ASSOCIATION OF URACIL WITH Zn2+ AND THE HYDRATED Zn2+: A DFT INVESTIGATION

2007 ◽  
Vol 06 (02) ◽  
pp. 197-212 ◽  
Author(s):  
NANA WANG ◽  
PING LI ◽  
YI HU ◽  
YUXIANG BU ◽  
WEIHUA WANG ◽  
...  
Keyword(s):  
Density Functional ◽  
Coordination Mode ◽  
Coordination Complexes ◽  
Carbonyl Oxygen ◽  
Water Molecules ◽  
Bidentate Coordination ◽  
Hydration Effect ◽  
The Density Functional Theory ◽  
Before And After ◽  
Monodentate Coordination

The association behaviors between Uracil and Zn 2+ in vacuum and in the presence of extra water molecules have been investigated systematically using the density functional theory (DFT). In these systems, the interaction of Zn 2+ with the carbonyl oxygen O 4 is systematically favored relative to O 2. For Uracil- Zn 2+ complexes, the more stable coordination mode among the possible complexes corresponds to the bidentate one, where the monodentate coordination mode is about 37 kcal/mol higher in energy relative to the bidentate case. Correspondingly, the stabilities of these structures are enhanced due to the formations of the four-membered chelate ring in the bidentate coordination processes. In the monodentate coordination complexes, the hydration effects are larger than those in the bidentate coordination complexes. The most basic center in the Uracil remains the same regardless of whether introducing the water molecules to Zn 2+ or not. The calculated Zn 2+ bonding energies in Uracil- Zn 2+( H 2 O ) complexes are reduced in comparison to those of the unhydrated Uracil- Zn 2+ complexes. Moreover, investigations of stepwise hydration of Zn 2+ in the most stable Uracil- Zn 2+ complex suggest that the successive hydration effect on the Zn 2+ site can enhance the strength of C = O bond in the Uracil- Zn 2+ complexes and reduce the association interaction of Uracil with Zn 2+. Additionally, the most acidic site of Uracil has been changed from N 1- to N 3– H group before and after introducing the Zn 2+ and there is a significant increase in the overall acidity of the system.

scholarly journals Poly[[nonaaquabis(μ-5-hydroxybenzene-1,3-dicarboxylato)(5-hydroxybenzene-1,3-dicarboxylato)dicerium(III)] hexahydrate]

2014 ◽  
Vol 70 (5) ◽  
pp. m181-m182 ◽  
Author(s):  
Xiao Fan ◽  
Carole Daiguebonne ◽  
Olivier Guillou ◽  
Magatte Camara
Keyword(s):  
Coordination Polymer ◽  
Coordination Mode ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Bidentate Coordination ◽  
Metal Atoms ◽  
Carboxylate Groups ◽  
Dicarboxylate Ligand ◽  
Monodentate Coordination ◽  
Trigonal Prismatic

In the title coordination polymer, {[Ce2(C8H4O5)3(H2O)9]·6H2O}n, the asymmetric unit is formed by two CeIIIatoms, three 5-hydroxybenzene-1,3-dicarboxylate ligands, nine coordinating water molecules and six water molecules of crystallization. The two CeIIIatoms are bridged by 5-hydroxybenzene-1,3-dicarboxylate ligands acting in a bis-bidentate coordination mode, generating infinite chains along [101]. Both independent metal atoms are nine-coordinated, one by four O atoms from the carboxylate groups of two bridging 5-hydroxybenzene-1,3-dicarboxylate ligands and five O atoms from water molecules, generating a tricapped trigonal–prismatic geometry. The coordination around the second CeIIIatom is similar, except that one of the water molecules is replaced by an O atom from an additional 5-hydroxybenzene-1,3-dicarboxylate ligand acting in a monodentate coordination mode and forming a capped square-antiprismatic geometry.

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 Solvent influence on intramolecular interactions and aromaticity in meta and para nitroanilines

2020 ◽  
Vol 31 (5) ◽  
pp. 1717-1728
Author(s):  
Krzysztof K. Zborowski ◽  
Halina Szatyłowicz ◽  
Tadeusz M. Krygowski
Keyword(s):  
Cluster Model ◽  
Density Functional ◽  
Intramolecular Interactions ◽  
Water Molecules ◽  
Amino Groups ◽  
Functional Theory ◽  
Hydration Effect ◽  
Solvent Influence ◽  
Solvation Models ◽  
Solvent Molecules

