Summaries of FY 1997 Research in the Chemical Sciences

The objective of this program is to expand, through support of basic research, knowledge of various areas of chemistry, physics and chemical engineering with a goal of contributing to new or improved processes for developing and using domestic energy resources in an efficient and environmentally sound manner. Each team of the Division of Chemical Sciences, Fundamental Interactions and Molecular Processes, is divided into programs that cover the various disciplines. Disciplinary areas where research is supported include atomic, molecular, and optical physics; physical, inorganic, and organic chemistry; chemical energy, chemical physics; photochemistry; radiation chemistry; analytical chemistry; separations science; heavy element chemistry; chemical engineering sciences; and advanced battery research. However, traditional disciplinary boundaries should not be considered barriers, and multi-disciplinary efforts are encouraged. In addition, the program supports several major scientific user facilities. The following summaries describe the programs

Interaction of Natural Organic Matter with Layered Minerals: Recent Developments in Computational Methods at the Nanoscale

The role of mineral surfaces in the adsorption, transport, formation, and degradation of natural organic matter (NOM) in the biosphere remains an active research area owing to the difficulties in identifying proper working models of both NOM and mineral phases present in the environment. The variety of aqueous chemistries encountered in the subsurface (e.g., oxic vs. anoxic, variable pH) further complicate this field of study. Recently, the advent of nanoscale probes such as X-ray adsorption spectroscopy and surface vibrational spectroscopy applied to study such complicated interfacial systems have enabled new insight into NOM-mineral interfaces. Additionally, due to increasing capabilities in computational chemistry, it is now possible to simulate molecular processes of NOM at multiple scales, from quantum methods for electron transfer to classical methods for folding and adsorption of macroparticles. In this review, we present recent developments in interfacial properties of NOM adsorbed on mineral surfaces from a computational point of view that is informed by recent experiments

High conductance values in p -folded molecular junctions

Folding processes play a crucial role in the development of function in biomacromolecules. Recreating this feature on synthetic systems would not only allow understanding and reproducing biological functions but also developing new functions. This has inspired the development of conformationally ordered synthetic oligomers known as foldamers. Herein, a new family of foldamers, consisting of an increasing number of anthracene units that adopt a folded sigmoidal conformation by a combination of intramolecular hydrogen bonds and aromatic interactions, is reported. Such folding process opens up an efficient through-space charge transport channel across the interacting anthracene moieties. In fact, single-molecule conductance measurements carried out on this series of foldamers, using the scanning tunnelling microscopy-based break-junction technique, reveal exceptionally high conductance values in the order of 10(-1) G(0) and a low length decay constant of 0.02 angstrom(-1) that exceed the values observed in molecular junctions that make use of through-space charge transport pathways.We thank Dr J.I. Miranda (University of the Basque Country) for assistance on NMR characterization. We are grateful to the Basque Science Foundation for Science (Ikerbasque), POLYMAT, the University of the Basque Country (SGIker and UFI11/23), the Deutsche Forschungsgemeinschaft (AU 373/3-1 and MA 5215/4-1), Gobierno de Espana (Ministerio de Economia y Competitividad CTQ2016-77970-R, CTQ2015-71936-REDT, CTQ2015-71406-ERC, CTQ2015-64579-C3-3P, CTQ-2014-54464-R and CTQ-2015-68148), Gobierno Vasco (BERC programme, Consolidated Groups IT520-10 and PC2015-1-01(06-37)), Diputacion Foral de Guipuzcoa (OF215/2016(ES)), CICECO-Aveiro Institute of Materials, POCI-01-0145-FEDER-007679 (FCT ref. UID/CTM/50011/2013), ON2 (NORTE-07-0162-FEDER-000086) and the European Union (ERA Chemistry, Marie Curie Career Integration Grant No. 618247, and FET-Open (2D-INK) Grant No. 664878)

Structural Studies of Biomolecular Building Blocks and Molecular Aggregates

Esta tesis recoge el trabajo de doctorado realizado en el Departamento de Química Física y Química Inorgánica de la Universidad de Valladolid entre septiembre de 2010 y agosto de 2014. Asimismo, y con el fin de obtener la mención de Tesis de Doctorado Internacional, la memoria recoge los trabajos realizados en varias estancias científicas internacionales, en particular en la Università di Bologna. La investigación llevada a cabo durante esta tesis doctoral ha comprendido el estudio teórico y experimental de diferentes unidades estructurales que juegan papeles importantes como bloques constructivos de diversos compuestos bioquímicos de relevancia, empleando técnicas de Química computacional y Espectroscopía de rotación. Asimismo, se han llevado a cabo estudios de varios agregados débilmente enlazados generados en chorros supersónicos. De esta manera se han analizado tanto los factores intramoleculares responsables de las estructuras moleculares de cada monómero, como las interacciones de carácter intermoleculares que se ponen en juego en el caso de los agregados (en particular, enlaces de hidrógeno e interacciones dispersivas). Se han estudiado tres familias de moléculas diferentes: tropanos, aminoésteres y decanos bicíclicos. A la primera familia molecular pertenece la escopina y la pseudopeletierina, que tienen en común el azabiciclo de tropano que aparece en muchas moléculas de interés farmacológico. Al igual que en estudios previos llevados a cabo en nuestro grupo como la tropinona y la escopolina, para ambas moléculas se encontró que las estructuras estables eran las asociadas a configuraciones piperidínicas tipo silla, con el grupo metilamino en configuraciones axial o ecuatorial.Departamento de Química Física y Química Inorgánic

Dynamical Excimer Formation in Rigid Carbazolophane via Charge Transfer State

Formation dynamics of intramolecular excimer in dioxa[3.3](3, 6)carbazolophane (CzOCz) was studied by time-resolved spectroscopic methods and computational calculations. In the ground state, the most stable conformer in CzOCz is the anti-conformation where two carbazole rings are in antiparallel alignment. No other isomers were observed even after the solution was heated up to 150 °C, although three characteristic isomers were found by the molecular mechanics calculation: the first is the anti-conformer, the second is the syn-conformer where two carbazole rings are stacked in the same direction, and the third is the int-conformer where two carbazole rings are aligned in an edge-to-face geometry. Because of the anti-conformation, the interchromophoric interaction in CzOCz is negligible in the ground state. Nonetheless, the intramolecular excimer in CzOCz was dynamically formed in an acetonitrile (MeCN) solution, indicating strong interchromophoric interaction and the isomerization from the anti- to syn-conformation in the excited state. The excimer formation in CzOCz is more efficient in polar solvents than in less polar solvents, suggesting the contribution of the charge transfer (CT) state to the excimer formation. The stabilization in the excited state is discussed in terms of molecular orbital interaction between two carbazole rings. The solvent-polarity-induced excimer formation is discussed in terms of the CT character in the int-conformation

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

New cysteine protease inhibitors : electrophilic (het)arenes and unexpected prodrug identification for the trypanosoma protease rhodesain

Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the SNAr addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (Ki = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the SNAr reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation

Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems

Rational design of supramolecular systems for application in photonic devices requires a clear understanding of both the mechanism of energy and electron transfer processes and how these processes can be manipulated. Central to achieving these goals is a detailed picture of their electronic structure and of the interaction between the constituent components. We review several approaches that have been taken towards gaining such understanding, with particular focus on the physical techniques employed. In the discussion, case studies are introduced to illustrate the key issues under consideration