Geometry Optimization, UV/Vis, NBO, HOMO and LUMO, Excited State and Antioxidant Evaluation of Pyrimidine Derivatives

2020 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Evgeni Kvasyuk ◽  
Aliaksei G. Sysa ◽  
Radwan Alnajjar ◽  
...  
Keyword(s):  
Density Functional ◽  
Antioxidant Properties ◽  
Geometry Optimization ◽  
Dft Method ◽  
Oscillator Strengths ◽  
Equilibrium Geometry ◽  
Pyrimidine Derivatives ◽  
Excitation Energies ◽  
Solvent Water ◽  
Homo And Lumo

: In this research, the four pyrimidine derivatives have been studied by using density functional theory (DFT/B3LYP/6-31G*) in solvent water for the first time. After quantum-chemical calculations, the title compounds have been synthesized. The electronic spectra of the new derivatives in a solvent water were performed by time-dependent DFT (TD-DFT) method. The equilibrium geometry, the HOMO and LUMO orbitals, MEP, excitation energies, natural charges, oscillator strengths for the molecules have also been calculated. NBO analysis has been calculated in order to elucidate the intramolecular, rehybridization and delocalization of electron density. These molecules have high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds. Antioxidant properties of the title compounds have been investigated and discussed.

scholarly journals GEOMETRIC and ELECTRONIC PROPERTIES of OLIGOMERS BASED ON LUORINATED THIOPHENES and 1H-PHOSPHOLES: N- VERSUS P-TYPE MATERIALS

2010 ◽  
Vol 13 (2) ◽  
pp. 28-44
Author(s):  
Nguyen Tran Nguyen Pham ◽  
Quan Phung ◽  
Khung Moc ◽  
Thanh Tho Bui ◽  
Tho Minh Nguyen
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Dft Method ◽  
Excitation Energies ◽  
Geometrical Structures ◽  
Functional Theory ◽  
Homo And Lumo ◽  
Reorganization Energies ◽  
P Type ◽  
Geometric And Electronic Properties

A series of oligothiophenes and novel oligophospholes, consisting of fluorinated and perfluoroarene-substituted structures, were investigated by using density functional theory (DFT) method. The study focused on the geometrical structures and electronic properties. The degree of -conjugation in the neutral oligomers was studied by different approaches including analysis of predicted Raman spectra. The character of the charge carrier of the new substituted oligomers, either electron (n-type doping) or hole (p-type doping) transport, was predicted by comparing their properties, including the HOMO and LUMO energies, excitation energies, and reorganization energies, with those of their non-substituted parent oligomers. The DFT results are consistent with the available experimental data on the oligothiophenes for both geometries and conductivity properties. The results strongly suggest that an effective way of designing new materials with n-type conductivity is to introduce electron-withdrawing groups into the oligomer backbone. Interesting results were also obtained for oligomers based on 1H-phospholes, which are predicted to have interesting properties as new semiconductor materials..

A density functional approach toward structural features and properties of C20…N2X2 (X = H, F, Cl, Br, Me) molecules

2014 ◽  
Vol 13 (04) ◽  
pp. 1450023 ◽  
Author(s):  
Reza Ghiasi ◽  
Morteza Zaman Fashami ◽  
Amir Hossein Hakimioun
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Structural Features ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Homo And Lumo ◽  
Lowest Unoccupied Molecular Orbitals

In this work, the interaction of C 20 with N 2 X 2 ( X = H , F , Cl , Br , Me ) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C 20… N 2 H 2 interaction is stronger than the interaction of other N 2 X 2 ( X = F , Cl , Br , Me ) with C 20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C 20… N 2 X 2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14 N NQR parameters of the C 20… N 2 X 2 molecules are predicted.

scholarly journals Unraveling the Effects of Co-Crystallization on the UV/Vis Absorption Spectra of an N-Salicylideneaniline Derivative. A Computational RI-CC2 Investigation

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4512
Author(s):  
Jean Quertinmont ◽  
Tom Leyssens ◽  
Johan Wouters ◽  
Benoît Champagne
Keyword(s):  
Optical Properties ◽  
Crystal Field ◽  
Indirect Effects ◽  
Density Functional ◽  
Crystal Packing ◽  
Density Functional Theory Method ◽  
Oscillator Strengths ◽  
Excitation Energies ◽  
Keto Form ◽  
Cell Parameters

