiently in vacuum, rather than with a solvent model.

scholarly journals Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

Nanomaterials ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 274
Author(s):  
Alexey Sulimov ◽  
Danil Kutov ◽  
Ivan Ilin ◽  
Vladimir Sulimov
Keyword(s):  
Quantum Chemical ◽  
Chemical Method ◽  
Wide Spectrum ◽  
Semiempirical Methods ◽  
Implicit Solvent ◽  
Quantum Chemical Method ◽  
Dispersion Interactions ◽  
Ligand Complex ◽  
High Quality Protein ◽  
Solvent Model

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

scholarly journals Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

2017 ◽  
Vol 2017 ◽  
pp. 1-6 ◽  
Author(s):  
A. V. Sulimov ◽  
D. C. Kutov ◽  
E. V. Katkova ◽  
V. B. Sulimov
Keyword(s):  
Force Field ◽  
Quantum Chemical ◽  
Semiempirical Method ◽  
Ligand Complex ◽  
Water Solvent ◽  
Global Energy Minimum ◽  
Combined Use ◽  
Pcm Model ◽  
Almost All ◽  
Native Ligand

Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

Solvation of ions by dipolar aprotic solvents and water. A CNDO/2 study

1985 ◽  
Vol 50 (11) ◽  
pp. 2493-2508 ◽  
Author(s):  
Petr Kyselka ◽  
Zdeněk Havlas ◽  
Ivo Sláma
Keyword(s):  
Binary Mixtures ◽  
Quantum Chemical ◽  
Chemical Method ◽  
Molecular Structures ◽  
Dimethyl Sulphoxide ◽  
Ternary Mixtures ◽  
Aprotic Solvents ◽  
Quantum Chemical Method ◽  
Solvation Of Ions ◽  
Dipolar Aprotic Solvents

Solvation of Li+, Be2+, Na+, Mg2+, and Al3+ ions has been studied in binary mixtures with dimethyl sulphoxide, dimethylformamide, acetonitrile and water, and in ternary mixtures of the organic solvents with water. The CNDO/2 quantum chemical method was used to calculate the energies of solvation, molecular structures and charge distributions for the complexes acetonitrile...ion (1:1, 2:1, 4:1), dimethyl sulphoxide...ion (1:1), dimethylformamide...ion (1:1), and acetonitrile (dimethyl sulphoxide, dimethylformamide)...ion...water (1:1:1).

The optoelectronic properties of π-conjugated organic molecules based on terphenyl and pyrrole for BHJ solar cells: DFT / TD-DFT theoretical study

2021 ◽  
Vol 10 (4) ◽  
pp. 489-502 ◽  
Author(s):  
M. Raftani ◽  
T. Abram ◽  
W. Loued ◽  
R. Kacimi ◽  
A. Azaid ◽  
...  
Keyword(s):  
Solar Cells ◽  
Quantum Chemical ◽  
Chemical Method ◽  
Chemical Reactivity ◽  
Optoelectronic Properties ◽  
Oscillator Strengths ◽  
Frontier Molecular Orbital ◽  
Bandgap Energy ◽  
Quantum Chemical Method ◽  
Td Dft

In the present paper, four π-conjugated materials, based on terphenyl and pyrrole, with A–D–A structure have been theoretically studied to propose new organic compounds to be used in the organic solar cell field. Moreover, the geometrical and optoelectronic properties of the designed molecules M1, M2, M3 and M4 have been computed after optimization in their fundamental states, using the quantum chemical method DFT / B3LYP/ 6−311G (d, p). Different parameters including HOMO and LUMO energy levels, bandgap energy, frontier molecular orbital (FMO), chemical reactivity indices, the density of states (DOS), Voc, electrostatic potential (ESP), and thermodynamic parameters at several temperatures in the range of 0-500 K have been determined. The absorption properties including the transition energy, the wavelengths (λmax), the excitation vertical energy, and the corresponding oscillator strengths of these molecules have been studied using the quantum chemical method TD−DFT / CAM–B3LYP / 6–311G (d, p). The obtained results of our studied compounds show that M3 (with 2H, 2'H-1, 1'-biisoindole moiety) as a donor group has special optoelectronic, absorption, and good photovoltaic characteristics. Thus, they can be utilized as an electron-donating in organic solar cells BHJ type.

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