scholarly journals Modeling the Effect of Hydration on the Electronic and Vibrational Properties of AZT

2020 ◽  
Vol 11 (2) ◽  
pp. 9253-9265
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Hydration Shell ◽  
Water Molecules ◽  
Functional Theory ◽  
Hydration Shells ◽  
Immunodeficiency Virus ◽  
Ir Frequencies ◽  
Homo Lumo

The 3'-azido-3'-deoxythymidine, which is termed AZT, was introduced as anti-human immunodeficiency virus HIV. AZT is supposed to interact with water molecules forming two hydration shells. In the first shell, five water molecules were surrounding five active sites. Each water molecule then further interacted with two water molecules forming the second hydration shell. The computational note is dedicated on the basis of density functional theory (DFT). So that, DFT:B3LYP/6-31G(d,p) was used to follow up on the changes in AZT as a result of hydration. The DFT was used to calculate total dipole moment (TDM), HOMO/LUMO bandgap energies, molecular electrostatic potential (MESP), and IR frequencies.

scholarly journals Computational notes on the molecular modeling analyses of flutamide

2020 ◽  
Vol 9 (2) ◽  
pp. 1099-1102
Keyword(s):  
Molecular Modeling ◽  
Active Sites ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Band Gap Energy ◽  
Total Dipole Moment ◽  
Functional Theory ◽  
Hartree Fock ◽  
Homo Lumo ◽  
Important Drug

Flutamide is one of the recommended and important drug for treating prostate cancer. In spite of this there some scientific reports that recommending against this drug according to some side effects. This is in turn paves the way towards investigating electronic properties of the drug with conventional molecular modeling methods. So that, density functional theory at B3LYP as well as Hartree-Fock HF together with PM3 were utilized to study the drug. Some important parameters are computed in this computational note including total dipole moment, HOMO/LUMO band gap energy and the contour of molecular electrostatic potential in order to map the active sites of the studied drug in terms the charge distributions. Finally, the infrared assignment of the flutamide is introduced based on B3LYP model.

scholarly journals Solvatochromism and Theoretical Studies of Dicyanobis(phenylpyridine)iridium(III) Complex Using Density Functional Theory

2021 ◽  
Vol 21 (3) ◽  
pp. 769
Author(s):  
Noorshida Mohd Ali ◽  
Anthony J. H. M. Meijer ◽  
Michael D. Ward ◽  
Norlinda Daud ◽  
Norhayati Hashim ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Good Description ◽  
Photophysical Properties ◽  
Hydration Shell ◽  
Water Molecules ◽  
Singlet Ground State ◽  
Absorption Bands ◽  
Functional Theory

Luminescent cyanometallate [Ir(ppy)2(CN)2]– (ppy = C6H5C5H4N) has recently gained attention due to its desired photophysical properties. Our research group reported that the [Ir(ppy)2(CN)2]– has shown a negative solvatochromism like [Ru(bipy)(CN)4]2–, resulting in a blue-shift of the UV-Vis absorption bands in the water. Therefore, to gain insight into the specific solvent-solute interaction governed by the hydrogen bond in the solvation hydration shell, density functional theory (DFT) calculations were performed on the singlet ground state of the [Ir(ppy)2(CN)2]– and its solvent environment in the water at B3LYP level theory. It was demonstrated, seven water molecules provided a good description of the relevant spectra: IR and UV-Vis. The calculation reproduced the positions and intensities of the observed n(CºN) bands at 2069 and 2089 cm–1. The calculated MLCT transition wavelength was 366 nm vs. a measured value of 358 nm, differing by 8 nm. The study revealed the water molecules interacted with cyanide ligands through CN⋯H-OH type hydrogen bonds and water-water interactions (HO-H⋯OH2 type hydrogen bonds) were involved in the solvation hydration shell around the [Ir(ppy)2(CN)2]–.

scholarly journals Cluster modeling and coordination structures of Cu+ ions in Al-incorporated Cu-MEL catalysts – a density functional theory study

