Solvent-Dependent Spectral Properties in Diverse Solvents, Light Harvesting and Antiviral Properties of Mono-azo Dye (Direct Yellow-27): A Combined Experimental and Theoretical Study

2021 ◽  
pp. 1-12
Author(s):  
Babita Bisht ◽  
Venkataramana Imandi ◽  
Sanjay Pant ◽  
Anik Sen
Keyword(s):  
Solar Cell ◽  
Electronic Absorption ◽  
Azo Dye ◽  
Density Functional ◽  
Light Harvesting ◽  
Visible Region ◽  
Docking Studies ◽  
Binding Energies ◽  
Td Dft ◽  
Antiviral Activities

In this paper, we have discussed for the first time a detailed electronic absorption study of the mono-azo dye Direct Yellow 27 [C[Formula: see text]H[Formula: see text]N4Na2O9S3] (DY-27) with five different homogeneous media by applying experimental and theoretical techniques along with some new characteristics of DY-27 in the field of solar cells as well as antiviral activities. A clear absorption band in the UV-visible region was observed, although the absorption maxima lie in the visible region. The electronic absorption transitions observed in our study were fully spin and symmetry allowed transitions with [Formula: see text]–[Formula: see text] character. Time-dependent density functional theory (TD-DFT) analysis has been done for understanding the electronic and the charge transfer performance. Moreover, the impacts of polar protic and polar aprotic solvents in the structural variation of DY-27 have been reported here. Further, applications of the dye in the field of solar cell, as well as antiviral activity, were performed using molecular modeling approaches. The dye exhibited a D–[Formula: see text]–A–A structure with a high light-harvesting efficiency (LHE) and good injection efficiency acts as an effective dye sensitized solar cell (DSSC). Molecular docking studies of the dye DY-27 performed with M-protease of the different corona viruses, MERS, SARS-CoV-1 and SARS-CoV-2 indicated comparable binding energies with the controlled inhibitors and best interactions are observed for the SARS-CoV-1.

Donor Functionalized Perylene and Different π-Spacers Based Sensitizers for DSSC Applications - A Theoretical Approach

2021 ◽  
Author(s):  
D. Nicksonsebastin ◽  
P. Pounraj ◽  
Prasath M
Keyword(s):  
Density Functional Theory ◽  
Solar Cell ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Dye Sensitized Solar Cell ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Td Dft ◽  
Organic Sensitizers

Abstract Perylene based novel organic sensitizers for the Dye sensitized solar cell applications are investigated by using Density functional theory (DFT) and time dependant density functional theory (TD-DFT).The designed sensitizers have perylene and dimethylamine (DM) and N-N-dimethylaniline(DMA) functionalized perylene for the dssc applications.π-spacers are thiophene andcyanovinyl groups and cyanoacrylic acid is chosen as the acceptor for the designed sensitizers. The studied sensitizers were fully optimized by density functional theory at B3LYP/6-311G basis set on gas phase and DMF phase. The electronic absorption of the sensitizers is analyzed by TD-DFT at B3LYP/6-311G basis set in both gas and DMF phase.

scholarly journals DFT Calculations and Molecular Docking Studies on a Chromene Derivative

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Najet Aouled Dlala ◽  
Younes Bouazizi ◽  
Houcine Ghalla ◽  
Naceur Hamdi
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Noncovalent Interactions ◽  
Chemical Shifts ◽  
Molecular Geometry ◽  
Docking Studies ◽  
Fukui Functions ◽  
Td Dft ◽  
Molecular Electrostatic Potential Surface ◽  
Reduced Density

Chromenes and their derivatives have been considered as an important class of oxygen-containing heterocycles. There has been an increasing interest in the study of chromenes due to their biological activity. Herein, the structural, electronic, and vibrational properties of a chromene derivative, entitled 2‐amino‐5‐oxo‐4‐phenyl‐4,5‐dihydropyrano[3,2‐c]chromene‐3‐carbonitrile and abbreviated as Chrom-D, have been reported. The FT-IR, UV-vis, and 1H-NMR and 13C-NMR chemical shifts’ measurements were recorded. The molecular geometry and the vibrational frequencies are computed in the frame of density functional theory at the B3LYP/6-311++G(d,p) level of theory. The noncovalent interactions in the crystal lattice which are responsible to the 3D crystal structure of Chrom-D are investigated based on Hirshfeld surfaces and topological reduced density gradient (RDG) analysis. Molecular electrostatic potential surface, Mulliken charges, and Fukui functions are computed in order to find out the electrophilic and nucleophilic sites. The electronic properties of the title compound have been studied based on the TD-DFT calculations. Finally, Chrom-D has been evaluated as a multifunctional agent against Alzheimer’s disease (AD).

