Computerkemi

This brief offers an introduction to the fascinating new field of quantitative read-across structure-activity relationships (q-RASAR) as a cheminformatics modeling approach in the background of quantitative structure-activity relationships (QSAR) and read-across (RA) as data gap-filling methods. It discusses the genesis and model development of q-RASAR models demonstrating practical examples. It also showcases successful case studies on the application of q-RASAR modeling in medicinal chemistry, predictive toxicology, and materials sciences. The book also includes the tools used for q-RASAR model development for new users. It is a valuable resource for researchers and students interested in grasping the development algorithm of q-RASAR models and their application within specific research domains.

This monograph describes the new quantum theory called the weakest bound electron theory (WBE theory) proposed by Prof. Neng-Wu Zheng and its applications. It starts with the fundamentals of quantum mechanics and then illustrates the key points of WBE theory and the mathematical expressions of WBE theory. Finally, it presents a wide range of applications of WBE theory to the chemical and physical properties of atoms and molecules, including energy levels, transition properties, the difference law of ionization energies etc. It appeals to a broad readership, particularly researchers and academics in chemistry, physics, and materials science.

This textbook is designed for students and researchers who are interested in materials and catalysts informatics with little to no prior experience in data science or programming languages. Starting with a comprehensive overview of the concept and historical context of materials and catalysts informatics, it serves as a guide for establishing a robust materials informatics environment. This essential resource is designed to teach vital skills and techniques required for conducting informatics-driven research, including the intersection of hardware, software, programming, machine learning within the field of data science and informatics. Readers will explore fundamental programming techniques, with a specific focus on Python, a versatile and widely-used language in the field. The textbook explores various machine learning techniques, equipping learners with the knowledge to harness the power of data science effectively. The textbook provides Python code examples, demonstrating materials informatics applications, and offers a deeper understanding through real-world case studies using materials and catalysts data. This practical exposure ensures readers are fully prepared to embark on their informatics-driven research endeavors upon completing the textbook. Instructors will also find immense value in this resource, as it consolidates the skills and information required for materials informatics into one comprehensive repository. This streamlines the course development process, significantly reducing the time spent on creating course material. Instructors can leverage this solid foundation to craft engaging and informative lecture content, making the teaching process more efficient and effective.

This book highlights various aspects of geochemical and geological processes. In brief, it facilitates to understand the geochemical behavior of major, trace and rare earth elements in rocks to identify the magmatic processes involved in present-day magma generation and their relation to global tectonic regimes as well as geothermal studies. Therefore, the book provides a comprehensive view of the generation of magma types (mafic to felsic in composition) and their role in the petrogenesis. The book also covers the development of new geosoftware to effectively process the geochemical data before its interpretation.

"Molecular Mechanisms in Brain Regeneration" written by Abhipradnya Bipin is an essential resource for researchers and clinicians interested in the field of neuroregeneration. The book covers the various molecular mechanisms involved in the process of brain regeneration, with a focus on the role of neural stem cells, neurotrophic factors, and extracellular matrix in facilitating regeneration. The book delves into the complex mechanisms of axon growth, myelin formation, synaptic plasticity, and inflammation, and discusses the vital role of glial cells in brain regeneration. The author also explores the crucial impact of epigenetic modifications on neuronal migration, differentiation, and proliferation, as well as on the survival or apoptosis of cells. The book further covers the critical signaling pathways that are essential for neurogenesis and the roles of oligodendrocytes, Schwann cells, astrocytes, and microglia in the process of brain regeneration. It also discusses the challenges that arise from the blood-brain barrier in facilitating regeneration. The book also focuses on the potential of neuroregenerative therapies for treating neurological disorders, such as traumatic injury, stroke, neurodegenerative diseases, including Alzheimer's, Parkinson's, Huntington's, and prion diseases, epilepsy, and neuropsychiatric disorders such as depression, anxiety, schizophrenia, and addiction. The author also discusses the potential of gene therapy and biomaterials in promoting brain regeneration. Overall, "Molecular Mechanisms in Brain Regeneration" provides a comprehensive and in-depth understanding of the complex processes involved in brain regeneration, highlighting the promising potential for new therapies to treat a wide range of neurological disorders.

This book introduces the innovatively advanced crystalline metal oxide catalysts that have multi-catalytic functions on the basis of spatially placed elements in crystal structure. With authors who are experts in their fields, the chapters of the book are organized according to catalytic function, on the basis of crystal structure. The book also covers the structure determination of micro-nano-sized metal oxide crystals that are now standard in most catalytic materials and new trends in catalyst development using materials informatics and catalytic informatics. The information contained here will guide researchers who are eager to carry out sustainable catalytic processes and ultimately to achieve a sustainable society in their quest for catalyst development.

