scholarly journals Quantum chemical studies of interactions between Au6 cluster and DNA bases

2020 ◽  
Vol 4 (2) ◽  
pp. First
Author(s):  
Nhat Vu Pham ◽  
Nguyen Thanh Si ◽  
Mai Mac Son ◽  
Pham Thi Bich Thao ◽  
Nguyen Van Hong ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Energy Gap ◽  
Gold Cluster ◽  
Water Environment ◽  
Gold Surface ◽  
Electrical Signal ◽  
Binding Energies ◽  
Basis Set ◽  
Dna Bases

Density functional theory (DFT) is employed to examine the adsorption mechanism of DNA bases (adenine, guanine, cytosine, and thymine) on the gold surface using Au6 cluster as model reactant. Geometries of resulting complexes are optimized using the PBE functional in conjunction with the cc-pVTZ-PP consistent-correlation pseudopotential basis set for gold and the cc-pVTZ basis set for the non-metals. The binding sites and energies, along with several quantum chemical indicators are also investigated at the same level of theory. The binding energies between Au6 cluster and DNA bases are computed to be around 14–25 kcal/mol in gas-phase and slightly reduced to 10 – 20 kcal/mol in the water environment. Cytosine has the highest affinity with gold cluster, decreasing as follows cytosine > adenine  guanine > thymine. If a visible light with a frequency of Hz (500 nm) is applied, the time for the recovery of Au6 from the complexes will be in the range of   (for thymine) to 10 (for cytosine) seconds at 298 K in water. In addition, the geometric structures of both the gold cluster and DNA bases are almost unchanged during the complexation. The gold cluster is found to benefit from a larger change of energy gap that could be converted to an electrical signal for the detection of these molecules. Current results could provide us with fundamentals for understanding the DNA bases absorption on gold nanoparticle surfaces at the atomic and molecular levels.

scholarly journals Structural and quantum chemical studies on aryl sulfonyl piperazine derivatives

2019 ◽  
Vol 9 (1-s) ◽  
pp. 88-97 ◽  
Author(s):  
Tahar Abbaz ◽  
Amel Bendjeddou ◽  
Didier Villemin
Keyword(s):  
Electrostatic Potential ◽  
Quantum Chemical ◽  
Density Functional ◽  
Energy Gap ◽  
Nbo Analysis ◽  
Basis Set ◽  
Linear Optics ◽  
Hydrogen Atoms ◽  
Charge Delocalization ◽  
Piperazine Derivatives

The optimized molecular structure and electronic features of aryl sulfonyl piperazine derivatives 1-4 have been investigated theoretically using Gaussian 09 software package and DFT/B3LYP method with 6-31G (d,p) basis set. The reactivity of the title molecules was investigated and both the positive and negative centers of the molecules were identified using molecular electrostatic potential (MEP) analysis which the results illustrate that the regions reveal the negative electrostatic potential are localized in sulfamide function while the regions presenting the positive potential are localized in the hydrogen atoms. The energies of the frontier molecular orbitals and LUMO-HOMO energy gap are measured to explain the electronic transitions. Global reactivity parameters of the aryl sulfonyl piperazine derivatives molecules were predicted to find that the more reactive and softest compound is the compound 3. Mulliken’s net charges have been calculated and results show that 3N is the more negative and 33S is the more positive charge, which Indicates extensive charge delocalization in the entire molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization (π→π transitions) has been analyzed using NBO analysis. Fist hyperpolarizability is calculated in order to find its importance in non-linear optics and the results show that the studied molecules have not the NLO applications. Keywords: sulfamide; density functional theory; computational chemistry; electronic structure; quantum chemical calculations.

scholarly journals A computational study of cysteine and glutathione binding to small gold cluster Au8

2020 ◽  
Vol 23 (1) ◽  
Author(s):  
Si Thanh Nguyen ◽  
Pham Nhat Vu
Keyword(s):  
Gas Phase ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Computational Study ◽  
Gold Cluster ◽  
Gold Surface ◽  
Basis Set ◽  
Functional Theory ◽  
Adsorption Behaviors ◽  
Energy Surfaces