scholarly journals Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

2020 ◽  
Vol 22 (19) ◽  
pp. 10500-10518 ◽  
Author(s):  
Beatrix M. Bold ◽  
Monja Sokolov ◽  
Sayan Maity ◽  
Marius Wanko ◽  
Philipp M. Dohmen ◽  
...  
Keyword(s):  
Long Range ◽  
Density Functional ◽  
Light Harvesting ◽  
Tight Binding ◽  
Time Dependent ◽  
Light Harvesting Complexes ◽  
Benchmark Study ◽  
Td Dft ◽  
And Performance ◽  
Dependent Density

In the present work, we perform a benchmark study on both the isolated chromophores retinal and BChl a as well as on the biological systems, to determine the accuracy of LC-TD-DFT and LC-TD-DFTB for describing color-tuning effects.

Acceptors/linkers effects on dye sensitized solar cell: Theoretical investigations of structure-property relationship for design of efficient dye sensitizers

2014 ◽  
Vol 13 (07) ◽  
pp. 1450062
Author(s):  
Ying Guo ◽  
Huaxin Zhu ◽  
Guofeng Yang ◽  
Guilin Liu ◽  
Hunmin Yan ◽  
...  
Keyword(s):  
Solar Cell ◽  
Density Functional ◽  
Organic Dyes ◽  
Dye Sensitized Solar Cell ◽  
Structure Property ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Theoretical Investigations ◽  
Td Dft ◽  
Ground State Structures

A series of carbazole-based organic dyes such as CzFCA, CzTCA, CzSeCA, CzFRA, CzTRA and CzSeRA with introduction of various linkers (furan, thiophene and selenophen) and acceptor (cyanoacrylic acid and rhodanine-3-acetic acid) groups, were designed and theoretically investigated by density functional theory (DFT) and time dependent DFT (TD-DFT). The ground state structures and absorption spectra (both in vacuum and solvated form) were optimized by using DFT-B3LYP/6-31G(d,p), TD-B3LYP/6-311G(d,p) and PCM-TD-B3LYP/6-311G(d,p) levels of theory. Substitution of linker groups from furan to selenophen, resulted in red-shift of absorption band. CzTRA and CzSeRA exhibited superior electron injection capabilities. The finding of this study can be helpful to obtain dye-sensitized solar cell (DSSC) with superior conversion efficiency.

scholarly journals Solar Driven Photocatalytic Activity of Porphyrin Sensitized TiO2: Experimental and Computational Studies

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3131
Author(s):  
Sebastian Otieno ◽  
Anabel E. Lanterna ◽  
John Mack ◽  
Solomon Derese ◽  
Edith K. Amuhaya ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Visible Region ◽  
Solar Spectrum ◽  
Visible Spectrum ◽  
Functional Theory ◽  
Td Dft ◽  
Depth Study ◽  
Photocatalytic H2 Generation

The absence of a secure long-term sustainable energy supply is recognized as a major worldwide technological challenge. The generation of H2 through photocatalysis is an environmentally friendly alternative that can help solve the energy problem. Thus, the development of semiconductor materials that can absorb solar light is an attractive approach. TiO2 has a wide bandgap that suffers from no activity in the visible spectrum, limiting its use of solar radiation. In this research, the semiconductor absorption profile was extended into the visible region of the solar spectrum by preparing porphyrin-TiO2 (P-TiO2) composites of meso-tetra(4-bromophenyl)porphyrin (PP1) and meso-tetra(5-bromo-2-thienyl)porphyrin (PP2) and their In(III), Zn(II) and Ga(III) metal complexes. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were performed on the porphyrins to gain insight into their electron injection capability. The results demonstrate that P-TiO2 systems merit further in-depth study for applications that require efficient photocatalytic H2 generation.

