Intramolecular Hydrogen Bonding 2021

This book describes the results of both theoretical and experimental research on many topical issues in intramolecular hydrogen bonding. Its great advantage is that the presented research results have been obtained using many different techniques. Therefore, it is an excellent review of these methods, while showing their applicability to the current scientific issues regarding intramolecular hydrogen bonds. The experimental techniques used include X-ray diffraction, infrared and Raman spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), nuclear quadrupole resonance spectroscopy (NQR), incoherent inelastic neutron scattering (IINS), and differential scanning calorimetry (DSC). The solvatochromic and luminescent studies are also described. On the other hand, theoretical research is based on ab initio calculations and the Car–Parrinello Molecular Dynamics (CPMD). In the latter case, a description of nuclear quantum effects (NQE) is also possible. This book also demonstrates the use of theoretical methods such as Quantum Theory of Atoms in Molecules (QTAIM), Interacting Quantum Atoms (IQA), Natural Bond Orbital (NBO), Non-Covalent Interactions (NCI) index, Molecular Tailoring Approach (MTA), and many others

A Perspective Distilled from Seventy Years of Research

Physical organic chemistry might be regarded as officially recognized as a distinct discipline through the publication of L. P. Hammett’s book of that title, although substantial earlier work can be traced back to the turn of the 20th century. Many of the instrumental tools that helped the discipline develop in so many different ways began to appear in the late thirties and during World War II and were soon built to be increasingly operated in the “hands-on” mode. This development became very popular in academia, where instruments are not operated for you by an expert, but even if you are an undergraduate, you can more or less be the expert yourself and take many varieties of data on instruments usually available on a 24 h basis. It has been my privilege and joy to begin research in chemistry just as these waves of change began to grow and to savor the great contribution that the new methods, such as measurement of 14C, UV−vis, IR, NMR, and hands-on use of computers, made in facilitating our research programs at MIT and later at Caltech. Among those programs, which will be discussed, were 14C tracing of carbocation rearrangements and benzyne formation, electrical effects of substituents, Grignard reagents, synthesis of small-ring compounds, (2 + 2) cycloaddition reactions of halogenated ethylenes, assisting in development of ^(19)F, ^(13)C, and ^(15)N NMR for conformational analysis, other structural, kinetic, and tracer studies, as well as helping through textbooks to bring Hückel MO theory and the elements of NMR to familiarity for organic chemists. From the very beginning of my research career, I have been the beneficiary of personal mentoring which has been very crucial to my success in research and is an important theme in what follows

Speciation of organoarsenicals in aqueous solutions by Raman spectrometry and quantum chemical calculations

.Knowledge about the existence and stability of different species of organoarsenicals in solution is of the most significant interest for fields so different as chemical, environmental, biological, toxicological and forensic. This work provides a comparative evaluation of the Raman spectra of four organoarsenicals (o-arsanilic acid, p-arsanilic acid, roxarsone and cacodylic acid) in aqueous solutions under acidic, neutral and alkaline conditions. Speciation of some of these organoarsenicals is possible by Raman spectrometry at different selected pHs. Further, we examine the proficiency of computational chemistry to obtain the theoretical Raman spectra of the four organoarsenicals compounds. To this end, we employ a computational protocol that includes explicit water molecules and conformational sampling, finding that the calculated organoarsenicals spectra agree reasonably well with those experimentally obtained in an aqueous solution in the whole pH range covered. Finally, we highlight the effectiveness of quantum chemical calculations to identify organoarsenicals in an aqueous solution.S

Proceedings of the Thirteenth International Conference on Time-Resolved Vibrational Spectroscopy