Introduction: Understanding the binding mechanism between gold and is a fundamental step for numerous applications in biosensors and targeted drug delivery. This study aims to clarify the adsorption behaviors of CYS and GSH on the gold surface using a small gold Au8 cluster as a model reactant. Methods: Here, we examine in details the molecular interaction between Au8 cluster with (CYS) and (GSH) by means of density functional theory (DFT). The PBE functional is employed in combination with the basis set for non-metal atoms and the basis set for gold. Harmonic frequencies are also computed to confirm optimized geometries as local minima or transition states on the potential energy surfaces. Results: The calculated results show that these molecules prefer to anchor on the gold cluster via the sulfur atom with the adsorption energies of 20.3 and 30.8 / for CYS and GSH, respectively, in gas phase. In water, such values are considerably reduced, namely 19.0 / for CYS and 26.4 / for GSH. If a visible light with a frequency of v = 6x1014 Hz (500 nm) is applied, the time for the recovery of CYS and GSH from the most stable complexes will be about 1.24 and 6.03x107 seconds at 298 K in gas phase. Conclusion: The Au8 cluster could be a promising material for designing sensor in CYS and GSH selective detection.

scholarly journals Molecular Structure, Homo-Lumo and Vibrational Analysis Of Ergoline By Density Functional Theory

2021 ◽  
Vol 14 (14) ◽  
pp. 21-30
Author(s):  
Bhawani Datt Joshi ◽  
Ghanshyam Thakur ◽  
Manoj Kumar Chaudhary
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Graphical Representation ◽  
Energy Gap ◽  
Quantum Chemical Study ◽  
Vibrational Analysis ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
Functional Theory

In this work, quantum chemical study on a natural product ergoline has been presented using density functional theory (DFT) employing 6-311++G(d,p) basis set. A complete vibrational assignment has been performed for the theoretical FT-IR and Raman wavenumbers along with the potential energy distribution (PED) with the result of quantum chemical calculations. The structure–activity relationship has been interpreted by mapping electrostatic potential surface (MEP). Graphical representation of frontier molecular orbitals with their energy gap have been analyzed theoretically for both the gaseous and solvent environment employing time dependent density functional theory (TDDFT) employing 6-31G basis set.

Spectroscopic investigations and DFT studies of synthesized 4-acetamidophenyl 3,4,5-trimethoxybenzoate and 4-acetyl phenyl 3,4,5-trimethoxybenzoate a novel conjugate of gallic acid

2020 ◽  
Vol 17 ◽  
Author(s):  
Sangeeta Srivastava ◽  
Nadeem Ahmad Ansari ◽  
Sadaf Aleem
Keyword(s):  
Gallic Acid ◽  
Density Functional ◽  
Energy Gap ◽  
Basis Set ◽  
Major Constituent ◽  
Orbital Energy ◽  
Reactivity Descriptors ◽  
Homo And Lumo ◽  
Electrophilic Reactivity ◽  
Global And Local

: Gallic acid is abundantly found in amla (Phyllanthus emblica), a deciduous of the family phyllanthaceae. Gallic acid, the major constituent of the plant was methylated to 3,4,5 trimethoxy gallic acid, which then underwent steglich esterification first with paracetamol and then with 4-hydroxy acetophenone to yield 4-acetamidophenyl 3,4,5-trimethoxybenzoate and 4-acetyl phenyl 3,4,5-trimethoxybenzoate “respectively”. 1H NMR, 13C NMR, UV, FT-IR and mass spectroscopy were used to characterize the synthesized compounds. Density functional theory (B3YLP) using 6-31G (d,p) basis set have been used for quantum chemical calculations. AIM (Atom in molecule) approach depicted weak molecular interactions within the molecules whereas the reactive site and reactivity within the molecule were examined by global and local reactivity descriptors. The HOMO and LUMO energies and frontier orbital energy gap were calculated by time dependant DFT approach using IEFPCM model. Small value for HOMO–LUMO energy gap indicated that easier charge transfer occurs within compound 4. The nucleophilic and electrophilic reactivity were determined by MEP (molecular electrostatic potential) experiment. Polarizability, dipole moment, and first hyperpolarizability values were calculated to depict the NLO (nonlinear optical) property of both the synthesized compounds. The antimicrobial activity was also carried out and broad spectrum antibacterial activity against several strains of bacteria and certain unicellular fungi were exhibited by synthesized compound 3.

