From Chemical Topology To Three Dimensional Geometry
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From Chemical Topology to Three-Dimensional Geometry by Alexandru T. Balaban Pdf
Even high-speed supercomputers cannot easily convert traditional two-dimensional databases from chemical topology into the three-dimensional ones demanded by today's chemists, particularly those working in drug design. This fascinating volume resolves this problem by positing mathematical and topological models which greatly expand the capabilities of chemical graph theory. The authors examine QSAR and molecular similarity studies, the relationship between the sequence of amino acids and the less familiar secondary and tertiary protein structures, and new topological methods.
Topology is becoming increasingly important in chemistry because of its rapidly growing number of applications. Here, its many uses are reviewed and the authors anticipate what future developments might bring. This work shows how significant new insights can be gained by representing molecular species as topological structures known as topographs. The text explores carbon structures, establishing how the stability of fullerene species can be accounted for and also predicting which fullerenes will be most stable. It is pointed out that molecular topology, rather than molecular geometry, characterizes molecular shape and various tools for shape characterization are described. Several of the fascinating ideas that arise from regarding topology as a unifying principle in chemical bonding theory are discussed, and in particular, the novel concept of the molecular topoid is shown to have numerous uses. The topological description of polymers is examined and the reader is gently guided through the realms of branched and tangled polymers. Overall, this work outlines the fact that topology is not only a theoretical discipline but also one that has practical applications and high relevance to the whole domain of chemistry.
Three Dimensional QSAR by Jean Pierre Doucet,Annick Panaye Pdf
As a result of new statistical and mathematical approaches, improved visualization tools, and recognition by international regulatory groups, quantitative structure-activity relationships (QSARs) now play important roles in pharmacology for the design of new drugs as well as in toxicology and ecotoxicology for hazard identification and risk assessm
Topological Indices and Related Descriptors in QSAR and QSPR by James Devillers,Alexandru T Balaban Pdf
Topological Indices and Related Descriptors in QSAR and QSPR reviews the state of the art in this field and highlights the important advances in the generation of descriptors calculated directly from the structure of molecules. This long-awaited comprehensive book provides all the necessary information to calculate and use these descriptors for deriving structure-activity and structure-property relationships. Written by leading experts in the field, this book discusses the physicochemical significance, strengths, and weaknesses of these indices and presents numerous examples of applications. This book will be a valuable reference for anyone involved in the use of QSAR and QSPR in the pharmaceutical, applied chemical, and environmental sciences. It is also suitable for use as a supplementary textbook on related graduate level courses.
Advances in Dendritic Macromolecules by G.R. Newkome Pdf
The series Advances in Dendritic Macromolecules aims to cover the synthesis and supramolecular chemistry of dendritic or cascade super-molecules as well as their less perfect hyperbranched cousins. The field of hyperbranched macromolecules, specifically dendrimers, has continued to expand at an amazing rate. The synthetic aspects, which were assumed to be over several years ago, have opened new avenues into the mesomolecular regime. The synthetic ingenuity of chemical artists has afforded new monomers and their diverse combinations to give rise to (poly)functionalized materials that embrace new supramolecular concepts in areas such as molecular recognition, assembly, encapsulation, and inclusion; catalysts; coatings; drug delivery systems; and in essence opens up the field of suprasupermolecular chemistry. In chapter 1 the synthesis of organometallic and related transition metal-cotaining dendrimers is summarized and their novel properties and useful applications are described. Chapter 2 covers work on the commercial poly(propylene imine)s, including the "dendritic box", dendrimer-based superamphiphiles, and unimolecular inverse micelles. The next chapter looks at aspects of chirality in dendritic systems and this is followed by a look inside dendrimers from a molecular topologist's point-of-view.
Solved and Unsolved Problems of Structural Chemistry by Milan Randic,Marjana Novic,Dejan Plavsic Pdf
Solved and Unsolved Problems of Structural Chemistry introduces new methods and approaches for solving problems related to molecular structure. It includes numerous subjects such as aromaticity—one of the central themes of chemistry—and topics from bioinformatics such as graphical and numerical characterization of DNA, proteins, and proteomes. It also outlines the construction of novel tools using techniques from discrete mathematics, particularly graph theory, which allowed problems to be solved that many had considered unsolvable. The book discusses a number of important problems in chemistry that have not been fully understood or fully appreciated, such as the notion of aromaticity and conjugated circuits, the generalized Hückel 4n + 2 Rule, and the nature of quantitative structure–property–activity relationships (QSARs), which have resulted in only partially solved problems and approximated solutions that are inadequate. It also describes advantages of mathematical descriptors in QSAR, including their use in screening combinatorial libraries to search for structures with high similarity to the target compounds. Selected problems that this book addresses include: Multiple regression analysis (MRA) Insufficient use of partial ordering in chemistry The role of Kekulé valence structures The problem of protein and DNA alignment Solved and Unsolved Problems of Structural Chemistry collects results that were once scattered in scientific literature into a thoughtful and compact volume. It sheds light on numerous problems in chemistry, including ones that appeared to have been solved but were actually only partially solved. Most importantly, it shows more complete solutions as well as methods and approaches that can lead to actualization of further solutions to problems in chemistry.
