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 Study of the Interplay Among Non covalent Interactions in Structural Determination of Gas Phase Cluster Ions written by Charlotte Ann Corbett and published by . This book was released on 2001 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 Non covalent Interactions in the Synthesis and Design of New Compounds written by Abel M. Maharramov and published by John Wiley & Sons. This book was released on 2016-04-18 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to overview the role of non-covalent interactions, such as hydrogen and halogen bonding, π-π, π-anion and electrostatic interactions, hydrophobic effects and van der Waals forces in the synthesis of organic and inorganic compounds, as well as in design of new crystals and function materials. The proposed book should allow to combine, in a systematic way, recent advances on the application of non-covalent interactions in synthesis and design of new compounds and functional materials with significance in Inorganic, Organic, Coordination, Organometallic, Pharmaceutical, Biological and Material Chemistries. Therefore, it should present a multi- and interdisciplinary character assuring a rather broad scope. We believe it will be of interest to a wide range of academic and research staff concerning the synthesis of new compounds, catalysis and materials. Each chapter will be written by authors who are well known experts in their respective fields.
Download or read book Anion Sensing written by Eric V. Anslyn and published by Springer Science & Business Media. This book was released on 2005-05-06 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: with contributions by numerous experts
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 Serpin Structure and Evolution written by and published by Academic Press. This book was released on 2011-11-07 with total page 562 pages. Available in PDF, EPUB and Kindle. Book excerpt: Serpins are a group of proteins with similar structures that were first identified as a set of proteins able to inhibit proteases. This volume in the Methods in Enzymology series comprehensively covers this topic. With an international board of authors, this volume covers subjects such as Crystallography of serpins and serpin complexes, Serpins as hormone transporters, and Production of serpins using cell free systems. This volume in the Methods in Enzymology series comprehensively covers the topic of serpins With an international board of authors, this volume covers subjects such as Crystallography of serpins and serpin complexes, Serpins as hormone transporters, and Production of serpins using cell free systems
Download or read book Non covalent Interactions in Quantum Chemistry and Physics written by Alberto Otero de la Roza and published by Elsevier. This book was released on 2017-06-15 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: Non-covalent Interactions in Quantum Chemistry and Physics: Theory and Applications provides an entry point for newcomers and a standard reference for researchers publishing in the area of non-covalent interactions. Written by the leading experts in this field, the book enables experienced researchers to keep up with the most recent developments, emerging methods, and relevant applications. The book gives a comprehensive, in-depth overview of the available quantum-chemistry methods for intermolecular interactions and details the most relevant fields of application for those techniques. Theory and applications are put side-by-side, which allows the reader to gauge the strengths and weaknesses of different computational techniques. Summarizes the state-of-the-art in the computational intermolecular interactions field in a comprehensive work Introduces students and researchers from related fields to the topic of computational non-covalent interactions, providing a single unified source of information Presents the theoretical foundations of current quantum mechanical methods alongside a collection of examples on how they can be applied to solve practical problems
Download or read book Comprehensive Supramolecular Chemistry II written by George W. Gokel and published by Elsevier. This book was released on 2017-06-22 with total page 4627 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Supramolecular Chemistry II, Second Edition, Nine Volume Set is a ‘one-stop shop’ that covers supramolecular chemistry, a field that originated from the work of researchers in organic, inorganic and physical chemistry, with some biological influence. The original edition was structured to reflect, in part, the origin of the field. However, in the past two decades, the field has changed a great deal as reflected in this new work that covers the general principles of supramolecular chemistry and molecular recognition, experimental and computational methods in supramolecular chemistry, supramolecular receptors, dynamic supramolecular chemistry, supramolecular engineering, crystallographic (engineered) assemblies, sensors, imaging agents, devices and the latest in nanotechnology. Each section begins with an introduction by an expert in the field, who offers an initial perspective on the development of the field. Each article begins with outlining basic concepts before moving on to more advanced material. Contains content that begins with the basics before moving on to more complex concepts, making it suitable for advanced undergraduates as well as academic researchers Focuses on application of the theory in practice, with particular focus on areas that have gained increasing importance in the 21st century, including nanomedicine, nanotechnology and medicinal chemistry Fully rewritten to make a completely up-to-date reference work that covers all the major advances that have taken place since the First Edition published in 1996
Download or read book Noncovalent Forces written by Steve Scheiner and published by Springer. This book was released on 2015-04-16 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methods, and in particular quantum chemistry, have taken the lead in our growing understanding of noncovalent forces, as well as in their categorization. This volume describes the current state of the art in terms of what we now know, and the current questions requiring answers in the future. Topics range from very strong (ionic) to very weak (CH--π) interactions. In the intermediate regime, forces to be considered are H-bonds, particularly CH--O and OH--metal, halogen, chalcogen, pnicogen and tetrel bonds, aromatic stacking, dihydrogen bonds, and those involving radicals. Applications include drug development and predictions of crystal structure.
Download or read book An Experimental and Computational Study of Noncovalent Interactions in Gas Phase Ion Solvation written by Orlando Manuel Cabarcos and published by . This book was released on 1998 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mass Spectrometry written by Dominic M. Desiderio and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: In response to the growing use of mass spectrometry in the clinical and biomedical fields, this book collects recent research involving electrospray ionization, neuronal systems, and structural modifications of proteins. The significant advances in instrumentation, methodology, experimentation presented herein will serve to expand the current concept of clinical mass spectrometry.
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 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 Nuclear Magnetic Resonance written by Krystyna Kamienska-Trela and published by Royal Society of Chemistry. This book was released on 2012-03-12 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a spectroscopic method, nuclear magnetic resonance (NMR) has seen spectacular growth, both as a technique and in its applications. Today's applications of NMR span a wide range of scientific disciplines, from physics to biology to medicine. Each volume of Nuclear Magnetic Resonance comprises a combination of annual and biennial reports which together provide comprehensive coverage of the literature on this topic. This Specialist Periodical Report reflects the growing volume of published work involving NMR techniques and applications, in particular NMR of natural macromolecules, which is covered in two reports: NMR of Proteins and Nucleic Acids and NMR of Carbohydrates, Lipids and Membranes. In his foreword to the first volume, the then editor, Professor Robin Harris announced that the series would be a discussion on the phenomena of NMR and that articles will be critical surveys of the literature. This has certainly remained the case throughout the series, and in line with its predecessors, Volume 40 aims to provide a comprehensive coverage of the relevant NMR literature. For the current volume this relates to publications appearing between June 2009 and May 2010 (the nominal period of coverage in volume 1 was July 1970 to June 1971). Compared to the previous volume there are some new members of the reporting team. Theoretical Aspects of Spin-Spin Couplings are covered by J. Jazwinski, while E. Swiezewska and J.Wojcik provide an account of NMR of Carbohydrates, Lipids and Membranes.
