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.

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 Regional and local variations in atmospheric aerosols using ground-based sun photometry during Distributed Regional Aerosol Gridded Observation Networks (DRAGON) in 2012

2016 ◽  
Vol 16 (22) ◽  
pp. 14795-14803 ◽  
Author(s):  
Itaru Sano ◽  
Sonoyo Mukai ◽  
Makiko Nakata ◽  
Brent N. Holben
Keyword(s):  
Atmospheric Aerosols ◽  
Urban Areas ◽  
Regional Scale ◽  
Reanalysis Data ◽  
Aerosol Dynamics ◽  
Aerosol Mass ◽  
Combined Use ◽  
Environmental Prediction ◽  
Almost All ◽  
Observation Networks

Abstract. Aerosol mass concentrations are affected by local emissions as well as long-range transboundary (LRT) aerosols. This work investigates regional and local variations of aerosols based on Distributed Regional Aerosol Gridded Observation Networks (DRAGON). We constructed DRAGON-Japan and DRAGON-Osaka in spring of 2012. The former network covers almost all of Japan in order to obtain aerosol information in regional scale over Japanese islands. It was determined from the DRAGON-Japan campaign that the values of aerosol optical thickness (AOT) decrease from west to east during an aerosol episode. In fact, the highest AOT was recorded at Fukue Island at the western end of the network, and the value was much higher than that of urban areas. The latter network (DRAGON-Osaka) was set as a dense instrument network in the megalopolis of Osaka, with a population of 12 million, to better understand local aerosol dynamics in urban areas. AOT was further measured with a mobile sun photometer attached to a car. This transect information showed that aerosol concentrations rapidly changed in time and space together when most of the Osaka area was covered with moderate LRT aerosols. The combined use of the dense instrument network (DRAGON-Osaka) and high-frequency measurements provides the motion of aerosol advection, which coincides with the wind vector around the layer between 700 and 850 hPa as provided by the reanalysis data of the National Centers for Environmental Prediction (NCEP).

Influence of Morphology on Mechanical Properties under the Combined Use of SEBS and EOr as Elastomer in PP/Elastomer/Filler Ternary Composites

2011 ◽  
Vol 19 (9) ◽  
pp. 725-732
Author(s):  
Shigeki Hikasa ◽  
Kazuya Nagata ◽  
Yoshinobu Nakamura
Keyword(s):  
Mechanical Properties ◽  
Impact Strength ◽  
Triblock Copolymer ◽  
Continuous Phase ◽  
Dispersed Phase ◽  
Impact Properties ◽  
Combined Use ◽  
Poly Ethylene ◽  
Almost All ◽  
The Impact

The influences of combined elastomers on impact properties and morphology of polypropylene (PP)/elastomer/CaCO3 ternary composites were investigated. In the case that polystyrene- block-poly(ethylene-butene)- block-polystyrene triblock copolymer (SEBS) and poly(ethylene- co-octene) (EOR) were used as elastomers, a sea-island structure consisting of EOR dispersed phase and SEBS continuous phase was formed. The elastomer and the CaCO3 particles were separately dispersed in PP matrix. In the case that carboxylated SEBS (C-SEBS) and EOR were used, the C-SEBS particles were dispersed in the EOR particles. Almost all of the CaCO3 particles were dispersed in the PP matrix, although some of the CaCO3 particles were dispersed in the C-SEBS/EOR combined particles. Impact strength improved with an increase of incorporated CaCO3 particles. The effect of elastomer on the impact strength was SEBS ≥ SEBS/EOR > EOR = C-SEBS/EOR > C-SEBS. The morphology formed by elastomer and CaCO3 particles strongly affected the impact properties of the ternary composites.

scholarly journals Deprotonation Mechanism of Methyl Gallate: UV Spectroscopic and Computational Studies

2018 ◽  
Vol 19 (10) ◽  
pp. 3111 ◽  
Author(s):  
Liangliang Zhang ◽  
Yuchen Liu ◽  
Yongmei Wang
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Acid Dissociation ◽  
Acid Dissociation Constant ◽  
Methyl Gallate ◽  
Deprotonated Form ◽  
Ph Influence ◽  
Combined Use ◽  
Deprotonation Reaction ◽  
Uv Visible

In the present paper, methyl gallate (MeG), a simple polyphenol and also the monomer of hydrolysable tannins, was selected to study the deprotonation process for the hydroxyls of the galloyl group by the combined use of spectroscopic measurements and quantum chemical calculations. The results of quantum chemical calculations show that the deprotonated form of methyl gallate undergoes the para-quinoid localization in the benzene ring, compared with free methyl gallate. The predicted spectra obtained from the free and deprotonated methyl gallate models are in agreement with the experimental UV-visible (UV-vis) absorption spectra. In the same way, the vibrational spectra of the para-quinoid MeG models validate the proposed mechanism of the deprotonation of MeG molecule. The pH influence on the deprotonation reaction and oxidization of phenolic groups has been also investigated. The pKa values of MeG were evaluated using the chemometric modeling method. The first acid dissociation constant (pKa1) for MeG was evaluated to be 4.20 ± 0.01, and the second one (pKa2) was 10.78 ± 0.06.

Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

2008 ◽  
Vol 57 (3) ◽  
pp. 499-505 ◽  
Author(s):  
L. S. Khaikin ◽  
O. E. Grikina ◽  
B. V. Lokshin ◽  
K. P. Dyugaev ◽  
A. M. Astakhov
Keyword(s):  
Force Field ◽  
Vibrational Spectra ◽  
Quantum Chemical ◽  
Chemical Force

A general intermolecular force field based on tight-binding quantum chemical calculations

2017 ◽  
Vol 147 (16) ◽  
pp. 161708 ◽  
Author(s):  
Stefan Grimme ◽  
Christoph Bannwarth ◽  
Eike Caldeweyher ◽  
Jana Pisarek ◽  
Andreas Hansen
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Tight Binding ◽  
Intermolecular Force

scholarly journals Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Igor V. Oferkin ◽  
Ekaterina V. Katkova ◽  
Alexey V. Sulimov ◽  
Danil C. Kutov ◽  
Sergey I. Sobolev ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Quantum Chemical ◽  
Target Function ◽  
Binding Energies ◽  
Low Energy ◽  
Implicit Solvent ◽  
Energy Calculation ◽  
Solvent Models ◽  
Docking Program

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

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