scholarly journals Radiation-Induced Oxidation Reactions of 2-Selenouracil in Aqueous Solutions: Comparison with Sulfur Analog of Uracil

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 133
Author(s):  
Konrad Skotnicki ◽  
Ireneusz Janik ◽  
Klaudia Sadowska ◽  
Grazyna Leszczynska ◽  
Krzysztof Bobrowski
Keyword(s):  
Absorption Band ◽  
Absorption Spectra ◽  
Density Functional ◽  
Transient Absorption ◽  
Dft Method ◽  
Transient Absorption Spectrum ◽  
Oxidation Reactions ◽  
Radiation Induced ◽  
High Concentrations ◽  
The Stability

One-electron oxidation of 2-selenouracil (2-SeU) by hydroxyl (●OH) and azide (●N3) radicals leads to various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by the density functional theory (DFT) method. The transient absorption spectra recorded in the reactions of ●OH with 2-SeU are dominated by an absorption band with an λmax = 440 nm, the intensity of which depends on the concentration of 2-SeU and pH. Based on the combination of conductometric and DFT studies, the transient absorption band observed both at low and high concentrations of 2-SeU was assigned to the dimeric 2c-3e Se-Se-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of a selenyl-type radical (6●) with 2-SeU, and both radicals are in equilibrium with Keq = 1.3 × 104 M−1 at pH 4 (below the pKa of 2-SeU). Similar equilibrium with Keq = 4.4 × 103 M−1 was determined for pH 10 (above the pKa of 2-SeU), which admittedly involves the same radical (6●) but with a dimeric 2c-3e Se-Se bonded radical in anionic form (2●−). In turn, at the lowest concentration of 2-SeU (0.05 mM) and pH 10, the transient absorption spectrum is dominated by an absorption band with an λmax = 390 nm, which was assigned to the ●OH adduct to the double bond at C5 carbon atom (3●) based on DFT calculations. Similar spectral and kinetic features were also observed during the ●N3-induced oxidation of 2-SeU. In principle, our results mostly revealed similarities in one-electron oxidation pathways of 2-SeU and 2-thiouracil (2-TU). The major difference concerns the stability of dimeric radicals with a 2c-3e chalcogen-chalcogen bond in favor of 2-SeU.

scholarly journals Radiation Induced One-Electron Oxidation of 2-Thiouracil in Aqueous Solutions

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4402
Author(s):  
Skotnicki ◽  
Taras-Goslinska ◽  
Janik ◽  
Bobrowski
Keyword(s):  
Absorption Band ◽  
Absorption Spectra ◽  
Sulfur Atom ◽  
Density Functional ◽  
Transient Absorption ◽  
Dft Method ◽  
Broad Absorption Band ◽  
Transient Absorption Spectra ◽  
Td Dft ◽  
Type Radical

Oxidative damage to 2-thiouracil (2-TU) by hydroxyl (•OH) and azide (N3) radicals produces various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by time-dependent density functional theory (TD-DFT) method. The transient absorption spectra recorded in the reactions of •OH with 2-TU depend on the concentration of 2-TU, however, only slightly on pH. At low concentrations, they are characterized by a broad absorption band with a weakly pronounced maxima located at λ = 325, 340 and 385 nm, whereas for high concentrations, they are dominated by an absorption band with λmax ≈ 425 nm. Based on calculations using TD-DFT method, the transient absorption spectra at low concentration of 2-TU were assigned to the ●OH-adducts to the double bond at C5 and C6 carbon atoms (3●, 4●) and 2c-3e bonded ●OH adduct to sulfur atom (1…●OH) and at high concentration of 2-TU also to the dimeric 2c-3e S-S-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of thiyl-type radical (6●) with 2-TU and both radicals are in an equilibrium with Keq = 4.2 × 103 M−1. Similar equilibrium (with Keq = 4.3 × 103 M−1) was found for pH above the pKa of 2-TU which involves admittedly the same radical (6●) but with the dimeric 2c-3e S-S bonded radical in anionic form (2●−). In turn, ●N3-induced oxidation of 2-TU occurs via radical cation with maximum spin location on the sulfur atom which subsequently undergoes deprotonation at N1 atom leading again to thiyl-type radical (6●). This radical is a direct precursor of dimeric radical (2●).

scholarly journals Singlet and Triplet Exciton Dynamics of Violanthrone

2021 ◽  
Author(s):  
Elham Gholizadeh ◽  
Shyamal Prasad ◽  
Lara Gillan ◽  
Dane R. McCamey ◽  
Murad J. Y. Tayebjee ◽  
...  
Keyword(s):  
Triplet State ◽  
Ground State ◽  
Density Functional ◽  
Transient Absorption ◽  
Density Functional Theory Calculations ◽  
Emission Feature ◽  
Stimulated Emission ◽  
Transient Absorption Spectrum ◽  
Exciton Dynamics ◽  
Solid Film