Abstract Theoretical density functional theory (B3LYP/6-31G**) was used to study the intra- and intermolecular interactions of nitrobenzene, aniline, and meta and para nitroaniline in various solvation models. The studied molecules were solvated by one or two water molecules in the presence of continuum solvation (the PCM model) or without it. Finally, the studied molecules were surrounded by a cluster of water molecules. For comparison, calculations were also made for separated molecules. Geometries, energies, hydrogen bonding between solutes and solvent molecules, atomic charges, and aromaticity were examined. The analysis was based on the Atoms in Molecules methodology and the Harmonic Oscillator Model of Aromaticity (HOMA) index. As a result, an extensive description of the solvation of nitro and amino groups and the effect of solvation on mutual interactions between these groups in meta and para nitroanilines is provided. It was found that in general, the PCM description of the hydration effect on the electronic structure of the studied systems (substituents) is consistent with the approach taking into account all individual interactions (cluster model).

scholarly journals Role of Basic Surface Groups of Activated Carbon in Chlordecone and β-Hexachlorocyclohexane Adsorption: A Molecular Modelling Study

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6969
Author(s):  
Kenia Melchor-Rodríguez ◽  
Chayan Carmenate-Rodríguez ◽  
Anthuan Ferino-Pérez ◽  
Sarra Gaspard ◽  
Ulises J. Jáuregui-Haza
Keyword(s):  
Activated Carbon ◽  
Molecular Modelling ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Water Molecules ◽  
Surface Groups ◽  
Hydration Effect ◽  
Multiple Minima ◽  
Modelling Study

The influence of nitrogen-containing surface groups (SGs) onto activated carbon (AC) over the adsorption of chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) was characterized by a molecular modelling study, considering pH (single protonated SGs) and hydration effect (up to three water molecules). The interactions of both pollutants with amines and pyridine as basic SGs of AC were studied, applying the multiple minima hypersurface (MMH) methodology and using PM7 semiempirical Hamiltonian. Representative structures from MMH were reoptimized using the M06-2X density functional theory. The quantum theory of atoms in molecules (QTAIM) was used to characterize the interaction types in order understanding the adsorption process. A favorable association of both pesticides with the amines and pyridine SGs onto AC was observed at all pH ranges, both in the absence and presence of water molecules. However, a greater association of both pollutants with the primary amine was found under an acidic pH condition. QTAIM results show that the interactions of CLD and β-HCH with the SGs onto AC are governed by Cl···C interactions of chlorine atoms of both pesticides with the graphitic surface. Electrostatic interactions (H-bonds) were observed when water molecules were added to the systems. A physisorption mechanism is suggested for CLD and β-HCH adsorption on nitrogen-containing SGs of AC.

Ab Initio Study of Water Clusters Adsorption on Graphite Surface

2010 ◽  
Vol 105-106 ◽  
pp. 499-501
Author(s):  
Bing Bing Fan ◽  
Hai Long Wang ◽  
Li Guan ◽  
De Liang Chen ◽  
Rui Zhang
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Water Clusters ◽  
Density Functional Theory Method ◽  
Graphite Surface ◽  
Water Molecules ◽  
Geometrical Structures ◽  
Graphite Sheet ◽  
The Density Functional Theory ◽  
Formed Hydrogen

Using the density functional theory method, we have characterized the geometrical structures and adsorption energy of water clusters adsorption on graphite surface. When one water molecule inter- acts with graphite surface, one of the H-O bonds formed hydrogen-bond with carbon atom in graphite sheet; in the two water molecules structure, the linear dimmer nearly parallel to the graphite surface, and also formed the hydrogen-bond; when the number of water molecules increased to six, all the H-O bond that point to the graphite surface has formed Hydrogen-bond with it. The binding energy of the water clusters with a graphite surface depends only on the number of water molecules that form hydrogen bond.

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 SYNTHESIS, CHARACTERIZATION, DFT MODELING AND IN VITRO ANTIMYCOBACTERIAL ACTIVITY ASSAYS OF A SILVER(I)-ISONIAZID COMPLEX

Química Nova ◽  
2020 ◽  
Author(s):  
José Paris Junior ◽  
Maurício Cavicchioli ◽  
Rachel Machado ◽  
Fernando Pavan ◽  
Douglas Hideki Nakahata ◽  
...  
Keyword(s):  
Density Functional ◽  
Antimycobacterial Activity ◽  
Nitrate Anion ◽  
Functional Theory ◽  
Bidentate Coordination ◽  
Anion Coordination ◽  
Dft Modeling ◽  
The Density Functional Theory ◽  
Strain H37rv

