Download or read book Gas phase Non covalent Complex written by Xin Cong and published by . This book was released on 2006 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Non covalent Interactions in the Gas Phase written by Jeremy Thomas O'Brien and published by . This book was released on 2012 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mass Spectrometry of Non Covalent Complexes written by Christoph A. Schalley and published by John Wiley & Sons. This book was released on 2009-09-08 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: Details the many benefits of applying mass spectrometry to supramolecular chemistry Except as a method for the most basic measurements, mass spectrometry (MS) has long been considered incompatible with supramolecular chemistry. Yet, with today's methods, the disconnect between these two fields is not warranted. Mass Spectrometry and Gas-Phase Chemistry of Non-Covalent Complexes provides a convincing look at how modern MS techniques offer supramolecular chemists a powerful investigatory toolset. Bringing the two fields together in an interdisciplinary manner, this reference details the many different topics associated with the study of non-covalent complexes in the gas phase. The text begins with brief introductions to supramolecular chemistry and such relevant mass spectrometric methods as ionization techniques, analyzers, and tandem MS experiments. The coverage continues with: How the analyte's transition into the gas phase changes covalent bonding How limitations and pitfalls in analytical methods may produce data misinterpretations Artificial supramolecular aggregates and their examination Biomolecules, their complexes, and their examination After the general remarks making up the first section of the book, the following sections describe specific experimental procedures and are illustrated with numerous examples and short tutorials. Detailed citations end each chapter. Mass spectrometrists, supramolecular chemists, students in these fields, and interested readers from other disciplines involving the study of non-covalent bonds will all value Mass Spectrometry and Gas-Phase Chemistry of Non-Covalent Complexes as an innovative and practical resource.

Download or read book Non covalent Interactions written by Pavel Hobza and published by Royal Society of Chemistry. This book was released on 2010 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Co-authored by an experimentalist (Klaus M3ller-Dethlefs ) and theoretician (Pavel Hobza), the aim of this book is to provide a general introduction into the science behind non-covalent interactions and molecular complexes using some important experimental and theoretical methods and approaches.

