Download or read book Characterization of Several Small Biologically Relevant Molecules by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations written by Sabrina M. Martens and published by . This book was released on 2011 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt: Infrared multiple photon dissociation (IRMPD) spectroscopy has been coupled with electronic structure calculations in order to elucidate the structures of several small biological molecules including: uracil, 5-fluorouracil, 5-fluorocytosine, ferulic acid, and a number of their related analogs. IRMPD is a powerful technique, that when combined with electronic structure calculations can provide convincing evidence for the structural characterization of ions in the gas phase. Isomers of uracil and 5-fluorouracil (5-FU) have been characterized by calculations performed at the MP2(full)/aug-cc-pVTZ level of theory; however, infrared multiple photon dissociation spectroscopy experiments proved to be unsuccessful for these species. Geometry optimization and frequency calculations have isolated the dominant isomer(s) for neutral and deprotonated uracil and 5-fluorouracil, along with several cluster interactions involving water, methanol, ammonia, and methylamine. For both uracil and 5-FU, a single relevant neutral isomer was determined, with each isomer existing in the diketo, as opposed to the enol form. Following the deprotonation of this neutral isomer, both uracil and 5-FU were permitted to form anionic cluster ions with water, methanol, ammonia, or methylamine, and based on the relative Gibbs free energies (298 K) of the calculated isomers, relevant cluster interactions were determined. For each cluster, several sites of intramolecular interaction were found to exist; however, interaction at the site of deprotonation was the most favourable in every instance. Ionic hydrogen bond interactions have been found in several clusters formed by 5-fluorocytosine (5-FC).
Download or read book Mass selected Infrared Multiple photon Dissociation as a Structural Probe of Gaseous Ion molecule Complexes written by Richard Alexander Marta and published by . This book was released on 2009 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass-selected infrared multiple photon spectroscopy (IRMPD), Fourier transform ion cyclotron resonance (FT-ICR) kinetic experiments, RRKM and electronic structure calculations have been performed in order to propose a complex mechanism involving the formation of the proton-bound dimer of water (H5O2) from 1,1,3,3-tetrafluorodimethyl ether. It has been found that the reaction is facilitated by a series of sequential exothermic bimolecular ion-molecule reactions. Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF2, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF), to lose formyl fluoride and yield protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate which decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). The 1,4-elimination of hydrogen fluoride is found to be strongly supported by the results of both RRKM theory and electronic structure calculations. Lastly, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2 (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition and product species was obtained using MP2/aug-cc-pVQZ//MP2(full)/6-31G(d) level of theory.
Download or read book Chiral Analysis written by Kenneth W. Busch and published by Elsevier. This book was released on 2011-10-13 with total page 721 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chiral Analysis covers an important area of analytical chemistry of relevance to a wide variety of scientific professionals. The target audience is scientific professionals with an undergraduate background in chemistry or a related discipline, specifically organic chemists, researchers in drug discovery, pharmaceutical researchers involved with process analysis or combinatorial libraries, and graduate students in chemistry. Chapters have been written with the nonspecialist in mind so as to be self-contained. * Broad coverage - spectroscopic and separation methods covered in a single volume * Up-to-date and detailed review of the various techniques available and/or under development in this field * Contributions from leading experts in the field
Download or read book Chemical Characterization of Mass selected Ions by Infrared Multiple Photon Dissociation Spectroscopy written by Warren K. Mino (Jr) and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Nonetheless, photodissociation of more strongly-bound ions is found to be much more challenging. A custom-built mass spectrometer is presented, where the ions are irradiated in a reduced pressure (10−5 mbar) "Paul-type" quadrupole ion trap (QIT). The compact ion cloud is subjected to focused laser beams. Comparison of IRMPD of protonated tryptophan in the Penning and Paul traps shows that required laser irradiation times are considerably shorter and that weaker modes become visible. Furthermore, the fragmentation pathways of protonated tryptophan in collision-induced dissociation conditions are interrogated by IRMPD spectroscopy, assisted by quantum-chemical calculations. The loss of NH3 is shown to be mediated by a nucleophilic attack from carbon C3 on the indole side chain. The subsequent CH2CO loss product is also structurally characterized. These results demonstrate that strongly-bound ions and reaction products from collision-induced dissociation in particular, can now be routinely characterized by IRMPD spectroscopy using a benchtop infrared laser. It is expected that these developments will make the technique of IRMPD spectroscopy more accessible to the wider mass spectrometry community, as opposed to being limited to a few user facilities.
