Download or read book Design of Molecular Mechanics Modeling Techniques for Exploring Molecular Recognition Using Cyclodextrins written by and published by . This book was released on 2003 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular mechanics modeling techniques have been developed to study the behavior of cyclodextrins (CDs) in capillary electrophoresis (CE) separations. Using the commercial computational package, Sybyl, the mechanisms of molecular recognition between organic analytes and CDs are investigated. Cyclodextrin-modified capillary electrochromatography (CDCE) experiments were conducted to separate neutral derivitized naphthalene solutes using carboxymethylbeta-cyclodextrin (CM-[beta]-CD). Grid conformation-searching programs were developed to explore the interaction space between CD and solute and to calculate their interaction energies using molecular mechanics. The interaction energies correlated remarkably well with the separation behavior. It was found that extensive minimization (more than 3000 iterations) was required at each of the docking positions to achieve the best agreement between computational and experimental distribution coefficients (Kd)[d subscript]. Molecular modeling techniques were also used to guide the development of a new charged cyclodextrin resolving agent, heptakis (6-O-carboxymethyl-2,3-dimethyl)-[beta]-cyclodextrin (HDMCM-[beta]-CD). Molecular computer aided design (MolCAD) analysis and docking techniques revealed that HDMCM-[beta]-CD would be superior to commercially available CDs for forming inclusion complexes with the target naphthalene derivative analytes. Molecular modeling studies also showed that significant intermolecular CD-CD interactions can occur under certain conditions, explaining some anomalous experimental findings. Additionally, the grid conformation-searching modeling technique was applied to chiral CDCE separations of dansyl amino acids (AAs) to explain separation behavior and to investigate different CD-CD interactions.

Download or read book Molecular Recognition Modeling written by Wanli You and published by . This book was released on 2017 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular recognition is fundamentally important in biological chemistry. Nowadays, with the rapid development of computational technology and algorithm, molecular modeling has become a powerful tool in studying molecular recognition, such as exploring molecular interactions and understanding biological dynamic processes, making significant contributions to modern biology and drug discovery. The state-of-the-art techniques of computational chemistry and molecular modeling can be applied to study a wide range of chemical and biological systems of interest. This enables us to study structural details at the atomic level and obtain chemical/biological information which is not available by experimental measurements. This dissertation project focused on modeling the recognition mechanisms of biomolecules and their conjugated ligands. Multiple computational techniques, such as molecular dynamics simulation, enhanced sampling methods and free energy calculation were applied. The model systems included signaling domains (BRCT domain), kinase (p38 kinase), enzyme system (TRPS) and small biomolecular system (cyclodextrin). The details of protein-ligand interactions, including both enthalpic and entropic contribution within protein domain-phosphopeptide systems were investigated, based on which new inhibitors were proposed. Several enhanced sampling methods like accelerated molecular dynamics simulation, pathway search guided by internal motions (PSIM) and umbrella sampling, were applied to explore the dissociation pathway of kinase-ligand systems and the motions of kinase during dissociation process were studied both thermodynamically and kinetically, protein conformational rearrangement was found to differentiate slow and fast unbinding inhibitors, casting light on high efficacy inhibitor design. Furthermore, using full structural molecular modeling, we explored how the position of a single proton can change the overall protein dynamics and further activate or inactivate enzyme catalysis, elucidating the catalytic mechanism of TRPS. In addition, we performed systematically evaluation to the performance of umbrella sampling, investigated the influence of subtle changes in the dissociation pathways and conformational sampling methods that provide the initial conformations, paving way for future improvement of umbrella sampling. This project studies the details of receptor-ligand interaction and provides a more complete picture of molecular recognition.

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2005 with total page 860 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book A Molecular Mechanics Analysis of Molecular Recognition by Cyclodextrin Mimics of Alpha Chymotrypsin written by C. A. Venanzi and published by . This book was released on 1989 with total page 44 pages. Available in PDF, EPUB and Kindle. Book excerpt: The method of molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by Beta-cyclodextrin and capped Beta -cyclodextrin models of alpha -chymotrypsin. Since capped Beta -cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N-methyformamide cap substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X-ray structure of the Beta -cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. the results indicate that the addition of the caps to the Beta -cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by Beta -cyclodextrin and capped Beta -cyclodextrin are similar. Keywords: Artificial enzymes, Enzyme models, Serine protease mimic. (aw).