This volume brings together internationally leading researchers in this interdisciplinary field to explore and exchange ideas, both experimental and theoretical, to further our understanding of the fundamental properties of water at interfaces.

Medicinal chemistry is the study of molecular aspects of drug actions. It encompasses molecules, their structures, designs, and their pharmacological activities. A molecule's potency is determined by its structure. The structural activity relationship is a sub-branch of medicinal chemistry that estimates a molecule's potential to display any pharmacological activity. Computational methods play a significant role in the development of molecules that are therapeutically significant. These methods can be categorized into ligand-based and structure-based methods. Ligand-based methods make use of ligand information for the prediction of activity based on the similarities and dissimilarities compared to previously known active ligands. Generally utilized ligand-based methods include quantitative structure-activity relationships, molecular descriptors, and ligand-based pharmacophores. These methods are analogous towards high-throughput screening, where information regarding ligand and target structure both is important. Structure-based methods include ligand design methods, pharmacophore, and ligand docking. This book contains some path-breaking studies in the field of medicinal chemistry. It will provide interesting topics for research on the computational methods for drug design, which interested readers can take up. This book will serve as a reference source for a broad spectrum of readers.

Computer-aided drug discovery and design technologies have played a critical role in the development of therapeutically important small compounds. These technologies involve computational tools and sources which are used for storing, managing, analyzing and modeling compounds. These approaches can be divided into two categories: structure-based and ligand-based. Computer-aided drug design (CADD) is an important tool for speeding up and saving money in the expensive and time-consuming process of drug discovery and development. There has been a surge in protein and ligand structural data in recent years. As a result, the number of databases and bioinformatics tools available to handle and process the data has increased dramatically. For the discovery and development of new medications, the best use of the broad array of available computational techniques is critical. This book is a compilation of research works that discuss the emerging trends in computational drug discovery and design. It will help the readers in keeping pace with the rapid changes taking place in this field.

Computational pharmaceutics is a new discipline that integrates big data, artificial intelligence, and multi-scale modeling techniques into pharmaceutics. It facilitates the understanding of drug delivery mechanisms, and the development of various novel systems in drug delivery. The conventional trial-and-error experiments, which are still used for formulation development in drug delivery systems, are time-consuming, costly and unpredictable. There are various molecular modeling techniques that are widely used to develop new drug delivery systems. These include solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein, and non-viral gene delivery systems. This book contains some path-breaking studies in the field of computational pharmaceutics. The various studies that are constantly contributing towards the application of molecular modeling in drug delivery are examined in detail. Scientists and students actively engaged in this field will find this book full of crucial and unexplored concepts.

This book summarizes the state-of-the-art advances in the area of computational modelling of molecule-based magnets. Nowadays, various computational tools based on DFT, ab initio methods and other techniques are gaining attention in molecular nanomagnets and are successfully used to solve several outstanding problems in this area. This contributed volume discusses the theoretical foundation of the modelling of molecular magnets, starting from fitting the experimental magnetic data of very large molecules to the theory of pseudo-spin Hamiltonian approach and spin-phonon relaxations mechanisms, while it also presents examples of contemporary applications of both transition metal and lanthanide molecular magnets. In addition, the transport characteristics of molecules when placed at an interface and how these assemble on surfaces are also reviewed. This book is a great tool for researchers working in the fields of molecular magnetism and computational/theoretical chemistry and will also benefit graduate students specializing in physical-inorganic chemistry and molecular modelling.Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Machine Learning and Hybrid Modelling for Reaction Engineering summarises latest research and fills a gap in methodology development of hybrid models for reaction engineering applications.

This second edition provides new and updated methods and techniques for identification of drug target, binding sites prediction, high- throughput virtual screening, lead discovery and optimization, conformational sampling, prediction of pharmacokinetic properties using computer-based methodologies. Chapters also focus on the application of the latest artificial intelligence technologies for computer aided drug discovery. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Drug Discovery and Design, Second Edition aims to effectively utilize computational methodologies in discovery and design of novel drugs.

This volume presents the current status of software development in the field of computational and theoretical chemistry and gives an overview of the emerging trends. The challenges of maintaining the legacy codes and their adaptation to the rapidly growing hardware capabilities and the new programming environments are surveyed in a series of topical reviews written by the core developers and maintainers of the popular quantum chemistry and molecular dynamics programs. Special emphasis is given to new computational methodologies and practical aspects of their implementation and application in the computational chemistry codes. Modularity of the computational chemistry software is an emerging concept that enables to bypass the development and maintenance bottleneck of the legacy software and to customize the software using the best available computational procedures implemented in the form of self-contained modules. Perspectives on modular design of the computer programs for modeling molecular electronic structure, non-adiabatic dynamics, kinetics, as well as for data visualization are presented by the researchers actively working in the field of software development and application. This volume is of interest to quantum and computational chemists as well as experimental chemists actively using and developing computational software for their research.Chapters "e;MLatom 2: An Integrative Platform for Atomistic Machine Learning"e; and "e;Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol"e; are available open access under a CC BY 4.0 License via link.springer.com.

