Download or read book Structural and Energetic Studies of Hydrated Gas phase Ions and Biomolecules Using Electrospray Ionization Mass Spectrometry written by Sandra Enid Rodriguez-Cruz and published by . This book was released on 1999 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Assigning Structures to Ions in Mass Spectrometry written by John L. Holmes and published by CRC Press. This book was released on 2006-12-26 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Assigning Structures to Ions in Mass Spectrometry describes the tools currently available for determining gas-phase ion structures. It surveys current experimental methods for ion production and separation as well as those designed to reveal qualitative and quantitative aspects of gas-phase ions. It also examines how and when to apply computational chemistry and theoretical calculations. Selected case studies illustrate specific challenges associated with ion structure assignment and thermochemical problems. Bringing together key results collected over the past four decades, the book contains the data for describing or identifying ions containing C alone and C with H, O, N, S, P, halogens, and small organic cations.
Download or read book Development of Ion Mobility mass Spectrometry Instrumentation to Probe the Conformations and Capture the Solution to Gas Phase Transition of Electrosprayed Biomolecules written by Joshua A Silveira and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent progress has been made developing ion mobility-mass spectrometry (IM-MS) instruments for biophysical studies; however, experimental techniques that can probe the structure and/or dynamics of biomolecules at intermediate extents of hydration are limited and little is known about the final stages of desolvation during electrospray ionization (ESI). Here, ion optical devices, analytical methodology, and instrument platforms are developed to study the conformations of structurally labile biomolecules (i.e., peptides and proteins) produced upon ESI and provide new insight into their solution to gas phase evolution. First, fundamental principles of periodic focusing ion mobility spectrometry are comprehensively discussed. Radial ion confinement is attributed to a collisionally dampened effective potential that ultimately results in high ion transmission. Detailed equations of motion are derived that culminate into useful methodology for accurate determination of peptide and protein collision cross section values via inclusion of a mobility dampening coefficient. Second, evaporation of water from extensively hydrated protons and peptides formed by ESI is examined for the first time using a new cryogenic (80 K) IM-MS instrument platform. Key parameters that influence the cluster distributions are critically examined. In agreement with previous studies, the findings indicate that water evaporation is largely dependent upon the particular charge-carrying species within the cluster. IM-MS results for protonated water clusters suggest that the special stability of the well-known H+(H2O)[subscript n] (n = 21) "magic number" cluster is attributed to the presence of a compact clathrate cage isomer produced upon ESI. Peptide studies are also presented in which specific and nonspecific solvation is observed for gramicidin S [GS + 2H]2+ (H2O)[subscript n] (n = 0 to 26) and bradykinin [BK + 2H]2+ (H2O)[subscript n] (n = 0 to 73), respectively. However in the case of substance P, [SP + 3H]3+, the results demonstrate that a compact dehydrated conformer population (resulting from the evaporative ESI process) can be kinetically trapped on the time scale of several milliseconds, even when an extended coil conformation is energetically favorable in the gas phase. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/151729
Download or read book Gas Phase Ion Chemistry written by Michael T. Bowers and published by Academic Press. This book was released on 2013-10-22 with total page 363 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gas Phase Ion Chemistry, Volume 2 covers the advances in gas phase ion chemistry. The book discusses the stabilities of positive ions from equilibrium gas-phase basicity measurements; the experimental methods used to determine molecular electron affinities, specifically photoelectron spectroscopy, photodetachment spectroscopy, charge transfer, and collisional ionization; and the gas-phase acidity scale. The text also describes the basis of the technique of chemical ionization mass spectrometry; the energetics and mechanisms of unimolecular reactions of positive ions; and the photodissociation of gas-phase ions. The applications of molecular beam techniques to the study of ion-molecule collisions; as well as the variational treatment of charge transfer reactions are also encompassed. Chemists and biochemists will find the book invaluable.