In the present work, a silver(I) complex with the antimycobacterial drug isoniazid (inh) is described. Elemental and thermogravimetric analyses confirmed a 1:1 metal:ligand ratio for the silver-isoniazid (Ag-inh) complex with molecular composition AgC6H7N3O·NO3. Infrared (IR) analysis suggests a bidentate coordination of isoniazid to silver by the nitrogen of the NH2 group and by the oxygen of the C=O group, and also confirms the presence of free nitrate anion. Coordination by the NH2 group was reinforced by NMR measurements. Computational simulations using the density functional theory (DFT) reinforced that the ligand coordinates to the silver atom by the NH2 and C=O groups. The silver complex presented a minimal inhibitory concentration (MIC90) of 0.78 μg/mL against the standard Mycobacterium tuberculosis strain H37Rv. The data reported herein warrants further investigation on Ag-inh complex as a potential agent against tuberculosis.

scholarly journals The Rattling and Rotation Behaviours of the Hydrated Excess Proton in Water

2019 ◽  
Author(s):  
Shuping Bi
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Zero Point ◽  
Water Molecules ◽  
Rotational Behaviour ◽  
Functional Theory ◽  
Solvent Water ◽  
Grotthuss Mechanism ◽  
The Density Functional Theory ◽  
Migration Mechanism

<p><b>The rattling and rotation behaviours of the hydrated excess proton (H<sup>+</sup>) in water are investigated using the density functional theory–quantum chemical cluster model (DFT-CM) method. The rattling pathways for the target proton <sup>*</sup>H<sup>+</sup> between two adjacent O atoms in the form of Zundel configurations with symmetrical solvation environments are obtained. The zero-point contribution reduces the reaction energy barrier and enables the rattling to occur spontaneously at room temperature. The rotational behaviour of <sup>*</sup>H<sup>+</sup> in the form of <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> is found. Upon <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>* </sup>rotation, <sup>*</sup>H<sup>+</sup> changes its position accompanied by concerted displacement of surrounding solvent water molecules and the breaking and formation of hydrogen bonds. The “<sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> rotating migration mechanism” is proposed for the proton transfer mechanism in water — the same <sup>*</sup>H<sup>+</sup> migrates via <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> rotation through void in solvent water, rather than different protons hopping along water hydrogen bond chains as known as the Grotthuss mechanism.</b></p><p><b> </b></p>

scholarly journals The Rattling and Rotation Behaviours of the Hydrated Excess Proton in Water

2019 ◽  
Author(s):  
Shuping Bi
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Zero Point ◽  
Water Molecules ◽  
Rotational Behaviour ◽  
Functional Theory ◽  
Solvent Water ◽  
Grotthuss Mechanism ◽  
The Density Functional Theory ◽  
Migration Mechanism

<p><b>The rattling and rotation behaviours of the hydrated excess proton (H<sup>+</sup>) in water are investigated using the density functional theory–quantum chemical cluster model (DFT-CM) method. The rattling pathways for the target proton <sup>*</sup>H<sup>+</sup> between two adjacent O atoms in the form of Zundel configurations with symmetrical solvation environments are obtained. The zero-point contribution reduces the reaction energy barrier and enables the rattling to occur spontaneously at room temperature. The rotational behaviour of <sup>*</sup>H<sup>+</sup> in the form of <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> is found. Upon <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>* </sup>rotation, <sup>*</sup>H<sup>+</sup> changes its position accompanied by concerted displacement of surrounding solvent water molecules and the breaking and formation of hydrogen bonds. The “<sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> rotating migration mechanism” is proposed for the proton transfer mechanism in water — the same <sup>*</sup>H<sup>+</sup> migrates via <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> rotation through void in solvent water, rather than different protons hopping along water hydrogen bond chains as known as the Grotthuss mechanism.</b></p><p><b> </b></p>

First Principle Calculation of CO Chemisorption on δ-Pu(001) Surface

2014 ◽  
Vol 556-562 ◽  
pp. 380-384
Author(s):  
Ru Song Li ◽  
Bin He ◽  
Peng Xu ◽  
Feng Tao Zhao
Keyword(s):  
Density Of States ◽  
Density Functional ◽  
Generalized Gradient ◽  
Surface Band ◽  
First Principle Calculation ◽  
Repulsion Energy ◽  
The Density Functional Theory ◽  
Spin Polarized ◽  
Before And After ◽  
Chemisorption Energy

Chemisorption of CO molecule on the (001) surface of δ-Pu using the generalized gradient approximation of the density functional theory with the Perdew-Burke-Ernzerhof exchange-correlation functional has been investigated without spin-orbit coupling at the non-spin-polarized level to better understand the interaction and chemical reaction of CO with Pu surface. Band structure and density of states before and after CO molecule chemisorption on the bridge position of the (001) surface have been compared and analyzed. The result shows that s and p states of CO molecule hybrid with Pu 6d states. Chemisorption energy for this adsorption site and repulsion energy between CO molecules are 0.615046eV and 0.96768eV, respectively.Key words: density functional;chemisorption;energy band;density of states;repulsion energy

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