Understanding and Measurement for the Binding Energy of Hydrogen bonds of Biomass-Derived Hydroxyl Compounds

2018 ◽  
Vol 122 (3) ◽  
pp. 843-848 ◽  
Author(s):  
Yang Luo ◽  
Hong Ma ◽  
Yuxia Sun ◽  
Penghua Che ◽  
Xin Nie ◽  
...  
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Energy Of Hydrogen Bonds ◽  
Hydroxyl Compounds

scholarly journals Molecular Dynamics Simulations for Effects of Fluoropolymer Binder Content in CL-20/TNT Based Polymer-Bonded Explosives

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4876
Author(s):  
Shenshen Li ◽  
Jijun Xiao
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Correlation Function ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Bond Length ◽  
Pair Correlation Function ◽  
Pair Correlation ◽  
Binder Content ◽  
Polymer Bonded Explosives

In order to better understand the role of binder content, molecular dynamics (MD) simulations were performed to study the interfacial interactions, sensitivity and mechanical properties of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) based polymer-bonded explosives (PBXs) with fluorine rubber F2311. The binding energy between CL-20/TNT co-crystal (1 0 0) surface and F2311, pair correlation function, the maximum bond length of the N–NO2 trigger bond, and the mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that binding energy increases with increasing F2311 content. Additionally, according to the results of pair correlation function, it turns out that H–O hydrogen bonds and H–F hydrogen bonds exist between F2311 molecules and the molecules in CL-20/TNT. The length of trigger bond in CL-20/TNT were adopted as theoretical criterion of sensitivity. The maximum bond length of the N–NO2 trigger bond decreased very significantly when the F2311 content increased from 0 to 9.2%. This indicated increasing F2311 content can reduce sensitivity and improve thermal stability. However, the maximum bond length of the N–NO2 trigger bond remained essentially unchanged when the F2311 content was further increased. Additionally, the calculated mechanical data indicated that with the increase in F2311 content, the rigidity of CL-20/TNT based PBXs was decrease, the toughness was improved.

IN VITRO AND IN SILICO ALPHA-AMYLASE INHIBITION POTENTIAL (ANTI-DIABETIC ACTIVITY) OF PSEUDERANTHEMUM BICOLOR (SIMS) RADIK

2020 ◽  
pp. 157-161
Author(s):  
RAMESH BS ◽  
LOKESH RAVI
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Ethyl Acetate ◽  
Bioactive Compounds ◽  
Methyl Ether ◽  
Docking Study ◽  
Alpha Amylase ◽  
Ligand Docking ◽  
Standard Drug ◽  
Reference Drug

Objective: Aim of this study is to evaluate theanti-diabetic activity of Pseuderanthemum bicolor commonly called limang-sugat by inhibiting alpha-amylase protein. Methods: Leaves of P. bicolor were extracted with methanol, chloroform, and ethyl acetate. The extracts were subjected for alpha-amylase inhibition assay and gas chromatography–mass spectrometry (GC–MS) analysis. Phytochemical compounds identified by GC-MS were subjected for protein-ligand docking study against alpha-amylase protein. Acarbose was used as a positive standard drug. Results: The major bioactive compounds obtained from methanol, chloroform, and ethyl acetate extracts were 1,6;2,3-Dianhydro-4-Deoxy-Beta-D-Ribo-Hexopyranose, Pseduosarsasapogenin-5,20-Dien, methyl ether/Hexatriacontane, Di-N-decylsulfone/Octadecanal, and squalene, respectively. A total of 19 secondary metabolites were subjected for protein–ligand docking study against the alpha-amylase protein. The reference drug acarbose demonstrated binding energy of −7.8 Kcal/mol and formed 20 hydrogen bonds with the enzyme. Acarbose signified high polar interaction with the amylase enzyme. Among the 19 test ligands, “2,2-Dibromocholestanone” from ethyl acetate extract exemplified the highest binding energy of −9.3 Kcal/mol. The next highest remarkable inhibition was showed by “Pseduosarsasapogenin-5,20-Dien Methyl Ether” present in the methanol extract, with a binding energy of -9.3 Kcal/mol with the formation of 2 hydrogen bonds. Conclusion: From the result, it could be concluded that the P. bicolor leaves contain various bioactive compounds which are considered as a good anti-diabetic drug.

scholarly journals MOLECULAR DOCKING TERPINEN-4-OL SEBAGAI ANTIINFLAMASI PADA ATEROSKLEROSIS SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 221
Author(s):  
N. M. P. Susanti ◽  
N. P. L. Laksmiani ◽  
N. K. M. Noviyanti ◽  
K. M. Arianti ◽  
I K. Duantara
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Endothelial Dysfunction ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Inflammatory Process ◽  
Mapk Pathway ◽  
Chronic Inflammatory Disease ◽  
Mitogen Activated Protein Kinase ◽  
Mitogen Activated Protein

Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction, it caused fat accumulation and plaque growth in the inner arteries walls. Endothelial dysfunction will activate the Mitogen Activated Protein Kinase (MAPK) pathway involving ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, as well as the Nuclear Factor Kappa B (NF-kB) pathway involving IKK proteins. Terpinen-4-ol is constituent found in the bangle rhizome. The purpose of this study were to determine the affinity and mechanisms of terpinen-4-ol against ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins as anti-inflammatory in atherosclerosis performed using molecular docking method. The study was conducted exploratively with several steps such as preparation and optimization of terpinen-4-ol structure, preparation of 3D ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, validation method of molecular docking, and docking terpinen-4-ol in these proteins. The docking result are assessed from the binding energy and hydrogen bonds formed between terpinen-4-ol and proteins. The smaller value of binding energy terpinen-4-ol with target proteins showed the complex that form more stable. The result showed that terpinen-4-ol and has activity in inhibiting the inflammatory process because it is able to disturb ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins with respective bond energy values -5,12; -5,24; -5,08; -5,88; and -4,99 Kcal/mol. The molecular mechanism in inhibiting the activity of ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins is through the formation of hydrogen bonds in these proteins. These results show that terpinen-4-ol have the potential to inhibit inflammatory process and the formation of atherosclerotic plaque can be obstructed. Keywords : atherosclerosis, terpinen-4-ol, molecular docking, in silico

The energy of hydrogen bonds in aqueous suspensions of nanodiamonds with different surface functionalization

2018 ◽  
Vol 50 (3) ◽  
pp. 387-395 ◽  
Author(s):  
K.A. Laptinskiy ◽  
A.N. Bokarev ◽  
S.A. Dolenko ◽  
I.L. Plastun ◽  
O.E. Sarmanova ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Surface Functionalization ◽  
Aqueous Suspensions ◽  
Energy Of Hydrogen Bonds

Tuning the Interaction Energy of Hydrogen Bonds: The Effect of the Substituent

2011 ◽  
Vol 115 (45) ◽  
pp. 12561-12571 ◽  
Author(s):  
Ignasi Mata ◽  
Elies Molins ◽  
Ibon Alkorta ◽  
Enrique Espinosa
Keyword(s):  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Energy Of Hydrogen Bonds

scholarly journals ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

2020 ◽  
pp. 152-155
Author(s):  
RACHAEL EVANGELINE ◽  
NIHAL AHMED
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Water Extract ◽  
Docking Study ◽  
Persea Americana ◽  
Ligand Docking ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Free Binding Energy

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study. Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results. Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active. Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

Molecular Docking Studies on the Anti-Fungal Activity of Allium Sativum (Garlic) Against Mucormycosis (Black Fungus) by BIOVIA Discovery Studio Visualizer 21.1.0.0

2021 ◽  
Author(s):  
Shaweta Sharma ◽  
Akhil Sharma ◽  
Utsav Gupta
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Docking Studies ◽  
Binding Energies ◽  
Inhibition Constant ◽  
Beta Glucan ◽  
Glucan Synthase ◽  
Fungal Protein ◽  
Discovery Studio ◽  
Black Fungi

Abstract Background: The COVID-19 pandemic is a major concern. However, its association and rising cases of mucormycosis, also known as black fungus make the scenario even more troublesome. In addition, no specific medication against mucormycosis/black fungus makes things even worse.Objective: Garlic phytoconstituents have shown remarkable antifungal properties against various fungal species in various studies. Thus, the objective of the study was to check the potency of garlic phytoconstituents against the 1,3-beta-glucan synthase fungal protein using in-silico methods.Method: Auto Dock was used to evaluate selected garlic phytochemical molecules against 1,3-beta-glucan synthase fungal protein, and Discovery studio visualizer was used to create 3D and 2D interaction photos.Results: Five out of 9 phytoconstituents were found to form conventional hydrogen bonds, and only alliin formed the highest number of hydrogen bonds. However, the binding energy and inhibition constant of all nine phytoconstituents were determined. Interestingly, Z-ajoene showed the lowest binding energy of -5.07 kcal/mol and inhibition constant of 192.57µM.Conclusion: The results of our investigation suggested that garlic phytochemicals can have a good impact against black fungi, pertaining to the significant binding energies of phytoconstituents during blind docking. Specifically, Z-ajoene could be a good alternate against black fungi. However, detailed research is required to explore the antifungal activity of garlic against mucormycosis.

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