Study of the Interplay Among Non-covalent Interactions in Structural Determination of Gas Phase Cluster Ions PDF Download

Author: Charlotte Ann Corbett
Publisher:
ISBN:
Category :
Languages : en
Pages : 600

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Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 868

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Author: Pavel Hobza
Publisher: Royal Society of Chemistry
ISBN: 1847558534
Category : Science
Languages : en
Pages : 239

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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.

Author: Terrence Chang
Publisher:
ISBN:
Category :
Languages : en
Pages : 109

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Book Description
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.

Author:
Publisher:
ISBN:
Category : Dissertation abstracts
Languages : en
Pages : 776

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Author: Adam C. Pearcy
Publisher:
ISBN:
Category : Mass spectrometry
Languages : en
Pages :

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Gas phase molecular clusters present an ideal medium for observing factors that drive chemical reactions without outside interferences from excessive solvent molecules. Introducing an ion into the cluster promotes ion-molecule interactions that may manifest in a variety of non-covalent or even covalent binding motifs and are of significant importance in many fields including atmospheric and astronomical sciences. For instance, in outer space, molecules are subject to ionizing radiation where ion-molecule reactions become increasingly competitive to molecule-molecule interactions. To elucidate individual ion-molecule interaction information, mass spectrometry was used in conjunction with appropriate theoretical calculations. Three main categories of experiment were conducted in this dissertation. The first of which were thermochemical equilibrium measurements where an ion was introduced to an ion mobility drift cell wherein thermalizing collisions occur with helium buffer gas facilitating a reversible reaction with a neutral molecule allowing the standard changes in enthalpy and entropy to be determined. The second type of experiment was an ion mobility experiment where an ionized homo- or hetero-cluster was injected into the drift cell at specific conditions allowing the reduced mobility and collisional cross-section to be evaluated. Thirdly, kinetics measurements were taken following injection of an ion into the drift cell were an irreversible reaction ensued with the neutral species hindering equilibrium, but prompting rate constant assessment. Previous research has laid the groundwork for this dissertation as the results and discussion contained herein will build upon existing data while maintaining originality. For example, past work has given support for ion-molecule reactions involving precursor species such as acetylene and hydrogen cyanide to form more complex organics, perhaps leading to biologically relevant species. The chemical systems studied for this research are either ionized substituted benzenes like phenylacetylene and benzonitrile or polycyclic aromatic nitrogen-containing hydrocarbons like quinoline and quinoxaline interacting with a variety of neutral species. Hydrogen bonding and its many sub-sections are of the utmost importance to the kinds of reactions studied here. Past work has shown the tendency of organic radical cations to form conventional and unconventional ionic hydrogen bonds with gas phase solvents. Other non-covalent modes of interaction have also been detected in addition to the formation of covalently bound species. Gas phase reactions studied here will explore, via mass-selected ion mobility, reversible and irreversible reactions leading to binding enthalpy and entropy and rate constant determination, respectively, in addition to collisional cross-section determination.

Author:
Publisher: Elsevier
ISBN: 0080471862
Category : Science
Languages : en
Pages : 325

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Advances in Physical Organic Chemistry provides the chemical community with authoritative and critical assessments of the many aspects of physical organic chemistry. The field is a rapidly developing one, with results and methodologies finding application from biology to solid state physics.

Author: James Stephen Prell
Publisher:
ISBN:
Category :
Languages : en
Pages : 474

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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.

Author: Christoph A. Schalley
Publisher: John Wiley & Sons
ISBN: 0470131152
Category : Science
Languages : en
Pages : 593

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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.

Author: Alisa G. Woods
Publisher: Springer
ISBN: 3030159507
Category : Science
Languages : en
Pages : 813

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This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease, and psychiatry. Additional chapters focus on methodology, technologies and instrumentation, as well as on analysis of protein-protein interactions, protein quantitation, and protein post-translational modifications. Various omics fields such as proteomics, metabolomics, glycomics, lipidomics, and adductomics are also covered. Applications of mass spectrometry in biotechnological and pharmaceutical industry are also discussed. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research, but also to initiate and improve their own work. This book acts as a technical guide as well as a conceptual guide to the newest information in this exciting field.