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)

pH-related fluorescence quenching mechanism of pterin derivatives and the effects of 6-site substituents

2018 ◽  
Vol 96 (4) ◽  
pp. 404-410
Author(s):  
Lei Liu ◽  
Bingqing Sun
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Fluorescence Quenching ◽  
Density Functional ◽  
Relaxation Processes ◽  
Quenching Mechanism ◽  
Functional Theory ◽  
Td Dft ◽  
Fluorescence Quenching Mechanism ◽  
Acidic Conditions

2-Amino-4-hydroxypteridine (pterin) and its derivatives serve as photooxidants and exhibit strong fluorescence. When they interact with hydrogen acceptors such as acetate and phosphate, their fluorescences are significantly quenched in acidic conditions (pH 4.9–5.5) but are retained in basic conditions (pH 10.0–10.5). This pH-related fluorescence quenching mechanism of pterin and its derivatives are fully investigated by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Pterin and its derivatives are demonstrated to show favorable excited-state proton transfer (ESPT) abilities in acidic conditions that induce the experimentally observed fluorescence quenching. In contrast, the ESPT processes are found to be retarded due to the lack of strong hydrogen-bonding interactions in basic environments, which sustain their fluorescence. Interestingly, these ESPT processes are found to show different site specificities depending on the 6-site substituents. The introduction of electron-donating substituent activates the N1 site, making it the preferred ESPT site. By contrast, the introduction of an electron-withdrawing substituent activates the N5 site, making it the favorable ESPT site. The substitutions of different functional groups are found to affect the locations of acidic centers during the excitation and relaxation processes. This further affects the hydrogen-bonding patterns and ultimately brings site specificity to the ESPT process.

scholarly journals Structure, electronic properties, NBO, NLO and chemi-cal reactivity of bis (1, 4-dithiafulvalene) derivatives: functional density theory study

2017 ◽  
Vol 6 (1) ◽  
pp. 18
Author(s):  
Tahar Abbaz ◽  
Amel Bendjeddou ◽  
Didier Villemin
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Computational Study ◽  
Molecular Geometry ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Reactivity Descriptors ◽  
Nlo Property ◽  
Functional Density Theory ◽  
Nucleophilic Reactivity

In this work, through computational study based on density functional theory (DFT/B3LYP) using basis set 6-31G (d,p) a number of global and local reactivity descriptors for a series of molecules containing a TTF function which are bis (1,4-dithiafulvalene) derivatives. They were computed to predict the reactivity and the reactive sites on the molecules. The molecular geometry and the electronic properties in the ground state such as frontier molecular orbital (HOMO and LUMO), ionization potential (I) and electron affinity (A) were investigated to get a better insight of the molecular properties. Molecular electrostatic potential (MEP) for all compounds were determined to check their electrophilic or nucleophilic reactivity. Fukui index, polarizability, hyperpolarizability, second order NLO property and natural bond orbital (NBO) analyses have also employed to determine the reactivity of bis (1,4-dithiafulvalene) derivatives.

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.

scholarly journals Hetarylazopyrazolone Dyes Based on Benzothiazole and Benzimidazole Ring Systems: Synthesis, Spectroscopic Investigation, and Computational Study

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Ebru Aktan ◽  
Tahsin Uyar
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Study ◽  
Benzimidazole Ring ◽  
Acid Base ◽  
Functional Theory ◽  
Ring Systems ◽  
Td Dft ◽  
Elemental Analyses ◽  
Experimental Values

In this study, the synthesized coupling component 1-(2-benzothiazolyl)-3-methylpyrazol-5-one reacted with diazotised heterocyclic amines to afford six novel hetarylazopyrazolone dyes. These azo dyes based on benzothiazole and benzimidazole ring systems were characterized by spectral methods and elemental analyses. The solvatochromic behaviors of these dyes in various solvents were evaluated. The ground state geometries of the dyes were optimized using density functional theory (DFT). Solvent, acid-base, and substituent influences on the wavelength of the maximum absorption were examined in detail. Time-dependent density functional theory (TD-DFT) calculations were performed to obtain the absorption spectra of the dyes in various solvents and the results compared with experimental values. Besides, frontier molecular orbitals (FMO) analysis for the dyes is also described from the computational process.

scholarly journals Computational Study of some Double Headed Acyclo-C-Nucleosides

2015 ◽  
Vol 61 ◽  
pp. 1-11
Author(s):  
Sarah Amara ◽  
Noureddine Tchouar ◽  
Salah Belaidi
Keyword(s):  
Electronic Properties ◽  
Ground State ◽  
Density Functional ◽  
Computational Study ◽  
Experimental Studies ◽  
Functional Theory ◽  
Hartree Fock ◽  
Structural And Electronic Properties ◽  
Semi Empirical

