Download or read book Atomistic Studies of Structure and Dynamics of Aggregation in Solution written by Sebastian Schöttl and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Structure and Dynamics of Solutions written by H. Ohtaki and published by Elsevier. This book was released on 2013-10-22 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in the study of structural and dynamic properties of solutions have provided a molecular picture of solute-solvent interactions. Although the study of thermodynamic as well as electronic properties of solutions have played a role in the development of research on the rate and mechanism of chemical reactions, such macroscopic and microscopic properties are insufficient for a deeper understanding of fast chemical and biological reactions. In order to fill the gap between the two extremes, it is necessary to know how molecules are arranged in solution and how they change their positions in both the short and long range. This book has been designed to meet these criteria. It is possible to develop a sound microscopic picture for reaction dynamics in solution without molecular-level knowledge of how reacting ionic or neutral species are solvated and how rapidly the molecular environment is changing with time. A variety of actual examples is given as to how and when modern molecular approaches can be used to solve specific solution problems. The following tools are discussed: x-ray and neutron diffraction, EXAFS, and XANES, molecular dynamics and Monte Carlo computer simulations, Raman, infrared, NMR, fluorescence, and photoelectron emission spectroscopic methods, conductance and viscosity measurements, high pressure techniques, and statistical mechanics methods. Static and dynamic properties of ionic solvation, molecular solvation, ion-pair formation, ligand exchange reactions, and typical organic solvents are useful for bridging the gap between classical thermodynamic studies and modern single-molecule studies in the gas phase. The book will be of interest to solution, physical, inorganic, analytical and structural chemists as well as to chemical kineticists.

Download or read book Atomistic Modelling of Structure and Dynamics of Pure Blends and Doped Chromonic Solutions written by Oscar Matus Rivas and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Lyotropic chromonic liquid crystals are an emerging class of mesogenic materials under current intense research and development due to their exceptional phase properties and promising advanced materials and devices’ applications. Although remarkable progress has been achieved in characterizing chromonic phases, a comprehensive understanding of the underlying mechanisms governing their spontaneous self-assembly and aggregation, miscibility capabilities and phase properties is still not entirely understood at the atomistic scale. These challenges arise from the inherent difficulty of characterizing chromonic behaviour at the molecular level with traditional experimental methods. This thesis aims to evaluate and characterize the structural and dynamical properties of relevant pure, blends, and doped chromonic liquid crystal solutions prepared with Disodium Cromoglycate, Sunset Yellow, and Bordeaux dye mesogens using atomistic molecular dynamics simulations. The relationship between equilibrium stacking structure and chromonic molecular architecture is examined, resolved and explained in detail. The formation of structured water around chromonic columnar aggregates via hydrogen bonding interactions and its crucial dynamic role on the aggregation and stability of chromonic mesogens are rigorously investigated. Additionally, molecular mixing affinity rules are determined for binary chromonic blends. Finally, the influence of doping agents, such as NaCl and MgCl2 ionic salts and L-alanine amino acid chiral additive, on the structure and dynamics of chromonic solutions is evaluated. Taken together, the results presented throughout this work provide an in-depth description of the atomistic-level mechanisms controlling the self-assembly and phase properties of lyotropic chromonic liquid crystal solutions, in addition to insights for the development of future experimental and simulation methodologies for expanding chromonics research and applications. These findings represent substantial contributions to the fundamental understanding of chromonic aggregation rules, which are crucial for the fabrication of innovative chromonic functionalities based on the fine-tuning of noncovalent interactions by designing novel custom-made chromonic mesogens"--

Download or read book Aggregation Processes in Solution written by Evan Wyn-Jones and published by Elsevier Science & Technology. This book was released on 1983 with total page 652 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Studies of Solution Structure and Dynamics by Molecular Spectroscopy written by Michael Walter Balk and published by . This book was released on 1980 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Modelling Molecules for Shape driven Aggregation written by Giovanni Doni and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The exploitation of self-assembling for the development of reliable technological platforms depends on the characterisation of the interactions between molecules. The possibility of tuning these interactions in order to create complex aggregates bearing specific chemical/ physical properties at the macroscopic level, is of crucial importance for the development of nanotechnology. In this framework, atomistic simulations constitute a powerful tool capable of providing fundamental contributions. Following this line, the present work combines three distinct studies carried out on as many molecular systems, where the use of a common set of computational techniques, based on classical potentials and Density Functional Theory (DFT), was addressed to understand the aggregation mechanisms displayed by poly-aromatic gelators, poly-aromatic hydrocarbons and nucleic acids. This thesis is structured as follows. In the first chapter, a review of the main computational techniques used throughout this study is presented. The foundations of Molecular Dynamics (MD) are introduced first, with particular attention to the atomistic classical potentials and the main algorithms used for the integration of the equation of motions, the generation of the correct ensemble and for the solvation energies. An overview of DFT is also presented, completing the overview of the investigation methods adopted. In the second chapter, the results of the research carried out to characterise the interactions between a particular type of poly-aromatic gelators, is presented. In particular, the study focuses on the individuation of a set of binding configurations able to provide a rationale for the sensitivity of gel formation to the enantiopurity of the solution. The third chapter focuses on the work conducted in collaboration with the British Petroleum.

