DFT, RHF and MP2 based study of the thermodynamic, electronic and non-optical properties of DNA nucleobases

Gidado, A. S.; Abubakar, Salihu Abdullahi; Shariff, M.A.

doi:10.4314/bajopas.v10i1.17

Cited by 2 publications

(4 citation statements)

References 1 publication

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“…"The applicability of DFT ranges from atoms, molecules and solids to nuclei and quantum and classical fluids. DFT predicts a great variety of molecular properties: molecular structures, vibrational frequencies, atomization energies, ionization energies, electric and magnetic properties, reaction paths and so on" [20][21].…”

Section: Density Functional Theorymentioning

confidence: 99%

“…"Density functional approach is based on a strategy of modelling the electron correlation via general functional of the electron density. Following the work by Kohn and Sham, the approximate functional employed by current DFT methods separate the electronic energy into several terms" [20][21]. (1) where is the kinetic energy term, includes terms describing the potential energy of the nuclear-electron attraction and of the repulsion between pairs of nuclei, is the electronelectron repulsion term, and is the exchange-correlation term and includes the remaining part of the electron-electron interactions.…”

Section: Density Functional Theorymentioning

confidence: 99%

“…The infrared intensities can be computed with the equation [21] where is the self-consistent field energy, f is the electric field, a is a nuclear coordinate, is the one-electron atomic orbital integral, U a is related to the derivative of the molecular orbital coefficients with respect to a by (9)…”

Section: Vibrational Frequencymentioning

confidence: 99%

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Effects of Mono-Halogen-Substitution on the Electronic and Non-Linear Optical Properties of Poly(3-hexylthiophene-2,5-diyl) for Solar Cell Applications: A DFT Approach

Maigari

Suleiman²,

Gidado³

et al. 2022

JENRR

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Poly(3-hexylthiophene-2,5-diyl) with the acronym P3HT and its derivatives are p-type conjugated semiconductor polymers that have been proved to be good organic semiconductors. They have several applications in many areas, such as photovoltaic systems, organic light-emitting diodes, and so on. The instability of organic molecules under ambient conditions is one factor deterring the commercialization of such organic semiconductor devices. Here we present a theoretical study using density functional theory (DFT) approach with Gaussian 09 and GaussView 5.0, to investigate the effects of halogens (Bromine, Chlorine, Fluorine and Iodine) on the electronic and nonlinear optical properties of poly(3-hexylthiophene-2,5-diyl) (P3HT). This is to enable us to address the issue of instability in the molecule. The bond lengths and bond angles of the mono-halogenated molecules were found to be less than that of the isolated Poly(3-hexylthiophene-2,5-diyl). Iodine doped P3HT was found to be the most stable amongst the studied molecule for having the least bond angles and bond lengths. The calculated band gap for iodine doped P3HT and fluorine doped P3HT were observed to have the lowest energy gap of 3.519 eV and 3.545 eV respectively thus proving that iodine doped P3H is the most stable and this makes it more suitable for photovoltaic applications. The molecule with the highest value of chemical hardness was obtained to be the isolated P3HT with a chemical hardness of 1.937eV. This is followed by bromine doped P3HT, chlorine doped P3HT, fluorine doped P3HT and iodine doped P3HT with values as 1.925 eV, 1.813 eV, 1.773 eV, and 1.7595 eV respectively. All the substituted molecules results were found to be more reactive than their isolated form for having lower values of chemical hardness. The results for the nonlinear optical (NLO) properties show that the first-order hyper-polarizability of chlorine doped P3HT and iodine doped P3HT as and respectively were found to be about eight times more than that of the urea value (0.3728 x10-30 esu), which is commonly used for the comparison of NLO properties with other materials. This makes them very good NLO materials. The open circuit voltage was also calculated. The highest values of the calculated open circuit voltage were found to be (PCBM C60) in chloroP3HT and 1.3134 eV (PCBM C60) in flouroP3HT. The results of the IR frequency show that the doped molecules are more stable than the isolated molecule. Zero-point vibrational energy (ZPVE), total entropy (S) and molar heat capacity (Cv) were also calculated and presented. We also observe that the entropy and heat capacity of the doped materials are higher than those of the original molecule, which confirms that the charge dynamics of the doped molecules are higher than those of the original molecule at the same temperature. This result further demonstrates that these doped materials have a high chemical reactivity and a high thermal resistivity, hence their application in the fields of organic electronics. By and large the overall results confirm that there is a good electron transfer within the doped molecules which makes them have potential applications in photovoltaic devices.

