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.

scholarly journals Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N2reduction

2018 ◽  
Vol 115 (45) ◽  
pp. E10521-E10530 ◽  
Author(s):  
Simone Raugei ◽  
Lance C. Seefeldt ◽  
Brian M. Hoffman
Keyword(s):  
Electrostatic Interactions ◽  
Density Functional ◽  
Computational Analysis ◽  
Reductive Elimination ◽  
Water Molecules ◽  
Computational Investigation ◽  
Functional Theory ◽  
Elimination Mechanism ◽  
Femo Cofactor

Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N2→ 2NH3reduction involves the reductive elimination (re) of H2from two [Fe–H–Fe] bridging hydrides bound to the catalytic [7Fe–9S–Mo–C–homocitrate] FeMo-cofactor (FeMo-co). These studies rationalize the Lowe–Thorneley kinetic scheme’s proposal of mechanistically obligatory formation of one H2for each N2reduced. They also provide an overall framework for understanding the mechanism of nitrogen fixation by nitrogenase. However, they directly pose fundamental questions addressed computationally here. We here report an extensive computational investigation of the structure and energetics of possible nitrogenase intermediates using structural models for the active site with a broad range in complexity, while evaluating a diverse set of density functional theory flavors. (i) This shows that to prevent spurious disruption of FeMo-co having accumulated 4[e−/H+] it is necessary to include: all residues (and water molecules) interacting directly with FeMo-co via specific H-bond interactions; nonspecific local electrostatic interactions; and steric confinement. (ii) These calculations indicate an important role of sulfide hemilability in the overall conversion ofE0to a diazene-level intermediate. (iii) Perhaps most importantly, they explain (iiia) how the enzyme mechanistically couples exothermic H2formation to endothermic cleavage of the N≡N triple bond in a nearly thermoneutralre/oxidative-addition equilibrium, (iiib) while preventing the “futile” generation of two H2without N2reduction: hydrideregenerates an H2complex, but H2is only lost when displaced by N2, to form an end-on N2complex that proceeds to a diazene-level intermediate.

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).

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

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

<p>This work reports a computational analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of the chlorohydrins CH<sub>3</sub>CHClOH (1ClEtOH) and CH<sub>2</sub>ClCH<sub>2</sub>OH (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 <b><i>n</i></b> 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.</p>

Symmetry-adapted perturbation theory study for some magnesium complexes

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.

scholarly journals Perturbation of Hydrogen Bonding Networks over Supported Lipid Bilayers by Poly (Allylamine Hydrochloride)

2019 ◽  
Author(s):  
Naomi Dalchand ◽  
Merve Dogangun ◽  
Paul E. Ohno ◽  
Emily Ma ◽  
Alex Martinson ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Electrostatic Interactions ◽  
Supported Lipid Bilayers ◽  
Water Molecules ◽  
Interfacial Water ◽  
Sum Frequency ◽  
Biochemical Processes ◽  
Zwitterionic Lipids ◽  
Allylamine Hydrochloride

<div><div><div><p>Water is vital to many biochemical processes and is necessary for driving many fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation (SFG) spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine, PC) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly (allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane disrupting polycations, or to transfection.</p></div></div></div>

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

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

<p>This work reports a computational analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of the chlorohydrins CH<sub>3</sub>CHClOH (1ClEtOH) and CH<sub>2</sub>ClCH<sub>2</sub>OH (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 <b><i>n</i></b> 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.</p>

scholarly journals Two Faces of Water in the Formation and Stabilization of Multicomponent Crystals of Zwitterionic Drug-Like Compounds

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 425
Author(s):  
Artem O. Surov ◽  
Nikita A. Vasilev ◽  
Andrei V. Churakov ◽  
Olga D. Parashchuk ◽  
Sergei V. Artobolevskii ◽  
...  
Keyword(s):  
Density Functional ◽  
General Scheme ◽  
Density Functional Theory Calculations ◽  
Cooh Group ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
Functional Theory ◽  
Bader Analysis ◽  
Empirical Approaches

Two new hydrated multicomponent crystals of zwitterionic 2-aminonicotinic acid with maleic and fumaric acids have been obtained and thoroughly characterized by a variety of experimental (X-ray analysis and terahertz Raman spectroscopy) and theoretical periodic density functional theory calculations, followed by Bader analysis of the crystalline electron density) techniques. It has been found that the Raman-active band in the region of 300 cm−1 is due to the vibrations of the intramolecular O-H...O bond in the maleate anion. The energy/enthalpy of the intermolecular hydrogen bonds was estimated by several empirical approaches. An analysis of the interaction networks reflects the structure-directing role of the water molecule in the examined multicomponent crystals. A general scheme has been proposed to explain the proton transfer between the components during the formation of multicomponent crystals in water. Water molecules were found to play the key role in this process, forming a “water wire” between the COOH group of the dicarboxylic acid and the COO– group of the zwitterion and the rendering crystal lattice of the considered multicomponent crystals.

THEORETICAL MECHANISMS AND KINETICS FOR THE REACTION OF DIMETHYL SULFIDE AND OZONE IN WATER VAPOR

2005 ◽  
Vol 04 (04) ◽  
pp. 1101-1117 ◽  
Author(s):  
ANGELA SHIH ◽  
CALINA CIOBANU ◽  
FU-MING TAO
Keyword(s):  
Water Vapor ◽  
Transition State ◽  
Rate Constants ◽  
Energy Barrier ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
State Theory ◽  
Second Order ◽  
Water Molecules ◽  
Phase Reaction

The reaction mechanisms and kinetics for DMS + O 3 ⇒ DMSO + O 2 in water vapor are studied using density functional theory. A series of reaction pathways are determined with molecular clusters containing the reacting species and up to three water molecules. The results show that the energy barrier, defined as the energy difference between the reactant complex and the transition state, decreases progressively as each water molecule is added to the reacting system. A decreasing energy barrier is attributed to favorable electrostatic interactions between the reacting species and water at the transition state and at the more polar product. Rate constants for the second-order reactions, involving different combinations of hydrated reactants up to three water molecules, are calculated using transition state theory with Eckart tunneling corrections. Effective rate constants for DMS + O 3 ⇒ DMSO + O 2 are obtained using the calculated second-order rate constants and the concentrations of hydrated reactants present in saturated water vapor. The results show that the rate of reaction for DMS + O 3 ⇒ DMSO + O 2 increases dramatically in the presence of water vapor, by up to seven orders of magnitude for reactions involving three water molecules. The study implies that the gas-phase reaction of DMS with ozone is significant in the troposphere and can greatly influence the global climate.

scholarly journals Perturbation of Hydrogen Bonding Networks over Supported Lipid Bilayers by Poly (Allylamine Hydrochloride)

2019 ◽  
Author(s):  
Naomi Dalchand ◽  
Merve Dogangun ◽  
Paul E. Ohno ◽  
Emily Ma ◽  
Alex Martinson ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Electrostatic Interactions ◽  
Supported Lipid Bilayers ◽  
Water Molecules ◽  
Interfacial Water ◽  
Sum Frequency ◽  
Biochemical Processes ◽  
Zwitterionic Lipids ◽  
Allylamine Hydrochloride

<div><div><div><p>Water is vital to many biochemical processes and is necessary for driving many fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation (SFG) spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine, PC) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly (allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane disrupting polycations, or to transfection.</p></div></div></div>

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