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La presente tesis doctoral se centra en el estudio de técnicas de mejora de resolución de la espectroscopía por Resonancia Magnética Nuclear (RMN) para una más simple y precisa elucidación estructural de moléculas pequeñas. El trabajo se ha presentado como un compendio de siete publicaciones escritas para diversas prestigiosas revistas científicas. Las publicaciones desarrollan en profundidad la aplicación de las mejoras de resolución para i) una medida precisa y eficiente de las constantes de acoplamiento tanto homo- como heteronucleares e ii) la optimización de las medidas de parámetros anisotrópicos a través de medios débilmente alineados. Estos dos tópicos se desarrollan mediante: 1.La aplicación de modernas técnicas de RMN para la mejora de laresolución, tanto digital como de señal, en experimentos 2D sin comprometer el tiempo experimental. 2.El diseño de nuevas secuencias de pulsos para la medida de conectividades de largo alcance heteronuclear. 3.La implementación de secuencias de pulsos ya existentes y el diseño de nuevas para el estudio de muestra en medio aniostrópicos. 4.El estudio de nuevos métodos en RMN para la discriminación mediante parámetros anisotrópicos. 5.La aplicación de protocolos para la automatización y simplificación de las medidas de contantes de acomplamientos en medio isotrópicos y anisotrópicos.
Ultra-high resolution nuclear magnetic resonance (NMR) methods refer to advanced techniques used to obtain detailed structural information about molecules. These methods use high-field magnets and specialized pulse sequences to achieve very high resolution in the NMR spectrum, allowing for the detection of very small chemical shifts and coupling constants. One of the main applications of ultra-high resolution NMR methods is in the study of biological macromolecules, such as proteins and nucleic acids. These methods can be used to determine the three-dimensional structure of these molecules, which is important for understanding their function and for drug design. Ultra-high resolution NMR methods can also be used for the study of small molecules. These methods can be used to determine the conformation of a molecule in solution, which is important for understanding the properties of a molecule and for designing new materials. In addition, ultra-high resolution NMR can be used for quantitative analysis of complex mixture. The high resolution of the spectrum allows for the detection of very small amounts of impurities or contaminants, and can also be used to determine the concentration of a component in a mixture. Overall, ultra-high resolution NMR methods are powerful tools that can provide detailed structural information about molecules and can be used in a wide range of applications, including biology, chemistry, and materials science. Nuclear magnetic resonance (NMR) spectroscopy is a potent analytical tool to comprehend physical and chemical nature (mobility, dynamics and kinetics) of small to medium size molecules for an extensive range of samples under variety of conditions such as temperature, concentration, and pH. A wealth of information related to molecular properties and interactions can be furnished by using NMR which could consequently provide utility in molecular structural identification. However, low sensitivity along with low resolution is a concern in application of NMR. Within the past few decades, NMR sensitivity has improved significantly through advancement in instrumentation as well as methodological developments. Recent upgrade in NMR instrumentation such as cryogenically cooled probes[1] has led to increase sensitivity and three to four-times better signal /noise ratio in comparison to room temperature probes leading to faster acquisition times and improved sensitivity. Resolution of spectrum is additionally improved in a high magnetic field which disperses the chemical shifts over the broad frequency range (in Hz). Nevertheless, signal overlaps continue being a limiting factor for characterizing complicated spectra. Therefore, a steady development of new pulse sequences and enhancements of the existing ones are of vital importance in improving the overall performance of NMR spectroscopy.
Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins. To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the soft- ware also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multi-dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at C? positions in proteins, using the CPMG dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals. To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of EphB2 and its signaling mechanism.
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.
Nuclear Magnetic Resonance Spectroscopy (NMR) is now widely regarded as having evolved into a subscience. The field has become immensely diverse, ranging from medical use through solid state NMR to liquid state applications, with countless books and scientific journals devoted to these topics. Theoretical as well as experimental advance continues to be rapid, and has in fact accelerated by many novel innovations. This multi-authored book focuses on the latest developments in the rapidly evolving field of high resolution NMR, specifically with a view to applications on the structure elucidation of organic molecules of moderate molecular weight. Conceptually it differs from basic educational texts, hard-core scientific papers and regular review articles in that each chapter may be regarded as the authors' personal account of their special insights and results that crystallised after several years of research into a given topic. The book revolves around several themes and offers a handful of scientific "gems" of various colors, reflecting the great diversity of NMR. It contains 16 loosely connected chapters written by some of today's most accomplished NMR scientists in the world. Each chapter is a unique synthesis of the authors' previous research results in the given field, and thus projects special insights. Much emphasis has been given to the latest developments in NMR, in particular to selective pulses and pulsed field gradients. As a part of the series "Analytical Spectroscopy Library", with subsequent editions coming along this book should provide a platform for future research accounts of similar flavor. The material is presented in a mostly non-mathematical fashion, and is intended mainly for chemists, application NMR scientists and students with already some background in NMR. Some of the chapters slightly overlap in the discussed topics, which is particularly exciting in terms of gaining insight into the same area from different angles.