This contributed volume overviews recently presented approaches for carrying out QSPR/QSAR analysis by using a simplifying molecular input-line entry system (SMILES) to represent the molecular structure. In contrast to traditional SMILES, quasi-SMILES is a sequence of special symbols-codes that reflect molecular features and codes of experimental conditions. SMILES and quasi-SMILES serve as a basis to develop QSPR/QSAR as well Nano-QSPR/QSAR via the Monte Carlo calculation that provides the so-called optimal descriptors for QSPR/QSAR models. The book presents a reliable technology for developing Nano-QSPR/QSAR while it also includes the description of the algorithms of the Monte Carlo optimization. It discusses the theory and practice of the technique of variational authodecoders (VAEs) based on SMILES and analyses in detail the index of ideality of correlation (IIC) and the correlation intensity index (CII) which are new criteria for the predictive potential of the model. The mathematical apparatus used is simple so that students of relevant specializations can easily follow. This volume is a valuable contribution to the field and will be of great interest to developers of models of physicochemical properties and biological activity, chemical technologists, and toxicologists involved in the area of drug design.

The book provides a unique analysis of current air pollution in Germany by correlating results from chemical transport modelling and accumulation monitoring by moss.Results of most recent modelling of atmospheric concentration and deposition of the metal elements Cd, Hg and Pb are compared with the results of technical measurements and bioindication with mosses. These modelling results with status 2020 have a higher spatial resolution of 0.1° x 0.1° than the modelling results valid up to then (50 km x 50 km). This leads to partly slightly higher correlations between the findings of the modelling and those of the moss monitoring. In this study, descriptive and correlation-statistical parameters are calculated, results and recommendations drawn described. A statistically adequately deepened analysis and evaluation of the highresolution modelling results requires additional methodological tools, which are outlined in summary. It is particularly important to link the exposure data from modelling, technical measurements and the findings from moss monitoring with information on the receptors, the ecosystem types. This is the only way to ensure that the results of the present project contribute to a more differentiated assessment of the impacts on ecosystems from atmospheric heavy metal deposition than has been the case to date, thus enabling a targeted further development of risk assessments for German

This volume brings together internationally leading researchers in the fields of synthesis, materials, and catalysis, particularly involving systems where non-covalent interactions are a crucial factor.

This book covers the design and development of glucocorticoid receptor modulators (GRM) from cortisol to antibody-drug conjugate payloads over the last 70 years. The author starts with an introduction to the background of glucocorticoid receptor modulators as potential therapeutic modalities. This is followed by seven chapters in which he collates and discusses the medicinal chemistry journey of GRMs, reviewing topics such as cortisol-based glucocorticoids, the different approaches that have been pursued to enable chronic dosing of GRM compounds by inactivation in plasma and the liver, the application of prodrugs to GRMs, selective GRMs, targeted delivery of GRMs using polymers and nanoparticles, and rational drug design approaches applied in the development of GRMs. Particular attention is given to the development of glucocorticoid receptor modulators as immunology antibody-drug conjugate payloads. In the book¿s final chapter, the author critiques the medicinal chemistry progress madesince the discovery of cortisone and the promise of the latest antibody-drug conjugates that release a GRM payload. In this book, readers will also find an overview of the X-ray structures of glucocorticoid receptor antagonists and a list of all the earlier reviews that cover part of the medicinal chemistry story of GRM collated by keywords organized in a table. With several examples of crystal structures and molecular modeling, this book illustrates the huge effort by multiple companies and research groups to develop glucocorticoid receptor modulators. Professionals and scholars alike will find it a handy tool, and appreciate the latest research findings that it presents.

