Pauling’s Conceptions of Hybridization and Resonance in Modern Quantum Chemistry

Glendening, Eric D.; Weinhold, Frank

doi:10.3390/molecules26144110

Cited by 20 publications

(14 citation statements)

References 87 publications

(118 reference statements)

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“…The sets of 5-10 ps runs were performed with harmonic potentials centered at different values of reaction coordinates. The force constant of the harmonic potential ½•K•(ξ − ξ0) 2 was usually set to 40 kcal/mol/Å 2 , and additional trajectories with the K = 80 kcal/mol/Å 2 in transition state regions were calculated in several runs. The harmonic potentials were centered in every 0.2-0.3 Å segment along the reaction coordinates.…”

Section: Models and Methodsmentioning

confidence: 99%

“…The important paper by Glendening and Weinhold [2] presents the natural resonance theory (NRT) analysis for the formamide-formimidic acid tautomerization, exemplifying the simplest reaction with the N-C=O peptide bond. In our study, we deal with a considerably more complex reaction, in which the N-C=O peptide group is involved (see Figure 1).…”

Section: The First Reaction Step: the Nbo Analysismentioning

confidence: 99%

“…It is interesting to compare results of the second order perturbation theory analysis of the Fock matrix in the NBO basis, which provides stabilization energies of the interaction between different NBO patterns, accounting for the presence of the minor resonance state and their population [2]. The n N → π CO * interactions account for the delocalization between structures I and III, whereas the n O → π CN * interactions quantify delocalization between structures II and III (Table 4).…”

Section: Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…In this respect, the Natural Bond Orbital (NBO) analysis developed by Frank Weinhold and his colleagues is an indispensable tool. The most recent papers [1,2] on this subject and references in the latter give an essential understanding of the significance of the NBO analysis. Enzyme-catalyzed reactions are literally complex multistep processes that require a careful consideration of each elementary step using adequate instruments.…”

Section: Introductionmentioning

confidence: 99%

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Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

2021

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We report the results of a computational study of the hydrolysis reaction mechanism of N-acetyl-l-aspartyl-l-glutamate (NAAG) catalyzed by glutamate carboxypeptidase II. Analysis of both mechanistic and electronic structure aspects of this multistep reaction is in the focus of this work. In these simulations, model systems are constructed using the relevant crystal structure of the mutated inactive enzyme. After selection of reaction coordinates, the Gibbs energy profiles of elementary steps of the reaction are computed using molecular dynamics simulations with ab initio type QM/MM potentials (QM/MM MD). Energies and forces in the large QM subsystem are estimated in the DFT(PBE0-D3/6-31G**) approximation. The established mechanism includes four elementary steps with the activation energy barriers not exceeding 7 kcal/mol. The models explain the role of point mutations in the enzyme observed in the experimental kinetic studies; namely, the Tyr552Ile substitution disturbs the “oxyanion hole”, and the Glu424Gln replacement increases the distance of the nucleophilic attack. Both issues diminish the substrate activation in the enzyme active site. To quantify the substrate activation, we apply the QTAIM-based approaches and the NBO analysis of dynamic features of the corresponding enzyme-substrate complexes. Analysis of the 2D Laplacian of electron density maps allows one to define structures with the electron density deconcentration on the substrate carbon atom, i.e., at the electrophilic site of reactants. The similar electronic structure element in the NBO approach is a lone vacancy on the carbonyl carbon atom in the reactive species. The electronic structure patterns revealed in the NBO and QTAIM-based analyses consistently clarify the reactivity issues in this system.

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Section: Models and Methodsmentioning

confidence: 99%

Section: The First Reaction Step: the Nbo Analysismentioning

confidence: 99%

Section: Structurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

2021

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Facilitating Layered Oxide Cathodes Based on Orbital Hybridization for Sodium‐Ion Batteries: Marvelous Air Stability, Controllable High Voltage, and Anion Redox Chemistry

Jia,

Wang,

Liu

et al. 2024

Advanced Materials

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Layered oxides have become the research focus of cathode materials for sodium‐ion batteries (SIBs) due to the low cost, simple synthesis process, and high specific capacity. However, the poor air stability, unsteady phase structure under high voltage, and slow anionic redox kinetics hinder their commercial application. In recent years, the concept of manipulating orbital hybridization has been proposed to simultaneously tune the microelectronic structure and modify the surface chemistry environment intrinsically. In this review, the hybridization modes between atoms in 3d/4d transition metal (TM) orbitals and O 2p orbitals near the region of the Fermi energy level (EF) were summarized based on orbital hybridization theory and first‐principles calculations as well as various sophisticated characterizations. Furthermore, the underlying mechanisms are explored from macro‐scale to micro‐scale, including enhancing air stability, modulating high voltage, and stabilizing anionic redox chemistry. Meanwhile, the origin, formation conditions, and different types of orbital hybridization, as well as its application in layered oxide cathodes are presented, which provide insights into the design and preparation of cathode materials. Ultimately, the main challenges in the development of orbital hybridization and its potential for the production application are also discussed, pointing out the route for high‐performance practical sodium layered oxide cathodes.This article is protected by copyright. All rights reserved

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Exploring the structural and optical characteristics of the charge transfer complex 2,3-dimethylquinoxaliniumpicrate: a comprehensive investigation through experimental and computational approaches

Ramesh,

Munusamy,

Saravanakumar

et al. 2024

J Mater Sci: Mater Electron

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Pauling’s Conceptions of Hybridization and Resonance in Modern Quantum Chemistry

Cited by 20 publications

References 87 publications

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

Facilitating Layered Oxide Cathodes Based on Orbital Hybridization for Sodium‐Ion Batteries: Marvelous Air Stability, Controllable High Voltage, and Anion Redox Chemistry

Exploring the structural and optical characteristics of the charge transfer complex 2,3-dimethylquinoxaliniumpicrate: a comprehensive investigation through experimental and computational approaches

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