The thirteenth meeting in a long-standing series of “Time-Resolved Vibrational Spectroscopy” (TRVS) conferences was held May 19th to 25th at the Kardinal Döpfner Haus in Freising, Germany, organized by the two Munich Universities - Ludwig-Maximilians-Universität and Technische Universität München. This international conference continues the illustrious tradition of the original in 1982, which took place in Lake Placid, NY. The series of meetings was initiated by leading, world-renowned experts in the field of ultrafast laser spectroscopy, and is still guided by its founder, Prof. George Atkinson (University of Arizona and Science and Technology Advisor to the Secretary of State). In its current format, the conference contributes to traditional areas of time resolved vibrational spectroscopies including infrared, Raman and related laser methods. It combines them with the most recent developments to gain new information for research and novel technical applications. The scientific program addressed basic science, applied research and advancing novel commercial applications. The thirteenth conference on Time Resolved Vibrational Spectroscopy promoted science in the areas of physics, chemistry and biology with a strong focus on biochemistry and material science. Vibrational spectra are molecule- and bond-specific. Thus, time-resolved vibrational studies provide detailed structural and kinetic information about primary dynamical processes on the picometer length scale. From this perspective, the goal of achieving a complete understanding of complex chemical and physical processes on the molecular level is well pursued by the recent progress in experimental and theoretical vibrational studies. These proceedings collect research papers presented at the TRVS XIII in Freising, German

Probing the Structure and Photophysics of Porphyrinoid Systems for Functional Materials

Porphyrins (Pors) and their many cousins, including phthalocyanines (Pcs), corroles (Cors), subphthalocyanines (SubPcs), porphyrazines (Pzs), and naphthalocyanines (NPcs), play amazingly diverse roles in biological and non-biological systems because of their unique and tunable physical and chemical properties. These compounds, collectively known as porphyrinoids, can be employed in any number of functional devices that have the potential to address the challenges of modern society. Their incorporation into such devices, however, depends on many structural factors that must be well understood and carefully controlled in order to achieve the desired behavior. Self-assembly and self-organization are key processes for developing these new technologies, as they will allow for inexpensive, efficient, and scalable designs. The overall goal of this dissertation is to elucidate and ultimately control the interplay between the hierarchical structure and the photophysical properties of these kinds of systems. This includes several case studies concerning the design and spectroscopic analysis of supramolecular systems formed through simple, scalable synthetic methods. We also present detailed experimental and computational studies on some porphyrin and phthalocyanine compounds that provide evidence for fundamental changes in their molecular structure. In addition to their impact on the photophysics, these changes also have implications for the organization of these molecules into higher order materials and devices. It is our hope that these findings will help to drive chemists and engineers to look more closely at every level of hierarchical structure in the search for the next generation of advanced materials

Computational Approach to Aluminum Biochemistry and Development of New Chelation Strategies

299 p.DIPC:Donostia International Physics Center SmartLigs Bioinformatica Universidade do Port

Conformational studies on some nitrogen containing compounds.

Some N.M.R. techniques used in conformational analysis, the principal factors peculiar to heterocyclic conformational analysis, and the background to conformational effects in alkyl substituted hydroxylamines are reviewed. The synthesis of N-carbethoxy- and N-methyl-tetrahydro-1,2- oxazines is discussed. The mechanism of formation of N-carbethoxytetrahydro-1,2-oxazines from the condensation of 1,4 dibromo-alkanes with N-hydroxyurethan under basic conditions is found to proceed by initial attack of the oxy-anion tautomer, formed from N-hydroxyurethane, on the more reactive bromo-substituted carbon. The preferred conformations of several N-methyl-tetrahydro1,2-oxazines are deduced from their N.M.R. spectra, and a measure of the free energy difference between the equatorial and axial positions for a methyl group substituted on any one of the four ring carbon atoms is estimated. A qualitative rationalisation of the variation in free energy difference with the point of substitution is given. The N-methyl group is found to strongly prefer the equatorial position. The stereochemistry of the B/C ring junction of the alkaloid geneserine is deduced from its N.M.R. spectra, and is found to be cis. The conformational equilibrium at nitrogen in some N,N-dimethyl-hexahydropyrimidines is studied by N.M.R. For N,N-dimethyl hexahydropyrimidine and l,3,5-trimethyl-hexahydropyrimidine a free energy difference between an equatorial and axial N-methyl group of ca. 0.5 kcal./mol. is found. A new method of measuring rate constants by N.M.R. using a small digital computer is tested by studying the barriers to internal rotation in the N,N-dimethyl amides of the three pyridine carboxylic acids. The method is found to be satisfactory, and the free energies of activation for the rotational process at 25°C are 17.9 kcal./mol. for N ,N-dimethyl picolinamide, 15,9 kcal./mol. for N,N-dimethyl nicotinamide, and 16.6 kcal./mol. for N,N-dimethyl isonicotinamide. The error on these values is considered to be less than 0.1 kcal./mol

