Theoretical investigation of the derivatives of favipiravir (T-705) as potential drugs for Ebola virus

2018 ◽  
Vol 3 (9) ◽  
Author(s):  
Lydia Rhyman ◽  
Mahir Tursun ◽  
Hassan H. Abdallah ◽  
Yee Siew Choong ◽  
Cemal Parlak ◽  
...  
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Ebola Virus ◽  
Dft Method ◽  
Basis Set ◽  
Functional Theory ◽  
Experimental Parameters ◽  
Good Comparison ◽  
Free Energy Of Binding ◽  
Derivatives Of

Abstract Density functional theory (DFT) method was used to compute the structural and vibrational parameters of favipiravir (T-705) in the gas phase. The functional used was B3LYP in conjuction with the 6–311++G(d,p) basis set. We also computed these parameters for unsubstituted T-705 and derivatives of T-705 by substituting fluorine by chlorine, bromine and the cyanide group. There is a good comparison between the computed and experimental parameters for T-705 and therefore, the predicted data should be reliable for the other compounds for which experimental data is not available. We extended our DFT study to include molecular docking involving the Ebola virus viral protein 35 (VP35). The docking results indicate that the T-705 and its chlorine and bromine analogues have comparable free energy of binding with VP35. Graphical Abstract:

scholarly journals Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation

2015 ◽  
Vol 93 (7) ◽  
pp. 708-714 ◽  
Author(s):  
Margarida S. Miranda ◽  
Darío J.R. Duarte ◽  
Joaquim C.G. Esteves da Silva ◽  
Joel F. Liebman
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Proton Affinities ◽  
Functional Theory ◽  
Heterocyclic Derivatives ◽  
Gas Phase Basicities ◽  
Derivatives Of

A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species using density functional theory with the B3LYP functional and the 6-31G(2df,p) basis set. More accurate enthalpy values were obtained from G4 calculations. Proton affinities and gas-phase basicities were accordingly derived.

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.

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 DFT Visualization and Experimental Evidence of BHT-Mg-Catalyzed Copolymerization of Lactides, Lactones and Ethylene Phosphates

Polymers ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1641 ◽  
Author(s):  
Ilya Nifant’ev ◽  
Andrey Shlyakhtin ◽  
Maxim Kosarev ◽  
Dmitry Gavrilov ◽  
Stanislav Karchevsky ◽  
...  
Keyword(s):  
Ring Opening ◽  
Density Functional ◽  
Point Of View ◽  
Basis Set ◽  
Random Copolymers ◽  
Key Factors ◽  
Functional Theory ◽  
Cyclic Esters ◽  
Dft Modeling ◽  
Derivatives Of

Catalytic ring-opening polymerization (ROP) of cyclic esters (lactides, lactones) and cyclic ethylene phosphates is an effective way to process materials with regulated hydrophilicity and controlled biodegradability. Random copolymers of cyclic monomers of different chemical nature are highly attractive due to their high variability of characteristics. Aryloxy-alkoxy complexes of non-toxic metals such as derivatives of 2,6-di-tert-butyl-4-methylphenoxy magnesium (BHT-Mg) complexes are effective coordination catalysts for homopolymerization of all types of traditional ROP monomers. In the present paper, we report the results of density functional theory (DFT) modeling of BHT-Mg-catalyzed copolymerization for lactone/lactide, lactone/ethylene phosphate and lactide/ethylene phosphate mixtures. ε-Caprolactone (ε-CL), l-lactide (l-LA) and methyl ethylene phosphate (MeOEP) were used as examples of monomers in DFT simulations by the Gaussian-09 program package with the B3PW91/DGTZVP basis set. Both binuclear and mononuclear reaction mechanistic concepts have been applied for the calculations of the reaction profiles. The results of calculations predict the possibility of the formation of random copolymers based on l-LA/MeOEP, and substantial hindrance of copolymerization for ε-CL/l-LA and ε-CL/MeOEP pairs. From the mechanistic point of view, the formation of highly stable five-membered chelate by the products of l-LA ring-opening and high donor properties of phosphates are the key factors that rule the reactions. The results of DFT modeling have been confirmed by copolymerization experiments.