Download or read book Fundamentals of Gas Phase Ion Chemistry written by K.R. Jennings and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 439 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents the proceedings of the 1990 Advanced Study Institute entitled "Fundamentals of Gas Phase Ion Chemistry" held at Mont Ste. Odile , Alsace, France, 25th June -6th July, 1990. The Institute brought together over 100 physicists, physical and organic chemists working on a wide variety of topics with gas-phase ion chemistry as the common theme. Many different viewpoints, making use of very different experimental and theoretical approaches, were brought to bear on the subject and provided a stimulating and up-to-date account of the subject. Although the Institute was built around the invited lectures, many specific points were addressed in workshops which consisted of informal discussion groups which were organised by participants during the Institute. This volume therefore contains not only chapters based on the lectures but summaries of many of the workshops which adds considerably to the diversity of information presented. This Advanced Study Institute was the fifth in a series of NATO-sponsored institutes devoted to various aspects of the physics and chemistry of gas phase ions. These meetings have been held every four years since the first, held in Biarritz in 1974, considered "Interactions between Ions and Molecules". The five volumes which comprise the proceedings of these meetings illustrate very clearly the many advances in theory and experiment which have taken place over the last 20 years.
Download or read book Investigation on Gas phase Structures of Biomolecules Using Ion Mobility mass Spectrometry written by Lei Tao and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: IM-MS is a 2-D technique which provides separations based on ion shape (ionneutralcollision cross-section, [omega]) and mass (m/z ratio). Ion structures can be deducedfrom the measured collision cross-section ([omega]meas) by calculating the collision crosssections([omega]calc) of candidates generated by molecular dynamics (MD) and compared withthe experiment results. A database of [omega]s for singly-charged peptide ions is presented. Standard proteins are digested using different enzymes (trypsin, chymotrypsin and pepsin), resulting in peptides that differ in amino acid composition. The majority (63%) of the peptide ion correlates well with the globular structures, but some exhibit [omega]s that are significantly larger or smaller than the average correlation. Of the peptide ions having larger [omega]s, approximately 71% are derived from trypsin digestion, and most of the peptide ions that have smaller [omega]s are derived from pepsin digestion, and most of the peptide ions that have smaller [omega]s are deroved from pepson digestion (90%). We use computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH2-Met-Ile-Phe-Ala- Gly-Ile-Lys-COOH) formed by both MALDI and ESI and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H] ions formed by MALDI have a predominantly turn structure even though the low energy ions prefer partial helical conformers. Although the ions formed by ESI have [omega]s that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester, as well as addition of Boc or Fmoc groups) of MIFAGIK, alter the distribution of various conformers. The most dramatic changes are observed for the [M + Na] ion, which show a strong preference for random coil conformers, owing to the strong solvation by the backbone amide groups. [Omega]meas of oligodeoxynucleotides in different length have been measured in both positive and negative modes. For a given molecular weight and charge state, [omega]meas of the oligodeoxynucleotide, ions are smaller than those of the peptides, indicating their different packing efficiency. A novel generalized non-Boltzman sampling MD has been utilized to investigate the gas-phase ion conformations of dGGATC based on the free energy values. Theory predicts only one low-energy conformer for the zwitterionic form of dGGATC− while dGGATC+ ions have several stable conformers in both canonical and zwitterionic form in the gas phase, in good agreement with the experiment.
