5,683 research outputs found

    Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide

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    This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond donors suggest a comstructural motif in all of the hydrogen bonded complexes. In particular, the arrangement of hydrogen bonds with TMAO\u27s oxygen atom appears to dictate the extended hydrogen bonded network and is likely the origin of TMAO\u27s osmolytic strength via the indirect effect. Hyperconjugation is observed in both TMAO and the hydrogen bonded solvent molecules. This charge transfer leads to blue shifts in TMAO\u27s C-H stretching modes and a dramatic red shift in methanol\u27s symmetric stretch. The effect is larger in the case of water and is likely the origin of TMAO\u27s blue shifted C-H stretching modes in solution

    THEORETICAL STUDIES OF BILIPROTEIN CHROMOPHORES AND RELATED BILE PIGMENTS BY MOLECULAR ORBITAL AND RAMACHANDRAN TYPE CALCULATIONS

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    Ramachandran calculations have been used to gain insight into steric hindrance in bile pigments related to biliprotein chromophores. The high optical activity of denatured phycocyanin, as compared to phycoerythrin, has been related to the asymmetric substitution at ring A, which shifts the equilibrium towards the P-helical form of the chromophore. Geometric effects on the electronic structures and transitions have then been studied by molecular orbital calculations for several conjugation systems including the chromophores of phycocyanin. phytochrome P,, cations, cation radicals and tautomeric forms. For these different chromophores some general trends can be deduced. For instance, for a given change in the gross shape (e.g. either unfolding of the molecule from a cyclic-helical to a fully extended geometry, or upon out-of-plane twists of the pyrrole ring A) of the molecules under study, the predicted absorption spectra all change in a simikar way. Nonetheless, there are characteristic distinctions between the different n-systems, both in the transition energies and the charge distribution, which can be related to their known differences in spectroscopic properties and their reactivity

    The Magnitude and Mechanism of Charge Enhancement of CH∙∙O H-bonds

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    Quantum calculations find that neutral methylamines and thioethers form complexes, with N-methylacetamide (NMA) as proton acceptor, with binding energies of 2–5 kcal/mol. This interaction is magnified by a factor of 4–9, bringing the binding energy up to as much as 20 kcal/mol, when a CH3+ group is added to the proton donor. Complexes prefer trifurcated arrangements, wherein three separate methyl groups donate a proton to the O acceptor. Binding energies lessen when the systems are immersed in solvents of increasing polarity, but the ionic complexes retain their favored status even in water. The binding energy is reduced when the methyl groups are replaced by longer alkyl chains. The proton acceptor prefers to associate with those CH groups that are as close as possible to the S/N center of the formal positive charge. A single linear CH··O hydrogen bond (H-bond) is less favorable than is trifurcation with three separate methyl groups. A trifurcated arrangement with three H atoms of the same methyl group is even less favorable. Various means of analysis, including NBO, SAPT, NMR, and electron density shifts, all identify the +CH··O interaction as a true H-bond

    Characterization Of Charge Accommodation In Biologically Important Hydrogen-Bonded Clusters

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    The underlying motivation of chemical physics and physical chemistry is to understand naturally occurring chemical and physical processes from the nanoscopic molecular level to the macroscopic condensed phase. Over the past half-century, experimentalists have developed a number of laser-based analytical techniques to bridge the gap between the bulk phase and the single molecule. Here, we look at bulk phase and gas phase clusters to compare the local hydrogen-bonded network. To better understand the role noncovalent interactions have on biologically relevant building blocks in a natural environment, we compare the microhydration of gas phase cluster ions to condensed phase spectra. The accommodation of excess charge plays an essential character in a number of biochemical processes involving peptides, nucleobases, aerosols, etc. A time-of-flight mass spectrometer was constructed to isolate discrete numbers of solute and solvent molecules for spectroscopic interrogation via light-matter interactions. We also employed high-resolution Raman spectroscopy for vibrational interrogation of temperature dependence in crystalline lattice modes as well as effects of surface-enhanced Plasresonances. Electronic structure methods were employed for accurate spectral assignment and identification of structural motifs