Three-Dimensional Geometry and Topology, Volume 1 by William P. Thurston Pdf
This book develops some of the extraordinary richness, beauty, and power of geometry in two and three dimensions, and the strong connection of geometry with topology. Hyperbolic geometry is the star. A strong effort has been made to convey not just denatured formal reasoning (definitions, theorems, and proofs), but a living feeling for the subject. There are many figures, examples, and exercises of varying difficulty. This book was the origin of a grand scheme developed by Thurston that is now coming to fruition. In the 1920s and 1930s the mathematics of two-dimensional spaces was formalized. It was Thurston's goal to do the same for three-dimensional spaces. To do this, he had to establish the strong connection of geometry to topology--the study of qualitative questions about geometrical structures. The author created a new set of concepts, and the expression "Thurston-type geometry" has become a commonplace. Three-Dimensional Geometry and Topology had its origins in the form of notes for a graduate course the author taught at Princeton University between 1978 and 1980. Thurston shared his notes, duplicating and sending them to whoever requested them. Eventually, the mailing list grew to more than one thousand names. The book is the culmination of two decades of research and has become the most important and influential text in the field. Its content also provided the methods needed to solve one of mathematics' oldest unsolved problems--the Poincaré Conjecture. In 2005 Thurston won the first AMS Book Prize, for Three-dimensional Geometry and Topology. The prize recognizes an outstanding research book that makes a seminal contribution to the research literature. Thurston received the Fields Medal, the mathematical equivalent of the Nobel Prize, in 1982 for the depth and originality of his contributions to mathematics. In 1979 he was awarded the Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by the National Science Foundation.
Handbook of Molecular Descriptors by Roberto Todeschini,Viviana Consonni Pdf
Quantitative studies on structure-activity and structure-property relationships are powerful tools in directed drug research. In recent years, various strategies have been developed to characterize and classify structural patterns by means of molecular descriptors. It has become possible not only to assess diversities or similarities of structure databases, but molecular descriptors also facilitate the identification of potential bioactive molecules from the rapidly increasing number of compound libraries. They even allow for a controlled de-novo design of new lead structures. This is the most comprehensive collection of molecular descriptors and presents a detailed review from the origins of this research field up to present day. This practically oriented reference book gives a thorough overview of the different molecular descriptors representations and their corresponding molecular descriptors. All descriptors are listed with their definition, symbols and labels, formulas, some numerical examples, data and molecular graphs, while numerous figures and tables aid comprehension of the definitions. Cross-references throughout, a list of acronyms and notations allow easy access to the information needed to solve a specific research problem. Examples of descriptor calculations along with tables of descriptor values for a set of selected reference compounds and an up-to-date reference list add to the practical value of the book, making it an invaluable guide for all those dealing with bioactive molecules as well as for researchers.
This volume addresses a number of topological themes of direct relevance to chemists. Topological concepts are now regularly applied in wide areas of chemistry including molecular engineering and design, chemical toxicology, the study of molecular shape, crystal and surface structures, chemical bonding, macromolecular species such as polymers and DNA, and environmental chemistry. Currently, the design and synthesis of new drugs and agrochemicals are of especial importance. The book's prime focus is on the role played by topological indices in the description and characterisation of molecular species. The Wiener index along with a variety of other major topological indices, are discussed with particular reference to the powerful and much used connectivity indices. In this book an international team of leading experts review their respective fields and present their findings.The considerable benefits offered by topological indices in the investigation of chemical problems in science, medicine, and industry are highlighted. The volume records proceedings of the Harry Wiener Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001, and serves as a fitting tribute to the chemical contributions of the late Harry Wiener. Focuses on the role played by topological indices in the description and characterisation of molecular species Records the proceedings of the Harry Weiner Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001 Along with a variety of other major topological indices, the Wiener index is discussed with particular reference to the powerful and much-used connectivity indices
Molecular Descriptors for Chemoinformatics by Roberto Todeschini,Viviana Consonni Pdf
The number-one reference on the topic now contains a wealth of new data: The entire relevant literature over the past six years has been painstakingly surveyed, resulting in hundreds of new descriptors being added to the list, and some 3,000 new references in the bibliography section. Volume 1 contains an alphabetical listing of more than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties, while the second volume lists over 6,000 references selected from 450 journals. To make the data even more accessible, the introductory section has been completely re-written and now contains several "walk-through" reading lists of selected keywords for novice users.
Statistical Modelling of Molecular Descriptors in QSAR/QSPR by Matthias Dehmer,Kurt Varmuza,Danail Bonchev Pdf
This handbook and ready reference presents a combination of statistical, information-theoretic, and data analysis methods to meet the challenge of designing empirical models involving molecular descriptors within bioinformatics. The topics range from investigating information processing in chemical and biological networks to studying statistical and information-theoretic techniques for analyzing chemical structures to employing data analysis and machine learning techniques for QSAR/QSPR. The high-profile international author and editor team ensures excellent coverage of the topic, making this a must-have for everyone working in chemoinformatics and structure-oriented drug design.