This work aims at unraveling the effects of co-crystallization on the optical properties of an N-salicylideneaniline-derived molecular switch transforming between an enol and a keto form. This is achieved by way of a two-step multi-scale method where (i) the molecular geometry and unit cell parameters are optimized using a periodic boundary conditions density functional theory method and (ii) the optical properties are computed for a selection of clusters embedded in an array of point-charges that reproduce the crystal field electronic potential. The optical properties (vertical excitation energies and oscillator strengths) are obtained at the RI-CC2/def2-TZVPD level of approximation. This method allows us to decompose the effects of co-crystallization into (i) indirect effects, the geometry changes of the chromophore due to crystal packing with the coformer, and (ii) direct ones, the polarization due to the interacting coformer and to the crystal field. For the former effects, variations of a crucial torsion angle lead to modification of the π-conjugation and therefore to the decrease or increase of the excitation energies. About the latter, they are antagonistic: (i) the coformer is not directly involved in the excitations but its polarization decreases the excitation energies while (ii) the crystal field has the opposite effect. For the co-crystals with succinic and fumaric acids, combining these direct and indirect effects leads to a hypsochromic shift of the first absorption band with respect to the reference crystal, in agreement with experimental data.

scholarly journals DFT Studies on the Antioxidant Activity of Naringenin and Its Derivatives: Effects of the Substituents at C3

2019 ◽  
Vol 20 (6) ◽  
pp. 1450 ◽  
Author(s):  
Yan-Zhen Zheng ◽  
Geng Deng ◽  
Rui Guo ◽  
Da-Fu Chen ◽  
Zhong-Min Fu
Keyword(s):  
Antioxidant Activity ◽  
Density Functional ◽  
Radical Scavenging Activity ◽  
Resonance Effect ◽  
Antioxidant Properties ◽  
Radical Scavenging ◽  
Dft Method ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Selection Of

The radical scavenging activity of a flavonoid is largely influenced by its structure. The effects of the substituents at C3 position on the antioxidant activity of naringenin were carried out using the density functional theory (DFT) method. The reaction enthalpies related with the three well-established mechanisms were analyzed. Excellent correlations were found between the reaction enthalpies and Hammett sigma constants. Equations obtained from the linear regression can be helpful in the selection of suitable candidates for the synthesis of novel naringenin derivatives with enhanced antioxidant properties. In the gas and benzene phases, the antioxidant activity of naringenin was enhanced by the electron-donating substituents via weakening the bond dissociation enthalpy (BDE). In the water phase, it was strengthened by electron-withdrawing groups—via lowering the proton affinity (PA). The electronic effect of the substituent on the BDE of naringenin is mainly governed by the resonance effect, while that on the ionization potential (IP) and PA of naringenin is mainly controlled by the field/inductive effect.

scholarly journals ABSORPTION OF SOME SMALL SILVER CLUSTERS: DFT AND CASPT2 CALCULATIONS

2018 ◽  
Vol 55 (6A) ◽  
pp. 72
Author(s):  
Ngo Tuan Cuong
Keyword(s):  
Absorption Spectra ◽  
Density Functional ◽  
Noble Gas ◽  
Silver Cluster ◽  
Dft Method ◽  
Basis Sets ◽  
Silver Clusters ◽  
Excitation Energies ◽  
Complete Active Space ◽  
Td Dft

Two quantum chemical methods which are the time-dependent density functional theory (TD-DFT) and the complete active space CASPT2/CASSCF have been used in modeling absorption spectra of silver clusters Agn (n = 2, 3, 4, 6, 8). There is an overall good agreement between TD-DFT and CASPT2 results for transition energies. The absorption spectra of the Agn clusters examined can reasonably be simulated using the excitation energies obtained by either TD-DFT or CASPT2 method.  The main result emerged from this calculation is that the TD-DFT method is suitable for treatment of excited states of Ag clusters. The choice of specific functionals and basis sets to be used in some cases induces important effects on the calculated spectra. It is also noteworthy to mention that for some clusters, the neutral Ag6 for instance, the effect of noble gas environment is significant, while for some others such as the neutral Ag8, it is not. Therefore, carrying out TD-DFT calculations to reproduce and to assign a given structure to an experimental absorption spectrum of a silver cluster, it is not only to select suitable functionals but also to take enough effects of environments into account. 

scholarly journals Study of Substituent Effect on Properties of Platinum(II) Porphyrin Semiconductor Using Density Functional Theory

2018 ◽  
Vol 18 (4) ◽  
pp. 742
Author(s):  
Harno Dwi Pranowo ◽  
Fadjar Mulya ◽  
Hafiz Aji Aziz ◽  
Grisani Ambar Santoso
Keyword(s):  
Substituent Effect ◽  
Density Functional ◽  
Geometry Optimization ◽  
Dft Method ◽  
Band Gap Energy ◽  
Functional Theory ◽  
Substituent Group ◽  
Partial Charges ◽  
Visible Spectra ◽  
Uv Visible