A computational study of the SNAr reaction of 2-ethoxy-3,5-dinitropyridine and 2-methoxy-3,5-dinitropyridine with piperidine

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Oluwakemi A. Oloba-Whenu ◽  
Idris O. Junaid ◽  
Chukwuemeka Isanbor
Keyword(s):  
Hydrogen Bonding ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Method ◽  
Basis Set ◽  
Slow Step ◽  
Functional Theory ◽  
Snar Reaction ◽  
Hybrid Density Functional

AbstractA computational study of the chemical kinetics and thermodynamics study of the SNAr between 3,5-dinitroethoxypyridine 1a and 3,5-dinitromethoxypyridine 1b with piperidine 2 in the gas phase is reported using hybrid density functional theory method B3PW91 and 6–31G(d,p) basis set. The reaction was modeled via both the catalyzed and base-catalyzed pathways which proceeded with the initial attack of the nucleophile 2 on the substrates 1 to yield the Meisenheimer complex intermediate that is stabilized with hydrogen bonding. Calculations show that the reaction goes via the formation and decomposition of a Meisenheimer complex, which was observed to be stabilized by hydrogen bonding. Along the uncatalyzed pathway, the decomposition of the Meisenheimer complex was the slow step and requires about 28 kcal/mol. This barrier was reduced to about 14.8 kcal/mol with the intervention of the base catalyst, thus making the formation of the Meisenheimer complex rate determining. All reactions were calculated to be exothermic, about −6.5 kcal/mol and −0.6 kcal/mol, respectively, for the reaction of 1a and 1b with 2.

scholarly journals Vibrational spectra of aniline in gas phase: An ab-initio study

2010 ◽  
Vol 7 (2) ◽  
pp. 449-455
Author(s):  
S. D. S. Chauhan ◽  
A.K. Sharma ◽  
R. Kumar ◽  
D. Kulshreshtha ◽  
R. Gupta ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Basis Sets ◽  
Ab Initio Study ◽  
Functional Theory ◽  
Hartree Fock ◽  
Modes Of Vibration ◽  
Experimental Findings

Vibrational frequencies of aniline in gas phase have been calculated and each of their modes of vibration assigned properly at RHF and DFT with 6-31G(d) basis set. In the present study, it has been observed that the 6-31G(d) basis set at both RHF and DFT levels of calculations provides better agreement to the experimental findings as compared to other basis sets. Simultaneously, Density functional theory is found to be superior to its counterpart Hartree Fock method.

scholarly journals Ultrasound Assisted Synthesis, Molecular Structure,UV-Visible Assignments, MEP and Mulliken Charges Study of (E)-3-(4-chlorophenyl)-1-(4-methoxyphenyl) prop-2-en-1-one: Experimental and DFT Correlational

2021 ◽  
Vol 18 (1) ◽  
pp. 86-96
Author(s):  
Rohit S. Shinde
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Method ◽  
Atomic Charge ◽  
Dft Method ◽  
Basis Set ◽  
Geometrical Parameters ◽  
Functional Theory ◽  
Vibrational Assignments ◽  
Uv Visible

Present investigation deals with the synthesis and density functional theory study (DFT) of a chalcone derivative; (E)-3-(4-chlorophenyl)-1-(4-methoxyphenyl)prop-2-en-1-one (CPMPP). The synthesis of a CPMPP has been carried out by the reaction of 4-methoxyacetophenone and 4-chlorobenzalehyde in ethanol at 30 ℃ under ultrasound irradiation. The structure of a synthesized chalcone is affirmed on the basis of FT-IT, 1H NMR and 13C NMR. The geometry of a CPMPP is optimized by using the density functional theory method at the B3LYP/6-31G(d,p) basis set. The optimized geometrical parameters like bond length and bond angles have been computed. The absorption energies, oscillator strength, and electronic transitions have been derived at the TD-DFT method at the B3LYP/6-31G(d,p) level of theory for B3LYP/6-31G(d p) optimized geometries. The effect of polarity on the absorption energies is discussed by computing UV-visible results in dichloromethane (DCM). Since theoretically obtained wavenumbers are typically higher than experimental wavenumbers, computed wavenumbers were scaled with a scaling factor, and vibrational assignments were made by comparing experimental wavenumbers to scaled theoretical wavenumbers. Quantum chemical parameters have been determined and examined. Molecular electrostatic potential (MEP) surface plot analysis has been carried out at the same level of theory. Mulliken atomic charge study is also discussed in the present study.