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Section: Density Functional Theorymentioning

confidence: 99%

Section: Density Functional Theorymentioning

confidence: 99%

See 1 more Smart Citation

Effects of Mono-Halogen-Substitution on the Electronic and Non-Linear Optical Properties of Poly(3-hexylthiophene-2,5-diyl) for Solar Cell Applications: A DFT Approach

Maigari

Suleiman²,

Gidado³

et al. 2022

JENRR

View full text Add to dashboard Cite

show abstract

“…The similar kind of quantum calculations and reactivity descriptor derivation approach has been used by several groups for different kind of molecules like nucleobases, small chemical compounds and their derivatives [65][66][67][68][69]. We have used this strategy for studying antisense modifications at the monomer level.…”

Section: Global Reactivity Descriptorsmentioning

confidence: 99%

Quantum Chemical Calculations on Locked Nucleic Acid based Antisense Modifications: A Density Functional Theory (DFT) Study at Monomer Level

N¹,

Dowerah²,

Sonavane³

et al. 2020

Preprint

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<p>Antisense technology has been developed as the next generation drug discovery methodology by which unwanted gene expression can be inhibited by targeting mRNA specifically with antisense oligonucleotides. It has been observed that a good number of these molecules entered into clinical trials at a faster rate and some of them got approved. The computational studies of antisense modifications based on phosphorothioate (PS), methoxyethyl (MOE), locked nucleic acids (LNA) may help to design better novel modifications. In the present study, newer LNA based modifications have been proposed. The conformational search and density functional theory (DFT) calculations have been used to investigate the quantum chemical parameters of PS, LNA, MOE, and novel LNA based proposed modifications. The conformational search has been done to identify the most and alternative stable conformations. The geometry optimization followed by single point energy calculation has been done at B3LYP/6-31G(d,p) level for gas phase and B3LYP/6-311G(d,p) level for the solvent phase of all modifications. The electronic properties and the quantum chemical descriptors for the frontier molecular orbitals of all the antisense modifications were derived and compared. The local and global reactivity descriptors, such as hardness, chemical potential, electronegativity, electrophilicity index, Fukui function calculated at DFT level for the optimized geometries. These are used for understanding the reactive nature and reactive sites of the modifications. A comparison of global reactivity descriptors confirmed that LNA based modifications are the most reactive modifications and prone to the chemical reactions. It may form stable duplex when it is bound to complementary nucleotides, compared to other modifications. Therefore, we are proposing that one of our proposed antisense modification (A3) may show strong binding to the complementary nucleotide as LNA and may also show reduced toxic effects like MOE.</p>

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DFT, RHF and MP2 based study of the thermodynamic, electronic and non-optical properties of DNA nucleobases

Abstract: ABSTRACT

Cited by 2 publications

References 1 publication

Effects of Mono-Halogen-Substitution on the Electronic and Non-Linear Optical Properties of Poly(3-hexylthiophene-2,5-diyl) for Solar Cell Applications: A DFT Approach

Effects of Mono-Halogen-Substitution on the Electronic and Non-Linear Optical Properties of Poly(3-hexylthiophene-2,5-diyl) for Solar Cell Applications: A DFT Approach

Quantum Chemical Calculations on Locked Nucleic Acid based Antisense Modifications: A Density Functional Theory (DFT) Study at Monomer Level

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