2017 ◽  
Vol 61 (1) ◽  
Author(s):  
Mehdi Ghambarian ◽  
Zahra Azizi ◽  
Mohammad Ghashghaee
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Zeolite Catalyst ◽  
Energy Gap ◽  
Structural Features ◽  
Lumo Energy ◽  
Functional Theory ◽  
Cluster Modeling ◽  
Homo Lumo ◽  
Cu Ions

<p>A density-functional-based cluster modeling was implemented on the Al-incorporated Cu-MEL zeolite catalyst (Cu-ZSM-11) to probe the electronic, energetic and structural features of the active sites of the catalyst at the B3LYP/6-311+G* and M06/Def2-TZVP levels. The HOMO–LUMO energy gap fell into the range of 3.31–5.15 eV at TD-BH&amp;HLYP/6-311+G* with the lowest magnitude for the I–Cu and M1–Cu clusters. Population-averaged values for the exchange enthalpy and binding energy were also calculated, being approximately 125 and 171 kcal/mol, respectively.</p>

A First-Principles Computational Comparison of the Aqueous Anatase TiO2 (001) Interface and the Disordered, Fluorinated TiO2 Interface

2018 ◽  
Author(s):  
Kyle Reeves ◽  
Damien Dambournet ◽  
Christel Laberty-Robert ◽  
Rodolphe Vuilleumier ◽  
Mathieu Salanne
Keyword(s):  
Density Of States ◽  
Density Functional ◽  
Water Dissociation ◽  
Water Molecules ◽  
Chemical Doping ◽  
Charge Balance ◽  
Functional Theory ◽  
Adsorption Of Water ◽  
Properties Of Materials ◽  
Computational Comparison

Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO<sub>2</sub> with charge balance achieved via the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a<br>monolayer of water via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1eV of the Fermi energy for various steps throughout the simulation, and we determine that the<br>variation in this representation of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in<br>the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules at the surface.

A First-Principles Computational Comparison of the Aqueous Anatase TiO2 (001) Interface and the Disordered, Fluorinated TiO2 Interface

2018 ◽  
Author(s):  
Kyle Reeves ◽  
Damien Dambournet ◽  
Christel Laberty-Robert ◽  
Rodolphe Vuilleumier ◽  
Mathieu Salanne
Keyword(s):  
Density Of States ◽  
Density Functional ◽  
Water Dissociation ◽  
Water Molecules ◽  
Chemical Doping ◽  
Charge Balance ◽  
Functional Theory ◽  
Adsorption Of Water ◽  
Properties Of Materials ◽  
Computational Comparison

Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO<sub>2</sub> with charge balance achieved via the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a<br>monolayer of water via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1eV of the Fermi energy for various steps throughout the simulation, and we determine that the<br>variation in this representation of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in<br>the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules at the surface.

scholarly journals Hyaluronan orders water molecules in its nanoscale extended hydration shells

2021 ◽  
Vol 7 (10) ◽  
pp. eabf2558
Author(s):  
J. Dedic ◽  
H. I. Okur ◽  
S. Roke
Keyword(s):  
Second Harmonic ◽  
Hydration Shell ◽  
Water Molecules ◽  
Temperature Dependent ◽  
Flexible Chain ◽  
Optical Modeling ◽  
Hydration Shells ◽  
Second Harmonic Scattering ◽  
Nuclear Quantum Effects ◽  
Extracellular Environment

