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 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.

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.

Chemische Bindung und Spektroskopie sind sehr wichtige Themen der Chemie. Ein Verständnis von diesen ist nicht ohne ein Verständnis der Quantentheorie möglich, und deswegen ist eine Einführung in Quantentheorie und deren Anwendungen für Chemiestudierende essentiell. Das vorliegende Lehrbuch bietet eine solche Einführung an, die sich für ein Bachelorkurs in einem Semester im 2ten Studienjahr geeignet ist, und die wenige Vorkenntnisse verlangt. Das Buch bringt zuerst eine Einführung in Grundlagen der Quantentheorie, und anschließend wird sie für verschiedene, chemisch relevante Systeme verwendet. Vor allem werden die elektronischen Eigenschaften von Atomen und Molekülen sowie die Grundlagen der chemischen Bindungen behandelt. Letztendlich werden auch die Grundlagen der verschiedenen, sehr häufig eingesetzten Methoden der Computerrechnungen behandelt, womit Eigenschaften von Atomen, Molekülen und Kristallen berechnet werden können. Solche Rechnungen sind heutzutage Standard der chemischen Forschung.

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 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.

Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity.The fourth volume of this series features four chapters covering natural lead compounds, computer aided drug discovery methods in Parkinson's Disease therapy, studies of aminoacyl tRNA synthetase inhibition in bacteria, computational modeling of halogen bonds in biological systems and molecular classification of caffeine and its metabolites.

In Periodic Nanostructures, the authors demonstrate that structural periodicity in various nanostructures has been proven experimentally. The text covers the coalescence reactions, studied by electronic microscopy, and shows that the nanoworld is continuous, giving rise to zero- (fullerenes), one- (tubules), two-(graphite) and three-(diamond, spongy carbon) dimensional carbon allotropes.The authors explore foam-like carbon structures, which relate to 'schwarzites', and which represent infinite periodic minimal surfaces of negative curvature. They show that these structures contain polygons (with dimensions larger than hexagons w.r.t. to graphite) that induce this negative curvature. The units of these structures appear as nanotube junctions (produced via an electron beam) that have wide potential molecular electronics applications. Self-assembled supramolecular structures (of various tessellation) and diamond architectures are also proposed. The authors propose that the periodicity of close repeat units of such structures is most evident not only in these formations but also present in all of the carbon allotropes. It is also shown that depending on the lattice tessellation, heteroatom type, and/or doping, metal nanostructures (nanotubes in particular) can display both metallic and semiconductor characteristics. Therefore, their properties can be manipulated by chemical functionalization. The authors therefore suggest that nanostructures have heralded a new generation of nanoscale biological, chemical, and physical devices.The text also provides literature and data on the field of nanostructure periodicity and the authors' own results on nanostructure building and energy calculations as well as topological characterization by means of counting polynomials of periodic nanostructures. The aromaticity of various coverings of graphitic structures is also discussed.This book is aimed at scientists working in the field of nanoscience and nanotechnology, Ph.D. and MSc. degree students, and others interested in the amazing nanoarchitectures that could inspire the cities of the future.

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

Computer Modelling techniques have developed very rapidly during the last decade, and interact with many contemporary scientific disciplines. One of the areas of greatest activity has concerned the modelling of condensed phases, including liquids solids and amorphous systems, where simulations have been used to provide insight into basic physical processes and in more recent years to make reliable predictions of the properties of the systems simulated. Indeed the predictive role of simulations is increasingly recognised both in academic and industrial contexts. Current active areas of application include topics as diverse as the viscosity of liquids, the conformation of proteins, the behaviour of hydrogen in metals, the diffusion of molecules in porous catalysts and the properties of micelles. This book, which is based on a NATO ASI held at the University of Bath, UK, from September 5th-17th, 1988, aims to give a general survey of this field, with detailed discussions both of methodologies and of applications. The earlier chapters of the book are devoted mainly to techniques and the later ones to recent simulation studies of fluids, polymers (including biological molecules) and solids. Special attention is paid to the role of interatomic potentials which are the fundamental physical input to simulations. In addition, developments in computer hardware are considered in depth, owing to the crucial role which such developments are playing in the expansion of the horizons of computer modelling studies.

In Silico Chemistry and Biology: Current and Future Prospects provides a compact overview on recent advances in this highly dynamic branch of chemistry. Various methods of protein modelling and computer-assisted drug design are presented, including fragment- and ligand-based approaches. Many successful practical applications of these techniques are demonstrated. The authors also look to the future and describe the main challenges of the field.

Chemoinformaticä, o informatica chimica, si riferisce all¿uso di ¿metodi informatici per risolvere problemi chimici¿: ha come oggetto ¿strutture molecolari¿ e descrizioni, proprietà e dati ad esse collegate.Grazie a questo volume, pensato e scritto per docenti, studenti e professionisti che desiderino arricchire le proprie conoscenze in una o più aree di applicazione della ¿Chemoinformaticä, termini, sigle e acronimi come DOE, virtual docking and screening, QSAR, structure-based design, ADMET predictions e molti altri, non saranno più velati da un¿ombra di mistero e diventeranno accessibili. Senza bisogno di prerequisiti né di competenze o esperienze specifiche, al lettore è offerta, da una parte, una panoramica adeguatamente ampia del settore ¿Chemoinformaticö e, dall¿altra, sufficienti informazioni utili nella eventualità che desideri approfondire specifici argomenti di interesse incontrati nel volume.Agli inizi degli anni ¿80 del secolo scorso la grafica molecolare iniziava a diffondersi; il ¿computer-aided drug design¿ veniva utilizzato dalle prime aziende farmaceutiche negli USA ed era ancora perlopiù sconosciuto in Italia; la ¿Chemoinformaticä non esisteva nemmeno come termine; internet era di là a venire: esisteva in germe come rete di comunicazione gestita dal Dipartimento della Difesa statunitense. Dai calcolatori di seconda generazione che non utilizzavano i transistor ma ancora le schede perforate, a quelli di terza generazione caratterizzati dall¿avvento del terminale, ai ¿portatili¿ di oggi, dai primi centri di calcolo a quelli di super-calcolo, al ¿grid computing¿ e ¿cloud computing¿ di oggi, la gamma delle soluzioni software e la complessità dei calcoli, delle simulazioni e delle ricerche in database ora possibili, sono aumentate in modo entusiasmante nel settore della ¿Chemoinformaticä. Sempre più dati ¿ sperimentali, virtuali, testuali, numerici, chimico-strutturali,chimico-fisici, analitici, spettrali, biologici, farmacologici, biomedici, etc. ¿ vengono generati, e aumenta così la necessità di archiviarli, ricercarli, renderli facilmente fruibili, per trasformare i dati in informazione e l¿informazione in conoscenza.