Study of substituent effect on properties of platinum(II) porphyrin had been performed using DFT method. The aim of the study is to investigate the effect of substituent group on the electronic and optical properties of the platinum(II) porphyrin. Geometry optimization was conducted using DFT/B3LYP/LANL2DZ to obtain molecular structure, electronic structure and energy profile. Band gap energy (Eg), the density of states (DOS), and UV-visible spectra are the semiconductor parameters to study. Computational results show that platinum(II) porphyrin and substituted platinum(II) porphyrin have properties of semiconductor based on Eg value, DOS, and UV-visible spectra. The results show that Mulliken partial charges of electron withdrawing substituents are higher than the electron donating substituents (CH3, OH, and NH2). Eg values of the complexes with respect to the substituents follow this order: NH2 < OH < NO2 < COOH < I < CH3 < Br < F < H, for DOSHOMO values, the order is CH3 < NO2 < I < OH < F < NH2 < COOH < Br < H and the maximum wavelength (λmax) for UV-visible adsorption spectra follows this order: NH2 > OH > COOH > NO2 > I > Br > CH3 > F > H. Molecules with smaller Eg and DOSHOMO values and higher λmax are considered as the most appropriate semiconductor materials. Our results show that Pt(II)P-NH2 has the smallest Eg and the highest λmax among other substituted platinum(II) porphyrin molecules. Therefore, Pt(II)P-NH2 are the most suitable semiconductor material based on the aforementioned criteria.

scholarly journals Enamine Barbiturates and Thiobarbiturates as a New Class of Bacterial Urease Inhibitors

2020 ◽  
Vol 10 (10) ◽  
pp. 3523
Author(s):  
M. Ali ◽  
Assem Barakat ◽  
Ayman El-Faham ◽  
Abdullah Mohammed Al-Majid ◽  
Sammer Yousuf ◽  
...  
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Docking Study ◽  
Acetohydroxamic Acid ◽  
Urease Inhibitors ◽  
Pyrimidine Derivatives ◽  
Functional Theory ◽  
New Class ◽  
The Density Functional Theory ◽  
Privileged Structure

Urease is a therapeutic target associated with several important diseases and health problems. Based on our previous work on the inhibition of glucosidase and other enzymes and exploiting the privileged structure assigned to the (thio)barbiturate (pyrimidine) scaffold, here we tested the capacity of two (thio)barbiturate-based compound collections to inhibit urease. Several compounds showed more activity than acetohydroxamic acid as a standard tested compound. In addition, by means of a conformational study and using the Density Functional Theory (DFT) method, we identified energetically low-lying conformers. Finally, we undertook a docking study to explore the binding mechanism of these new pyrimidine derivatives as urease inhibitors.

scholarly journals OS100: A Benchmark Set of 100 Digitized UV-Visible Spectra and Derived Experimental Oscillator Strengths

2021 ◽  
Author(s):  
Astrid Tarleton ◽  
Jorge Garcia-Alvarez ◽  
Anah Wynn ◽  
Cade Awbrey ◽  
Tomas Roberts ◽  
...  
Keyword(s):  
Density Functional ◽  
Oscillator Strengths ◽  
Learning Approaches ◽  
Excitation Energies ◽  
Absorption Bands ◽  
Visible Absorption ◽  
Plain Text ◽  
Solvent Model ◽  
Visible Spectra ◽  
Uv Visible

Excited-state quantum chemical calculations typically report excitation energies and oscillator strengths, ƒ, for each electronic transition. On the other hand, UV-visible spectrophotometric experiments report energy-dependent molar extinction/attenuation coefficients, ε(v), that determine the absorption band line shapes. ε(v) and ƒ are related, but this relation is complicated by various broadening and solvation effects. We fit and integrated experimental UV-visible spectra to obtain ƒexp values for absorption bands and estimated the uncertainty in the fitting. We derived 164 ƒexp values from 100 organic molecules ranging in size from 6-34 atoms. The corresponding computed oscillator strengths (ƒcomp) were obtained with time-dependent density functional theory and a polarizable continuum solvent model. By expressing experimental and computed absorption strengths using a common quantity, we directly compared ƒcomp and ƒexp. While ƒcomp and ƒexp are well correlated (linear regression R2=0. 921), ƒcomp in most cases significantly overestimates ƒexp (regression slope=1.34). The agreement between absolute ƒcomp and ƒexp values was substantially improved by accounting for a solvent refractive index factor, as suggested in some derivations in the literature. The 100 digitized UV-visible spectra are included as plain text files in the supporting information to aid in benchmarking computational or machine-learning approaches that aim to simulate realistic UV-visible absorption spectra.

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