Quantum Computational, Spectroscopic, NHO and Molecular Docking Studies on 1-Methyl-nicotinamide (MNA): An Antithrombotic, Anti-inflammatory, Gastroprotective and Vasoprotective Compound

2021 ◽  
Vol 6 (2) ◽  
pp. 128-140
Author(s):  
Mukesh Kumar ◽  
Satyavir Singh ◽  
Nazia Siddiqui ◽  
Saleem Javed
Keyword(s):  
Molecular Docking ◽  
Density Functional ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Binding Energies ◽  
Basis Set ◽  
Theory Approach ◽  
Fukui Functions ◽  
Donor And Acceptor ◽  
Ligand Interactions

In present work, 1-methylnicotinamide (1-MNA) has been investigated theoretically by density functional theory approach and investigated its vibrational spectroscopy. To complete the structure optimization, determination of vibrational frequencies and other valuable parameters, B3LYP method used with the 6-311++G(d,p) basis set. Atoms in molecules theory (AIM) had been used to evaluate ellipticity, isosurface projection by electron localization function and binding energies. The IR and Raman spectra have also been calculated computationally. NBO analysis employed to determine interactions of donor and acceptor. Fukui functions and molecular electrostatic potential (MEP) showed reactive regions of the molecule. UV-vis spectrum calculated using TD-DFT/PCM methods with different solvents. Thermodynamic properties like free energy, enthalpy and entropy with various temperature were calculated. By the use of the electrophilicity index, the probability of the bioactive nature of the molecule was proved theoretically. Protein-ligand interactions calculated and established by molecular docking. The biological investigations for druglikeness also employed for the (1-MNA).

Combined Virtual Screening, DFT Calculations and Molecular Dynamics Simulations to Discovery of Potent MMP-9 Inhibitors

2019 ◽  
Vol 16 (8) ◽  
pp. 892-903
Author(s):  
Hamed Bahrami ◽  
Hafezeh Salehabadi ◽  
Zahra Nazari ◽  
Massoud Amanlou
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Virtual Screening ◽  
Dft Calculations ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Docking Studies ◽  
Binding Energies ◽  
Energy Calculations ◽  
Dynamics Simulations

Background: Matrix metalloproteinase-9 (MMP-9) plays a crucial role in the development and progression of cancer. Therefore, identifying its inhibitors has enjoyed numerous attentions. In this report, a hybrid approach, including pharmacophore-based virtual screening, docking studies, and density functional theory (DFT) binding energy calculations followed by molecular dynamics simulations, was used to identify potential MMP-9 inhibitors. Methods: Pharmacophore modeling based on ARP101, as a known MMP-9 inhibitor, was performed and followed by virtual screening of ZINC database and docking studies to introduce a set of new ligands as candidates for potent inhibitors of MMP-9. The binding energies of MMP-9 and the selected ligands as well as ARP101, were estimated via the DFT energy calculations. Subsequently, molecular dynamics simulations were applied to evaluate and compare the behavior of ARP101 and the selected ligand in a dynamic environment. Results: (S,Z)-6-(((2,3-dihydro-1H-benzo[d]imidazol-2-yl)thio)methylene)-2-((4,6,7- trimethylquinazolin- 2-yl)amino)-1,4,5,6-tetrahydropyrimidin-4-ol, ZINC63611396, with the largest DFT binding energy, was selected as a proper potent MMP-9 inhibitor. Molecular dynamics simulations indicated that the new ligand was stable in the active site. Conclusion: The results of this study revealed that compared to the binding energies achieved from the docking studies, the binding energies obtained from the DFT calculations were more consistent with the intermolecular interactions. Also, the interaction between the Zinc ion and ligand, in particular the Zn2+-ligand distance, played a profound role in the quantity of DFT binding energies.

scholarly journals DFT and TD-DFT Study of [Tris(dithiolato)M]3- Complexes[M= Cr, Mn and Fe]: Electronic Structures, Properties and Analyses

2019 ◽  
Vol 67 (1) ◽  
pp. 63-68
Author(s):  
Mohammad A Matin ◽  
Mohammad Alauddin ◽  
Tapas Debnath ◽  
M Saiful Islam ◽  
Mohammed A Aziz
Keyword(s):  
Experimental Data ◽  
Density Functional Theory ◽  
Charge Transfer ◽  
Metal Ions ◽  
Molecular Orbital ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Binding Energies ◽  
Functional Theory ◽  
Td Dft

