scholarly journals Molecular Modeling Studies of Some Uracil and New Deoxyuridine Derivatives

2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Yousra Abdel-Mottaleb ◽  
M. S. A. Abdel-Mottaleb
Keyword(s):  
Molecular Modeling ◽  
Density Functional ◽  
Biological Activities ◽  
Quantitative Relationship ◽  
Molecular Properties ◽  
Molecular Systems ◽  
Biological Potential ◽  
Td Dft ◽  
Molecular Modeling Studies ◽  
Bioactive Agents

Molecular modeling results reported in this paper are crucial in highlighting the quantitative relationship between the optimized structure and computed molecular properties related to four newly synthesized uracil derivatives with promising biological potential as anticancer bioactive agents. Moreover, 5-fluorouracil (5-FU) and its tautomers and thiouracils molecular properties are studied and correlated with their biological activities. The great medical importance of these and similar molecular systems requires research on their quantitative structure-activity relationships (QSAR) in order to further improve our knowledge about how receptor binding, selectivity, and pharmacological effects are achieved. Modeling is performed in the ground and the first singlet excited states using density functional theory (DFT) and its time-dependent extension (TD-DFT), respectively.

Molecular Modeling Studies on Molecular Properties of Mutagenic Flavonoids

2013 ◽  
Vol 10 (6) ◽  
pp. 1385-1390
Author(s):  
Vinícius G. Maltarollo ◽  
Miriam Sannomiya ◽  
Káthia M. Honório
Keyword(s):  
Molecular Modeling ◽  
Molecular Properties ◽  
Modeling Studies ◽  
Molecular Modeling Studies

scholarly journals Structural and Electronic Properties of Adenine-Thymine Basepair : A Computational Study

2019 ◽  
Vol 67 (1) ◽  
pp. 51-54
Author(s):  
Mohammad Alauddin ◽  
Tapas Debnath ◽  
Mohammed A Aziz
Keyword(s):  
Hydrogen Bonding ◽  
Electronic Properties ◽  
Density Functional ◽  
Computational Study ◽  
Double Helix ◽  
Molecular Systems ◽  
Td Dft ◽  
Life Phenomena ◽  
Dna Double Helix ◽  
Adenine Thymine

It is well known that stability of deoxyribo-nucleic acid (DNA) double helix depends on hydrogen bonding (HB) between adenine-thymine and guanine-cytosine. HB plays an important role in molecular systems, particularly in biological systems because all lives on the earth may be viewed as a matter of hydrogen-bonding supramolecular systems. Since HBs have a central role on the mechanism of life phenomena including the structure and functions, it is essential to understand the molecular-level aspects of HB systems. Therefore, we studied the structural properties of adenine-thymine (A-T) basepair theoretically using DFT/B3LYP/6-31G level of theory. Theoretically we found four isomers of A-T basepair and the most stable isomer is one in which adenine and thymine are connected via two hydrogen bonding. The electronic properties were calculated by Time Dependent Density Functional Theory (TD-DFT) approach. Dhaka Univ. J. Sci. 67(1): 51-54, 2019 (January)

scholarly journals Theoretical Study of a New Diarylic Ligand for M2+ Cations Detection

Proceedings ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 45
Author(s):  
Carla M. Ormachea ◽  
Cristián A. Ferretti ◽  
Pablo Noriega ◽  
Leandro Gutierrez ◽  
Pedro M. E. Mancini ◽  
...  
Keyword(s):  
Density Functional ◽  
Theoretical Study ◽  
Polarizable Continuum Model ◽  
Ligand Complex ◽  
Hydrazone Ligand ◽  
Molecular Systems ◽  
The Density Functional Theory ◽  
Td Dft ◽  
Structural Electronics ◽  
Polarizable Continuum

A novel byphenyl hydrazone ligand developed as a chemosensor for the detection of Cu2+ was studied using a theoretical analysis based on the density functional theory (DFT) and time-dependent DFT (TD-DFT). The geometries of the ligand (L) and the Cu2+-ligand complex were optimized at the CAM-B3LYP/631+G(d,p) level of theory in dimethyl sulfoxide, using the conductor-like polarizable continuum model. The adsorption spectra of these molecular systems were analyzed and compared with the experimental data. Theoretical study of the structural, electronics and optical properties allowed us to understand the chemical changes that the ligand undergoes in the complexation process with the Cu+2 ion.

