Motion in the Solid State Studied by NMR and Extended Time Scale MD Simulation PDF Download
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Author: Andrew John Ilott
Publisher:
ISBN:
Category : Molecular dynamics
Languages : en
Pages :
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Book Description
The ability to characterise dynamic processes in the solid state is crucial to our understanding of many important materials. Nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are two, highly complementary techniques that can be used in this pursuit, with NMR providing robust measurements of kinetic parameters across a large range of time-scales while MD can give insight into the form that the motion takes. The aim of the work presented in this thesis has been to demonstrate the extent of this complementarity by combining both techniques to investigate interesting systems, and also to expand upon it by implementing extended time scale MD methods that allow slower dynamic processes to be accurately simulated. Atomistic simulations of a urea inclusion compound and of octafluoronaphthalene (OFN), a molecular solid, illustrate the dynamic range and complicated nature of motions that can be present in solid phases of matter, and the inherent difficulty of modeling them without explicit knowledge of their form. Whilst the MD simulation can provide this information, there are computational limits to the range of time-scales it can conventionally access. The OFN system provides an example of this limit, as slow molecular motions observed by NMR experiments are shown to be inaccessible to long, ambient temperature simulations. To combat this deficiency, the metadynamics extended time scale technique has been implemented, allowing rare dynamic events to be observed in very short simulations, and the effects of complex correlated motions to be explored.
Author: Andrew John Ilott
Publisher:
ISBN:
Category : Molecular dynamics
Languages : en
Pages :
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Book Description
The ability to characterise dynamic processes in the solid state is crucial to our understanding of many important materials. Nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are two, highly complementary techniques that can be used in this pursuit, with NMR providing robust measurements of kinetic parameters across a large range of time-scales while MD can give insight into the form that the motion takes. The aim of the work presented in this thesis has been to demonstrate the extent of this complementarity by combining both techniques to investigate interesting systems, and also to expand upon it by implementing extended time scale MD methods that allow slower dynamic processes to be accurately simulated. Atomistic simulations of a urea inclusion compound and of octafluoronaphthalene (OFN), a molecular solid, illustrate the dynamic range and complicated nature of motions that can be present in solid phases of matter, and the inherent difficulty of modeling them without explicit knowledge of their form. Whilst the MD simulation can provide this information, there are computational limits to the range of time-scales it can conventionally access. The OFN system provides an example of this limit, as slow molecular motions observed by NMR experiments are shown to be inaccessible to long, ambient temperature simulations. To combat this deficiency, the metadynamics extended time scale technique has been implemented, allowing rare dynamic events to be observed in very short simulations, and the effects of complex correlated motions to be explored.
Author: Melinda J. Duer
Publisher: John Wiley & Sons
ISBN: 0470999381
Category : Science
Languages : en
Pages : 592
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Book Description
This book is for those familiar with solution-state NMR who are encountering solid-state NMR for the first time. It presents the current understanding and applications of solid-state NMR with a rigorous but readable approach, making it easy for someone who merely wishes to gain an overall impression of the subject without details. This dual requirement is met through careful construction of the material within each chapter. The book is divided into two parts: "Fundamentals" and "Further Applications." The section on Fundamentals contains relatively long chapters that deal with the basic theory and practice of solid-state NMR. The essential differences and extra scope of solid-state NMR over solution-state is dealt with in an introductory chapter. The basic techniques that all chapters rely on are collected into a second chapter to avoid unnecessary repetition later. Remaining chapters in the "Fundamentals" part deal with the major areas of solid-state NMR which all solid-state NMR spectroscopists should know about. Each begins with an overview of the topic that puts the chapter in context. The basic principles upon which the techniques in the chapter rely are explained in a separate section. Each of these chapters exemplifies the principles and techniques with the applications most commonly found in current practice. The "Further Applications" section contains a series of shorter chapters which describe the NMR techniques used in other, more specific areas. The basic principles upon which these techniques rely will be expounded only if not already in the Fundamentals part.
