Geometrical and vibrational DFT studies of HOBr·(H2O)n clusters (n = 1–4)

2003 ◽  
Vol 81 (9) ◽  
pp. 961-970 ◽  
Author(s):  
Cristina Maria P Santos ◽  
Roberto B Faria ◽  
Wagner B De Almeida ◽  
Juan O Machuca-Herrera ◽  
Sérgio P Machado
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Vibrational Spectra ◽  
Low Frequency ◽  
Binding Energies ◽  
Basis Sets ◽  
Dft Studies ◽  
Geometrical Structures ◽  
Stable Structures

The geometrical structures and the vibrational spectra of the HOBr·(H2O)n clusters (n = 1–4) have been calculated at the DFT level of theory, using the pBP method and the DN* and DN** numerical basis sets. The results showed that the interaction involving the H of the HOBr and the O of the water molecule represent the preferred arrangements for these hydrated compounds. Both HOBr·H2O and HOBr·(H2O)2 clusters presented stable structures with syn and anti conformations, the syn being the most stable. The HOBr·(H2O)3 and the HOBr·(H2O)4 clusters have presented stable cyclic structures. In the HOBr·H2O and HOBr·(H2O)2 clusters, low-frequency stretching values could be assigned to hydrogen bonds, but the same could not be done so clearly for the HOBr·(H2O)3 and the HOBr·(H2O)4 cyclic clusters. The binding energies were also determinated for these HOBr hydrated clusters, showing that the addition of a water molecule to the HOBr·H2O and HOBr·(H2O)2 clusters increases the binding energy by approximately 4 kcal mol–1, while the addition of a water molecule to the HOBr·(H2O)3 cluster decreases this value by 4 kcal mol–1.Key words: DFT, numerical basis, HOBr·(H2O)n, clusters.

Gas-Phase Clustering of NO+ with H2S and H2O

2007 ◽  
Vol 72 (8) ◽  
pp. 1122-1138 ◽  
Author(s):  
Milan Uhlár ◽  
Ivan Černušák
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Gas Phase ◽  
Saddle Points ◽  
Solvent Molecule ◽  
Local Minima ◽  
Additional Water ◽  
Three Body ◽  
Rain Formation ◽  
Stable Structures

The complex NO+·H2S, which is assumed to be an intermediate in acid rain formation, exhibits thermodynamic stability of ∆Hº300 = -76 kJ mol-1, or ∆Gº300 = -47 kJ mol-1. Its further transformation via H-transfer is associated with rather high barriers. One of the conceivable routes to lower the energy of the transition state is the action of additional solvent molecule(s) that can mediate proton transfer. We have studied several NO+·H2S structures with one or two additional water molecule(s) and have found stable structures (local minima), intermediates and saddle points for the three-body NO+·H2S·H2O and four-body NO+·H2S·(H2O)2 clusters. The hydrogen bonds network in the four-body cluster plays a crucial role in its conversion to thionitrous acid.

A STUDY OF THE STRUCTURES AND VIBRATIONAL SPECTRA OF THE N2O⋯(HX)2 AND ON2⋯(HX)2 WITH X = F, Cl, Br AND CN

2013 ◽  
Vol 12 (05) ◽  
pp. 1350044 ◽  
Author(s):  
NATHÁLIA B. D. LIMA ◽  
MÁRCIA K. D. L. BELARMINO
Keyword(s):  
Nitrous Oxide ◽  
Vibrational Spectra ◽  
Theoretical Calculations ◽  
Bond Formation ◽  
Binding Energies ◽  
Vibrational Modes ◽  
Out Of Plane ◽  
Usual Behavior ◽  
Bending Modes ◽  
Stable Structures

Theoretical calculations 6-311++G(d,p) have been performed in order to obtain binding energies and molecular properties of complexes involving nitrous oxide ( N2O ) and two HX (X = F, Cl, Br and CN ) molecules. Our calculations have revealed the existence of eleven stable structures. The vibrational changes which take place in the HX acid after complexation follow the usual behavior: the HX stretching frequency is shifted downward whereas its IR intensity is much enhanced. The new vibrational modes arising upon H-bond formation, were verified, especially, those associated with the out-of-plane and in-plane HX bending modes, which are pure rotations in the HX isolated molecule.

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.

scholarly journals Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods

2021 ◽  
Author(s):  
Nazli Irmak Giritlioglu ◽  
Gizem Koprululu Kucuk
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Protein Complexes ◽  
Protein Product ◽  
Binding Energies ◽  
Spike Protein ◽  
Web Based