Download or read book Gas phase Reactivity Studies of Non covalent Complexes Diazonium Ions and Grignard Reagents written by Ana K. Vrkic and published by . This book was released on 2004 with total page 946 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Recognition in Gas Phase written by Andrey Dyachenko and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biomolecules and Their Noncovalent Complexes in the Gas Phase written by Rebecca Ann Jockusch and published by . This book was released on 2001 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Structural Influences of Noncovalent Interactions in the Gas Phase written by Terrence Chang and published by . This book was released on 2014 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt: The physical properties of molecules in solution, such as basicity and structure, depend on the cooperation and competition of noncovalent intra- and intermolecular interactions. Studying these interactions in the condensed phase is made difficult by the presence of competing influences from counterions and impurities. In the gas phase, however, specific ions, ion complexes and hydration states can be isolated and studied by Fourier transform mass spectrometry coupled with infrared (IR) laser spectroscopy. Using these two techniques, it is possible to isolate specific ions before inducing dissociation via absorption of IR photons. The extent of absorption at a given wavelength correlates to the relative abundance of product ions produced via dissociation, which can be measured using mass spectrometry. The absorption of IR photons only occurs at specific wavelengths depending on which functional groups are present and how their vibrational modes are influenced by interactions such as hydrogen bonding. Structural information is obtained from these spectra by interpreting the presence of certain bands and their frequencies. In addition, information can also be obtained by comparing the spectra from ions of interest to the spectra of reference ions, with known structures, or the simulated spectra of computed geometries. These types of studies provide valuable insight into how noncovalent interactions govern the structure of biomolecules and hydrogen-bonded networks. This dissertation reports experiments utilizing IR spectroscopy to study how water-ion interactions can affect both the structure of an ion solvated by an aqueous nanodrop as well as the hydrogen-bonding network of the nanodrop itself. In addition, the structural effects of ion-peptide interactions, which are relevant to understanding how ions influence biological processes, are also investigated. In order to study the ability of water to stabilize protonation sites on larger molecules, I investigated the influence of sequential hydration on the structure of protonated p-aminobenzoic acid (PABAH+), which has different preferred aqueous solution and gas-phase protonation sites. The preferred protonation site of PABA is the amine in aqueous solution, but the preferred protonation site is the carbonyl O atom of the carboxylic acid in the gas phase. The spectrum of PABAH+*(H2O)1 contains an absorption band at a particular photon energy indicating that protonation occurs at the carboxylic acid, i.e. there is a spectroscopic signature for the O-protonated structure. This absorption band persists for PABAH+*(H2O)2-6, indicating that these ions have a population of O-protonated isomers as well. Spectra for PABAH+*(H2O)6 are also consistent with presence of a second isomer, in which the amine is protonated. These results indicate that PABAH+ exists in the preferred gas-phase structure for PABAH+*(H2O)1-6, but there is a transition to the preferred solution-phase structure when the ion is solvated by six or more water molecules. In isolation, the excess charge associated with protonation at the carbonyl O atom of the carboxylic acid can be resonantly stabilized and delocalized into the phenyl ring and amine. When six or more water molecules are attached, however, a more favorable hydrogen-bonding network can be formed at the protonated amine than at the carboxylic acid. In contrast to PABAH+, protonation for m-aminobenzoic acid (MABA) occurs at the amine site even when solvated by only one water molecule due to orientation of the amine and carboxylic acid group. This orientation prevents the positive charge from being delocalized into the amine. Thus, MABAH+ serves as an ideal model for the solvation of the N- and C-termini of a protonated amino acid, for which the N- and C-termini typically interact with each other. The measured spectra for MABAH+*(H2O)1,2 are consistent with the attachment of water to a H atom of the protonated amine. For MABAH+*(H2O)3, the measured spectrum indicates that the dominant isomer has a hydrogen-bonded water bridge between the amine and carbonyl O atom of the carboxylic acid. This result indicates that the formation of this water bridge is more energetically favorable than the formation of a third ionic hydrogen bond to the amine group. The spectra for MABAH+*(H2O)n also indicate that water molecules attach to the carboxylic acid H atom, i.e. the ion is fully hydrogen-bonded when there are ≥6 water molecules attached. Ion spectroscopy can also be used to study how ion-water interactions influence hydration structures. Certain positive ions are known to induce cage-like clathrate structures when hydrated by 20 water molecules. The hydration of NH4+ as well as selected, protonated primary, secondary and tertiary amines solvated by 19 - 21 water molecules was investigated in order to elucidate details about how amines can stabilize clathrate structures. The spectra of NH4+ as well as monomethyl-, n-heptyl-, and tert-butylammonium+ with 20 water molecules attached are consistent with the nearly exclusive presence of clathrate structures, whereas nonclathrate structures are present for the more highly substituted amines. By comparison, nonclathrate structures are observed for all ions when 19 or 21 water molecules are attached. Spectroscopic evidence for clathrate structures for NH4+*(H2O)20 has been previously reported, but the location of the ion, whether at the surface or the interior, was difficult to determine based on the IR spectrum of this ion alone. Thus, the spectra of NH4+, monomethyl- and n-heptylammonium+ solvated by 20 water molecules were compared to those for Rb+ and tert-butylammonium+, which serve as references for clathrate structures with the ion located in the interior or at the surface, respectively. These comparisons indicate that NH4+ goes to the interior, whereas protonated primary amines are located at the surface, irrespective of the size of the alkyl group. In addition to ion-water interactions, ion-biomolecule interactions can also be probed by ion spectroscopy. Although there are several studies that have used ion spectroscopy to investigate cations coordinated to amino acids and peptides, there are fewer studies focused on these same biomolecules complexed with anion adducts. The ions Gly3*X-, Ala3*X- and Leu3*X- (X = Cl, Br and I) were studied in order to investigate how the size of anion adducts and alkyl side chains influence the coordination of halide anions to aliphatic peptides. The spectra of Gly3*Cl-, Ala3*Cl- and Leu3*Cl- suggest that all three complexes adopt similar structures, where Cl- coordinates to the peptides by accepting three or four hydrogen bonds from the amides as well as the N- and C-termini. These results indicate that the size of the alkyl chain does not have a significant influence on the coordination geometry of these complexes. These structures are "inverted" in comparison to previously reported structures for Gly3*Na+ and Ala3*Na+, where the Na+ coordinates to lone pair electrons of the N atom of the N-terminus, or the carbonyl O atoms of the amides and C-terminus. The spectra of Gly3*X-, Ala3*X- and Leu3*X- each appear similar to each other within each peptide, indicating that the size of the anion does not significantly affect the coordination geometry.

Download or read book Non covalent Interactions written by James Stephen Prell and published by . This book was released on 2011 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experiments investigating the role of non-covalent interactions in the structure, properties, and reactivity of gas-phase ion-biomolecule, ion-water, and water-biomolecule complexes in the gas phase are presented and discussed in this dissertation. Ions generated using electrospray ionization and trapped using Fourier transform ion cyclotron resonance mass spectrometers at the University of California, Berkeley, and the FOM Institute for Plasma Physics Rijnhuizen in Nieuwegein, The Netherlands, are probed using infrared photodissociation/infrared multiple photon dissociation (IRPD/IRMPD) spectroscopy and kinetics and electron capture dissociation. IRMPD spectra of alkali metal cationized dipeptides, protonated dipeptides, and trivalent lanthanide cationized polypeptides reported here reveal the role of ion size, formal charge site geometry, peptide sequence, gas-phase basicity, and competition between carbonyl groups and aromatic groups in the structures of these complexes. IRPD spectra of hydrated hydrophobic ions in the gas phase reveal a hydrogen bonding motif that contrasts strongly with those typically seen for more strongly hydrated ions. The role of ion charge state and size in the structures of gas-phase "nanodrops" is discussed based on their IRPD spectra and a computationally inexpensive point-charge model, as well as the dependence of these spectra on the electric field of the ion. These results show that ions can intrinsically affect the hydrogen bond structure of the water network out to three or more solvation shells, in contrast to many recent reports that only the first solvation shell is affected for ions in bulk solution. A new method using IRPD/IRMPD kinetics is demonstrated for directly measuring relative populations of spectroscopically distinguishable ion isomers, and a method for extending IRPD spectroscopic techniques to extensively hydrated ions that dissociate quickly is illustrated. This photodissociation kinetic method is demonstrated for several ion-biomolecule complexes and hydrated biomolecular ions, and relative Gibbs free energies, entropies, and enthalpies for nearly isoenergetic thermal ion populations are obtained with unprecedented precision. Ion nanocalorimetry is used to measure appearance energies for products of the exothermic reaction of a hydrated, doubly protonated dipeptide in the gas phase with a low-energy free electron, and nearly complete quenching of peptide fragmentation is achieved with a very small number of water molecules in the precursor ion complex.

