Importance of van der Waals Descriptions on Accurate Isomerization Energy Calculations of Thiourea Compounds: LCgau-BOP+LRD Method

2019 ◽  
Vol 123 (32) ◽  
pp. 7034-7041 ◽  
Author(s):  
Dae-Hwan Ahn ◽  
Takeshi Sato ◽  
Jong-Won Song ◽  
Kimihiko Hirao
Keyword(s):  
Van Der Waals ◽  
Energy Calculations ◽  
Isomerization Energy

About the overestimation of the basis set superposition error on interaction energy calculations for van der Waals systems

1986 ◽  
Vol 84 (9) ◽  
pp. 5077-5080 ◽  
Author(s):  
F. J. Olivares del Valle ◽  
S. Tolosa ◽  
J. J. Esperilla ◽  
E. A. Ojalvo ◽  
A. Requena
Keyword(s):  
Interaction Energy ◽  
Van Der Waals ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Energy Calculations

Medium-Size Polarized Basis Sets Applicability for Interaction Energy Calculations: He2 and Be2 van der Waals Systems

1993 ◽  
Vol 58 (8) ◽  
pp. 1739-1750
Author(s):  
Andrzej Nowek
Keyword(s):  
Interaction Energy ◽  
Van Der Waals ◽  
Basis Set ◽  
Basis Sets ◽  
Medium Size ◽  
Dispersion Energy ◽  
Energy Calculations ◽  
Polarized Basis Sets ◽  
Standard Energy

Polarized bases set approach has been applied for preparation of medium-size contracted GTO basis sets starting from various standard energy-optimized and even-tempered isotropic atomic basis sets. Their usefulness for calculation of the SCF interaction energy and its components as well as dispersion energy consistently determined within the dimer basis set were studied for He2 and Be2 systems for intermediate internuclear separations. The results obtained with polarized basis sets indicate their good performance in comparison with property oriented ones.

scholarly journals Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

2020 ◽  
Author(s):  
Md Fulbabu Sk ◽  
Rajarshi Roy ◽  
Nisha Amarnath Jonniya ◽  
Sayan Poddar ◽  
Parimal Kar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Binding Free Energy ◽  
Van Der Waals ◽  
Antiviral Drug ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Main Protease ◽  
Dynamics Simulations

<div>The recent outbreak of novel “coronavirus disease 2019” (COVID-19) has spread rapidly</div><div>worldwide, causing a global pandemic. In the absence of a vaccine or a suitable</div><div>chemotherapeutic intervention, it is an urgent need to develop a new antiviral drug to fight this</div><div>deadly respiratory disease. In the present work, we have elucidated the mechanism of binding</div><div>of two inhibitors, namely α-ketoamide and Z31792168 to SARS-CoV-2 main protease (Mpro</div><div>or 3CLpro) by using all-atom molecular dynamics simulations and free energy calculations. We</div><div>calculated the total binding free energy (ΔGbind) of both inhibitors and further decomposed</div><div>ΔGbind into various forces governing the complex formation using the Molecular</div><div>Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal</div><div>that α-ketoamide is more potent (ΔGbind= - 9.05 kcal/mol) compared to Z31792168 (ΔGbind= -</div><div>3.25 kcal/mol) against COVID-19 3CLpro. The increase in ΔGbind for α-ketoamide relative to</div><div>Z31792168 arises due to an increase in the favorable electrostatic and van der Waals</div><div>interactions between the inhibitor and 3CLpro. Further, we have identified important residues</div><div>controlling the 3CLpro-ligand binding from per-residue based decomposition of the binding free</div><div>energy. Finally, we have compared ΔGbind of these two inhibitors with the anti-HIV retroviral</div><div>drugs, such as lopinavir and darunavir. It is observed that α-ketoamide is more potent compared</div><div>to both lopinavir and darunavir. In the case of lopinavir, a decrease in the size of the van der</div><div>Waals interactions is responsible for the lower binding affinity compared to α-ketoamide. On</div><div>the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic</div><div>and van der Waals interactions contributes to lower affinity compared to α-ketoamide. Our</div><div>study might help in designing rational anticoronaviral drugs targeting the SARS-CoV-2 main</div><div>protease. </div>

