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The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, “naked” conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical 2E and 3E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5′ and OH-3′ are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3′ is “born free” in the “naked” lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining 2T1 conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for “life’s code” and suggest a mechanism by which the resulting freedom of OH-3′ (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5′-to-3′., The preferred conformations and populations of DNA ribopyranosides and furanosides were determined with atomic resolution in the gas phase and in water solution.

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

Tesis presentada para la obtención del título de Doctor por la Universidad del País Vasco., La espectroscopía rotacional es la técnica de mayor resolución que proporciona datos estructurales de las moléculas y pequeños agregados en fase gas, así como información sobre sus dinámicas moleculares. Esta tesis está mayoritariamente focalizada al estudio de azucares utilizando la combinación de la espectroscopia rotacional y los cálculos químico cuánticos. En la tesis se presentan varios estudios, partiendo del estudio de la eritrulosa en la que combinamos los datos obtenidos en el laboratorio con los datos de los radio-telescopios para su intento de detección en el medio interestelar y continuamos con varios estudios de azucares derivados de glucosa, galactosa y manosa. Nuestros resultados muestran como las pequeñas mutaciones en los azucares (de oxidaciones, lactonizaciones, oxidaciones) producen grandes cambios estructurales de la estructura intrínseca de los monosacáridos en fase gas.Por último, se presentan varios estudios de procesos químicos de relevante interés en la biología. Entre ellos la transferencia de protones en el dimero de ácido furoico y la micro-solvatación del metil benzoato.En general demostramos como la espectroscopia de rotación permite el estudio de las estructuras y de varios procesos de importancia en la biología.

Benzenesulfonamides are a class of molecules of extreme interest in the biochemical field because many of them are active against a variety of diseases. In this work, the pharmacophoric group benzensulfonamide, its derivatives para-toluensulfonamide and ortho-toluensulfonamide, and the bioactive molecule sulfanilamide, were investigated using rotational spectroscopy to determine their conformations and the influence of different substituents on their structures. For all species, the hyperfine structure due to the 14N atom was analyzed, and this provided crucial information for the unambiguous identification of the observed conformation of all molecules. In addition, for ortho-toluensulfonamide, the vibration–rotation hyperfine structure related to the methyl torsion was analyzed, and the methyl group rotation barrier was determined. For benzensulfonamide, partial rS and r0 structures were established from the experimental rotational constants of the parent and two deuterated isotopic species. In all compounds except ortho-toluensulfonamide, the amino group of the sulfonamide group lies perpendicular to the benzene plane with the aminic hydrogens eclipsing the oxygen atoms. In ortho-toluensulfonamide, where weak attractive interactions occur between the nitrogen lone pair and the methyl hydrogen atoms, the amino group lies in a gauche orientation, retaining the eclipsed configuration with respect to the SO2 frame. A comparison of the geometrical arrangements found in the PDB database allowed us to understand that the bioactive conformations are different from those found in isolated conditions. The conformations within the receptor are reached with an energy cost, which is balanced by the interactions established in the receptor.

The rotational spectra of the parent species and of four water isotopologues (-DOH, -HOD, -DOD, and -H(18)OH) of the adduct 3-fluoropyridine-water have been investigated using pulsed supersonic-jet Fourier-transform microwave spectroscopy. From the rotational constants, the structure of the adduct was deduced where the water is linked to the aromatic ring through an intermolecular O-H···N hydrogen bond with a bond distance of 1.9961(5) Å and an O-H···N angle of 156.8(1)°. The shape of the complex is such that the water oxygen is in the plane of the aromatic ring, on the opposite side of fluorine, and forming a C-H···N weak hydrogen bond with the adjacent aromatic hydrogen.

The conformational landscapes of β-ionone and two mutants (α-ionone and β-damascone) have been analyzed by means of state-of-the-art rotational spectroscopy and quantum-chemical calculations. The experiments performed at high resolution and sensitivity have provided a deep insight into their conformational spaces, assigning more than 8000 transitions corresponding to the rotational structures of 54 different species (3 isomers, 14 conformers, and 40 isotopologues). Methyl internal rotation dynamics were also observed and analyzed. The work proved the great flexibility of β-ionone due to its flatter potential energy surface. This feature confers on β-ionone a wider ability to interconvert between conformers with rather similar energies with respect to its mutants, allowing the retinal ligand to better adapt inside the binding pocket.

In order to facilitate its detection in astronomical observations, the measurement of the rotational spectrum of acrylic acid has been extended to 397 GHz using a free space cell at room temperature. 295 new lines were assigned to the s-cis conformer and 286 new lines to the s-trans conformer of acrylic acid. Using the determined experimental parameters, the predictions of the rotational transition frequencies up to 900 GHz and their intensities were obtained at temperatures of 100 and 200 K and at room temperature. Based on these predictions, a search of the most intense transitions of acrylic acid in star-forming regions was performed using published data from the HERSCHEL Science Archive. No lines were found but the possibility of observing rotational transitions of acrylic acid in astronomical objects is discussed.

The pure rotational spectrum of 1,2-dimethoxyethane was measured in the 6–18 and 59.6–74.4 GHz frequency ranges using a cavity-based pulsed jet Fourier transform microwave spectrometer and a Stark modulated free-jet millimeter-wave absorption spectrometer, respectively. Two conformers, TGT and TGG′, have been identified, together with their mono-substituted 13C isotopologues. Each rotational transition is split into several components due to the two methyl groups internal rotations. The corresponding V3 barriers have been experimentally determined. MP2/6-311++G(d,p) calculations have provided the determination of the conformational stabilities, structures and spectroscopic parameters.

The rotational spectrum of the weakly bound complex pentafluoropyridine·water has been investigated with pulsed jet Fourier transform microwave spectroscopy. From the analysis of the rotational parameters of the parent species and of three water isotopologues, the structural arrangement of the adduct has been unambiguously established. The results show that the full ring fluorination of pyridine has a dramatic effect on its binding properties: It inverts the electron density distribution above the ring, creating a π-hole, with respect to the typical π-cloud of benzene and pyridine. In the complex the water moiety lies above the aromatic ring with the oxygen lone pairs pointing toward its center. This lone pair···π-hole interaction stabilizes the adduct, and it is more stable than the in-plane O–H···N hydrogen bond normally found in the complexes involving nitrogen heterocyclic aromatic rings. Evidence of a large amplitude motion involving the weakly bound water molecule has also been observed and discussed.

The weakly bound 1:1 complex between acrylonitrile (CH2═CHCN) and water has been characterized spectroscopically in the millimeter wave range (59.6-74.4 GHz) using a Free Jet Absorption Millimeter Wave spectrometer. Precise values of the rotational and quartic centrifugal distortion constants have been obtained from the measured frequencies of the normal and isotopically substituted water moiety (DOH, DOD, H(18)OH). Structural parameters have been estimated from the rotational constants and their differences among isotopologues: the complex has a planar structure with the two subunits held together by a O-H···N (2.331(3) Å) and a C-H···O (2.508(4) Å) interaction. The ab initio intermolecular binding energy, obtained at the counterpoise corrected MP2/aug-cc-pVTZ level of calculation, is De = 24.4 kJ mol(-1).