Download or read book Non Covalent Interactions written by Pavel Hobza and published by Royal Society of Chemistry. This book was released on 2009-11-18 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to understand the main aspects of non-covalent chemistry (mainly in the gas phase) and specifically compares the experimental and theoretical data available for non-covalent complexes and subsequent problems associated with this comparison. The book is authored by an experimentalist (KMD) and theorist (PH), and their main philosophy in writing together is that any book on non-covalent interactions cannot be limited either to theory or experiment. Both approaches are nowadays so closely connected that one cannot exist without the other and vice versa and their mutual connection provides the consistent description of non-covalent processes in our world. This book will be of great assistance to researchers engaged in both theoretical and experimental aspects of non-covalent bonding and in macro- and supermolecular chemistry.

Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-03-02 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.

Download or read book Nucleic Acids in the Gas Phase written by Valérie Gabelica and published by Springer. This book was released on 2014-07-28 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives physical chemists a broader view of potential biological applications of their techniques for the study of nucleic acids in the gas phase. It provides organic chemists, biophysicists, and pharmacologists with an introduction to new techniques they can use to find the answers to yet unsolved questions. Laboratory sciences have bloomed with a variety of techniques to decipher the properties of the molecules of life. This volume introduces techniques used to investigate the properties of nucleic acids in the absence of solvent. It highlights the specificities pertaining to the studies of nucleic acids, although some of the techniques can similarly be applied to the study of other biomolecules, like proteins. The first part of the book introduces the techniques, from the transfer of nucleic acids to the gas-phase, to their detailed physico-chemical investigation. Each chapter is devoted to a specific molecular property, and illustrates how various approaches (experimental and theoretical) can be combined for the interpretation. The second part of the book is devoted to applying the gas-phase approaches to solve specific questions related to the biophysics, biochemistry or pharmacology of nucleic acids.

Download or read book Molecular Biophysics for the Life Sciences written by Norma Allewell and published by Springer Science & Business Media. This book was released on 2013-09-28 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides an overview of the development and scope of molecular biophysics and in-depth discussions of the major experimental methods that enable biological macromolecules to be studied at atomic resolution. It also reviews the physical chemical concepts that are needed to interpret the experimental results and to understand how the structure, dynamics, and physical properties of biological macromolecules enable them to perform their biological functions. Reviews of research on three disparate biomolecular machines—DNA helicases, ATP synthases, and myosin--illustrate how the combination of theory and experiment leads to new insights and new questions.

Download or read book Integration of structural biology data in lead drug discovery and optimization written by Marco Nardini and published by Frontiers Media SA. This book was released on 2023-03-03 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biophysical Approaches Determining Ligand Binding to Biomolecular Targets written by Alberto Podjarny and published by Royal Society of Chemistry. This book was released on 2011-04-01 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: The binding of small ligands to biological molecules is central to most aspects of biological function. The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. These methods have received increasing attention with the growth in more rational approaches to drug discovery and design. This book reviews the latest advances in the application of biophysics to the study of ligand binding. It provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand their binding mechanisms. Particular emphasis is given to the combined use of different techniques and their relative strengths and weaknesses. Consistency in the way each technique is described makes it easy for readers to select the most suitable protocol for their research. The introduction explains why some techniques are more suitable than others and emphasizes the possible synergies between them. The following chapters, all written by a specialist in the particular technique, focus on each method individually. The book finishes by describing how several complimentary techniques can be used together for maximum effectiveness. This book is suitable for biomolecular scientists at graduate or post-doctoral level in academia and industry. Biologists and chemists will also find it a useful introduction to the techniques available.

Download or read book Applied Electrospray Mass Spectrometry written by Birendra N. Pramanik and published by CRC Press. This book was released on 2002-02-28 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discussing strategies to determine the structure and machanisms of numerous compound classics, this book covers new chemical and elctrophoretic techniques for rapid sample preconcentration and separation. It summarizes breakthroughs in the theory and instrumentation of electrospray mass spectrometry in pharmaceutical and biomedical applications, provides practical examples for the characterization of peptides, proteins, and glycoproteins, includes applications in proteomics, combinatorial chemistry, and drug characterization. Topics include chemical and electrophoretic techniques for rapid sample preconcentration and separation, screening processes for proteins from libraries of compounds, protein folding and dynamics, and more.

Download or read book Mass Spectrometry in Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2005-05-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.