<div>The exciton dynamics of violanthrone-79 are investigated in solution and in the solid</div><div>state. In solution, the photo-prepared singlet is found to exhibit a strong ground-state bleach</div><div>and stimulated emission feature, but when sensitized in its triplet state, exhibits only a narrow</div><div>and weak ground-state bleach. As supported by density functional theory calculations,</div><div>this is explained by the triplet state having absorptions in the same region, with a similar</div><div>oscillator strength, as the ground state molecule. In solid films, the excited singlet is</div><div>found to survive only 100 ps, giving way to a long-lived transient absorption spectrum with</div><div>characteristics reminiscent of the triplet in solution. This is interpreted in terms of singlet</div><div>fission in the solid film.</div>

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. 

Phase Stability Study of the Shape Memory Alloy CuAl-X (X: Be, Zn, Ti, Ni, Ag and Au) by Ab Initio Calculations

2016 ◽  
Vol 879 ◽  
pp. 250-255
Author(s):  
Nassim Boudalia ◽  
Jean Marc Raulot ◽  
Etienne Patoor ◽  
Claude Esling
Keyword(s):  
Density Functional Theory ◽  
Shape Memory Alloys ◽  
Shape Memory ◽  
First Principles ◽  
Density Functional ◽  
Dft Method ◽  
Stability Study ◽  
Atomic Scale ◽  
Functional Theory ◽  
The Stability

Shape memory alloys (SMA) have been at the forefront of research in recent years. They have been used for a wide variety of applications in various fields. This work presents a brief study at the atomic scale of Cu-Al based Shape Memory Alloys. Using first-principles Density Functional Theory (DFT) method, the stability of different austenitic and martensitic phases of Cu3Al, the effect of intrinsic vacancies, the doping effect by an element X (X = Be, Zn, Ti, Ni, Ag and Au) have been studied.

Stability and Electronic Structures of Mg2Pb (100), (110) and (111) Surfaces

2015 ◽  
Vol 817 ◽  
pp. 690-697
Author(s):  
Yong Hua Duan ◽  
Yong Sun ◽  
Ming Jun Peng
Keyword(s):  
Density Functional Theory ◽  
Surface Energy ◽  
Density Of States ◽  
First Principles ◽  
Electronic Structures ◽  
Density Functional ◽  
Dft Method ◽  
Functional Theory ◽  
Charge Density Difference ◽  
The Stability

The stability and electronic properties of Mg2Pb (100), (110) and (111) surfaces were investigated by using the first-principles density functional theory (DFT) method. The calculated results showed that the orders of relaxation and surface energy are |∆d15(111)| < |∆d15(110)| < |∆d15(100)| andEsurf(100) >Esurf(110) >Esurf(111), respectively, indicating that Mg2Pb (111) surface is the most stable among these three low index surfaces. The Density of states (DOS) of Mg2Pb surfaces are mainly dominated by Pb-6, Mg-3s, and 2porbitals in the band ranging from-5 eV to Fermi level. It can be further obtained from results of the DOS and the charge density difference that Mg2Pb (111) surface is more stable than Mg2Pb (100) and (110) surfaces. The Mg2Pb (111) surface is the thermodynamically most favorable over all of the range of.

scholarly journals Singlet and Triplet Exciton Dynamics of Violanthrone

2021 ◽  
Author(s):  
Elham Gholizadeh ◽  
Shyamal Prasad ◽  
Lara Gillan ◽  
Dane R. McCamey ◽  
Murad J. Y. Tayebjee ◽  
...  
Keyword(s):  
Triplet State ◽  
Ground State ◽  
Density Functional ◽  
Transient Absorption ◽  
Density Functional Theory Calculations ◽  
Emission Feature ◽  
Stimulated Emission ◽  
Transient Absorption Spectrum ◽  
Exciton Dynamics ◽  
Solid Film

<div>The exciton dynamics of violanthrone-79 are investigated in solution and in the solid</div><div>state. In solution, the photo-prepared singlet is found to exhibit a strong ground-state bleach</div><div>and stimulated emission feature, but when sensitized in its triplet state, exhibits only a narrow</div><div>and weak ground-state bleach. As supported by density functional theory calculations,</div><div>this is explained by the triplet state having absorptions in the same region, with a similar</div><div>oscillator strength, as the ground state molecule. In solid films, the excited singlet is</div><div>found to survive only 100 ps, giving way to a long-lived transient absorption spectrum with</div><div>characteristics reminiscent of the triplet in solution. This is interpreted in terms of singlet</div><div>fission in the solid film.</div>

scholarly journals Comparison of the Stability of 2H Nanosurfaces by the Adsorption of Small Molecules : A DFT Study

