Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling

2018 ◽  
Vol 14 (2) ◽  
pp. 1020-1032 ◽  
Author(s):  
Arghya Chakravorty ◽  
Zhe Jia ◽  
Lin Li ◽  
Shan Zhao ◽  
Emil Alexov
Keyword(s):  
Dielectric Function ◽  
Solvation Energy ◽  
Ensemble Average ◽  
Single Structure ◽  
Macromolecular Modeling ◽  
Polar Solvation

scholarly journals On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function

2014 ◽  
Vol 13 (03) ◽  
pp. 1440002 ◽  
Author(s):  
Lin Li ◽  
Chuan Li ◽  
Emil Alexov
Keyword(s):  
Dielectric Constant ◽  
Dielectric Function ◽  
Solvation Energy ◽  
Bulk Water ◽  
Dielectric Medium ◽  
Water Phase ◽  
Polar Component ◽  
Implicit Methods ◽  
Inhomogeneous Dielectric ◽  
Polar Solvation

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule–water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (Li L, Li C, Zhang Z, Alexor E, On the dielectric constant of proteins: Smooth dielectric function for macromolecular modeling and its implementation in Delphi, J Chem Theory Comput9(4):2126–2136, 2013). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute–water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.

Molecular Dynamics Free Energy Simulation study to Investigate Binding Pattern of Isoliquiritigenin as PPAR𝛾 Agonist

2022 ◽  
Author(s):  
Amit Singh ◽  
Abha Mishra
Keyword(s):  
Diabetes Mellitus ◽  
Free Energy ◽  
Binding Energy ◽  
Electrostatic Interactions ◽  
Binding Free Energy ◽  
Solvation Energy ◽  
Bioactive Constituents ◽  
Binding Interaction ◽  
Pparγ Agonist ◽  
Polar Solvation

Abstract Phytochemicals are rich source of bioactive constituents and can be used as another alternative to currently used drugs for diseases like Diabetes mellitus. The potential of Isoliquiritigenin (a constituent of Pterocarpus marsupium) as PPAR𝛾 agonist was evaluated by in silico technique. Autodock results showed that Tyr327, and Tyr473 of the PPARγ forms H-bonds with Isoliquiritigenin (binding energy of -7.46 kcal/mol) and Troglitazone (known drug) showed H bond with Tyr327, Ser289, with binding energy of -11.01 kcal/mol. Isoliquiritigenin, binding energy in Extra precision (XP) was -6.74 kcal/mol while Troglitazone docking, gave binding energy in XP mode as -9.59 kcal/mol. The best Induced fit docking (IFD) score of the optimised PPARγ- Isoliquiritigenin complexes was -9.39 Kcal/mol. The important residues in IFD forming H bond were Cys 285, Arg 288, Tyr 327 and Leu 340. The post docking MM/GBSA free energy for PPARγ with Isoliquiritigenin and Troglitazone was -49.29 and -71.48 Kcal/mol respectively. Binding interaction in MD simulation and Principal Component Analysis studies revealed stable binding throughout 100 ns simulation. Post Simulation MM/PBSA free energy was calculated. The results indicated that compound possessed a negative binding free energy with -114.37KJ/mol. It was observed that van der Waals, electrostatic interactions and non-polar solvation energy negatively contributed to the total interaction energy while only polar solvation energy positively contributed to total free binding energy. The Isoliquiritigenin fulfils the criteria of drug-likeness property. Thus, study presents a systematic analysis on molecular mechanism of action of Isoliquiritigenin as PPARγ agonist in controlling Diabetes mellitus.

Main Provisions Of The Concept Of Technology Of Diamond Cutting And Drilling Of Building Structures

2019 ◽  
pp. 59-63
Keyword(s):  
Combustion Engine ◽  
Front Surface ◽  
The Body ◽  
Building Structures ◽  
Diamond Cutting ◽  
Variable Diameter ◽  
Diamond Drilling ◽  
Single Structure ◽  
New Construction ◽  
Non Destructive

The main provisions of the concept of technology of diamond cutting and drilling of building structures are considered. The innovativeness of the technology, its main possibilities and advantages are presented. Carrying out works with the help of this technology in underwater conditions expands its use when constructing and reconstructing hydraulic structure. The use of diamond drilling equipment with motors equipped with an internal combustion engine is considered. Drilling holes with a variable diameter during the reconstruction of the runways of airfields makes it possible to combine the landing mats into a single structure. The ability to cut inside the concrete mass, parallel to the front surface, has no analogues among the methods of concrete treatment. The use of this technology for producing blind openings in the body of concrete without weakening the structure is also unique. Work with precision quality in cutting and diamond drilling of concrete and reinforced concrete was noted by architects and began to be implemented in the manufacture of inter-room and inter-floor openings. Non-destructive approach to the fragmentation of building structures allows them to be reused. The technology of diamond cutting and drilling is located at the junction of new construction, repair, reconstruction of buildings and structures, and dismantling of structures. Attention is paid to the complexity and combinatorial application of diamond technology. Economic efficiency and ecological safety of diamond technology are presented. The main directions of further research for the development of technology are indicated.