Using Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) methods, transition metal complexes of benzene-1, 2-dithiolate (L2-) ligand from Cr to Fe have been studied theoretically. The ground state geometries, binding energies, UV-Visible spectra (UV-Vis), frontier molecular orbitals (FMOs) analysis, charge analysis and natural bond orbital (NBO) have been calculated. The structural parameters are in good accord with the experimental data. The metal-ligand binding energies are one (1) order of magnitude higher than the physisorption energy of a benzene-1, 2-dthiolate molecule on a metallic surface. In accordance with experiment the calculated electronic spectra of these tris complexes show bands at 565, 559 and 546 nm for Cr3+, Mn3+, and Fe3+ respectively which are mainly qualified to ligand-to metal charge transfer (LMCT) transitions. The electronic properties analysis demonstrate that the highest occupied molecular orbital (HOMO) is mostly centered on metal coordinated sulfur atoms whereas the lowest unoccupied molecular orbital (LUMO) is mainly located on the metal surface. By calculating natural bond orbital (NBO), the intramolecular interactions and electron delocalization was obtained. The results of NBO analysis illustrated the significant charge transfer from sulfur to central metal ions, as well as to the benzene of the complex. The calculated charges on metal ions are also reported at various charge schemes. The calculations show encouraging agreement with the available experimental data. Dhaka Univ. J. Sci. 67(1): 63-68, 2019 (January)

The Nature of S-N Bonding in Sulfonamides and Related Compounds: Insights into π-Bonding Contributions from Sulfur K-Edge XAS

2020 ◽  
Author(s):  
Tulin Okbinoglu ◽  
Pierre Kennepohl
Keyword(s):  
Density Functional ◽  
Chemical Properties ◽  
Functional Theory ◽  
Rotational Barriers ◽  
Td Dft ◽  
Nitrogen Bonds ◽  
X Ray Absorption ◽  
Related Compounds ◽  
And Chemical Properties

Molecules containing sulfur-nitrogen bonds, like sulfonamides, have long been of interest due to their many uses and chemical properties. Understanding the factors that cause sulfonamide reactivity is important, yet their continues to be controversy regarding the relevance of S-N π bonding in describing these species. In this paper, we use sulfur K-edge x-ray absorption spectroscopy (XAS) in conjunction with density functional theory (DFT) to explore the role of S<sub>3p</sub> contributions to π-bonding in sulfonamides, sulfinamides and sulfenamides. We explore the nature of electron distribution of the sulfur atom and its nearest neighbors and extend the scope to explore the effects on rotational barriers along the sulfur-nitrogen axis. The experimental XAS data together with TD-DFT calculations confirm that sulfonamides, and the other sulfinated amides in this series, have essentially no S-N π bonding involving S<sub>3p</sub> contributions and that electron repulsion and is the dominant force that affect rotational barriers.

In silico Discovery of Resveratrol Analogues as Potential Agents in Treatment of Metabolic Disorders

2019 ◽  
Vol 25 (35) ◽  
pp. 3776-3783
Author(s):  
Nebojša Pavlović ◽  
Maja Đanić ◽  
Bojan Stanimirov ◽  
Svetlana Goločorbin-Kon ◽  
Karmen Stankov ◽  
...  
Keyword(s):  
In Silico ◽  
Metabolic Disorders ◽  
Partial Agonist ◽  
Aqueous Solubility ◽  
Structural Similarity ◽  
Data Bank ◽  
Docking Studies ◽  
Binding Energies ◽  
Molegro Virtual Docker ◽  
Ppar Γ

Background: Resveratrol was demonstrated to act as partial agonist of PPAR-γ receptor, which opens up the possibility for its use in the treatment of metabolic disorders. Considering the poor bioavailability of resveratrol, particularly due to its low aqueous solubility, we aimed to identify analogues of resveratrol with improved pharmacokinetic properties and higher binding affinities towards PPAR-γ. Methods: 3D structures of resveratrol and its analogues were retrieved from ZINC database, while PPAR-γ structure was obtained from Protein Data Bank. Docking studies were performed using Molegro Virtual Docker software. Molecular descriptors relevant to pharmacokinetics were calculated from ligand structures using VolSurf+ software. Results: Using structural similarity search method, 56 analogues of resveratrol were identified and subjected to docking analyses. Binding energies were ranged from -136.69 to -90.89 kcal/mol, with 16 analogues having higher affinities towards PPAR-γ in comparison to resveratrol. From the calculated values of SOLY descriptor, 23 studied compounds were shown to be more soluble in water than resveratrol. However, only two tetrahydroxy stilbene derivatives, piceatannol and oxyresveratrol, had both better solubility and affinity towards PPAR-γ. These compounds also had more favorable ADME profile, since they were shown to be more metabolically stable and wider distributed in body than resveratrol. Conclusion: Piceatannol and oxyresveratrol should be considered as potential lead compounds for further drug development. Although experimental validation of obtained in silico results is required, this work can be considered as a step toward the discovery of new natural and safe drugs in treatment of metabolic disorders.

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