Density-functional theoretical study on hydrated DNA duplex: Effect of hydrating water molecules on HOMO distribution in DNA

This work reports a computational analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of the chlorohydrins CH3CHClOH (1ClEtOH) and CH2ClCH2OH (2ClEtOH). The goal of the study is to assess the role of the water solvent into the facilitation of the initial step for dehalogenation of these compounds, a process of interest in several contexts. Molecular orbital methods (MP2), density functional methods (B3LYP, M06 and wB97X-D) and composite model chemistries (CBS-QB3, G4) were employed to investigate the structure, electronic distribution and hydrogen-bonded structure of 7 monohydrates, 6 dihydrates, 5 trihydrates and 5 tetrahydrates of both species. Standard reaction enthalpy and standard Gibbs free reaction energy were computed for all aggregates with respect to n independent water molecules and with respect to the dimer, trimer and tetramer of water, respectively, in order to evaluate stability and hydrogen bonding network. The influence of the water chains on the length and vibrational frequencies, especially of the C-Cl and O-H bonds, was evaluated.

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Symmetry-adapted perturbation theory study for some magnesium complexes

Canadian Journal of Chemistry ◽

10.1139/v2012-062 ◽

2012 ◽

Vol 90 (10) ◽

pp. 819-827

Author(s):

Mehdi D. Esrafili ◽

Sirous Yourdkhani

Keyword(s):

Perturbation Theory ◽

Density Functional ◽

Theoretical Study ◽

Water Molecules ◽

Interaction Energies ◽

Unique Role ◽

Functional Methods ◽

Ligand Interactions ◽

Good Agreement

A systematic theoretical study on Mg–ligand interactions has been carried out employing both ab initio correlated wave function and density functional methods. The interactions of the Mg(CH3N2)2 moiety with BF, CO, N2, NH3, and H2O ligands have been investigated by performing calculations at the B3LYP, MP2, MP4, and CCSD(T)/6–311++G(3df,3pd) levels of theory. Results indicate that the interaction energies of the Mg(CH3N2)2–L complexes increase in the order NH3 > H2O > BF > CO > N2. Symmetry-adapted perturbation theory (SAPT) analysis has been carried out to understand the nature of the forces involved in the bonding. The SAPT results indicate that the stabilities of the Mg–L interactions are attributed mainly to electrostatic effects, while induction and dispersion forces also play a significant role. The evaluated SAPT interaction energies for the Mg(CH3N2)2–L complexes are generally in good agreement with those obtained using the supermolecule CCSD(T) methods, suggesting that SAPT is a proper method to study the intermolecular interactions in these complexes. The results also suggest an explanation for the unique role of Mg2+ as a carrier of water molecules that mediate enzymatic hydrolysis reactions.

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A density functional theoretical study of the influence of cavities and water molecules on tautomerism: The case of pyridones and 1,2,4-triazoles linked to crown ethers and esters

Journal of Heterocyclic Chemistry ◽

10.1002/jhet.5570380622 ◽

2001 ◽

Vol 38 (6) ◽

pp. 1387-1391 ◽

Cited By ~ 18

Author(s):

Ibon Alkorta ◽

José Elguero

Keyword(s):

Crown Ethers ◽

Density Functional ◽

Theoretical Study ◽

Water Molecules

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Supramolecular study, Hirshfeld analysis and theoretical study of 6-methoxyquinolineN-oxide dihydrate

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s0108270113011979 ◽

2013 ◽

Vol 69 (6) ◽

pp. 665-670 ◽

Cited By ~ 1

Author(s):

Rodolfo Moreno-Fuquen ◽

Geraldine Hernandez ◽

Alan R. Kennedy ◽

Catriona A. Morrison

Keyword(s):