An examination of density functional theories on isomerization energy calculations of organic molecules

2011 ◽  
Vol 130 (4-6) ◽  
pp. 851-857 ◽  
Author(s):  
Jong-Won Song ◽  
Takao Tsuneda ◽  
Takeshi Sato ◽  
Kimihiko Hirao
Keyword(s):  
Density Functional ◽  
Organic Molecules ◽  
Energy Calculations ◽  
Isomerization Energy

scholarly journals Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

2020 ◽  
Author(s):  
Md Fulbabu Sk ◽  
Rajarshi Roy ◽  
Nisha Amarnath Jonniya ◽  
Sayan Poddar ◽  
Parimal Kar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Binding Free Energy ◽  
Van Der Waals ◽  
Antiviral Drug ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Main Protease ◽  
Dynamics Simulations

<div>The recent outbreak of novel “coronavirus disease 2019” (COVID-19) has spread rapidly</div><div>worldwide, causing a global pandemic. In the absence of a vaccine or a suitable</div><div>chemotherapeutic intervention, it is an urgent need to develop a new antiviral drug to fight this</div><div>deadly respiratory disease. In the present work, we have elucidated the mechanism of binding</div><div>of two inhibitors, namely α-ketoamide and Z31792168 to SARS-CoV-2 main protease (Mpro</div><div>or 3CLpro) by using all-atom molecular dynamics simulations and free energy calculations. We</div><div>calculated the total binding free energy (ΔGbind) of both inhibitors and further decomposed</div><div>ΔGbind into various forces governing the complex formation using the Molecular</div><div>Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal</div><div>that α-ketoamide is more potent (ΔGbind= - 9.05 kcal/mol) compared to Z31792168 (ΔGbind= -</div><div>3.25 kcal/mol) against COVID-19 3CLpro. The increase in ΔGbind for α-ketoamide relative to</div><div>Z31792168 arises due to an increase in the favorable electrostatic and van der Waals</div><div>interactions between the inhibitor and 3CLpro. Further, we have identified important residues</div><div>controlling the 3CLpro-ligand binding from per-residue based decomposition of the binding free</div><div>energy. Finally, we have compared ΔGbind of these two inhibitors with the anti-HIV retroviral</div><div>drugs, such as lopinavir and darunavir. It is observed that α-ketoamide is more potent compared</div><div>to both lopinavir and darunavir. In the case of lopinavir, a decrease in the size of the van der</div><div>Waals interactions is responsible for the lower binding affinity compared to α-ketoamide. On</div><div>the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic</div><div>and van der Waals interactions contributes to lower affinity compared to α-ketoamide. Our</div><div>study might help in designing rational anticoronaviral drugs targeting the SARS-CoV-2 main</div><div>protease. </div>

The annealed (0001) α-alumina surface and its influence on thin-film growth

1995 ◽  
Vol 53 ◽  
pp. 336-337
Author(s):  
Michael W. Bench ◽  
Paul G. Kotula ◽  
C. Barry Carter
Keyword(s):  
Electron Microscopy ◽  
Surface Energy ◽  
Film Growth ◽  
Thin Film Growth ◽  
Energy Calculations ◽  
Transmission Electron ◽  
Reflection Electron Microscopy ◽  
Low Energy Electron ◽  
Surface Nature

The growth of semiconductors, superconductors, metals, and other insulators has been investigated using alumina substrates in a variety of orientations. The surface state of the alumina (for example surface reconstruction and step nature) can be expected to affect the growth nature and quality of the epilayers. As such, the surface nature has been studied using a number of techniques including low energy electron diffraction (LEED), reflection electron microscopy (REM), transmission electron microscopy (TEM), molecular dynamics computer simulations, and also by theoretical surface energy calculations. In the (0001) orientation, the bulk alumina lattice can be thought of as a layered structure with A1-A1-O stacking. This gives three possible terminations of the bulk alumina lattice, with theoretical surface energy calculations suggesting that termination should occur between the Al layers. Thus, the lattice often has been described as being made up of layers of (Al-O-Al) unit stacking sequences. There is a 180° rotation in the surface symmetry of successive layers and a total of six layers are required to form the alumina unit cell.

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