Relativistic time-dependent density functional theories

2018 ◽  
Vol 47 (12) ◽  
pp. 4481-4509 ◽  
Author(s):  
Wenjian Liu ◽  
Yunlong Xiao
Keyword(s):  
Excited States ◽  
Density Functional ◽  
Time Dependent ◽  
Heavy Elements ◽  
Molecular Systems ◽  
Relativistic Time ◽  
Td Dft ◽  
Dependent Density

The foundations, formalisms, technicalities, and practicalities of relativistic time-dependent density functional theories (R-TD-DFT) for spinor excited states of molecular systems containing heavy elements are critically reviewed.

scholarly journals A Theoretical and Experimental Study on the Potential Luminescent and Biological Activities of Diaminodicyanoquinodimethane Derivatives

2020 ◽  
Author(s):  
Edison Rafael Jimenez ◽  
Manuel Caetano ◽  
Nelson Santiago ◽  
F. Javier Torres ◽  
Thibault Terencio ◽  
...  
Keyword(s):  
Density Functional ◽  
Fluorescent Dyes ◽  
Biological Activities ◽  
Dipole Moments ◽  
Luminescent Properties ◽  
Oscillator Strengths ◽  
Fluorescence Properties ◽  
Quantum Yields ◽  
Td Dft ◽  
Emission Effect

Since the discovery of the aggregation-induced emission effect in 2001, diaminodicyanoquinone derivatives (DADQs) have presented interesting fluorescence properties, allowing them to be considered fluorescent dyes capable of showing quantum yields above 90%. Besides, the diaminodiacyanoquinone core represents a versatile building block propense either to modification or integration into different systems to obtain and provide them unique photophysical features. Herein, we carried out a theoretical study on the fluorescence properties of three different diaminodicyanoquinodimethane systems. Therefore, time-dependent density functional theory (TD-DFT) was used to obtain the values associated with the dipole moments, oscillator strengths, and the conformational energies between the ground and the first excited states of each molecule. The results suggest that only two of the three studied systems possess significant luminescent properties. In a further stage, the theoretical insights were confirmed by means of experimental measurements, which not only retrieved the luminescence of the DADQs, but also suggest a preliminary and promising antibacterial activity of these systems.

scholarly journals A Theoretical and Experimental Study on the Potential Luminescent and Biological Activities of Diaminodicyanoquinodimethane Derivatives

2021 ◽  
Vol 22 (1) ◽  
pp. 446
Author(s):  
Edison Rafael Jiménez ◽  
Manuel Caetano ◽  
Nelson Santiago ◽  
F. Javier Torres ◽  
Thibault Terencio ◽  
...  
Keyword(s):  
Excited States ◽  
Density Functional ◽  
Biological Activities ◽  
Dipole Moments ◽  
Luminescent Properties ◽  
Oscillator Strengths ◽  
Fluorescence Properties ◽  
Quantum Yields ◽  
Functional Theory ◽  
Td Dft

Recently, several studies have demonstrated that diaminodicyanoquinone derivatives (DADQs) could present interesting fluorescence properties. Furthermore, some DADQs under the solid state are capable of showing quantum yields that can reach values of 90%. Besides, the diaminodiacyanoquinone core represents a versatile building block propense either to modification or integration into different systems to obtain and provide them unique photophysical features. Herein, we carried out a theoretical study on the fluorescence properties of three different diaminodicyanoquinodimethane systems. Therefore, time-dependent density functional theory (TD-DFT) was used to obtain the values associated with the dipole moments, oscillator strengths, and the conformational energies between the ground and the first excited states of each molecule. The results suggest that only two of the three studied systems possess significant luminescent properties. In a further stage, the theoretical insights were confirmed by means of experimental measurements, which not only retrieved the photoluminescence of the DADQs, but also suggest a preliminary and promising antibacterial activity of these systems.

Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions ◽  
The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

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.

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