¿¿Molecular Association Studies On Novel Materials" is an insightful book written by N Dharani Rajan that explores the molecular properties and associations of novel materials. The book covers a broad range of topics, including the fundamental principles of molecular association, the properties of novel materials, and their applications in various fields. The book begins by introducing readers to the basics of molecular association and its importance in the study of novel materials. It then goes on to explore the various types of novel materials, including biomaterials, magnetic materials, and supramolecular materials, discussing their unique properties and structures. The author also discusses the various techniques used to study the molecular associations of novel materials, including X-ray diffraction, spectroscopy, and microscopy. The book concludes with a discussion on the applications of these materials in various fields such as biomedicine, energy storage, and environmental remediation. Overall, "Molecular Association Studies On Novel Materials" is an invaluable resource for students, researchers, and professionals in the field of materials science and engineering. It provides a comprehensive understanding of the molecular associations of novel materials and their potential applications, making it a must-read for anyone interested in this exciting and rapidly growing field. The book is written in a clear and concise manner, making it accessible to readers from a wide range of scientific backgrounds.

The book presents select proceedings of Global meet on 'Computational Modelling and Simulation, Recent Innovations, Challenges and Perspectives, 2020. This book covers leading-edge technologies from different domains such as computation in optimization and control, multiscale and multiphysics modeling and computation analysis, environmental modeling, modeling approaches to enterprise systems and services, finite element analysis, dependability and security, high-performance computation/cloud computing applications, computational biology and chemistry and computational mechanics. The primary goal of this book is to strengthen pre-eminence in computational modeling and simulation by catalyzing the transformative use of innovative developments in a wide range of disciplines to achieve lasting societal impact. The book discusses on how to perform simulation of large complex dynamic systems in an efficient manner using advanced computational analysis. The inter-disciplinary nature of the book would be a valuable reference for academicians and research scientists, industrialists interested in modelling and simulation driven by computational technology.

This book begins by providing a simplified version of the computational quantum chemistry sufficient to calculate the wavefunctions that are the basic input of NG-QTAIM. Enough basic (scalar) QTAIM theory is provided to understand the later chapters. In addition, our developments of scalar QTAIM are presented and activities at various levels of difficulty are provided for the readership to facilitate understanding. The topological origins of Quantum Theory of Atoms in Molecules (QTAIM) before explaining the highlights and consequences of the developments of Next-Generation QTAIM (NG-QTAIM) that is a 3-D vector-based realization of QTAIM. The book compiles all developments and extensions of Next-Generation QTAIM in one place for easy reference for those engaged in theoretical/computational chemistry. Essential insights into molecular switch functioning not available from the energy barrier or any scalar measures are presented along with a new measure toassess the efficiency of rotary molecular motors. The book also discusses how the treatment of external forces such as electric fields and laser irradiation is included in NG-QTAIM. This book benefits theoretical/computational chemists/physics/engineers, students (graduate and undergraduate) and chemical/pharmaceutical industry researchers who carry out chemical computations in universities and industries.Where appropriate, Target Learning Outcomes and Further Reading are provided along with a list of the scientific goals to be addressed in addition to a glossary table in the summary sections. Where applicable each chapter concludes by outlining benefits, limitations and suggestions for further investigations.All our NG-QTAIM publications are available as pre-prints in the form of .pdf files along with the corresponding supplementary materials at our BEACON website www.beaconresearch.org.

This book reviews recent physicochemical and biophysical techniques applied in drug discovery research, and it outlines the latest advances in computational drug design. Divided into 10 chapters, the book discusses about the role of structural biology in drug discovery, and offers useful application cases of several biophysical and computational methods, including time-resolved fluorometry (TRF) with Forster resonance energy transfer (FRET), X-Ray crystallography, nuclear magnetic resonance spectroscopy, mass spectroscopy, generative machine learning for inverse molecular design, quantum mechanics/molecular mechanics (QM/MM,ONIOM) and quantum molecular dynamics (QMT) methods. Particular attention is given to computational search techniques applied to peptide vaccines using novel mathematical descriptors and structure and ligand-based virtual screening techniques in drug discovery research. Given its scope, the book is a valuable resource for students, researchers and professionals from pharmaceutical industry interested in drug design and discovery.

Written chemical formulas, such as C2H6O, can tell us the constituent atoms a molecule contains but they cannot differentiate between the possible geometrical arrangements (isomers) of these models. Yet the chemical properties of different isomers can vary hugely. Therefore, to understand the world of chemistry we need to ask what kind of isomers can be produced from a given atomic composition, how are isomers converted into each other, how do they decompose into smaller pieces, and how can they be made from smaller pieces? The answers to these questions will help us to discover new chemistry and new molecules. A potential energy surface (PES) describes a system, such as a molecule, based on geometrical parameters. The mathematical properties of the PES can be used to calculate probable isomer structures as well as how they are formed and how they might behave.Exploration on Quantum Chemical Potential Energy Surfaces focuses on the PES search based on quantum chemical calculations. It describes how to explore the chemical world on PES, discusses fundamental methods and specific techniques developed for efficient exploration on PES, and demonstrates several examples of the PES search for chemical structures and reaction routes.