scholarly journals Supramolecular Complexes of Cucurbiturils with Second Group Metal Salts and Hydrates and Histamine

INEOS OPEN ◽  
2021 ◽  
Vol 4 ◽  
Author(s):  
Yu. A. Borisov ◽  
◽  
S. S. Kiselev ◽  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Metal Salts ◽  
Supramolecular Complexes ◽  
Water Molecules ◽  
Functional Theory ◽  
Guest Molecules ◽  
First Time ◽  
Formation Energies

The interaction of cucurbiturils (Q6, Q7, and Q8) with Ca and Ba chlorides and iodides are studied for the first time by density functional theory. The thermodynamic parameters for the formation of host–guest complexes are calculated. The structures of complexes of Q6 and Q7 with one and two guest molecules are established. The energy parameters for the transfer of Be2+ and Ba2+ cations from an aqueous solution into the cavity of Q7 containing n water molecules are defined. The dependences of the formation energies for complexes Q7WnBe2+ and Q7WnBa2+ on the number of water molecules are shown to be parabolic, with the energy minima at n = 5 and n = 6, respectively. It is found that Q7 can form in an aqueous solution supramolecular complexes with protonated histamine (HA) and neutral histamine in the presence of Ca2+ ions.

Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution

2017 ◽  
Vol 16 (04) ◽  
pp. 1750028 ◽  
Author(s):  
Martina Pola ◽  
Michal A. Kochman ◽  
Alessandra Picchiotti ◽  
Valentyn I. Prokhorenko ◽  
R. J. Dwayne Miller ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Energy Charge ◽  
Blue Shift ◽  
Water Molecules ◽  
Excitation Energies ◽  
Functional Theory ◽  
Vertical Excitation ◽  
Dna Nucleobases

Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.

On the aqueous solvation of AsO(OH)3vs. As(OH)3. Born–Oppenheimer molecular dynamics density functional theory cluster studies

2018 ◽  
Vol 20 (24) ◽  
pp. 16568-16578 ◽  
Author(s):  
A. Ramírez-Solís ◽  
J. I. Amaro-Estrada ◽  
C. I. León-Pimentel ◽  
J. Hernández-Cobos ◽  
S. E. Garrido-Hoyos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Functional Theory ◽  
Aqueous Solvation ◽  
First Time

BOMD simulations were used to reveal the hydration features of As(OH)3 and (for the first time) AsO(OH)3 in aqueous solution.

Density Functional Theory Study of Uranium(VI) Aquo Chloro Complexes in Aqueous Solution

2008 ◽  
Vol 112 (11) ◽  
pp. 2428-2436 ◽  
Author(s):  
Michael Bühl ◽  
Nicolas Sieffert ◽  
Volodymyr Golubnychiy ◽  
Georges Wipff
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Chloro Complexes

A complete ab initio thermodynamic and kinetic catalogue of the defect chemistry of hematite α-Fe2O3, its cation diffusion, and sample donor dopants

2021 ◽  
Author(s):  
Shehab Shousha ◽  
Sarah Khalil ◽  
Mostafa Youssef
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Defect Formation ◽  
Defect Chemistry ◽  
Cation Diffusion ◽  
Functional Theory ◽  
Migration Barriers ◽  
Hubbard U ◽  
And Migration ◽  
Formation Energies

This paper studies comprehensively the defect chemistry and cation diffusion in α-Fe2O3. Defect formation energies and migration barriers are calculated using density functional theory with a theoretically calibrated Hubbard U...

Oxygen vacancy migration in CSZ using density functional theory

2008 ◽  
Vol 1122 ◽  
Author(s):  
Byeong-Eon Lee ◽  
Dae-Hee Kim ◽  
Yeong-Cheol Kim
Keyword(s):  
Density Functional Theory ◽  
Oxygen Vacancy ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Nearest Neighbor ◽  
Functional Theory ◽  
The Third ◽  
Vacancy Migration ◽  
Neighbor Site ◽  
Formation Energies