DENSITY FUNCTIONAL CALCULATIONS OF BACKBONE 15N CHEMICAL SHIELDINGS IN PEPTIDES AND PROTEINS

In this dissertation, we describe computational and theoretical study of backbone 15N chemical shieldings in peptides and proteins. Comprehensive density functional calculations have been performed on systems of different complexity, ranging from model dipeptides to real proteins and protein complexes. We begin with examining the effects of solvation, hydrogen bonding, backbone conformation, and the side chain identity on 15N chemical shielding in proteins by density functional calculations. N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) were used as model systems for this purpose. The conducting polarizable continuum model was employed to include the effect of solvent in the calculations. We show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard &beta-sheet and standard &alpha-helical conformations ranges from 0.8 ppm to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins. Having applied density functional calculation successfully to model peptides, we develop a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone 15N in a protein. We present the application to selected &alpha-helical and &beta-sheet residues of protein G. The role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field is analyzed. We show that the dipole moment of the &alpha-helix can cause significant deshielding of 15N; therefore, it needs to be considered when calculating 15N chemical shielding. We emphasize the importance of including interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. For &alpha-helical residues, chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data. We also performed computational modeling of the chemical shift perturbations occurring upon protein-protein or protein-ligand binding. We show that the chemical shift perturbations in ubiquitin upon dimer formation can be explained qualitatively through computation. This dissertation hence demonstrates that quantum chemical calculations can be successfully used to obtain a fundamental understanding of the relationship between chemical shielding and the surrounding protein environment for the elusive case of 15N and therefore enhance the role of 15N chemical shift measurements in the analysis of protein structure and dynamics

A combined computational and NMR-spectroscopic approach for tautomer elucidation under extreme conditions towards investigating the robustness of genetic codes

The goal of this work was to establish a combined computational and experimental workflow for the prediction of tautomeric ratios of small molecules in solution under various environmental conditions. Quantum chemical (QC) calculations using the embedded cluster reference interaction site model (EC-RISM), which takes into account the solvent structure and the mutual polarization of solute and solvent and is able to incorporate environmental effects via appropriate correction terms, form the computational part of this workflow, NMR experiments the experimental part. Benchmarking of EC-RISM for the prediction of tautomeric ratios was performed using the SAMPL2 dataset and histamine, for which the workflow was extensively tested at ambient conditions and used to identify the nuclei most sensitive to tautomerism. This system was also used to develop an EC-RISM based force field (FF) reparametrization workflow. A temperature-dependent correction term for EC-RISM was developed, benchmarked, and used in conjunction with a pressure-dependent correction term to calculate NMR chemical shifts. Various computational NMR referencing methods were developed using reference shielding constants of trimethylsilylpropanesulfonate (DSS) and ammonia and their performance was tested on N-methyl-acetamide (NMA) and trimethylamine-N-oxide (TMAO). The tautomeric ratios of nucleobases were calculated at different pressures and temperatures for the natural species and the hachimoji expanded genetic alphabet. Initial steps were also taken towards the prediction of the tautomeric ratios of larger nucleic acid building blocks such as nucleotides