Progress in Biological Chirality by Gyula Palyi,Claudia Zucchi,Luciano Caglioti Pdf
Following on from Advances in BioChirality, Progress in Biological Chirality provides a unique summary and review of the most recent developments in the field of biochirality. Living organisms use only one enantiomer of chiral molecules in the majority of biologically important processes. The exact origin and mechanisms for this surprising selectivity are not yet known. This book discusses current research aimed at identifying the scientific reasons that may contribute to this phenomenon. Progress in Biological Chirality takes an interdisciplinary approach to this exciting field, covering a wide range of topics, such as, theory, palaeontology and food technology, to name but a few. This book presents findings via a broad spectrum of scientific approaches making it an excellent overview of Biological Chirality, suitable for postgraduate students, practitioners and researchers in the field of chemistry, biochemistry, biology, palaeontology, and food science with an interest in Chirality. This book contains 32 chapters written by Authors, who are leading authorities in the field Presents the most recent research taking place in this highly challenging field Contains both reference material for the specialist and provides an overview for those who are interested in the fundamental problems of biology and chemistry
Advances in Mathematical Chemistry and Applications: Volume 1 by Subhash C. Basak,Guillermo Restrepo,Jose L. Villaveces Pdf
Advances in Mathematical Chemistry and Applications highlights the recent progress in the emerging discipline of discrete mathematical chemistry. Editors Subhash C. Basak, Guillermo Restrepo, and Jose Luis Villaveces have brought together 27 chapters written by 68 internationally renowned experts in these two volumes. Each volume comprises a wise integration of mathematical and chemical concepts and covers numerous applications in the field of drug discovery, bioinformatics, chemoinformatics, computational biology, mathematical proteomics, and ecotoxicology. Volume 1 includes chapters on mathematical structural descriptors of molecules and biomolecules, applications of partially ordered sets (posets) in chemistry, optimal characterization of molecular complexity using graph theory, different connectivity matrices and their polynomials, use of 2D fingerprints in similarity-based virtual screening, mathematical approaches to molecular structure generation, comparability graphs, applications of molecular topology in drug design, density functional theory of chemical reactivity, application of mathematical descriptors in the quantification of drug-likeness, utility of pharmacophores in drug design, and much more. Brings together both the theoretical and practical aspects of the fundamental concepts of mathematical chemistry Covers applications in diverse areas of physics, chemistry, drug discovery, predictive toxicology, systems biology, chemoinformatics, and bioinformatics Revised 2015 edition includes a new chapter on the current landscape of hierarchical QSAR modelling About half of the book focuses primarily on current work, new applications, and emerging approaches for the mathematical characterization of essential aspects of molecular structure, while the other half describes applications of structural approach to new drug discovery, virtual screening, protein folding, predictive toxicology, DNA structure, and systems biology
Molecular Modeling and Prediction of Bioactivity by Klaus Gundertofte,Fleming Steen Jørgensen Pdf
Much of chemistry, molecular biology, and drug design, are centered around the relationships between chemical structure and measured properties of compounds and polymers, such as viscosity, acidity, solubility, toxicity, enzyme binding, and membrane penetration. For any set of compounds, these relationships are by necessity complicated, particularly when the properties are of biological nature. To investigate and utilize such complicated relationships, henceforth abbreviated SAR for structure-activity relationships, and QSAR for quantitative SAR, we need a description of the variation in chemical structure of relevant compounds and biological targets, good measures of the biological properties, and, of course, an ability to synthesize compounds of interest. In addition, we need reasonable ways to construct and express the relationships, i. e. , mathematical or other models, as well as ways to select the compounds to be investigated so that the resulting QSAR indeed is informative and useful for the stated purposes. In the present context, these purposes typically are the conceptual understanding of the SAR, and the ability to propose new compounds with improved property profiles. Here we discuss the two latter parts of the SARlQSAR problem, i. e. , reasonable ways to model the relationships, and how to select compounds to make the models as "good" as possible. The second is often called the problem of statistical experimental design, which in the present context we call statistical molecular design, SMD. 1.
Author : Mircea V. Diudea,Csaba L. Nagy Publisher : Springer Science & Business Media Page : 218 pages File Size : 49,6 Mb Release : 2007-08-23 Category : Technology & Engineering ISBN : 9781402060205
Periodic Nanostructures by Mircea V. Diudea,Csaba L. Nagy Pdf
These tiny structures could offer architectural designs for the cities of the future. The authors explore the foam-like carbon structures, which relate to ‘schwarzites’ and which are infinite periodic minimal surfaces of negative curvature. They show that the periodicity of close repeat units of such structures is evident not only in these formations but also in all of the carbon allotropes. The text provides literature and data on the field of nanostructure periodicity and the authors’ own results on nanostructure building and energy calculations.