    Rhenium(V)-Carbohydrate Complexes with Amino Acids

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    This thesis is about the coordination chemistry of rhenium(V) with small biomolecules. Such rhenium complexes may be of medical significance in the field of radiopharmacy, since radioactive isotopes such as 186Re or 188Re are used for the diagnosis or treatment of tumors. But fundamental research is still necessary for the attachment of radiometals to biologically active molecules. Most rhenium(V)-based radiopharmaceuticals lack stability (at physiological conditions) or selectivity (in terms of targeting cells, or in terms of preparing an exactly defined agent). In order to meet these requirements, a library of ligands was scanned to synthesize kinetically inert mixed-ligand rhenium(V) complexes. Most of the prepared complexes (22 out of 28) were built with tri- and bidentate chelating ligands (“3 + 2” approach). They were studied by means of single-crystal X-ray diffraction, NMR spectroscopy, mass spectrometry, elemental analysis and other methods. As tridentate chelators, nitrogen containing compounds such as diethylenetriamine, rac-2,3-diaminopropionic acid, L-histidine, L-carnosine and other ligands based on amino acids were used. As bidentate chelators, an oxygen donor library was used, covering simple diols such as ethanediol or anhydroerythritol, and more complex molecules such as nucleosides, pyranosides, mono- and disaccharides or glycoside antibiotics. The optimum was found for a compound derived from the reducing disaccharide D-isomaltose and the dipeptide L-carnosine. It was possible to transfer the synthesis from standard laboratory conditions (millimolar concentration range, methanol as solvent, alkaline pH) to labeling experiments with 188Re (nanomolar concentration range, water as solvent, physiological pH). With this work, the chemistry of coordination compounds with rhenium(V) is extended to physiological conditions and the synthesized compounds are promising candidates for prospective works in the field of radiopharmacy

    Definition of the Pnictogen Bond: A Perspective

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    This article proposes a definition for the term pnictogen bond and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intra-molecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.Comment: 15 page

    Computational Study About Noncovalent Bonding Systems Involving Halogen, Chalcogen and Pnicogen Bonds

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    First terms used in this thesis are introduced and defined as follows. In the periodic table, the elements in the 17th column are named halogen including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I). The elements in the 16th column are named chalcogen including oxygen (O), sulfur (S), selenium (Se) and tellurium (Te). The elements in the 15th column are named pnicogen including nitrogen (N), phosphorus (P), arsenic (As) and antimony (Sb). After hydrogen bonds (B-H⋅⋅⋅B) are well studied and understood by scientists and researchers, halogen bonds (R-X⋅⋅⋅B) have drawn attention due to the similarities in bonding format and geometries. However, it is not straightforward to understand how the overall negative halogen atoms interact with the electronegative chemical group, which is usually a Lewis base until scientists proved the existence of the positive region surrounding the halogen atom X directly opposite the R group by Molecular Electrostatic Potential analysis. This thesis studied the detailed structural, geometric and spectroscopic features quantitatively by computational chemistry. The research studied the halogen transfer in symmetric (between two same molecules) and asymmetric systems (between two different molecules). In either case, the potential contains a single symmetric well for short halogen bond length and transferred to a double well when the distance was increased. Furthermore, the partial transfer calculations of halogen as bridging atom between two molecules suggests the degree of halogen transfer to form an ion pair is small even when a strong acid is combined with a strong base. Moreover, the thesis extended the application of Badger-Bauer rules from hydrogen bonds to halogen, chalcogen and pnicogen bonds. Badger-Bauer rules states the spectroscopic change were linearly related to the bond strength of hydrogen bonds. The theory extension will improve the understanding of bond strength of a specific bond in the complicated systems by detecting the spectroscopic change

    Bioinorganic Chemistry

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    This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry

    Effects of Nonionic Surfactant Mixtures on Water Alignment at the Air-Water Interface

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