Download or read book Spectroscopy and Modeling of Biomolecular Building Blocks written by Jean-Pierre Schermann and published by Elsevier. This book was released on 2007-10-16 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Modeling of Biomolecular Building Blocks presents an overview of recent advances in the intertwining of the following research fields: photon and electron spectroscopy, quantum chemistry, modelling and mass-spectrometry. The coupling of these disciplines offers a new point of view to the understanding of isolated elementary building blocks of biomolecules and their assemblies. It allows the unambiguous separation between intrinsic properties of biomolecular systems and those induced by the presence of their environment. The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III). Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems. The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules. Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules Includes case studies of experimental investigations coupled to quantum or classical calculations
Download or read book Infrared Multiple photon Dissociation of Small Organic Sulfoxides written by Marko Peter Banjavčiʹc and published by . This book was released on 1999 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The infrared multiple-photon dissociation of several small organic sulfoxides was studied in order to provide some insight in the dissociative product channels for this class of molecules. Vibrational excitation was achieved with a TEA CO2 laser and photofragments were identified with a laser ionized time of light mass spectrometer. A beam of 10.5 eV photons generated in a static xenon gas tripling cell from a tightly focused Nd:YAG third harmonic beam of light was used to ionize the molecules and fragment species. The photoionization mass spectra were found to contain fewer fragmentation species than the corresponding electron impact ionization mass spectra. Numerous product species were observed from skeletal rearrangement reactions despite the lower level of energy excitation from the photoionization process. The infrared photolysis wavelength dependence of dimethyl sulfoxide indicated that the maximum abundance for the major fragmentation species occurred at (or near) 1085.8 cm−1. The major products at 1085.8 cm−1 were [H3CSO]+ and [CH3]+. Minor products were also observed at a higher output power threshold like the skeletal rearrangement species [H3CS]+ and [OCH3]+. With the infrared photolysis wavelength dependence of methyl phenyl sulfoxide, the major product species ([CH3]+ and [OSCH3]+) had a maximum abundance near 1086.9 cm−1 . Small mass fragment species (like [HCS]+, [C4H5]+ and [C4H3]+) had a maximum abundance near 1080 cm−1 while large mass fragment species ([C6H8S]+ and [C6H5SO]+) had a maximum abundance that was further red-shifted (1058.9 and 1050.4 cm−1 , respectively). The photolysis at 1085.8 cm−1 generated the high mass fragment species ([C6H5SO]+, [C6H8S]+ and [C5H5S]+) at all CO2 laser output powers but a plateau in the abundance was observed at higher output powers. The smaller mass fragmentation species only appeared after a threshold power was surpassed. The maximum abundance for the various fragmentation species of sec-butyl methyl sulfoxide occurred near 1072 cm−1. The CO2 laser output power dependence for the formation of the butane, butyl and butene ions indicated all three were generated at all output powers with an abundance plateau or decline occurring at higher output powers. Fragmentation species were observed from the butyl group primary products with the power threshold increasing for the sequentially smaller secondary species.
Download or read book Computational Chemistry Investigation of Gas phase Structures Infrared Spectroscopy and Dissociation Pathways of Isomeric Molecules written by Widana Kankanamge Dayangani Nirosha Kaushalya and published by . This book was released on 2020 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt: While chemical isomers typically have distinct properties, differentiating between them is often an analytical challenge, especially for mass spectrometric methods. Infrared multiple photon dissociation (IRMPD) spectroscopy and ion mobility spectrometry (IMS) can be useful in analysis of such isomeric compounds; however, experimental results alone do not directly provide in-depth structural information. In this thesis, computational chemistry is first used to explain experimental results and understand the conformational preference of the gas phase ions formed from the lithiation of cis-3, cis-4 and trans-4 hydroxyproline isomers and then used in a predictive manner to evaluate IRMPD spectroscopy and IMS as potential paths forward for the characterization of isomeric dye species. Finally, theoretical methods are used to begin to understand the dissociation pathways of lithiated hydroxyproline isomers in the gas phase, which is ongoing.
Download or read book Top Down Characterization of Proteins by Electron Capture Dissociation and Blackbody Infrared Radiative Dissociation Mass Spectrometry written by Ying Ge and published by . This book was released on 2002 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Infrared Multiple Photon Dissociation Spectroscopy on Biomolecular Ions written by Tjalling Sybren Joannes Antonius de Boer and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Use of Infrared Multiple Photon Dissociation and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry to Study the Thermochemical Dynamics of Dephosphorylation and the Spectral and Density Functional Theory Determined Structural Characteristics of Monosaccharide Isomers written by and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Photon (vibrationally resonant) induced dissociation or action spectra, spanning the C-H-and O-H stretch regions, were then acquired for four rubidium cation-bound glycosides. Comparison of the experimental and Density Functional Theory calculated spectra revealed a network of intermolecular hydrogen bonding and rubidium attachments that provided the means to differentiate D-glucoside and D-galactoside anomers in the O-H stretching region of the infrared spectrum. In the second project, two cw-CO2 lasers were also set up for gas-phase experiments. Dephosphorylation rate constants (at varying laser powers) were obtained for both positively and negatively charged phosphopeptide ions at three different wavelengths. In these experiments, the dissociation rate constants favored the negatively charged species at all wavelengths (a result of lower activation energies) as the overall Arrhenius activation energies were independent of vibrational mode intensities.