Download or read book Protein Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.

Download or read book Springer Handbook of Aerogels written by Michel A. Aegerter and published by Springer Nature. This book was released on 2023-10-01 with total page 1778 pages. Available in PDF, EPUB and Kindle. Book excerpt: This indispensable handbook provides comprehensive coverage of the current state-of-the-art in inorganic, organic, and composite aerogels – from synthesis and characterization to cutting-edge applications and their potential market impact. Built upon Springer’s successful Aerogels Handbook published in 2011, this handbook features extensive revisions and timely updates, reflecting the changes in this fast-growing field. Aerogels are the lightest solids known to man. Up to 1000 times lighter than glass and with a density only four times that of air, they possess extraordinarily high thermal, electrical, and acoustic insulation properties, and boast numerous entries in Guinness World Records. Originally based on silica, R&D efforts have extended this class of materials to incorporate non-silicate inorganic oxides, natural and synthetic organic polymers, carbon, metal, and ceramic materials. Composite systems involving polymer-crosslinked aerogels and interpenetrating hybrid networks have been developed and exhibit remarkable mechanical strength and flexibility. Even more exotic aerogels based on clays, chalcogenides, phosphides, quantum dots, and biopolymers such as chitosan are opening new applications for the construction, transportation, energy, defense and healthcare industries. Applications in electronics, chemistry, mechanics, engineering, energy production and storage, sensors, medicine, nanotechnology, military and aerospace, oil and gas recovery, thermal insulation, and household uses are being developed. Readers of this fully updated and expanded edition will find an exhaustive source for all aerogel materials known today, their fabrication, upscaling aspects, physical and chemical properties, and the most recent advances towards applications and commercial use. This key reference is essential reading for a combined audience of graduate students, academic researchers, and industry professionals.

Download or read book Atomistic Simulation of Anistropic Crystal Structures at Nanoscale written by Jia Fu and published by BoD – Books on Demand. This book was released on 2019-05-10 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multiscale simulations of atomistic/continuum coupling in computational materials science, where the scale expands from macro-/micro- to nanoscale, has become a hot research topic. These small units, usually nanostructures, are commonly anisotropic. The development of molecular modeling tools to describe and predict the mechanical properties of structures reveals an undeniable practical importance. Typical anisotropic structures (e.g. cubic, hexagonal, monoclinic) using DFT, MD, and atomic finite element methods are especially interesting, according to the modeling requirement of upscaling structures. It therefore connects nanoscale modeling and continuous patterns of deformation behavior by identifying relevant parameters from smaller to larger scales. These methodologies have the prospect of significant applications. I would like to recommend this book to both beginners and experienced researchers.

Download or read book Encyclopedia of Ionic Liquids written by Suojiang Zhang and published by Springer Nature. This book was released on 2023-02-03 with total page 1391 pages. Available in PDF, EPUB and Kindle. Book excerpt: The encyclopedia consists 13 subareas as follows: 1: Synthesis and Characterisation of Ionic Liquids (Section Editors: Prof. Fu-Wei Li and Prof. Zhen Li) 2: Physicochemical Properties of Ionic Liquids (Section Editors: Asso. Prof. Qing Zhou, Prof. Xingmei Lu and Prof. Xiaoyan Ji) 3: Computational and Theoretical Modeling of Ionic Liquids (Section Editors: Prof. Guang Feng and Prof. Peter T. Cummings) 4: Toxicology and Biodegradation of Ionic Liquids (Section Editors: Prof. Chunxi Li and Prof. Stefan Stolte) 5: Ionic Liquids in Electrochemistry (Section Editors: Prof. Yingying Lu, Prof. Houlong Zhuang and Prof. Chuan Zhao) 6. Ionic Liquids in Organic Reaction (Section Editors: Prof. Liang-Nian He and Prof. Bhalchandra M. Bhanage) 7. Ionic Liquids in Separation (Section Editors: Prof. Huabin Xing) 8. Ionic Liquids in Biomass and Biomolecules (Section Editors: Prof. Toshiyuki Itoh and Prof. Jian Sun) 9. Ionic Liquids in Materials Science (Section Editors: Prof. Sheng Dai and Prof. Tao Wang) 10. Ionic Liquids in Polymer Science (Section Editors: Asso. Prof. Jinming Zhang and Prof. Jun Zhang) 11. Ionic Liquids in Environmental Science (Section Editors: Prof. Tiancheng Mu, Prof. Arunprakash T. Karunanithi and Prof. Yingxiong Wang) 12. Ionic Liquids in Green Chemistry (Section Editors: Prof. Buxing Han and Prof. Peter Licence) 13. Emerging Applications of Ionic Liquids (Pharmacology, Food Science, Agriculture, Nuclear Science Technology, Optics) (Section Editors: Prof. Zhonghao Li and Prof. Maya Guncheva) This encyclopedia is systematic and comprehensive, with detailed descriptions about theory, technology, and industrial applications. This encyclopedia is valuable for students, researchers and industrial players, giving them a quick understanding and overview of ionic liquids in various aspects.