Theoretical investigation on tautomerism and NLO properties of Salicylideneaniline derivatives

2021 ◽  
Author(s):  
N. Daho ◽  
N. Benhalima ◽  
F. KHELFAOUI ◽  
O. SADOUKI ◽  
M. Elkeurti ◽  
...  
Keyword(s):  
Optical Properties ◽  
Density Functional ◽  
Energy Gap ◽  
Intramolecular Proton Transfer ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Molecular Orbital Calculations ◽  
Visible Absorption ◽  
Charge Delocalization ◽  
Intramolecular Hydrogen

In this work, a comprehensive investigation of the salicylideneaniline derivatives is carried out using density functional theory to determine their linear and non-linear optical properties. Geometry optimizations, for gas and solvent phases, of the tautomers (enol and keto forms) are calculated using B3LYP levels with 6–31G (d,p) basis set . An intramolecular proton transfer, for 1SA-E and 2SA-E, is performed by a PES scan process at the B3LYP/6-31G (d,p) level. The optical properties are determined and show that they have extremely high nonlinear optical properties. In addition, the RDG analysis, MEP, and gap energy are calculated. The low energy gap value indicates the possibility of intramolecular charge transfer. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the first-order hyperpolarizability (β = 59.6471 × 10-30 esu), confirming that the salicylideneaniline derivatives can be used as attractive future NLO materials. Therefore, the reactive sites are predicted using MEP and the visible absorption maxima are analyzed using a theoretical UV–Vis spectrum. Natural bond orbitals are used to investigate the stability, charge delocalization, and intramolecular hydrogen bond.

scholarly journals Theoretical Study of Solvent Effects on the Electronic and Thermodynamic Properties of Tetrathiafulvalene (TTF) Molecule Based on DFT

2021 ◽  
pp. 42-54
Author(s):  
Rabiu Nuhu Muhammad ◽  
N. M. Mahraz ◽  
A. S Gidado ◽  
A. Musa
Keyword(s):  
Thermodynamic Properties ◽  
Bond Length ◽  
Density Functional ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Basis Sets ◽  
Frontier Molecular Orbital ◽  
Orbital Energy ◽  
Chemical Hardness

Tetrathiafulvalene () is an organosulfur compound used in the production of molecular devices such as switches, sensors, nonlinear optical devices and rectifiers. In this work, a theoretical study on the effects of solvent on TTF molecule was investigated and reported based on Density Functional Theory (DFT) as implemented in Gaussian 03 package using B3LYP/6-31++G(d,p) basis set. Different solvents were introduced as a bridge to investigate their effects on the electronic structure. The HUMO, LUMO, energy gap, global chemical index, thermodynamic properties, NLO and DOS analysis of the TTF molecule in order to determine the reactivity and stability of the molecule were obtained. The results obtained showed that the solvents have effects on the electronic and non-linear-optical properties of the molecule. The optimized bond length revealed that the molecule has strong bond in gas phase with smallest bond length of about 1.0834Å than in the rest of the solvents. It was observed that the molecule is more stable in acetonitrile with HOMO-LUMO gap and chemical hardness of 3.6373eV and 1.8187eV respectively. This indicates that the energy gap and chemical hardness of TTF molecule increases with the increase in polarity and dielectric constant of the solvents. The computed results agreed with the results in the literature. The thermodynamics and NLO properties calculation also indicated that TTF molecule has highest value of specific heat capacity (Cv), total dipole moment () and first order hyperpolarizability () in acetonitrile, while acetone has the highest value of entropy and toluene has a slightly higher value of zero point vibrational energy (ZPVE) than the rest of the solvents. The results show that careful selection of the solvents and basis sets can tune the frontier molecular orbital energy gap of the molecule and can be used for molecular device applications.