Hyaluronan (HA) is an anionic, highly hydrated bio-polyelectrolyte found in the extracellular environment, like the synovial fluid between joints. We explore the extended hydration shell structure of HA in water using femtosecond elastic second-harmonic scattering (fs-ESHS). HA enhances orientational water-water correlations. Angle-resolved fs-ESHS measurements and nonlinear optical modeling show that HA behaves like a flexible chain surrounded by extended shells of orientationally correlated water. We describe several ways to determine the concentration-dependent size and shape of a polyelectrolyte in water, using the amount of water oriented by the polyelectrolyte charges as a contrast agent. The spatial extent of the hydration shell is determined via temperature-dependent measurements and can reach up to 475 nm, corresponding to a length of 1600 water molecules. A strong isotope effect, stemming from nuclear quantum effects, is observed when light water (H2O) is replaced by heavy water (D2O), amounting to a factor of 4.3 in the scattered SH intensity.

scholarly journals Study on the adsorption selection of CH$$_4$$ on CuO (110) versus (111) surfaces: a density functional theory study

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Adsorption Capacity ◽  
Active Sites ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Density Functional Theory Calculations ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Strong Adsorption ◽  
Selection Of

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.

scholarly journals Structure of aqueous sodium acetate solutions by X-Ray scattering and density functional theory

2020 ◽  
Vol 92 (10) ◽  
pp. 1627-1641
Author(s):  
Guangguo Wang ◽  
Yongquan Zhou ◽  
He Lin ◽  
Zhuanfang Jing ◽  
Hongyan Liu ◽  
...  
Keyword(s):  
Sodium Acetate ◽  
Density Functional ◽  
Hydration Shell ◽  
Ion Pair ◽  
Water Molecules ◽  
Sodium Acetate Solution ◽  
Acetate Solution ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

AbstractThe structure of aq. sodium acetate solution (CH3COONa, NaOAc) was studied by X-ray scattering and density function theory (DFT). For the first hydrated layer of Na+, coordination number (CN) between Na+ and O(W, I) decreases from 5.02 ± 0.85 at 0.976 mol/L to 3.62 ± 1.21 at 4.453 mol/L. The hydration of carbonyl oxygen (OC) and hydroxyl oxygen (OOC) of CH3COO− were investigated separately and the OC shows a stronger hydration bonds comparing with OOC. With concentrations increasing, the hydration shell structures of CH3COO− are not affected by the presence of large number of ions, each CH3COO− group binds about 6.23 ± 2.01 to 7.35 ± 1.73 water molecules, which indicates a relatively strong interaction between CH3COO− and water molecules. The larger uncertainty of the CN of Na+ and OC(OOC) reflects the relative looseness of Na-OC and Na-OOC ion pairs in aq. NaOAc solutions, even at the highest concentration (4.453 mol/L), suggesting the lack of contact ion pair (CIP) formation. In aq. NaOAc solutions, the so called “structure breaking” property of Na+ and CH3COO− become effective only for the second hydration sphere of bulk water. The DFT calculations of CH3COONa (H2O)n=5–7 clusters suggest that the solvent-shared ion pair (SIP) structures appear at n = 6 and become dominant at n = 7, which is well consistent with the result from X-ray scattering.

scholarly journals Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

The Quantum Length Dependence of Conductance in Molecular Device: An Ab Initio Study

2010 ◽  
Vol 663-665 ◽  
pp. 519-522
Author(s):  
Cai Juan Xia ◽  
Han Chen Liu ◽  
Ying Tang Zhang
Keyword(s):  
Electronic Transport ◽  
First Principles ◽  
Electronic Structures ◽  
Density Functional ◽  
Molecular Device ◽  
Functional Theory ◽  
Length Dependence ◽  
Molecular Conductance ◽  
Homo Lumo ◽  
Molecular Compounds

By Applying Nonequilibrium Green’s Function Formalism Combined First-Principles Density Functional Theory, we Investigate the Electronic Transport Properties of Thiophene and Furan Molecules with Different Quantum Length. the Influence of HOMO-LUMO Gaps and the Spatial Distributions of Molecular Orbitals on the Electronic Transport through the Molecular Device Are Discussed in Detail. the Results Show that the Transport Behaviors Are Determined by the Distinct Electronic Structures of the Molecular Compounds. the Length Dependence of Molecular Conductance Exhibits its Diversity for Different Molecules.

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