This book explores how nuclear magnetic resonance (NMR) spectroscopy may be used for spatial structural elucidation of novel compounds from fungal and synthetic sources. Readers will discover the exciting world of NOE (nuclear Overhauser effect), RDC (residual dipolar coupling) and J-coupling constants, both short- and long range. With emphasis on obtaining structural knowledge from these NMR observables, focus is moved from solving a static 3D structure to solving the structural space inhabited by small organic molecules. The book outlines the development and implementation of two Heteronuclear Multiple Bond Correlation-type NMR experiments, and the 3D structural elucidation of multiple known and novel compounds. In addition, a new method of back-calculating RDCs (allowing for more flexible structures to be investigated), and the synthesis and evaluation of novel chiral alignment media for ab initio determination of absolute stereochemistry of small molecules using RDCs are also included. Challenges that 3D structural generation of small compounds face are also covered in this work.
The progress in nuclear magnetic resonance (NMR) spectroscopy that took place during the last several decades is observed in both experimental capabilities and theoretical approaches to study the spectral parameters. The scope of NMR spectroscopy for studying a large series of molecular problems has notably broadened. However, at the same time, it requires specialists to fully use its potentialities. This is a notorious problem and it is reflected in the current literature where this spectroscopy is typically only used in a routine way. Also, it is seldom used in several disciplines in which it could be a powerful tool to study many problems. The main aim of this book is to try to help reverse these trends.This book is divided in three parts dealing with 1) high-resolution NMR parameters; 2) methods for understanding high-resolution NMR parameters; and 3) some experimental aspects of high-resolution NMR parameters for studying molecular structures. Each part is divided into chapters written by different specialists who use different methodologies in their work. In turn, each chapter is divided into sections. Some features of the different sections are highlighted: it is expected that part of the readership will be interested only in the basic aspects of some chapters, while other readers will be interested in deepening their understanding of the subject dealt with in them. - Shows how NMR parameters are useful for structure assignment as well as to obtain insight on electronic structures - Emphasis on conceptual aspects - Contributions by specialists who use the discussed methodologies in their everyday work
The contemplation of truth and beauty is the proper object for which we were created, which calls forth the most intense desires of the soul, and of which it never tires -Hazlitt In his Nobel lecture Purcell commented that when he saw snow in New England after the discovery of NMR, it appeared like "heaps of protons quietly precessing in earth's magnetic field. " If he were to make the comment in the context of how NMR is being used today, he could have conjured up an image of hydrogen, carbon, and nitrogen nuclei in proteins of an earthbound 8rganism subtly orchestrating a quiet symphony of frequencies, from 150 Hz to 2 kHz, carrying clues to the three-dimensional structure of the macromolecules. The manner in which the basic discoveries of Bloch and Purcell have led to the emergence of NMR, several decades later, as a major technique of biological and medical physics (and chemistry) is a striking example of the power of basic research. It is also a fascinating saga whereby whenever it was felt that the field had reached a plateau, new directions, new technologies, and sometimes serendipity produced new developments that revolutionized the technique and enhanced its capability. As Richard Ernst points out "NMR is intellectually attractive, . . . the practical importance of NMR is enormous, and can justify much of the playful activities of an addicted spectroscopist" (Nobel lecture).
The derivation of structural information from spectroscopic data is now an integral part of organic chemistry courses at all Universities. Over recent years, a number of powerful two-dimensional NMR techniques (e.g. HSQC, HMBC, TOCSY, COSY and NOESY) have been developed and these have vastly expanded the amount of structural information that can be obtained by NMR spectroscopy. Improvements in NMR instrumentation now mean that 2D NMR spectra are routinely (and sometimes automatically) acquired during the identification and characterisation of organic compounds. Organic Structures from 2D NMR Spectra is a carefully chosen set of more than 60 structural problems employing 2D-NMR spectroscopy. The problems are graded to develop and consolidate a student’s understanding of 2D NMR spectroscopy. There are many easy problems at the beginning of the collection, to build confidence and demonstrate the basic principles from which structural information can be extracted using 2D NMR. The accompanying text is very descriptive and focussed on explaining the underlying theory at the most appropriate level to sufficiently tackle the problems. Organic Structures from 2D NMR Spectra Is a graded series of about 60 problems in 2D NMR spectroscopy that assumes a basic knowledge of organic chemistry and a basic knowledge of one-dimensional NMR spectroscopy Incorporates the basic theory behind 2D NMR and those common 2D NMR experiments that have proved most useful in solving structural problems in organic chemistry Focuses on the most common 2D NMR techniques – including COSY, NOESY, HMBC, TOCSY, CH-Correlation and multiplicity-edited C-H Correlation. Incorporates several examples containing the heteronuclei 31P, 15N and 19F Organic Structures from 2D NMR Spectra is a logical follow-on from the highly successful “Organic Structures from Spectra” which is now in its fifth edition. The book will be invaluable for students of Chemistry, Pharmacy, Biochemistry and those taking courses in Organic Chemistry. Also available: Instructors Guide and Solutions Manual to Organic Structures from 2D NMR Spectra