AbstractWe studied oxygen migration in calcia-stabilized cubic zirconia (CSZ) using density functional theory. A Ca atom was substituted for a Zr atom in a 2×2×2 ZrO2 cubic supercell, and an oxygen vacancy was produced to satisfy the charge neutrality condition. We found that the formation energies of an oxygen vacancy, as a function of its location with respect to the Ca atom, were varied. The relative formation energies of the oxygen vacancies located at the first-, second-, third-, and fourth-nearest-neighbors were 0.0, −0.07, 0.19, and 0.19 eV, respectively. Therefore, the oxygen vacancy located at the second-nearest-neighbor site of the Ca atom was the most favorable, the oxygen vacancy located at the first-nearest-neighbor site was the second most favorable, and the oxygen vacancies at the third- and fourth-nearest-neighbor sites were the least favorable. We also calculated the energy barriers for the oxygen vacancy migration between oxygen sites. The energy barriers between the first and the second nearest sites, the second and third nearest sites, and the third and fourth nearest sites were 0.11, 0.46, and 0.23 eV, respectively. Therefore, the oxygen vacancies favored the first- and second-nearest-neighbor oxygen sites when they drifted under an electric field.

scholarly journals Hydration Dependent Band Gap Tunability of Self-Assembled Phenylalanine-Tryptophan Nanotubes

2020 ◽  
Author(s):  
Hugo Souza ◽  
Antonio Chaves Neto ◽  
Francisco Sousa ◽  
Rodrigo Amorim ◽  
Alexandre Reily Rocha ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Band Gap ◽  
Electronic Properties ◽  
Building Block ◽  
Density Functional ◽  
Tight Binding ◽  
Water Molecules ◽  
Confined Water ◽  
Functional Theory ◽  
Tight Binding Method

In this work, we investigate the effects of building block separation of Phenylalanine-Tryptophan nanotube induced by the confined water molecules on the electronic properties using density-functional theory based tight-binding method. <div><br></div>

scholarly journals Взаимодействие alpha-частиц keV-энергий с молекулами глицил-лейцина

2021 ◽  
Vol 47 (12) ◽  
pp. 23
Author(s):  
А.А. Басалаев ◽  
А.Г. Бузыкин ◽  
В.В. Кузьмичев ◽  
М.Н. Панов ◽  
А.В. Петров ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Cross Sections ◽  
Density Functional ◽  
Molecular Ions ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Singly Charged ◽  
Doubly Charged ◽  
First Time ◽  
Fragmentation Processes

Radiation damage to isolated glycyl-leucine (C8H16N2O3) molecules caused by interaction with He2+ ions was studied. For the first time, the relative cross sections of the main processes of changes in the charge state of the collision partners and the relative cross sections of the fragmentation processes of singly and doubly charged molecular ions formed during single collisions of glycyl-leucine molecules with ions have been obtained. The optimized geometry of the molecule and singly charged glycyl-leucine ion was calculated using the density functional theory (DFT).

scholarly journals Computational Evidence Suggests That 1-chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-chloroethanol into Acetaldehyde and HCl

2019 ◽  
Author(s):  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Oscar Ventura ◽  
Vincenzo Barone
Keyword(s):  
Aqueous Solution ◽  
Water Molecule ◽  
Gas Phase ◽  
Density Functional ◽  
Water Molecules ◽  
Functional Theory ◽  
Direct Transformation ◽  
The Density Functional Theory ◽  
Successive Step ◽  
The One

<p>The dehalogenation of 2-chloroethanol (2ClEtOH) in gas phase with and without participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route towards oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. This species is more stable than 2ClEtOH by about 6 kcal mol<sup>-1</sup>, and the reaction barrier is 22 kcal mol<sup>-1</sup> vs 55 kcal mol<sup>-1</sup> for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol<sup>-1</sup>) than that of VA to the same products (55 kcal mol<sup>-1</sup>). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol<sup>-1</sup>, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 6 kcal mol<sup>-1</sup>). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 22 to 12 kcal mol<sup>-1</sup>). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is competitive with the VA alcohol path.</p>

scholarly journals The mechanism of aquaporin inhibition by gold compounds elucidated by biophysical and computational methods

2017 ◽  
Vol 53 (27) ◽  
pp. 3830-3833 ◽  
Author(s):  
Andreia de Almeida ◽  
Andreia F. Mósca ◽  
Darren Wragg ◽  
Margot Wenzel ◽  
Paul Kavanagh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Computational Methods ◽  
Density Functional ◽  
Electrochemical Studies ◽  
Functional Theory ◽  
Mechanism Of Inhibition ◽  
Gold Compounds ◽  
First Time

The mechanism of inhibition of water and glycerol permeation via human aquaglyceroporin-3 (AQP3) by gold(iii) complexes has been described, for the first time, using molecular dynamics (MD), combined with density functional theory (DFT) and electrochemical studies.

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