Download or read book Large Ions written by Tomas Baer and published by John Wiley & Sons. This book was released on 1996 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in both experimental techniques and theoretical methodologies have meant that increasingly sophisticated studies concerning the formation, structures, energetics and reaction dynamics of state- or energy-selected molecular ions can now be performed. In order to better serve the ion chemistry and physics community, each volume of this series is dedicated to reviewing a specific topic, emphasizing new experimental and theoretical developments in the study of ions. The Wiley Series in Ion Chemistry and Physics will help stimulate new research directions and point to future opportunities in the field of ion chemistry and physics. This volume, the sixth in the series, concentrates on the area of large ions. The production, detection and analysis of large ions are areas which have taken on great importance in recent years, in particular in the biomedical and biochemical fields. The understanding of large ions presents unique and formidable challenges which are very different from those associated with the study of small ions. This volume focuses on some of the fundamental chemistry and physics associated with the behavior of large ions, with the contributors addressing the issues in a quantitative fashion, in order to elucidate clearly some of the key recent advances which have taken place. As such, Large Ions: Their Vaporization, Detection and Structural Analysis provides an excellent snapshot of current research in this fascinating and important area. The six chapters are written by some of the leading experts in the field, and together they will be of great interest to experts and newcomers, both of whom will benefit from the in-depth discussion of the latest methods and results.
Download or read book Ion Fragmentation Methods for Characterizing Peptides and Hydrated Ions in the Gas Phase written by Richard Li Chou Wong and published by . This book was released on 2003 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Gas Phase IR Spectroscopy and Structure of Biological Molecules written by Anouk M. Rijs and published by Springer. This book was released on 2015-06-03 with total page 409 pages. Available in PDF, EPUB and Kindle. Book excerpt: The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students.
Download or read book Advances in Gas Phase Ion Chemistry written by N.G. Adams and published by Elsevier. This book was released on 1998-04-23 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gas-phase ion chemistry is a broad field which has many applications and which encompasses various branches of chemistry and physics. An application that draws together many of these branches is the synthesis of molecules in interstellar clouds. This was part of the motivation for studies on the neutralization of ions by electrons and on isomerization in ion-neutral associations. The results of investigations of particular aspects of ion dynamics are presented in this volume. Solvation in ion-molecule reactions is discussed and extended to include multiply charged ions by the application of electrospray techniques. This volume also provides a wealth of information on reaction thermodynamics which is critical in determining reaction spontaneity and availability of reaction channels. More focused studies are also presented towards the end of this volume, relating to the ionization process and its nature.
Download or read book Fundamentals and Applications of Gas Phase Ion Chemistry written by K.R. Jennings and published by Springer Science & Business Media. This book was released on 1999 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book draws together leading workers in the fields of mass spectrometry and gas phase ion chemistry, providing a forum for the exchange of ideas and information. It contains 14 lecture summaries and accounts of seven workshops with contributions from Europe and North America.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2004 with total page 692 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural Elucidation of Biomolecular Ions in the Gas Phase Using Novel Mass Spectrometric and Computational Methods written by Yang Liu and published by . This book was released on 2019 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological molecules such as protein and DNA play critical roles in various cellular reactions and carry out essential biological functions. But the mechanisms of these reactions, and the essential molecular structures to facilitate them are often poorly understood. Many efforts have been applied to these problems, but due to their complexity and various limitations of existing methods, the elucidation of biological reaction mechanisms and biological molecule or complex structures is still considered a challenge today. Therefore, the scientific community has been highly motivated to invent new methods to tackle these problems devise new angles of approach to grain insights into biomolecular structure. This dissertation summarizes some recent work in characterizing cation-radical reactions, and structures of gas-phase molecular complexes using novel mass spectrometry methods in combination with theoretical computational modeling. The novel mass spectrometric methods presented in this work are gas-phase photo-dissociative crosslinking techniques and UV-visible photodissociation action spectroscopy. They have several unique advantages in tackling structure elucidation of weakly bound complexes and transient radical species. 