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2024 | Buch

Electron Localization-Delocalization Matrices

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This book builds bridges between two yet separated branches of theoretical and mathematical chemistry: Chemical Graph Theory and Electronic Structure Calculations. Although either of the fields have developed their own techniques, problems, methods, and favorite benchmark cases independent from each other, the authors have managed to bring them together by using the localization-delocalization matrix (LDM). The LDM is a novel molecular descriptor that fingerprints a molecule by condensing the complicated electronic information in one, mathematically manageable, object. In this book, the authors introduce the readers to modeling techniques based on LDMs. Their technique offers a high accuracy as well as robust predictive power, often dramatically surpassing the potential of either of the constituting methods on their own. In addition to the comprehensive and accessible introduction to this new field of theoretical chemistry, the authors offer their self-developed software free to download, so that readers can try running their own simulations. The described methods are very general and can easily be implemented for calculating various properties and parameters such as mosquito repelling activity, ionic liquid properties, local aromaticity of ring molecules, log P's, pKa's, LD50, corrosion inhibition activities, and Lewis acidities and basicities – to only name a few. The free downloadable software helps readers automate the analysis of the matrices described in this book and hence facilitates application of the described methodology.

Inhaltsverzeichnis

Frontmatter
Chapter 1. An Introduction to Electron Localization-Delocalization Matrices
Abstract
This book has been written with the practicing chemist in sight. It is not a book on theoretical chemistry but rather one that is primarily focused on making practical predictions starting from theoretical chemistry calculations.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 2. The Physics of Electron Localization and Delocalization
Abstract
In molecular chemistry, the terms localized/delocalized usually refer to electrons (atomic nuclei (exclusively protons) are rarely delocalized). Localized electrons are typically associated with a specific atom or pair of atoms; delocalized electrons are diffuse and spread out over several atomic nuclei. Typically, in an organic compound, electrons are localized in isolated bonds and delocalized over conjugated bonds.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 3. The Quantum Theory of Atoms in Molecules and Electron Localization and Delocalization
Abstract
The electron density (ρ) is a scalar field that determines the chemical, physical, and biological properties of macroscopic matter as we know it. An atom, a molecule, an ion, a crystal, all have in common that they interact with their surroundings through their electron density distributions. All chemistry is a reflection of an underlying electronic charge interaction, transfer, loss, gain, etc.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 4. Localization-Delocalization Matrix Representation of Molecules
Abstract
A network is a set of objects connected in a pairwise fashion. Frequently, the word network and graph are used interchangeably, even though some authors stress that the network is a set of identifiable connected objects, while the objects connected in a graph are identical. In this monograph, the two terms are used interchangeably.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 5. Molecular Fingerprinting using Localization-Delocalization Matrices: Computational Aspects
Abstract
Ismat Sumar of Saint Mary’s University, one of whom this book is dedicated, pioneered the first software implementation of an algorithm to automate the localization-delocalization matrices (LDMs) analysis of a series of molecules.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 6. Principal Component Analysis of Localization-Delocalization Matrices
Abstract
Principal Component Analysis (PCA) and one of its variants, Factor Analysis (FA), are dimensionality reduction statistical approaches that replace the original correlated variables in a data set with fewer new ones that are linear combinations of the old ones. These new fewer variables capture the majority of the variability in the original data set and hence reduce or eliminate the redundancy of the row data. The new variables are uncorrelated, i.e., orthogonal, in PCA; or less correlated in the case of FA. If the original data set contains uncorrelated random variables, then PCA and FA become irrelevant since there is no data reduction possible in this case.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 7. Localization-Delocalization Matrices Analysis for Corrosion Inhibition
Abstract
In this chapter, three case studies will be presented illustrating how to use electron localization-delocalization matrices (LDMs) analysis in the prediction of corrosion inhibitors’ activities. Furthermore, the analysis is shown to go beyond the mere prediction of activity to deepen our mechanistic understanding by uncovering the active molecular species (e.g., the protonation state or dimerization state) that are responsible for a given compound’s activity in inhibiting corrosion.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 8. Localization-Delocalization Matrices Analysis in Predicting Mosquito Repellency
Abstract
Insects are both humankind’s best friends and worst enemies. Modern agriculture could not survive without the presence of honeybees and other pollinators including mosquitoes. At the same time, mosquitoes are human’s worst enemy. They transmit the protozoan parasite that causes malaria and several viruses that cause dangerous infections such as dengue, yellow fever, West Nile, Chikungunya, encephalitis, and Zika.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 9. Modeling Enzyme-Substrate Interaction with Localization-Delocalization Matrices
Abstract
Enzymes are life’s catalysts par excellence. They are incredibly efficient and are mainly composed of protein—save prosthetic groups and/or nucleic acid components. They can enhance the rate of virtually all the chemical reactions within cells and by astronomical factors so much as to often limit reaction rates by diffusion, that is, the access of the substrate through its random walk to the active site of the enzyme. Enzymatically-catalyzed reactions are accelerated by typical factors of 108–1012.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 10. Localization-Delocalization Matrices of Large Systems
Abstract
In previous chapters, we have demonstrated the extraction of chemical information from molecular structures via the use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM) followed by the analysis of the electron localization-delocalization matrices by such methods as Principal Component Analysis (PCA) to predict useful properties.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Chapter 11. Closing Remarks
Abstract
This monograph presents a new approach to quantum chemically based quantitative structure-to-activity/property (QSAR/QSPR) relationships. The key for good model construction is to have good experimental (activity or property) data for as many compounds as possible.
Chérif F. Matta, Paul W. Ayers, Ronald Cook
Backmatter
Metadaten
Titel
Electron Localization-Delocalization Matrices
verfasst von
Chérif F. Matta
Paul W. Ayers
Ronald Cook
Copyright-Jahr
2024
Electronic ISBN
978-3-031-51434-0
Print ISBN
978-3-031-51432-6
DOI
https://doi.org/10.1007/978-3-031-51434-0

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