scholarly journals The Grotthuss mechanism for bifunctional proton transfer in poly(benzimidazole)

2021 ◽  
Vol 8 (12) ◽  
Author(s):  
Jittima Thisuwan ◽  
Phorntep Promma ◽  
Kritsana Sagarik
Keyword(s):  
Proton Transfer ◽  
Energy Barrier ◽  
Density Functional ◽  
State Theory ◽  
Ion Pair ◽  
Transition Structure ◽  
Energy Trap ◽  
Grotthuss Mechanism ◽  
Theoretical Results ◽  
Dielectric Environment

Poly(benzimidazole) (PBI) has received considerable attention as an effective high-temperature polymer electrolyte membrane for fuel cells. In this work, the Grotthuss mechanism for bifunctional proton transfer in PBI membranes was studied using density functional theory and transition state theory. This study focused on the reaction paths and kinetics for bifunctional proton transfer scenarios in neutral ([PBI] 2 ), single (H + [PBI] 2 ) and double-protonated (H 2+ [PBI] 2 ) dimers. The theoretical results showed that the energy barriers and strength for H-bonds are sensitive to the local dielectric environment. For [PBI] 2 with ε = 1, the uphill potential energy curve is attributed to extraordinarily strong ion-pair H-bonds in the transition structure, regarded as a ‘dipolar energy trap’. For ε = 23, the ion-pair charges are partially neutralized, leading to a reduction in the electrostatic attraction in the transition structure. The dipolar energy trap appears to prohibit interconversion between the precursor, transition and proton-transferred structures, which rules out the possibility for [PBI] 2 to be involved in the Grotthuss mechanism. For H + [PBI] 2 and H 2+ [PBI] 2 with ε = 1, the interconversion involves a low energy barrier, and the increase in the energy barrier for ε = 23 can be attributed to an increase in the strength of the protonated H-bonds in the transition structure: the local dielectric environment enhances the donor–acceptor interaction of the protonated H-bonds. Analysis of the rate constants confirmed that the quantum effect is not negligible for the N–H + … N H-bond especially at low temperatures. Agreement between the theoretical and experimental data leads to the conclusion that the concerted bifunctional proton transfer in H 2+ [PBI] 2 in a high local dielectric environment is ‘the rate-determining scenario’. Therefore, a low local dielectric environment can be one of the required conditions for effective proton conduction in acid-doped PBI membranes. These theoretical results provide insights into the Grotthuss mechanism, which can be used as guidelines for understanding the fundamentals of proton transfers in other bifunctional H-bond systems.

scholarly journals Caryolene-forming carbocation rearrangements

2013 ◽  
Vol 9 ◽  
pp. 323-331 ◽  
Author(s):  
Quynh Nhu N Nguyen ◽  
Dean J Tantillo
Keyword(s):  
Density Functional Theory ◽  
Proton Transfer ◽  
Energy Barrier ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Intramolecular Proton Transfer ◽  
The Other ◽  
Orbital Symmetry ◽  
Functional Theory ◽  
Biosynthetic Precursor

Density functional theory calculations on mechanisms of the formation of caryolene, a putative biosynthetic precursor to caryol-1(11)-en-10-ol, reveal two mechanisms for caryolene formation: one involves a base-catalyzed deprotonation/reprotonation sequence and tertiary carbocation minimum, whereas the other (with a higher energy barrier) involves intramolecular proton transfer and the generation of a secondary carbocation minimum and a hydrogen-bridged minimum. Both mechanisms are predicted to involve concerted suprafacial/suprafacial [2 + 2] cycloadditions, whose asynchronicity allows them to avoid the constraints of orbital symmetry.

Ethylenediamine Catalyzed Decarboxylation of Oxaloacetic Acid: A DFT Investigation

2013 ◽  
Vol 781-784 ◽  
pp. 253-258
Author(s):  
Ming Zhi Song ◽  
Zai Long Zhang ◽  
Chuan Gang Fan ◽  
Da Zhi Li ◽  
Shi Guo Zhang
Keyword(s):  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Water Solution ◽  
Membered Ring ◽  
Transition Structure ◽  
Functional Theory ◽  
Oxaloacetic Acid ◽  
Stepwise Mechanism ◽  
Rate Determining Step

The decarboxylation mechanism of oxaloacetic acid aided with ethylenediamine or without any catalyst is investigated employing Density Functional Theory (DFT). DFT calculations for both the gas phase and in water solution indicate a stepwise mechanism for each of the steps of the reactions. In the catalyzed mechanism, the dehydration of carbinolamine (IM1) is via a seven-membered ring transition structure (TS5), which is consistent with the structure proposed by Thalji, et al. The decarboxylation of the imine (IM6) is the rate determining step with an energy barrier of 16.46 kcal/mol, lower than the reaction without any catalysts or catalyzed with ions.