Download or read book Liquid Chromatography written by Salvatore Fanali and published by Elsevier. This book was released on 2017-06-23 with total page 840 pages. Available in PDF, EPUB and Kindle. Book excerpt: Liquid Chromatography: Applications, Second Edition,is a single source of authoritative information on all aspects of the practice of modern liquid chromatography. It gives those working in both academia and industry the opportunity to learn, refresh, and deepen their knowledge of the wide variety of applications in the field. In the years since the first edition was published, thousands of papers have been released on new achievements in liquid chromatography, including the development of new stationary phases, improvement of instrumentation, development of theory, and new applications in biomedicine, metabolomics, proteomics, foodomics, pharmaceuticals, and more. This second edition addresses these new developments with updated chapters from the most expert researchers in the field. Emphasizes the integration of chromatographic methods and sample preparation Explains how liquid chromatography is used in different industrial sectors Covers the most interesting and valuable applications in different fields, e.g., proteomic, metabolomics, foodomics, pollutants and contaminants, and drug analysis (forensic, toxicological, pharmaceutical, biomedical) Includes references and tables with commonly used data to facilitate research, practical work, comparison of results, and decision-making
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2007 with total page 960 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Infrared Multiple Photon Dissociation Mass Spectrometry of Monosaccharides Disaccharides Trisaccharides and Their Derivatives for Isomeric Differentiation written by Yanglan Tan and published by . This book was released on 2014 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sulfates which were structurally elucidated by IRMPD spectroscopy with a tunable OPO. The IRMPD spectra of monosaccharide derivative isomers displayed remarkable differences in the O-H and N-H stretching IR region. The results also suggested that gas-phase conformation, affected by ionization state or chemical modifications, exhibited diagnostic IR absorbances and characteristic photodissociation behavior. In Chapter 5, a top-down approach was employed to characterize isomeric variants of glucose-based trisaccharides. The trisaccharides were fragmented and mass selected to the key disaccharide fragments. The linkage and anomericity of the disaccharide substructures were then differentiated by wavelength-dependent IRMPD using the CO2 laser. On the basis of these results, variable-wavelength IRMPD provides a promising method to characterize carbohydrate structures and thus differentiate isomer variants by mass spectrometry.
Download or read book Energy Research Abstracts written by and published by . This book was released on 1985 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Scientific and Technical Aerospace Reports written by and published by . This book was released on with total page 1050 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Publications of the National Institute of Standards and Technology Catalog written by National Institute of Standards and Technology (U.S.) and published by . This book was released on 1983 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Polarization Dependent Two photon Absorption Properties of Chiral Molecules written by Carlos Toro and published by . This book was released on 2010 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecules that are non-superimposable on their mirror image are named chiral or optically active compound. Over the years, molecular chirality has played an essential role in the understanding of fundamental aspects associated the origin of life, drug and food technologies and, asymmetric catalysis, among others. Moreover, most of the groundbreaking discoveries and advances made in this field have happened due to the development of spectroscopic techniques based on the natural asymmetry of the enantiomers and their ability to preferentially absorb right or left polarized light. For instance, circular dichroism (CD), which measures the difference in absorption between these two states of polarized light, has emerged as one of the most useful spectroscopic methods to identify and characterize chiral compounds. Unfortunately, CD is based on linear absorption which, in most common organic molecules, takes place in the UV region of the spectrum where the majority of organic solvents absorb as well. This certainly imposes limitations in the indiscriminated applicability of this technique to the study of chiral chromophores of biological interest in non-aqueous solutions. Consequently, a systematic and comprehensive characterization of the electronic and optical properties of such molecular entities still remains a major issue to be addressed. On this regard, nonlinear optics offers new alternatives to overcome some of the shortcomings of the standard linear CD-based spectroscopy. In order to surmount the existent limitations in this field and deepen in the fundamental understanding of chiral systems, we have mainly directed the attention of our research to the experimental and theoretical study of the polarization dependent two-photon absorption (2PA) of several chiral azo-compounds and binaphthol derivatives in solution. The first part of this dissertation (Chapters I-IV) covers a full characterization of the linear and nonlinear optical properties of a series of non-chiral and chiral azo derivatives. The combination of experimental techniques such as absorption, fluorescence, excitation anisotropy, circular dichroism, two-photon absorption and two-photon absorption circular-linear dichroism in combination with density functional theory calculations allowed us to unambiguously distinguish and assign the spectral position of the main electronic transitions (n-[pi];* and [pi]-[pi]*) in azobenzene derivatives. Our results represent a major contribution to the understanding of the electronic structure of these organic chromophores which have been reported of potential interest in the design of optoelectronic devices. Then, Chapter V describes the development of a novel experimental technique called the synchronized double L-scan for the study of polarization dependent multiphoton absorption in chiral samples. The high sensitivity of this technique resides in the use of "twin" pulses to account for energy and mode fluctuations of the excitation pulse when determining absorption nonlinearities as a function of the light polarization. The robustness of this method was validated by measuring the first ever reported two-photon absorption circular dichroism (2PA-CD) spectrum on a chiral binaphthol derivative in solution. Finally, Chapters VI and VII compile an ample experimental and theoretical investigation of the chirality-dependent 2PA of axial enantiomers in solution. We combined the use of the synchronized double L-scan technique with state-of-the-art density functional theory calculations to provide a precise and reliable description of the contribution of the different electronic excited states to the 2PA-CD and 2PA-CLD spectra. Our findings are foreseen to have a tremendous impact in the comprehension of some of the most fundamental aspects of chiral phenomena.