Download or read book Molecular Materials with Specific Interactions Modeling and Design written by W. Andrzej Sokalski and published by Springer Science & Business Media. This book was released on 2007-05-06 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: Design of new molecular materials is emerging as a new interdisciplinary research field. Corresponding reports are scattered in literature, and this book constitutes one of the first attempts to overview ongoing research efforts. It provides basic information, as well as the details of theory and examples of its application, to experimentalists and theoreticians interested in modeling molecular properties and putting into practice rational design of new materials.

Download or read book Computer Aided Molecular Design written by Jean-Pierre Doucet and published by Elsevier. This book was released on 1996-03-05 with total page 517 pages. Available in PDF, EPUB and Kindle. Book excerpt: The computer-aided design of novel molecular systems has undoubtedly reached the stage of a mature discipline offering a broad range of tools available to virtually any chemist. However, there are few books coveringmost of these techniques in a single volume and using a language which may generally be understood by students or chemists with a limited knowledge of theoretical chemistry. The purpose of this book is precisely to review, in such a language, both methodological aspects and important applications of computer-aided molecular design (CAMD), with a special emphasis on drug design and protein modeling. Using numerous examples ranging from molecular models to shapes, surfaces, and volumes, Computer-Aided Molecular Design provides coverage of the role molecular graphics play in CAMD. The text also treats the very notion of the structure of molecular systems by presenting both the various experimental techniques giving access to it and the most common model builders based on force fields. Separate chapters are devoted to other important topics in CAMD, such as Monte Carlo and molecular dynamics simulations; most common quantum chemical methods; derivation and visualization of molecular properties; and molecular similarity. Finally, strategies used in protein modeling and drug design, such as receptor mapping and the pharmacophore approach, are presented and illustrated by several examples. The book is addressed to students and researchers who wish to enter this new exciting field of molecular sciences, but also practitioners in CAMD as a comprehensive source of refreshing information in their field. Key Features * Presents a comprehensive introduction to computer-aided molecular design * Describes applications of CAMD through the use of numerous examples * Emphasizes strategies used in protein modeling and drug design * Includes separate chapters devoted to other important topics in CAMD, such as: * Monte Carlo and molecular dynamics simulations * Common quantum chemical methods * Derivation and visualization of molecular properties * Molecular similarity

Download or read book Time dependent Electron Localization Function written by Tobias Burnus and published by Tobias Burnus. This book was released on 2008 with total page 90 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Chemistry and Molecular Modeling written by K. I. Ramachandran and published by Springer Science & Business Media. This book was released on 2008-05-20 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: The gap between introductory level textbooks and highly specialized monographs is filled by this modern textbook. It provides in one comprehensive volume the in-depth theoretical background for molecular modeling and detailed descriptions of the applications in chemistry and related fields like drug design, molecular sciences, biomedical, polymer and materials engineering. Special chapters on basic mathematics and the use of respective software tools are included. Numerous numerical examples, exercises and explanatory illustrations as well as a web site with application tools (http://www.amrita.edu/cen/ccmm) support the students and lecturers.

Download or read book DNA Interactions with Polymers and Surfactants written by Rita Dias and published by John Wiley & Sons. This book was released on 2008-07-14 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad overview of the interaction of DNA with surfactants and polymers Due to the potential benefits of biotechnology, interest in the interaction between DNA and surfactants and polymers has become increasingly significant. Now, DNA Interactions with Polymers and Surfactants provides an extensive, up-to-date overview of the subject, giving readers a basis for understanding the factors leading to complexation between DNA and different cosolutes, including metal ions, polyelectrolytes, spermine, spermidine, surfactants and lipids, and proteins. Topical coverage includes: Polyelectrolytes, physico-chemical aspects and biological significance Solution behavior of nucleic acids Single DNA molecules: compaction and decompaction Interaction of DNA with surfactants and cationic polymers Interactions of histones with DNA DNA-DNA interactions The hydration of DNA-amphiphile complexes DNA-surfactant/lipid complexes at liquid interfaces DNA and DNA-surfactant complexes at solid surfaces The role of correlation forces for DNA-cosolute interactions Simulations of polyions Cross-linked DNA gels and gel particles DNA as an amphiphilic polymer Lipid-DNA interactions Covering both theoretical and practical aspects of the subject, DNA Interactions with Polymers and Surfactants is an ideal resource for chemists and biochemists working in gene and DNA delivery research in industry and academia, as well as for cell biologists, chemical engineers, molecular biologists, and development biologists in the pharmaceutical industry.