Density Functional ◽

Theoretical Study ◽

Basis Sets ◽

Water Molecules ◽

Theoretical Studies ◽

Functional Theory ◽

Hartree Fock ◽

Hirshfeld Surfaces ◽

Hirshfeld Analysis ◽

Oxide Group

In the crystal structure of 6-methoxyquinolineN-oxide dihydrate, C10H9NO2·2H2O, (I), the presence of two-dimensional water networks is analysed. The water molecules form unusual water channels, as well as two intersecting mutually perpendicular columns. In one of these channels, the O atom of theN-oxide group acts as a bridge between the water molecules. The other channel is formed exclusively by water molecules. Confirmation of the molecular packing was performed through the analysis of Hirshfeld surfaces, and (I) is compared with other similar isoquinoline systems. Calculations of bond lengths and angles by the Hartree–Fock method or by density functional theory B3LYP, both with 6-311++G(d,p) basis sets, are reported, together with the results of additional IR, UV–Vis and theoretical studies.

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Theoretical Study of the Microhydration of 1-Chloro and 2-Chloro Ethanol as a Clue for Their Relative Propensity Toward Dehalogenation

10.26434/chemrxiv.7378445.v1 ◽

2018 ◽

Author(s):

George Petsis ◽

Zoi Salta ◽

Agnie M. Kosmas ◽

Oscar Ventura

Keyword(s):

Density Functional ◽

Theoretical Study ◽

Initial Step ◽

Water Molecules ◽

Water Solvent ◽

Functional Methods ◽

Electronic Distribution ◽

Standard Reaction ◽

Hydrogen Bonded

This work reports a computational analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of the chlorohydrins CH3CHClOH (1ClEtOH) and CH2ClCH2OH (2ClEtOH). The goal of the study is to assess the role of the water solvent into the facilitation of the initial step for dehalogenation of these compounds, a process of interest in several contexts. Molecular orbital methods (MP2), density functional methods (B3LYP, M06 and wB97X-D) and composite model chemistries (CBS-QB3, G4) were employed to investigate the structure, electronic distribution and hydrogen-bonded structure of 7 monohydrates, 6 dihydrates, 5 trihydrates and 5 tetrahydrates of both species. Standard reaction enthalpy and standard Gibbs free reaction energy were computed for all aggregates with respect to n independent water molecules and with respect to the dimer, trimer and tetramer of water, respectively, in order to evaluate stability and hydrogen bonding network. The influence of the water chains on the length and vibrational frequencies, especially of the C-Cl and O-H bonds, was evaluated.

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A First-Principles Computational Comparison of the Aqueous Anatase TiO2 (001) Interface and the Disordered, Fluorinated TiO2 Interface

10.26434/chemrxiv.7076816.v1 ◽

2018 ◽

Author(s):

Kyle Reeves ◽

Damien Dambournet ◽

Christel Laberty-Robert ◽

Rodolphe Vuilleumier ◽

Mathieu Salanne

Keyword(s):

Density Of States ◽

Density Functional ◽

Water Dissociation ◽

Water Molecules ◽

Chemical Doping ◽

Charge Balance ◽

Functional Theory ◽

Adsorption Of Water ◽

Properties Of Materials ◽

Computational Comparison

Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO2 with charge balance achieved via the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a monolayer of water via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1eV of the Fermi energy for various steps throughout the simulation, and we determine that the variation in this representation of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules at the surface.

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A First-Principles Computational Comparison of the Aqueous Anatase TiO2 (001) Interface and the Disordered, Fluorinated TiO2 Interface

10.26434/chemrxiv.7076816 ◽

2018 ◽

Author(s):

Kyle Reeves ◽

Damien Dambournet ◽

Christel Laberty-Robert ◽

Rodolphe Vuilleumier ◽

Mathieu Salanne

Keyword(s):

Density Of States ◽

Density Functional ◽

Water Dissociation ◽

Water Molecules ◽

Chemical Doping ◽

Charge Balance ◽

Functional Theory ◽

Adsorption Of Water ◽

Properties Of Materials ◽

Computational Comparison

Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO2 with charge balance achieved via the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a monolayer of water via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1eV of the Fermi energy for various steps throughout the simulation, and we determine that the variation in this representation of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules at the surface.