A Study on Maximum Fluctuation Width within a few Hours regarding Ensemble Average Insolation Observed at Multi-points in Large Area

2012 ◽  
Vol 132 (5) ◽  
pp. 452-458 ◽  
Author(s):  
Shinsuke Kumazawa ◽  
Takeyoshi Kato ◽  
Nobuyuki Honda ◽  
Masakazu Koaizawa ◽  
Shinichi Nishino ◽  
...  
Keyword(s):  
Ensemble Average ◽  
Large Area ◽  
Maximum Fluctuation

Optical properties of the Vanadium dioxide

2015 ◽  
Vol 8 (2) ◽  
pp. 2148-2155 ◽  
Author(s):  
Abderrahim Benchaib ◽  
Abdesselam Mdaa ◽  
Izeddine Zorkani ◽  
Anouar Jorio
Keyword(s):  
Energy Efficiency ◽  
Optical Properties ◽  
Critical Temperature ◽  
Thin Layer ◽  
Dielectric Function ◽  
Vanadium Dioxide ◽  
Ultra Violet ◽  
Index Of Refraction ◽  
Practical Utility ◽  
Infra Red

The vanadium dioxide is a material thermo chromium which sees its optical properties changing at the time of the transition from the phase of semiconductor state ↔ metal, at a critical temperature of 68°C. The study of the optical properties of a thin layer of VO₂ thickness 82 nm, such as the dielectric function, the index of refraction, the coefficient ofextinction, the absorption’s coefficient, the reflectivity, the transmittivity, in the photonic spectrum of energy ω located inthe interval: 0.001242 ≤ ω (ev) ≤ 6, enables us to control well its practical utility in various applications, like the intelligentpanes, the photovoltaic, paintings for increasing energy efficiency in buildings, detectors of infra-red (I.R) or ultra-violet(U.V). We will make simulations with Maple and compare our results with those of the literature

Computational Parameters in Correlation Analysis: Gas-Water Distribution Coefficient

1999 ◽  
Vol 64 (11) ◽  
pp. 1727-1747 ◽  
Author(s):  
George R. Famini ◽  
Dalia Benyamin ◽  
Christina Kim ◽  
Rattiporn Veerawat ◽  
Leland Y. Wilson
Keyword(s):  
Correlation Analysis ◽  
Distribution Coefficient ◽  
Water Distribution ◽  
Solvation Energy ◽  
Linear Solvation Energy Relationships ◽  
Linear Solvation Energy Relationship ◽  
Energy Relationships ◽  
Linear Solvation Energy ◽  
Water Equilibrium ◽  
Linear Solvation

Theoretical linear solvation energy relationships (TLSER) combine computational molecular parameters with the linear solvation energy relationship (LSER) of Kamlet and Taft to characterize and predict properties of compounds. This paper examines the correlation of the gas-water equilibrium constant for 423 compounds with the TLSER parameters. Also, it describes new parameters designed to improve the TLSER information content.

From Semiconductor to Metal in a Flash: Observing Ultrafast Laser-Induced Phase Transformations

1997 ◽  
Vol 481 ◽  
Author(s):  
J. P. Callan ◽  
A. M.-T. Kim ◽  
L. Huangt ◽  
E. N. Glezer ◽  
E. Mazur
Keyword(s):  
Phase Transformations ◽  
Dielectric Function ◽  
Spectral Range ◽  
Laser Excitation ◽  
Spectroscopic Technique ◽  
Ultrafast Laser ◽  
Lattice Heating ◽  
Fs Laser

ABSTRACTWe use a new broadband spectroscopic technique to measure ultrafast changes in the dielectric function of a material over the spectral range 1.5–3.5 eV following intense 70-fs laser excitation. The results reveal the nature of the phase transformations which occur in the material following excitation. We studied the response of GaAs and Si. For GaAs, there are three distinct regimes of behavior as the pump fluence is increased — lattice heating, lattice disordering, and a semiconductor-to-metal transition.

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