Download or read book Cold Ion Spectroscopy of Biological Molecules in the Gas Phase written by Natalia Nagornova and published by . This book was released on 2011 with total page 179 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 Novel Approaches in Cold Ion Spectroscopy for Structural Characterization of Biomolecules in the Gas Phase written by Vladimir Kopysov and published by . This book was released on 2016 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mots-clés de l'auteur: cold ion spectroscopy ; UV spectroscopy ; high-resolution mass spectrometry ; photodissociation ; Orbitrap ; UV-MS ; gas phase ; biomolecular ions ; isomers ; conformers ; FRET ; phosphorylated peptides ; opioid peptides ; ephedrine ; gramicidin S ; homatropine ; leucine enkephalin.
Download or read book The Effective Temperatures of Gas phase Biological Molecules Stored in a Quadrupole Ion Trap written by Geng Li and published by . This book was released on 2008 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt: The internal energy distribution undergoing collision-induced dissociation (CID) in the cell of a quadrupole ion trap (QIT) mass spectrometer can be characterized by the effective temperature, which would help determine the activation energy and entropy. Here, the relationship in a Bruker QIT has been reexamined based on kinetic measurements at two qz values. An observed linear relationship between ion effective temperatures and resonant activation amplitudes appears qualitatively different from simplified theoretical simulation, which is in agreement with previous results on Finnigan ion trap. However, the normalization process aiming to compensate for the m/z dependency of the required fragmentation energy that is used successfully in Finnigan-geometry traps is not entirely successful for use in Bruker-geometry trans. The calibration determined here roughly indicates the relationship between ion effective temperature, resonant excitation amplitude and ion m/z. However, Successful extraction of the dissociation energetics still requires a better accuracy of the calibration.
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 Photophysics of Ionic Biochromophores written by Steen Brøndsted Nielsen and published by Springer Science & Business Media. This book was released on 2013-10-16 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a concise overview of the photophysics and spectroscopy of bio chromophore ions. The book "Photophysics of Ionic Biochromophores" summarizes important recent advances in the spectroscopy of isolated biomolecular ions in vacuo, which has within the last decade become a highly active research field. Advanced instrumental apparatus and the steady increase in more and more powerful computers have made this development possible, both for experimentalists and theoreticians. Applied techniques described here include absorption and fluorescence spectroscopy, which are excellent indicators of environmental effects and can thus shed light on the intrinsic electronic structures of ions without perturbations from e.g. water molecules, counter ions, nearby charges, and polar amino acid residues. When compared with spectra of the chromophores in their natural environment, such spectra allow to identify possible perturbations. At the same time gas-phase spectra provide important benchmarks for quantum chemistry calculations of electronically excited states. This volume focuses on biological systems from protein biochromophores, e.g. the protonated Schiff-base retinal responsible for vision, and individual aromatic amino acids to peptides and whole proteins, studied using visible, ultraviolet and vacuum ultraviolet light. Work on DNA nucleotides and strands that are amenable to mass spectrometric studies because of the negatively charged sugarphosphate backbone are also presented. DNA strands represent an example of the interplay between multiple chromophores, which is even harder to model correctly than just single chromophores due to spatially extended excited states and weak coupling terms. The experimental techniques used to measure spectra and commonly used theoretical methods are described with a discussion on limitations and advantages. The volume includes an updated status of the field and interesting future directions such as cold ion spectroscopy.
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 Gas Phase NMR written by Karol Jackowski and published by Royal Society of Chemistry. This book was released on 2016-02-09 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the recent NMR studies with the application of gaseous molecules. Among the comprehensively discussed aspects of the area it includes in particular: new multinuclear experiments that deliver spectral parameters of isolated molecules and provide the most accurate values of nuclear magnetic shielding, isotropic spin–spin coupling and relaxation times; advanced, precise and correct theoretical descriptions of spectral parameters of molecules as well as the application of gas-phase NMR measurements to chemical analysis and medicine. The progress of research in these fields is enormous and has rapidly changed our knowledge and understanding of molecular parameters in NMR spectroscopy. For example, accurate studies of the shielding for isolated molecules allow the exact determination of nuclear magnetic dipole moments, the calculated values of spectral parameters can be verified by precise gas-phase NMR measurements, and the application of hyperpolarized noble gases provides excellent MRI pictures of lungs. Aimed at graduates and researchers in spectroscopy, analytical chemistry and those researching the applications of NMR in medicine, this book presents the connections between sophisticated experiments, the theory of magnetic parameters and the exploration of new methods in practice.
Download or read book Optical Spectroscopy of Mass selected Ions in the Gas Phase written by Matthew William Forbes and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-inducedfluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption. The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore of the green fluorescent protein (GFP), p-hydroxybenzylidene-2,3-dimethylimidazolone (HBDI). The body of work in this dissertation highlights the integration of gas-phase spectroscopy and mass spectrometry to elucidate the fundamental photophysical properties of biological and related ions.
Download or read book Optical Spectroscopy of Mass selected Ions in the Gas Phase written by and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-inducedfluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption. The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore o.
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 Optical Spectroscopy of Mass selected Ions in the Gas Phase written by Matthew W. Forbes and published by . This book was released on 2010 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-induced-fluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption.The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR-fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore of the green fluorescent protein (GFP), p-hydroxybenzylidene-2,3-dimethylimidazolone (HBDI). The body of work in this dissertation highlights the integration of gas-phase spectroscopy and mass spectrometry to elucidate the fundamental photophysical properties of biological and related ions.
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 Low Temperatures and Cold Molecules written by Ian W. M. Smith and published by Imperial College Press. This book was released on 2008 with total page 578 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book brings together, for the first time, the results of recent research in areas ranging from the chemistry of cold interstellar clouds (10-20 K), through laboratory studies of the spectroscopy and kinetics of ions, radicals and molecules, to studies of molecules in liquid helium droplets, to attempts to create molecular (as distinct from atomic) Bose-Einstein condensates.
Download or read book Ion molecule Interactions in the Gas Phase written by Richard D. Burton and published by . This book was released on 1997 with total page 284 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 Physical Chemistry of Cold Gas Phase Functional Molecules and Clusters written by Takayuki Ebata and published by Springer. This book was released on 2019-08-02 with total page 395 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes advanced research on the structures and photochemical properties of polyatomic molecules and molecular clusters having various functionalities under cold gas-phase conditions. Target molecules are crown ethers, polypeptides, large size protonated clusters, metal clusters, and other complex polyatomic molecules of special interest. A variety of advanced frequency and time-domain laser spectroscopic methods are applied. The book begins with the principle of an experimental setup for cold gas-phase molecules and various laser spectroscopic methods, followed by chapters on investigation of specific molecular systems. Through a molecular-level approach and analysis by quantum chemical calculation, it is possible to learn how atomic and molecular-level interactions (van der Waals, hydrogen-bonding, and others) control the specific properties of molecules and clusters. Those properties include molecular recognition, induced fitting, chirality, proton and hydrogen transfer, isomerization, and catalytic reaction. The information will be applicable to the design of new types of functional molecules and nanoparticles in the broad area that includes applied chemistry, drug delivery systems, and catalysts.