Synthesis and DFT Studies of Pyrimidin-1(2H)-ylaminofumarate Derivatives

2020 ◽  
Vol 42 (5) ◽  
pp. 746-746
Author(s):  
Murat Saracoglu Murat Saracoglu ◽  
Zulbiye Kokbudak Zulbiye Kokbudak ◽  
M Izzettin Yilmazer and Fatma Kandemirli M Izzettin Yilmazer and Fatma Kandemirli
Keyword(s):  
Quantum Chemical ◽  
Energy Gap ◽  
Basis Set ◽  
Chemical Hardness ◽  
Pyrimidine Derivatives ◽  
1H And 13C Nmr ◽  
Solvent Phase ◽  
B3lyp Method ◽  
Ft Ir ◽  
New Compounds

Pyrimidine derivatives have biological and pharmacological properties. Therefore, in this study we focused on the synthesis various Pyrimidine derivatives to make noteworthy contributions this class of heterocyclic compounds. In the present study, the new compounds (4-6) were obtained by the reactions of 1-amino-5-benzoyl-4-phenylpyrimidin-2(1H)-one (1), 1-amino-5-(4-methylbenzoyl)-4-(4-methylphenyl)pyrimidin-2(1H)-one (2) and 1-amino-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl)pyrimidin-2(1H)-one (3) with dimethyl acetylenedicarboxylate. The structures of these compounds were proved by elemental analysis, FT-IR, 1H and 13C-NMR spectra. In addition to, quantum chemical calculations were made to find molecular properties of the pyrimidin-1(2H)-ylaminofumarate derivatives (4-6) by using DFT/B3LYP method with 6-311++G(2d,2p) basis set. Quantum chemical features such as EHOMO, ELUMO, energy gap, ionization potential, chemical hardness, chemical softness, electronegativity etc. values for gas and solvent phase of neutral molecules were calculated and discussed.

SOLVENT EFFECTS ON THE ELECTRONIC STRUCTURE AND NON-LINEAR OPTICAL PROPERTIES OF PYRENE AND SOME OF ITS DERIVATIVES BASED ON DENSITY FUNCTIONAL THEORY

2021 ◽  
Vol 4 (4) ◽  
pp. 236-251
Author(s):  
A. S. Gidado ◽  
L. S. Taura ◽  
A. Musa
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Lumo Energy ◽  
Functional Theory ◽  
Organic Optoelectronic ◽  
Homo Lumo

Pyrene (C16H10) is an organic semiconductor which has wide applications in the field of organic electronics suitable for the development of organic light emitting diodes (OLED) and organic photovoltaic cells (OPV). In this work, Density Functional Theory (DFT) using Becke’s three and Lee Yang Parr (B3LYP) functional with basis set 6-311++G(d, p) implemented in Gaussian 03 package was  used to compute total energy, bond parameters, HOMO-LUMO energy gap, electron affinity, ionization potential, chemical reactivity descriptors, dipole moment, isotropic polarizability (α), anisotropy of polarizability ( Δ∝) total first order hyper-polarizability () and second order hyperpolarizability (). The molecules used are pyrene, 1-chloropyrene and 4-chloropyrene  in gas phase and in five different solvents: benzene, chloroform, acetone, DMSO and water. The results obtained show that solvents and chlorination actually influenced the properties of the molecules. The isolated pyrene in acetone has the largest value of HOMO-LUMO energy gap of and is a bit closer to a previously reported experimental value of  and hence is the most stable. Thus, the pyrene molecule has more kinetic stability and can be described as low reactive molecule. The calculated dipole moments are in the order of 4-chloropyrene (1.7645 D) < 1-chloropyrene (1.9663 D) in gas phase. The anisotropy of polarizability ( for pyrene and its derivatives were found to increase with increasing polarity of the solvents.  In a nutshell, the molecules will be promising for organic optoelectronic devices based on their computed properties as reported by this work.