Spectroscopic investigation, HOMO–LUMO energies, natural bond orbital (NBO) analysis and thermodynamic properties of two-armed macroinitiator containing coumarin with DFT quantum chemical calculations

2016 ◽  
Vol 94 (6) ◽  
pp. 583-593 ◽  
Author(s):  
Feride Akman
Keyword(s):  
Density Functional Theory ◽  
Molecular Orbital ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Dft Method ◽  
Basis Set ◽  
Orbital Method ◽  
Functional Theory ◽  
Homo Lumo

In the present work, two-armed macroinitiator containing coumarin were synthesized, characterized by Fourier transform infrared spectroscopy and 1H nuclear magnetic resonance techniques and investigated theoretically using density functional theory (DFT) calculations. The molecular geometry, fundamental vibrational frequencies, atomic charges obtained from atomic polar tensors and Mulliken were analyzed by means of structure optimizations based on the DFT method with 6-31G+(d, p) as a basis set. The 1H chemical shifts were calculated by the gauge-including atomic orbital method and compared with available experimental data. The electronic properties, such as highest occupied molecular orbital – lowest unoccupied molecular orbital (HOMO–LUMO) energies, electron affinity, electronegativity, ionization energy, hardness, chemical potential, global softness, and global electrophilicity were calculated by using the DFT method. The electrostatic potential and molecular electrostatic potential surfaces were performed to predict the reactive sites of the two-armed macroinitiator. The energy difference between acceptor and donor and stabilization energy were determined using natural bond orbital analysis. The results show that the occurrence of intramolecular charge transfers within the polymer. Time-dependent density functional theory calculations of visible spectra were analyzed at different solvents. Finally, thermodynamic functions, such as enthalpy, heat capacity, and entropy, of the two-armed macroinitiator at different temperatures were calculated and the relationship with temperature was investigated.

scholarly journals Molecular Structures and Spectral Properties of Natural Indigo and Indirubin: Experimental and DFT Studies

Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3831 ◽  
Author(s):  
Zixin Ju ◽  
Jie Sun ◽  
Yanping Liu
Keyword(s):  
Density Functional Theory ◽  
Spectral Properties ◽  
Density Functional ◽  
Dft Method ◽  
Molecular Structures ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Visible Absorption ◽  
Functional Theory ◽  
Uv Visible

This paper presents a comparative study on natural indigo and indirubin in terms of molecular structures and spectral properties by using both computational and experimental methods. The spectral properties were analyzed with Fourier transform infrared (FTIR), Raman, UV-Visible, and fluorescence techniques. The density functional theory (DFT) method with B3LYP using 6-311G(d,p) basis set was utilized to obtain their optimized geometric structures and calculate the molecular electrostatic potential, frontier molecular orbitals, FTIR, and Raman spectra. The single-excitation configuration interaction (CIS), time-dependent density functional theory (TD-DFT), and polarization continuum model (PCM) were used to optimize the excited state structure and calculate the UV-Visible absorption and fluorescence spectra of the two molecules at B3LYP/6-311G(d,p) level. The results showed that all computational spectra agreed well with the experimental results. It was found that the same vibrational mode presents a lower frequency in indigo than that in indirubin. The frontier molecular orbital analysis demonstrated that the UV-Visible absorption and fluorescence bands of indigo and indirubin are mainly derived from π → π* transition. The results also implied that the indigo molecule is more conjugated and planar than indirubin, thereby exhibiting a longer maximum absorption wavelength and stronger fluorescence peak.

Interatomic Potential and Thermodynamic Property of Diatomic Uranium

2012 ◽  
Vol 550-553 ◽  
pp. 2810-2813 ◽  
Author(s):  
Xiu Lin Zeng ◽  
Xue Hai Ju ◽  
Si Yu Xu
Keyword(s):  
Density Functional ◽  
Vibrational Energy ◽  
Interatomic Potential ◽  
Zero Point ◽  
Dft Method ◽  
Basis Set ◽  
Functional Theory ◽  
Lennard Jones ◽  
Anharmonicity Constant ◽  
The Relationship

Potential energy scan for U2 was performed by density functional theory (DFT) method at the B3LYP level in combination with the (ECP80MWB_AVQZ + 2f) basis set. The dissociation energy of U2, after being corrected for the zero-point vibrational energy, is 2.482 eV, which is in good agreement with the experiment. The calculated energy was fit to the typical potential functions of Morse, Lennard-Jones (L-J) and Rydberg. Both the Morse and Rydberg functions are good representatives of the potentials, but the Lennard-Jones function is not. The anharmonicity constant is very small. The anharmonic frequency is 113.99 cm–1. Thermodynamic properties of entropy and heat capacity at 298.2 K – 1500 K were calculated by using DFT-B3LYP computational results and Morse parameters, respectively. The relationship between entropy and temperature was established.

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