2021 ◽  
pp. 122-129
Author(s):  
Alev Sakarya ◽  
Seyfettin Dalgic ◽  
Serap Senturk Dalgic
Keyword(s):  
Small Molecules ◽  
Recovery Time ◽  
Density Functional ◽  
Hexagonal Phase ◽  
Gold Surface ◽  
Dft Method ◽  
Absorption Energy ◽  
Short Recovery Time ◽  
The Stability ◽  
2D Nanosheets

Density functional theory (DFT) calculations were carried out to understand the structural stability of 2D nanosheets of gold and silver in hexagonal phase of 2H by the adsorption of small molecules. In this work, we have obtained the bonding and adsorption properties of such small molecules as H2O, H2O2, and C2H5OH on 2H phase of gold and silver nanosurfaces, through DFT method using Quantum Expresso (QE) code. The high absorption energy values of (-2.45 eV, -2,46 eV, -2, 41 eV) for H2O, H2O2, and C2H5OH molecules on 2H-Au surfaces, respectively obtained than that of 2H-silver surfaces that the interaction between small molecules and both 2H nanosurfaces corresponds to physisorption. However, during the adsorption, the gold surface in the 2H phase (2H-Au) seems to preserve its atomic structure, while 2H-Ag surface changes from 2H to the fcc structure. Based on the analysis of electronic and physicochemical properties, the composite systems of 2H-gold/2H-silver-small molecules exhibit semiconductor behaviour. While 2H-Ag surfaces have short recovery time values for hydrogen peroxide (H2O2), this time is quite long for 2H-Au surfaces. Because of the long recovery time, Au-2H reported surfaces can be a candidate for possible applications of viral capture. Thus, the reported results are significant, and they would stimulate the experimental and further studies.

Investigation of the Adsorption Rubraca Anticancer Drug on the CNT(4,4-8) Nanotube as a Factor of Drug Delivery: A Theoretical Study Based on DFT Method

2019 ◽  
Vol 19 (7) ◽  
pp. 473-486 ◽  
Author(s):  
Masoome Sheikhi ◽  
Siyamak Shahab ◽  
Mehrnoosh Khaleghian ◽  
Mahin Ahmadianarog ◽  
Fatemeh Azarakhshi ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Dft Method ◽  
Nbo Analysis ◽  
Hydrogen Atoms ◽  
Functional Theory ◽  
Adsorption Effect ◽  
Chemical Shift Tensors ◽  
Td Dft ◽  
The Stability

Background: In the present study, the interaction between new drug Rubraca and CNT(4,4-8) nanotube by Density Functional Theory (DFT) calculations in an aqueous medium for first time have been investigated. Method and Results: According to calculations, the intermolecular hydrogen bonds take place between active positions of the molecule Rubraca and hydrogen atoms of the nanotube that plays an important role in the stability of the complex CNT(4,4- 8)/Rubraca. The non-bonded interaction effects of the molecule Rubraca with CNT(4,4- 8) nanotube on the electronic properties, chemical shift tensors and natural charge have been also detected. The natural bond orbital (NBO) analysis suggested that the molecule Rubraca as an electron donor and the CNT(4,4-8) nanotube plays the role an electron acceptor at the complex CNT(4,4-8)/Rubraca. The electronic spectra of the Rubraca drug and the complex CNT(4,4-8)/Rubraca were also calculated by Time Dependent Density Functional Theory (TD-DFT) for the investigation of adsorption effect of the Rubraca drug over nanotube. Conclusion: The use of CNT(4,4-8) nanotube for Rubraca delivery to the diseased cells have been established.

Theoretical reconsideration on the hydrogen bonding and coordination interactions of chlorophyll a in aqueous solution

2011 ◽  
Vol 15 (03) ◽  
pp. 202-210 ◽  
Author(s):  
Ji-Feng Liu
Keyword(s):  
Hydrogen Bonding ◽  
Absorption Band ◽  
Water Molecule ◽  
Chlorophyll A ◽  
Absorption Spectra ◽  
Density Functional ◽  
Theoretical Study ◽  
Absorption Bands ◽  
Hydrogen Bonding Interactions ◽  
Explicit Water

In the present work, explicit water molecule and solvent-field effects on the absorption spectrum of chlorophyll a have been studied using time-dependent density functional theory (TDDFT) method. Calculated results show that the one complex and two water coordinated complexes formed by concerted coordination and hydrogen-bonding interactions would be the most preferable conformations of chlorophyll a in aqueous surroundings. Moreover, four obvious absorption bands are assigned by comparing the theoretically simulated absorption spectra with the experimental ones. The theoretical study shows that the explicit water molecule interactions slightly influence the first absorption band. However, the water coordination and hydrogen-bonding interactions can significantly affect the second absorption band which has a strong red-shift. The solvent-field effect due to the polarity of water on absorptions in Q-bands is relatively smaller than that on absorptions in B-bands. As a consequence, our theoretical study on the absorption spectra in the 350–400 nm region presents that the absorption strength in this region was influenced by the explicit coordination and hydrogen bonding interactions from water molecules, significantly.

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