In the present paper we have a focus in a study of theoretical characterization of three double headed acyclo-C-nucleosides, which are a recent target of experimental studies. The structural and electronic properties of double headed acyclo-C-nucleosides, 1,4-bis (3-mercapto-1H-1,2,4-triazol-5-yl) butane-1,2,3,4-tetrol, 1,4-bis (4-amino-5-mercapto-4H-1,2,4-triazol-3-yl) butane-1,2,3,4-tetrol and 5,5'-(1,2,3,4-tetrahydroxybutane-1,4-diyl) bis (1,3,4-oxadiazole-2(3H)-thione), have been investigated theoretically by performing semi-empirical molecular orbital, ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) calculations. Geometries of the three molecules are optimized at the level of Austin Model 1 (AM1). The electronic properties and relative energies of the molecules have been calculated by HF and DFT in the ground state.

scholarly journals Virtual Screening of Marine Natural Compounds by Means of Chemoinformatics and CDFT-Based Computational Peptidology

2020 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Virtual Screening ◽  
Density Functional ◽  
Computational Study ◽  
Chemical Reactivity ◽  
Conceptual Density Functional Theory ◽  
Qsar Studies ◽  
Molecular Systems ◽  
Biological Targets ◽  
Global And Local

This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the Theopapuamides A-D family of marine peptides by making use of our own proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular systems. CP allowed for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea of the chemical reactivity properties of the marine natural products under study which are already known to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans in DFT) technique as well as the MN12SX/Def2TZVP/H2O model chemistry has been successfully verified. Together with several Chemoinformatic tools that can be used for the improvement of process of Virtual Screening, some additional properties of these marine peptides were identified related to their ability to behave as useful drugs. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the Theopapuamides A-D pharmacokinetics are also reported.

Aerobic photolysis of methylcobalamin: structural and electronic properties of the Cbl–O–O–CH3 intermediate

2020 ◽  
Vol 49 (13) ◽  
pp. 4114-4124 ◽  
Author(s):  
Arghya Pratim Ghosh ◽  
Piotr Lodowski ◽  
Aida Bazarganpour ◽  
Marzena Leks ◽  
Pawel M. Kozlowski
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Molecular Oxygen ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
Td Dft ◽  
Structural And Electronic Properties

Photolysis of methylcobalamin (MeCbl) in the presence of molecular oxygen (O2) has been investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT).

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.

BIS(BIPYRIDYL)-RU(II)-1-BENZOYL-3-(PYRIDINE-2-YL)-1H-PYRAZOLE AS POTENTIAL PHOTOSENSITISER: EXPERIMENTAL AND DENSITY FUNCTIONAL THEORY STUDY

2017 ◽  
Vol 79 (5-3) ◽  
Author(s):  
Wun-Fui Mark-Lee ◽  
Febdian Rusydi ◽  
Lorna Jeffery Minggu ◽  
Takashi Kubo ◽  
Mohammad Kassim
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Density Functional ◽  
Energy Levels ◽  
Spectroscopic Techniques ◽  
Functional Theory ◽  
Injection Process ◽  
Highest Occupied Molecular Orbital ◽  
Ligand Charge Transfer ◽  
Td Dft

Ru(II) complexes, [Ru(bpy)2(m-R-L)](PF6)2 where bpy = 2,2’-bipyridyl and  m-R-L= 1-(meta-R)-benzoyl-3-(pyridine-2-yl)-1H-pyrazole derivatives (R = H, CH3 and Cl) abbreviated as RuL, Ru(m-CH3-L) and Ru(m-Cl-L) complexes, respectively, were synthesized and characterized with spectroscopic techniques namely, infrared, UV-Vis and nuclear magnetic resonance (NMR), photoluminescence and mass spectroscopy. Density functional theory (DFT) and time-dependent (TD) DFT calculations were carried out to study the structural and electronic features of the molecules. These Ru(II) complexes exhibit photo-electronic properties required for a photosensitiser in a TiO2-catalysed photoelectrochemical (PEC) cell. In-depth understanding of the R-L fragment functionality is important to tune the photo-electronic properties of the Ru(II) complex. The highest-occupied molecular orbital (HOMO) is mainly localized at the Ru(II) centre, while the LUMO is dominantly spread across the R-L ligand. The Ru(II) complexes showed favourable metal-to-ligand charge transfer (MLCT) energy levels, which are comparably higher than the conduction band of TiO2 to facilitate electron injection process. Among the Ru(II) complexes, Ru(m-Cl-L) comparatively possesses the highest photoluminescence quantum yield and has the potential to be applied as photosensitiser in PEC systems.

Design of donor–acceptor copolymers for organic photovoltaic materials: a computational study

2018 ◽  
Vol 20 (5) ◽  
pp. 3581-3591 ◽  
Author(s):  
Haydar Taylan Turan ◽  
Oğuzhan Kucur ◽  
Birce Kahraman ◽  
Seyhan Salman ◽  
Viktorya Aviyente
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Time Dependent ◽  
Organic Photovoltaic ◽  
Functional Theory ◽  
Organic Chromophores ◽  
Photovoltaic Materials ◽  
Td Dft ◽  
Organic Photovoltaic Materials ◽  
Donor Acceptor

80 different push–pull type organic chromophores which possess Donor–Acceptor (D–A) and Donor–Thiophene–Donor–Thiophene (D–T–A–T) structures have been systematically investigated by means of density functional theory (DFT) and time-dependent DFT (TD-DFT) at the B3LYP/6-311G* level.

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