scholarly journals Theoretical Study of a Class of Organic D-π-A Dyes for Polymer Solar Cells: Influence of Various π-Spacers

Crystals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 163
Author(s):  
Nguyen Van Trang ◽  
Tran Ngoc Dung ◽  
Ngo Tuan Cuong ◽  
Le Thi Hong Hai ◽  
Daniel Escudero ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Solar Cells ◽  
Molecular Orbital ◽  
Density Functional ◽  
Energy Gap ◽  
Polymer Solar Cells ◽  
Basis Set ◽  
Structure Theory ◽  
Functional Theory ◽  
Alkyl Groups

A class of D-π-A compounds that can be used as dyes for applications in polymer solar cells has theoretically been designed and studied, on the basis of the dyes recently shown by experiment to have the highest power conversion efficiency (PCE), namely the poly[4,8-bis(5-(2-butylhexylthio)thiophen-2-yl)benzo[1,2-b:4,5-b’]dithiophene-2,6-diyl-alt-TZNT] (PBDTS-TZNT) and poly[4,8-bis(4-fluoro-5-(2-butylhexylthio)thiophen-2-yl)benzo[1,2-b:4,5-b’]dithiophene-2,6-diyl-alt-TZNT] (PBDTSF-TZNT) substances. Electronic structure theory computations were carried out with density functional theory and time-dependent density functional theory methods in conjunction with the 6−311G (d, p) basis set. The PBDTS donor and the TZNT (naphtho[1,2-c:5,6-c]bis(2-octyl-[1,2,3]triazole)) acceptor components were established from the original substances upon replacement of long alkyl groups within the thiophene and azole rings with methyl groups. In particular, the effects of several π-spacers were investigated. The calculated results confirmed that dithieno[3,2-b:2′,3′-d] silole (DTS) acts as an excellent π-linker, even better than the thiophene bridge in the original substances in terms of well-known criteria. Indeed, a PBDTS-DTS-TZNT combination forms a D-π-A substance that has a flatter structure, more rigidity in going from the neutral to the cationic form, and a better conjugation than the original compounds. The highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gap of such a D-π-A substance becomes smaller and its absorption spectrum is more intense and red-shifted, which enhances the intramolecular charge transfer and makes it a promising candidate to attain higher PCEs.

scholarly journals M(VI) Oxidation State Stabilization in Iron, Cobalt and Nickel Heteroligand Metal Chelates Containing 3,7,11,15-Tetraazaporphine and Two Axial Oxo Ligands: Quantum-Chemical Simulation

2020 ◽  
Vol 21 (4) ◽  
pp. 1494 ◽  
Author(s):  
Oleg V. Mikhailov ◽  
Denis V. Chachkov
Keyword(s):  
Oxidation State ◽  
Quantum Chemical ◽  
Density Functional ◽  
Chemical Elements ◽  
Basis Set ◽  
Chemical Calculation ◽  
Deprotonated Form ◽  
Iron Cobalt ◽  
Cobalt And Nickel ◽  
Oxo Ligands

The quantum-chemical calculation of iron, cobalt and nickel heteroligand complexes with the double deprotonated form of (NNNN)-donor atomic ligand—3,7,11,15-tetraazaporphine—and two oxo ligands has been carried out. Data on the structural and standard thermodynamic parameters, NBO analysis and multiplicity of the ground states of these complexes have been presented. The given calculation has been made by using the density functional theory (DFT) method with the OPBE/TZVP basis set. Based on the results of this calculation, the possibility of the existence of oxidation state VI for the chemical elements indicated above—unusual for iron and cobalt, and for nickel, unknown at all—has been shown.

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