Author: Sławomir Szymański
Publisher: Springer
ISBN: 3319907816
Category : Science
Languages : en
Pages : 406
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Book Description
The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As an introduction to this exciting research field, selected aspects of the quantum mechanics of isolated systems undergoing rotational tunnelling are reviewed, together with some basic information about quantum systems interacting with their condensed environment. The quantum theory of rate processes evidenced in the NMR lineshapes of molecular rotors is presented, and illustrated with appropriate experimental examples from both solid- and liquid-phase spectra. In this context, the everlasting problem of the quantum-to-classical transition is discussed at a quantitative level. The book will be suitable for graduate students and new and practising researchers using NMR techniques.
Author: Amir Goldbourt
Publisher: Frontiers Media SA
ISBN: 2832517404
Category : Science
Languages : en
Pages : 216
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Book Description
Author: John L. Markley
Publisher: Oxford University Press
ISBN: 0195357426
Category : Science
Languages : en
Pages : 375
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Book Description
This book presents a critical assessment of progress on the use of nuclear magnetic resonance spectroscopy to determine the structure of proteins, including brief reviews of the history of the field along with coverage of current clinical and in vivo applications. The book, in honor of Oleg Jardetsky, one of the pioneers of the field, is edited by two of the most highly respected investigators using NMR, and features contributions by most of the leading workers in the field. It will be valued as a landmark publication that presents the state-of-the-art perspectives regarding one of today's most important technologies.
Author: E.E. Burnell
Publisher: Springer Science & Business Media
ISBN: 9401702217
Category : Science
Languages : en
Pages : 465
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Book Description
NMR of Ordered Liquids gives a unique overview of the scope and limitations of the NMR of oriented liquids, based on contributions from acknowledged experts in the field. The book consists of four sections: -detailed general introduction which covers the basic principles and sophisticated experimental techniques; -wide variety of applications ranging from NMR studies of small atoms and molecules in anisotropic liquids to the utilization of residual dipolar couplings for structure determination of biological molecules; -summary of the sophisticated theoretical treatments, computer simulations, and phenomenological models for anisotropic intermolecular interactions that are widely used in the analysis of experimental results; -overview of the dynamical aspects and relaxation processes relevant for orientationally ordered molecules.
Author: Paul Hodgkinson
Publisher: Royal Society of Chemistry
ISBN: 1782628541
Category : Science
Languages : en
Pages : 452
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Book Description
Solid-state NMR covers an enormous range of material types and experimental techniques. Although the basic instrumentation and techniques of solids NMR are readily accessible, there can be significant barriers, even for existing experts, to exploring the bewildering array of more sophisticated techniques. In this unique volume, a range of experts in different areas of modern solid-state NMR explain about their area of expertise, emphasising the “practical aspects” of implementing different techniques, and illustrating what questions can and cannot be addressed. Later chapters address complex materials, showing how different NMR techniques discussed in earlier chapters can be brought together to characterise important materials types. The volume as a whole focusses on topics relevant to the developing field of “NMR crystallography” – the use of solids NMR as a complement to diffraction crystallography. This book is an ideal complement to existing introductory texts and reviews on solid-state NMR. New researchers wanting to understand new areas of solid-state NMR will find each chapter to be the equivalent to spending time in the laboratory of an internationally leading expert, learning the hints and tips that make the difference between knowing about a technique and being ready to put it into action. With no equivalent on the market, it will be of interest to every solid-state NMR researcher (academic and postgraduate) working in the chemical sciences.