Download or read book Protein Protein Interactions in Drug Discovery written by Alexander Dömling and published by John Wiley & Sons. This book was released on 2013-01-02 with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt: Treating protein-protein interactions as a novel and highly promising class of drug targets, this volume introduces the underlying strategies step by step, from the biology of PPIs to biophysical and computational methods for their investigation. The main part of the book describes examples of protein targets for which small molecule modulators have been developed, covering such diverse fields as cancer, autoimmune disorders and infectious diseases. Tailor-made for the practicing medicinal chemist, this ready reference includes a wide selection of case studies taken straight from the development pipeline of major pharmaceutical companies to illustrate the power and potential of this approach. From the contents: * Prediction of intra- and inter-species protein-protein interactions facilitating systems biology studies * Modulators of protein-protein interactions: The importance of Three-Dimensionality * Interactive technologies for leveraging the known chemistry of anchor residues * SH3 Domains as Drug Targets * P53 MDM2 Antagonists: Towards Non Genotoxic Anticancer Treatments * Inhibition of LFA-1/ICAM interaction for treatment of autoimmune diseases * The PIF-binding pocket of AGC kinases * Peptidic inhibitors of protein-protein interactions for cell adhesion receptors * The REPLACE Strategy for generating Non-ATP competitive Inhibitors of Cell-Cycle Protein Kinases and more

Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Download or read book Immunoglobulin G written by Michael Fortunato and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Immunoglobulin molecules are extremely effective at providing protection from foreign molecules or viruses; however, in certain cases the naturally occurring immune system cannot provide adequate protection. Monoclonal antibodies are designed to fill these gaps by engineering antigen binding regions capable of targeting and eliminating dangerous molecules. The monoclonal antibodies can function when isolated and able to travel through the blood stream. However, immunoglobulin efficiency decreases upon self-association for two reasons. First, the immune system may recognize the associated molecules and eliminate them depending on the size of the aggregates. Second, if the molecules associate in such a way that the antigen binding regions are no longer accessible they will be unable to function.This thesis discusses molecular simulation techniques that can be used to study the structural changes that occur due to intrinsic molecular flexibility in immunoglobulin molecules as well as the structure of small aggregates that form through self-association. One solvated immunoglobulin molecule was studied by explicitly representing every atom however coarse-graining techniques were required in order to study multiple molecules in the same system.The role of terminal galactose residues in the carbohydrate attached to the Fc domain in an atomisitc model of an antibody molecule was studied in this work. Carbohydrate mobility as well as the protein--carbohydrate hydrogen bonding interactions were compared between simulations with and without terminal galactose residues. It was shown that one of the two biantennary terminal galactose residues preferentially interacts with the protein when both were present; however, when both were removed the carbohydrate structure changed such that new protein--carbohydrate interactions formed. This change in solvent accessible protein surfaces will be an important area of study to both increase effector functions and decrease self-association involving the Fc domain.Understanding through which residues immunoglobulin molecules interact will lead to better designed monoclonal antibodies with increased aggregation resistance. To aid in this understanding, a previously developed residue level coarse-grained model was employed using the same model molecule from the previous atomistic studies. The residues most often involved in self-associationof the antibody were individually mutated to alanine and the resulting association frequencies were compared to the "native" immunoglobulin results to determine the residues most important in self-association. Because of the asymmetry in the three-dimensional structure of the model immunoglobulinmolecule used in this work, differences in aggregation behavior between two domains with identical amino acid sequence indicated that molecular structure can play a significant role in self-association.These simulation techniques were shown to be effective at studying molecular flexibility and protein--carbohydrate interactions with great chemical detail as well as the self-association with resolution at the residue level. The future combination of results from these types of studies will increase the understanding of the solution behavior of immunoglobulin molecules in order to develop more effective monoclonal antibodies.

Download or read book Molecular Dynamics Simulation written by Giovanni Ciccotti and published by MDPI. This book was released on 2018-10-08 with total page 627 pages. Available in PDF, EPUB and Kindle. Book excerpt: Printed Edition of the Special Issue Published in Entropy

Download or read book Structural Bioinformatics written by Zoltán Gáspári and published by Humana. This book was released on 2020-02-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics. Chapter 13 is available open access under a CC-BY 4.0 license via link.springer.com.

Download or read book Asphaltenes and Asphalts 2 written by T.F. Yen and published by Elsevier. This book was released on 2000-08-16 with total page 645 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the second volume in the series of Asphaltenes and Asphalts. Since the publication of the first volume in 1994, there has been a significant advancement in our knowledge. Knowledge of both asphaltenes and asphalts is needed by several disciplines, and often the progress is dictated by interdisciplinary sciences and technology. This includes material sciences, fuel sciences, chemical engineering, civil engineering, environmental engineering, polymer sciences, transportation engineering, petroleum engineering, chemistry, geological sciences, physics, geochemistry rheology, biological sciences, tribology, soil sciences, petroleum science. The development in this field is not based on our knowledge of chemistry or petroleum engineering alone, as many chemists and petroleum engineers believe. In this volume, therefore, significant contributions from different disciplines have been included.