Download or read book Cyclodextrins and Their Complexes written by Helena Dodziuk and published by John Wiley & Sons. This book was released on 2006-08-21 with total page 507 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering comprehensive and up-to-date know-how in one compact book, an experienced editor and top authors cover every aspect of these important molecules from molecular recognition to cyclodextrins as enzyme models. Chapters include reactivity and chemistry, chromatography, X-ray, NMR plus other physicochemical methods, as well as model calculations, rotaxane and catenane structures, and applications in the pharmaceutical industry. The book also discusses other applications such as in the cosmetics, toiletries, textile and wrapping industries, agrochemistry, electrochemical sensors, and devices. A must for everyone working with these substances.

Download or read book Cumulated Index Medicus written by and published by . This book was released on 2000 with total page 1840 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Index Medicus written by and published by . This book was released on 2004 with total page 2454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.

Download or read book Cyclodextrin written by Poonam Arora and published by BoD – Books on Demand. This book was released on 2018-04-18 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book is devoted to the highly versatile and potential ingredient Cyclodextrin, a family of cyclic oligosaccharides composed of ?-(1,4)-linked glucopyranose subunits. Its molecular complexation phenomena and negligible cytotoxic effects attribute toward its application such as in pharmaceuticals, cosmetics, food, agriculture, textile, separation process, analytical methods, catalysis, environment protection, and diagnostics. Efforts have also been made to concentrate on recent research outcomes along with future prospects of cyclodextrins to attract the interest of scientists from the industry and academia. The contributions of the authors are greatly acknowledged, without which this compilation would not have been possible.

Download or read book Cyclodextrin Chemistry written by Zheng-Yu Jin and published by World Scientific. This book was released on 2013 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cyclodextrin Chemistry covers the preparation of cyclodextrins and cyclodextrin derivatives (CDs), and their applications in industrial and non-industrial areas. An overall theme in the book is the screening of cyclodextrin glycosyltransferase (CGTase), the preparation of sugar-branched cyclodextrins and CDs, and the use of CDs for reconstructing various supermolecule systems. The specific content also includes preparation methods, spectroscopy techniques for CDs analysis, and potential applications in food packaging, nutrient fortification, medicine, cosmetics, textiles, chemicals, feed, agriculture, and environment. It summarizes the research merit of CDs in the past twenty years and also emphasizes hot topics and important areas of cyclodextrin chemistry in the future. Contents: Introduction (Jun-Rong Huang, Hai-Ning Zhuang and Zheng-Yu Jin); Enzymes in Preparing Cyclodextrins (Sheng-Jun Wu, Xiu-Ting Hu, Jin-Moon Kim and Jing Chen); Preparation and Analysis of Cyclodextrin (An-Wei Cheng, Jin-Peng Wang and Zheng-Yu Jin); Preparation of Branched-Cyclodextrins (Xing Zhou, Yao-Qi Tian and Zheng-Yu Jin); Preparation and Analysis of Cyclodextrin Derivatives (Chao Yuan, Yu-Xiang Bai and Zheng-Yu Jin); Basic Application of Cyclodextrins in Supermolecule Chemistry (Tao Feng, Ai-Quan Jiao and Zheng-Yu Jin); Use of Cyclodextrins in Food, Pharmaceutical and Cosmetic Industries (Yao-Qi Tian, Xing Zhou and Zheng-Yu Jin); Application of Cyclodextrins in Non-industrial Areas (Xue-Hong Li and Zheng-Yu Jin). Readership: Researchers and technicians in food, pharmaceutical, cosmetic and chemical industries, as well as in non-industry areas such as agriculture and environmental engineering, supermolecule and analytical chemistry.

Download or read book Chemical Abstracts written by and published by . This book was released on 2002 with total page 2668 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Theory of Solvation written by F. Hirata and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Theory of Solvation presents the recent progress in the statistical mechanics of molecular liquids applied to the most intriguing problems in chemistry today, including chemical reactions, conformational stability of biomolecules, ion hydration, and electrode-solution interface. The continuum model of "solvation" has played a dominant role in describing chemical processes in solution during the last century. This book discards and replaces it completely with molecular theory taking proper account of chemical specificity of solvent. The main machinery employed here is the reference-interaction-site-model (RISM) theory, which is combined with other tools in theoretical chemistry and physics: the ab initio and density functional theories in quantum chemistry, the generalized Langevin theory, and the molecular simulation techniques. This book will be of benefit to graduate students and industrial scientists who are struggling to find a better way of accounting and/or predicting "solvation" properties.

Download or read book Essentials of Computational Chemistry written by Christopher J. Cramer and published by John Wiley & Sons. This book was released on 2013-04-29 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.