1) The mass spectrometer (MS) is a universal detector which is widely used to characterize various kinds of biological molecules. 2) MS works with ions of interest that are generated and stored in the gas phase at low pressure of an inert gas (He). It is the perfect system to study reaction mechanisms because of low interference from the ambient environment, such as solvent, counterions, surfaces, etc. 3) Methods exist to generate cation radicals in the gas phase, and thanks to the low pressure inside a mass spectrometer, the produced species are kinetically stable on the experimental time scale of several milliseconds. 4) MS is a perfect tool for conducting gas-phase reactions because it allows one to manipulate the ion population and select and focus the ions. It is advantageous for crosslinking reactions that often suffer from low concentrations of reactants when the reaction is attempted in condensed phase. 5) The experimental action spectra can be interpreted using sophisticated computational techniques providing vibronic transitions of multiple isomeric candidates. The new data generated with these new mass spectrometry methods offer unique insights, but also pose challenges to experimental data interpretation. Various computational approaches are used to supplement the experimental data, and the results from the computations are used to guide the interpretation. This dissertation also includes several novel approaches on the computational front, introducing the customized modeling pipeline with a combination of Born-Oppenheimer dynamics, density functional theory calculations, and machine learning techniques. The first chapter introduces some basic terms and outlines the background for the topic of study, including a quick review of the current challenges and techniques in the field of structure elucidation of biomolecules. Also introduced are the fundamentals of mass spectrometer, commonly used and newly developed ion activation methods, and computational modeling. This chapter lays the foundation of the work described in later chapters. A small neuroprotective peptide Cys-Ala-Gln-Lys (CAQK) has recently been discovered to mitigate adverse effects of brain trauma in mice, possibly because of specific interactions with yet-to-be identified proteins. In Chapter 2, an application of photo-crosslinking is described to study the noncovalent interactions of CAQK with several model target peptide motifs. The experimental results in combination with Born-Oppenheimer molecular dynamics revealed the structural preferences for binding to the amino acid residues of potential target peptides. In Chapter 3, inspired by the biological significance of CAQK, we employed the photo-dissociative crosslinking techniques to probe its interactions with several dinucleotides as structure motifs of nuclear DNA. This lysine-containing peptide can be viewed as a simplified surrogate of a histone interacting with DNA. We were able to show that in interactions with CAQK ions, even simple dinucleotides differ in their binding efficiency and stereochemistry. We provided structures of selected complexes obtained by electronic structure theory calculations using density functional theory (DFT). UV and energetic particle radiation can ionize DNA creating electron deficiency (hole) at nucleobases. These holes can migrate along the strand, leading to lesions and DNA damage by follow up radical reactions. Chapter 4 and chapter 5 are focused on the characterization of DNA cation radicals in the guanine and cytosine containing dinucleotide as model systems in probing the electron transfer mechanisms in DNA radiation damage. Experimental action spectra were obtained for these small nucleotides and the absorption bands were interpreted by finding the closest match from the calculated spectra. The last chapter features an ongoing project in which we have made an attempt, using photo-crosslinking techniques, to probe noncovalent interactions within a complex consisting of a chiral agonist and its binding motifs. The experimental results revealed high binding affinity of the native agonist regardless of chirality, however the crosslinking fragment was not observed. Several DFT optimized low energy structure had shown a consistently low "contact" rate of the phototag with the target peptide. A further characterization of ion structures will be complemented from the collisional cross section analysis by ion mobility (IM) measurements.