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Structure of aqueous sodium acetate solutions by X-Ray scattering and density functional theory

Pure and Applied Chemistry ◽

10.1515/pac-2020-0402 ◽

2020 ◽

Vol 92 (10) ◽

pp. 1627-1641

Author(s):

Guangguo Wang ◽

Yongquan Zhou ◽

He Lin ◽

Zhuanfang Jing ◽

Hongyan Liu ◽

...

Keyword(s):

Sodium Acetate ◽

Density Functional ◽

Hydration Shell ◽

Ion Pair ◽

Water Molecules ◽

Sodium Acetate Solution ◽

Acetate Solution ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

AbstractThe structure of aq. sodium acetate solution (CH3COONa, NaOAc) was studied by X-ray scattering and density function theory (DFT). For the first hydrated layer of Na+, coordination number (CN) between Na+ and O(W, I) decreases from 5.02 ± 0.85 at 0.976 mol/L to 3.62 ± 1.21 at 4.453 mol/L. The hydration of carbonyl oxygen (OC) and hydroxyl oxygen (OOC) of CH3COO− were investigated separately and the OC shows a stronger hydration bonds comparing with OOC. With concentrations increasing, the hydration shell structures of CH3COO− are not affected by the presence of large number of ions, each CH3COO− group binds about 6.23 ± 2.01 to 7.35 ± 1.73 water molecules, which indicates a relatively strong interaction between CH3COO− and water molecules. The larger uncertainty of the CN of Na+ and OC(OOC) reflects the relative looseness of Na-OC and Na-OOC ion pairs in aq. NaOAc solutions, even at the highest concentration (4.453 mol/L), suggesting the lack of contact ion pair (CIP) formation. In aq. NaOAc solutions, the so called “structure breaking” property of Na+ and CH3COO− become effective only for the second hydration sphere of bulk water. The DFT calculations of CH3COONa (H2O)n=5–7 clusters suggest that the solvent-shared ion pair (SIP) structures appear at n = 6 and become dominant at n = 7, which is well consistent with the result from X-ray scattering.

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Theoretical Study of Zirconium Isomorphous Substitution into Zeolite Frameworks

Molecules ◽

10.3390/molecules24244466 ◽

2019 ◽

Vol 24 (24) ◽

pp. 4466

Author(s):

Duichun Li ◽

Bin Xing ◽

Baojun Wang ◽

Ruifeng Li

Keyword(s):

Acid Site ◽

Density Functional ◽

Theoretical Study ◽

Atomic Radius ◽

Acid Sites ◽

Isomorphous Substitution ◽

Dispersion Correction ◽

Brønsted Acidity ◽

Functional Theory ◽

Brönsted Acidity

Systematic periodic density functional theory computations including dispersion correction (DFT-D) were carried out to determine the preferred location site of Zr atoms in sodalite (SOD) and CHA-type topology frameworks, including alumino-phosphate-34 (AlPO-34) and silico-alumino-phosphate-34 (SAPO-34), and to determine the relative stability and Brönsted acidity of Zr-substituted forms of SOD, AlPO-34, and SAPO-34. Mono and multiple Zr atom substitutions were considered. The Zr substitution causes obvious structural distortion because of the larger atomic radius of Zr than that of Si, however, Zr-substituted forms of zeolites are found to be more stable than pristine zeolites. Our results demonstrate that in the most stable configurations, the preferred favorable substitutions of Zr in substituted SOD have Zr located at the neighboring sites of the Al-substituted site. However, in the AlPO-34 and SAPO-34 frameworks, the Zr atoms are more easily distributed in a dispersed form, rather than being centralized. Brönsted acidity of substituted zeolites strongly depends on Zr content. For SOD, substitution of Zr atoms reduces Brönsted acidity. However, for Zr-substituted forms of AlPO-34 and SAPO-34, Brönsted acidity of the Zr-O(H)-Al acid sites are, at first, reduced and, then, the presence of Zr atoms substantially increased Brönsted acidity of the Zr-O(H)-Al acid site. The results in the SAPO-34-Zr indicate that more Zr atoms substantially increase Brönsted acidity of the Si-O(H)-Al acid site. It is suggested that substituted heteroatoms play an important role in regulating and controlling structural stability and Brönsted acidity of zeolites.

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