A Molecular Dynamics Study for the Characteristics of Proton Transfer in Polymer Electrolyte Membrane

2011 ◽  
Author(s):  
Takashi Tokumasu ◽  
Taiki Yoshida
Keyword(s):  
Molecular Dynamics ◽  
Fuel Cell ◽  
Proton Transfer ◽  
Polymer Electrolyte ◽  
Energy Barrier ◽  
Density Functional ◽  
Polymer Electrolyte Membrane ◽  
Mean Square Displacement ◽  
Polymer Electrolyte Fuel Cell ◽  
Electrolyte Membrane

These days Polymer Electrolyte Fuel Cell (PEFC) is the most developed fuel cell. A polymer electrolyte membrane (PEM) is used in PEFC. Its efficiency is proportional to the proton transferring efficiency, which depends on the nanoscale structure of water. In this study, the property of proton transfer was analyzed by Molecular Dynamics (MD) method including Grotthus mechanism by Empirical Valence Bond (EVB) method. Nafion membrane was adopted as PEM. The potential energy barrier of proton hopping obtained by EVB method was adjusted to reproduce the energy barrier obtained by Density Functional Theory (DFT). In MD simulation, the distribution of water in Nafion was firstly analyzed. The results showed that liquid molecules gather around sulfo groups. Next, the property of proton transfer was analyzed by Mean Square Displacement (MSD).

Quantum mechanical tunnelling through the catalytic effects of A2451 ribosomal residue during a stepwise peptide bond formation

2019 ◽  
Vol 97 (4) ◽  
pp. 497-503
Author(s):  
Hadieh Monajemi ◽  
Sharifuddin Md. Zain ◽  
Toshimasa Ishida ◽  
Wan Ahmad Tajuddin Wan Abdullah
Keyword(s):  
Reaction Mechanism ◽  
Proton Transfer ◽  
Density Functional ◽  
Bond Formation ◽  
Peptide Bond ◽  
State Theory ◽  
Basis Set ◽  
Quantum Mechanical ◽  
Peptide Bond Formation ◽  
Quantum Mechanical Effects

The search for the mechanism of ribosomal peptide bond formation is still ongoing. Even though the actual mechanism of peptide bod formation is still unknown, the dominance of proton transfer in this reaction is known for certain. Therefore, it is vital to take the quantum mechanical effects on proton transfer reaction into consideration; the effects of which were neglected in all previous studies. In this study, we have taken such effects into consideration using a semi-classical approach to the overall reaction mechanism. The M06-2X density functional with the 6-31++G(d,p) basis set was used to calculate the energies of the critical points on the potential energy surface of the reaction mechanism, which are then used in transition state theory to calculate the classical reaction rate. The tunnelling contribution is then added to the classical part by calculating the transmission permeability and tunnelling constant of the reaction barrier, using the numerical integration over the Boltzmann distribution for the symmetrical Eckart potential. The results of this study, which accounts for quantum effects, indicates that the A2451 ribosomal residue induces proton tunnelling in a stepwise peptide bond formation.

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.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

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

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.

Steady-State Spectroscopy to Single Out the Contact Ion Pair in Excited-State Proton Transfer

2021 ◽  
Vol 12 (6) ◽  
pp. 1683-1689
Author(s):  
Alexander Grandjean ◽  
J. Luis Pérez Lustres ◽  
Stephan Muth ◽  
Daniel Maus ◽  
Gregor Jung
Keyword(s):  
Excited State ◽  
Steady State ◽  
Proton Transfer ◽  
Ion Pair ◽  
Contact Ion Pair ◽  
Excited State Proton Transfer

scholarly journals Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

2021 ◽  
Vol 22 (15) ◽  
pp. 8033
Author(s):  
Aneta Jezierska ◽  
Kacper Błaziak ◽  
Sebastian Klahm ◽  
Arne Lüchow ◽  
Jarosław J. Panek
Keyword(s):  
Monte Carlo ◽  
Perturbation Theory ◽  
Potential Energy ◽  
Proton Transfer ◽  
Ir Spectra ◽  
Quantum Monte Carlo ◽  
Density Functional ◽  
Theoretical Approaches ◽  
Study Results ◽  
Intramolecular Hydrogen

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

scholarly journals Theoretical insight on the treatment of β-hexachlorocyclohexane waste through alkaline dehydrochlorination

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alicia Bescós ◽  
Clara I. Herrerías ◽  
Zoel Hormigón ◽  
José Antonio Mayoral ◽  
Luis Salvatella
Keyword(s):  
Density Functional ◽  
Kinetic Studies ◽  
Alkaline Treatment ◽  
Functional Study ◽  
Reaction Intermediates ◽  
Preferential Formation ◽  
Reaction Intermediate ◽  
Rate Determining Step ◽  
Dehydrochlorination Reaction ◽  
Theoretical Results

AbstractThe occurrence of 4.8–7.2 million tons of hexachlorocyclohexane (HCH) isomers stocked in dumpsites around the world constitutes a huge environmental and economical challenge because of their toxicity and persistence. Alkaline treatment of an HCH mixture in a dehydrochlorination reaction is hampered by the low reactivity of the β-HCH isomer (HCl elimination unavoidably occurring through syn H–C–C–Cl arrangements). More intriguingly, the preferential formation of 1,2,4-trichlorobenzene in the β-HCH dehydrochlorination reaction (despite the larger thermodynamical stability of the 1,3,5-isomer) has remained unexplained up to now, though several kinetic studies had been reported. In this paper, we firstly show a detailed Density Functional study on all paths for the hydroxide anion-induced elimination of β-HCH through a three-stage reaction mechanism (involving two types of reaction intermediates). We have now demonstrated that the first reaction intermediate can follow several alternative paths, the preferred route involving abstraction of the most acidic allylic hydrogen which leads to a second reaction intermediate yielding only 1,2,4-trichlorobenzene as the final reaction product. Our theoretical results allow explaining the available experimental data on the β-HCH dehydrochlorination reaction (rate-determining step, regioselectivity, instability of some reaction intermediates).

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