Download or read book Advances in Gas Phase Ion Chemistry written by and published by Elsevier. This book was released on 1996-05-14 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Gas Phase Ion Chemistry
Download or read book Electrospray Ionization Mass Spectrometry written by and published by . This book was released on 2007 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation focused on using electrospray ionization mass spectrometry to study cluster ions and toxic metal ions in biology. In Chapter 2, it was shown that primary, secondary and quarternary amines exhibit different clustering characteristics under identical instrument conditions. Carbon chain length also played a role in cluster ion formation. In Chapters 3 and 4, the effects of solvent types/ratios and various instrumental parameters on cluster ion formation were examined. It was found that instrument interface design also plays a critical role in the cluster ion distribution seen in the mass spectrum. In Chapter 5, ESI-MS was used to investigate toxic metal binding to the [Gln11]-amyloid ?-protein fragment (1-16). Pb and Cd bound stronger than Zn, even in the presence of excess Zn. Hg bound weaker than Zn. There are endless options for future work on cluster ions. Any molecule that is poorly ionized in positive ion mode can potentially show an increase in ionization efficiency if an appropriate anion is used to produce a net negative charge. It is possible that drug protein or drug/DNA complexes can also be stabilized by adding counter-ions. This would preserve the solution characteristics of the complex in the gas phase. Once in the gas phase, CID could determine the drug binding location on the biomolecule. There are many research projects regarding toxic metals in biology that have yet to be investigated or even discovered. This is an area of research with an almost endless future because of the changing dynamics of biological systems. What is deemed safe today may show toxic effects in the future. Evolutionary changes in protein structures may render them more susceptible to toxic metal binding. As the understanding of toxicity evolves, so does the demand for new toxic metal research. New instrumentation designs and software make it possible to perform research that could not be done in the past. What was undetectable yesterday will become routine tomorrow.
Download or read book Novel Analytical Methods for Examining Biomolecular Complexes Using Electrospray Ionization Mass Spectrometry written by Tawnya Grace Flick and published by . This book was released on 2012 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several analytical strategies and investigations are presented in this dissertation to improve the quantification, sensitivity, and structural information that can be obtained for gaseous biomolecular ions in electrospray ionization (ESI) mass spectrometry (MS) experiments. Internal or external standards are commonly employed to quantify molecules in complex mixtures because molecular ion abundances cannot be directly related to the concentration of the molecules in solution. A new standard-free quantitation method is used to obtain the relative concentrations of components in a mixture using the abundances of large, nonspecific clusters formed by ESI. Large non-covalent clusters overcome differences in ionization efficiencies between molecules, and are representative of the solution-phase mixture. The sensitivity in MS experiments can be significantly lowered by the presence of high concentrations of salts in the ESI solution because nonspecific ion adduction to biomolecules distributes ion signal into different forms with various numbers of adducts. Studies here demonstrate the extent of both sodium ion and acid molecule adduction to proteins are inversely related, and both depend significantly on the proton affinity of the anion in the ESI solution. Several solution-phase additives that contain anions with low proton affinity values are shown to effectively desalt protein ions generated by ESI, which should result in improved detection limits, more accurate mass measurements, and improved tandem MS sensitivity. Additionally, a solution-phase additive (HClO4) is discovered that can be used to count the number of basic sites accurately in peptides and proteins based on the number of HClO4 adducts to low charge states. High charge states of peptides and proteins can be readily formed by ESI of aqueous solutions that contain trivalent metal ions, and fragmentation of these trivalent metal ion-peptide or protein complexes by electron capture dissociation can be used to increase the structural information obtained from these experiments. Metal ion-biomolecule interactions are ubiquitous in nature where they play a role in many biological processes. Here, nonspecific metal ion adduction to protein cation and anions is shown to result in more compact conformations compared to the bare protein ion, likely a result of salt-bridge interactions between the metal ion and the biomolecule.
Download or read book Generation and Analysis of Highly Hydrated Ions Using Electrospray Ionization Mass Spectrometry written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: A variety of highly hydrated ions were generated and studied using electrospray ionization mass spectrometry (ESI-MS) including proton, a series of triply charged lanthanide ions, the doubly charged lead ion and various methylated guanidinium ions. In each case large hydrated water clusters were mass selected and fragmented through collision induced dissociation (CID) to investigate their properties. The fragmentation of protonated water clusters highlighted the stability of the "magic" water cluster [H(H2O)21]+. Typically unstable triply charge lanthanide water clusters and the previously unobserved doubly charged lead water clusters were generated. Fragmentation studies indicated that both the charge density and the geometry of the clusters affect their stability. The charge reduction of triply charged lanthanide clusters led to the direct observation of ion evaporation. Finally, the dehydration of various methylated guanidinium ions indicated a structural basis for differences in their ability to hydrogen bond.