COVID-19 is a viral disease that has been a threat to the whole world since 2019. Although effective vaccines against the disease have been developed, there are still points to be clarified about the mechanism of SARS-CoV-2, which is the causative agent of COVID-19. In this study, we determined the binding energies and the bond types of complexes formed by open (6VYB) and closed (6VXX) forms of the Spike protein of SARS-CoV-2 and wild and mutant forms of IFITM1, IFITM2, and IFITM3 proteins using the molecular docking approach. First, all missense SNPs were found in the NCBI Single Nucleotide Polymorphism database (dbSNP) for IFITM1, IFITM2, and IFITM3 and analyzed with SIFT, PROVEAN, PolyPhen-2, SNAP2, Mutation Assessor, and PANTHER cSNP web-based tools to determine their pathogenicity. When at least four of these analysis tools showed that the SNP had a pathogenic effect on the protein product, this SNP was saved for further analysis. Delta delta G (DDG) and protein stability analysis for amino acid changes were performed in the web-based tools I-Mutant, MUpro, and SAAFEC-SEQ. The structural effect of amino acid change on the protein product was made using the HOPE web-based tool. HawkDock server was used for molecular docking and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and binding energies of all complexes were calculated. BIOVIA Discovery Studio program was utilized to visualize the complexes. Hydrogen bonds, salt bridges, and non-bonded contacts between Spike and IFITM protein chains in the complexes were detected with the PDBsum web-based tool. The best binding energy among the 6VYB-IFITM wild protein complexes belong to 6VYB-IFITM1 (-46.16 kcal/mol). Likewise, among the 6VXX-IFITM wild protein complexes, the most negative binding energy belongs to 6VXX-IFITM1 (-52.42 kcal/mol). An interesting result found in the study is the presence of hydrogen bonds between the cytoplasmic domain of the IFITM1 wild protein and the S2 domain of 6VYB. Among the Spike-IFITM mutant protein complexes, the best binding energy belongs to the 6VXX-IFITM2 N63S complex (-50.77 kcal/mol) and the worst binding energy belongs to the 6VXX-IFITM3 S50T complex (4.86 kcal/mol). The study suggests that IFITM1 protein may act as a receptor for SARS-CoV-2 Spike protein. Assays must be advanced from in silico to in vitro for the determination of the receptor-ligand interactions between IFITM proteins and SARS-CoV-2.

Mg2Cl5 - and Mg3Cl7 - Superhalogen Anions

2008 ◽  
Vol 61 (9) ◽  
pp. 712 ◽  
Author(s):  
Iwona Anusiewicz
Keyword(s):  
Green Function ◽  
Crystal Lattice ◽  
Global Minimum ◽  
Binding Energies ◽  
Basis Sets ◽  
Energy Structure ◽  
Electron Detachment ◽  
Geometrical Structures ◽  
Outer Valence ◽  
Electron Binding Energies

The vertical electron detachment energies of Mg2Cl5– and Mg3Cl7– superhalogen anions were calculated at the outer valence Green function level with 6–311+G(3df) basis sets. These species were found to form rather unusual geometrical structures, each of which corresponds to a stable anionic state exhibiting superhalogen nature. The global minimum structure of Mg2Cl5– was found to possess D3h symmetry, which can be described as a system in which two central magnesium atoms are linked via a symmetrical triangle formed by three chlorine atoms, whereas the lowest-energy structure for Mg3Cl7– was found to have C3v symmetry, which can be viewed as a fragment of chloromagnesite crystal lattice. Extremely large electron binding energies of these anions (exceeding 6.5 eV in all cases) were predicted and discussed.

Basis set convergence of binding energy with and without CP-correction utilizing PBE0 method: A benchmark study of X2 (X=Ge, As, Se, Sc, Ti, V, Cr, Mn, Co, Cu, Zn)

2019 ◽  
Vol 18 (08) ◽  
pp. 1950034
Author(s):  
S. Akbudak ◽  
G. Uğur ◽  
Ş. Uğur ◽  
H. Y. Ocak
Keyword(s):  
Binding Energy ◽  
Binding Energies ◽  
Basis Set ◽  
Basis Sets ◽  
Set Convergence ◽  
Hartree Fock ◽  
Counterpoise Correction ◽  
Benchmark Study ◽  
Complete Basis Set ◽  
Speed Up

A DFT study of homonuclear X2 ([Formula: see text], As, Se, Sc, Ti, V, Cr, Mn, Fe, Co, Cu, Zn) is presented using PBEO exchange (xc) functional which is a mixing of Perdew–Burke–Ernzerhof (PBE) and Hartree Fock (HF) exchange energy. However, we used cc-pVXZ and aug-cc-pVXZ basis sets where X is maximum angular momentum number in basis set. Convergence pattern of binding energy with respect to basis set was observed. Two-point extrapolations to complete basis set (CBS) limit were applied to speed up convergence and decrease the basis set incompleteness error (BSIE). Counterpoise correction (CP) method was utilized to alleviate basis set superposition errors (BSSE). Both CP-corrected and uncorrected binding energies were obtained and compared with the experimental and theoretical binding energy values in literature.

scholarly journals 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 ◽  
pp. 028-032
Author(s):  
Sharma Shaweta ◽  
Sharma Akhil ◽  
Gupta Utsav
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Docking Studies ◽  
Binding Energies ◽  
Inhibition Constant ◽  
Beta Glucan ◽  
Glucan Synthase ◽  
Fungal Protein ◽  
Discovery Studio ◽  
Black Fungi

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.

Density functional theory periodic slab calculations of adsorption and dissociation of H2O on the Cu2O(110):CuO surface

2013 ◽  
Vol 91 (12) ◽  
pp. 1101-1106 ◽  
Author(s):  
Sherin A. Saraireh ◽  
Mohammednoor Altarawneh
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Water Molecule ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Environmental Applications ◽  
Functional Theory ◽  
Adsorption And Dissociation

Interaction of water with Cu2O has many prominent industrial and environmental applications. This study represents detailed density-functional theory calculations investigating the adsorption of a water molecule on a Cu2O(110):CuO surface; one of the two most stable Cu2O surfaces under practical catalytic conditions of temperatures and pressures. We report herein structural geometries and binding energies for all plausible molecular and dissociative interaction of H2O with the surface. The water molecule is found to interact weakly with the Cu2O(110):CuO surface, forming several vertical and flat orientations where the latter was found to offer the most preferred site with a binding energy at 0.389 eV. Dissociation of a water molecule on this surface is found to incur a modest endothermcity of 0.71 eV.

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