Author: Alexandra Nemkevich
Publisher:
ISBN:
Category : Molecular crystals
Languages : en
Pages : 188
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Book Description
The subject of this thesis is the application of molecular dynamics (MD) techniques to study motion in organic molecular crystals. MD can provide a higher level of detail compared to experimental methods used to study molecular motion, such as crystallography and solid state NMR spectroscopy. However, due to the many simplifications and approximations involved, the results of MD simulations have uncertain reliability. The aim of this work was to assess the reliability of MD in simulating the structure and dynamics of simple organic crystals, and to explore the potential of using MD for understanding dynamics in more complicated crystalline systems. The range of possible applications of MD simulations of organic molecular crystals is very wide. They could include, for example, refinement of disordered crystal structures (including large biomolecules), obtaining anisotropic atomic displacement parameters (ADPs) for weakly scattering hydrogens in Xray structure determination, providing insight into some interesting physical phenomena that involve molecular motion and aiding the design of materials showing these phenomena, better understanding of drug-receptor interactions and reactivity in the solid state and helping to design molecular motors. This thesis is organised as a series of papers that have been published or prepared for publication and contains eight Chapters. Chapters 1 and 2 give a general introduction into the topics of molecular motion and computational chemistry. Chapter 1 contains an overview of the types of dynamical processes taking place in organic molecular crystals known from experiment and their relevance to crystal properties. Chapter 2 introduces molecular dynamics and related techniques and reviews their applications to date in studying motion in crystals. Chapter 3 provides an introduction into the experimental work presented in Chapters 4 to 7, which are written as journal articles. In Chapter 4 the reliability of molecular dynamics in reproducing crystal structure and dynamics is critically assessed using a number of force fields to study crystals of a range of compounds of differing polarity and rigidity. A number of simple reorientational motions is also observed and described here. Chapter 5 investigates the rotational frequencies of acetonitrile methyl groups in the clathrate of hydroquinone with acetonitrile, providing insight into which groups rotate with different frequencies and why, which was not available from experiment. Chapter 6 follows the reorientation of hydroxyls in the 6-membered hydrogen bonded rings of clathrates of Dianin's compound and hydroquinone. A consecutive mechanism is suggested for this process in the clathrate of Dianin's compound with ethanol as well as in the empty Dianin's compound framework. Ethanol is found to facilitate the reorientation. In hydroquinone clathrates the reorientation is found to be energetically unfavourable. Chapter 7 discusses guest transport in the clathrates of Dianin's compound and hydroquinone: its mechanism, associated free energy barriers and some other interesting transport related issues. Finally Chapter 8 contains conclusions and a general outline of the possible avenues for further investigations.
Author: Anne E. McDermott
Publisher: John Wiley & Sons
ISBN: 1118588886
Category : Science
Languages : en
Pages : 596
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Book Description
The content of this volume has been added to eMagRes (formerly Encyclopedia of Magnetic Resonance) - the ultimate online resource for NMR and MRI. The field of solid state NMR of biological samples [ssNMR] has blossomed in the past 5-10 years, and a cohesive overview of the technology is needed for new practitioners in industry and academia. This title provides an overview of Solid State NMR methods for studying structure dynamics and ligand-binding in biopolymers, and offers an overview of RF pulse sequences for various applications, including not only a systematic catalog but also a discussion of theoretical tools for analysis of pulse sequences. Practical examples of biochemical applications are included, along with a detailed discussion of the many aspects of sample preparation and handling that make spectroscopy on solid proteins successful. About EMR Handbooks / eMagRes Handbooks The Encyclopedia of Magnetic Resonance (up to 2012) and eMagRes (from 2013 onward) publish a wide range of online articles on all aspects of magnetic resonance in physics, chemistry, biology and medicine. The existence of this large number of articles, written by experts in various fields, is enabling the publication of a series of EMR Handbooks / eMagRes Handbooks on specific areas of NMR and MRI. The chapters of each of these handbooks will comprise a carefully chosen selection of articles from eMagRes. In consultation with the eMagRes Editorial Board, the EMR Handbooks / eMagRes Handbooks are coherently planned in advance by specially-selected Editors, and new articles are written (together with updates of some already existing articles) to give appropriate complete coverage. The handbooks are intended to be of value and interest to research students, postdoctoral fellows and other researchers learning about the scientific area in question and undertaking relevant experiments, whether in academia or industry. Have the content of this Handbook and the complete content of eMagRes at your fingertips! Visit: www.wileyonlinelibrary.com/ref/eMagRes View other eMagRes publications here
Author: Yuxi Pang
Publisher:
ISBN:
Category :
Languages : en
Pages : 320
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Book Description
