G2 and DFT rigorous description of the inversion process of oxane and thiane used as simple ring systems to model sugar components

Conformational structure of cationic tetrahydropyran by one-photon vacuum ultraviolet mass-analyzed threshold ionization spectroscopy

Isolating and identifying the conformational forms of molecules are imperative processes to investigate the chemical reaction pathways of individual conformers. Herein, we explored the conformational structures of tetrahydropyran in the neutral (S0) and cationic (D0) states by varying the supersonic expansion conditions using one-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy. The constructed 2D potential energy surfaces associated with conformational interconversion between the chair and boat forms in the S0 and D0 states revealed that the ionic transitions observed in the MATI spectra correspond to the most stable chair conformer. Accordingly, based on the 0-0 band in the VUV-MATI spectrum supported by the VUV photoionization efficiency curve, the adiabatic ionization energy for the conversion of the chair conformer to a cationic state was determined to be 74 687 ± 4 cm-1 (9.2600 ± 0.0005 eV). Definitive vibrational assignment of the measured MATI spectra using Franck-Condon fitting revealed the cationic structure of the twisted chair conformer. The geometrical change upon ionization promoted the vibrational modes associated with ring inversion and deformation motions in the cationic state. This behavior, which was attributed to the effect of electron removal from the highest occupied molecular orbital (HOMO) consisting of the nonbonding orbital of the oxygen atom, reveals the role of electrons in the HOMO.

Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions

Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied the equatorial/axial exchange of nitrogen and phosphorous bearing six-membered rings with different representative substituents by using quantum chemistry methods. Three possible routes, i.e. heteroatom inversion and two ring flipping modes were considered. The feasibility of equatorial/axial conversion (based on ΔE#) for the substituted piperidine rings with substituents was in the following order; H > CH 3> Cl ~ OH ~ F , whereas for the phosphorous bearing six-membered rings it was H ~ F > OH > Cl ~ CH 3. In the piperidine system hydrogen and methyl substituents preferred the atom inversion route while the other substituents ( Cl , F , OH ) favored C4 site ring flipping in equatorial/axial conversion. For the phosphorous bearing rings, however, phosphorous retards the atom inversion mechanism and heteroatom site ring flipping is the preferred route for all substituents. We demonstrate that charge transfer effect is one of the key factors that determines the favored route in the presence of various substituents. We show how wave function analysis by natural bond orbital (NBO) method can be used as a straightforward technique to explain the most favored route in the equatorial/axial conversion of substituted 6-membered rings.

Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design

Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.

Investigation of the effects of fine structure on the nanomechanical properties of pectin

Pectin is an important structural polysaccharide found in the cell walls of all land plants. While in detail its composition and its organization in muro are complex, it is predominantly a copolymer of galacturonic acid and its methylesterified counterpart. Previous single-molecule stretching studies carried out on a sparsely methylesterified pectin sample indicated the importance of force-induced conformational transitions of the pyranose ring during extension, and the possible biological role of such transitions was discussed. More heavily methylesterified samples are better biomimetic models of the polymeric components as found in the plant cell wall, in particular being less restricted by the shackles of the significant intermolecular interactions expected to constrain the behavior of bare galacturonic acid sequences. Density functional theory calculations revealed that upon extending galacturonic acid monomers, whether methylesterified or not, the initial ((4)C1) chair structure is transformed to a ((3)S5) skew boat and that subsequently upon further elongation, via an intermediate inverted skew boat ((5)S3), the inverted chair ((1)C4) is reached. Experimentally, the force-extension curve of highly methylesterified pectin was found to be solvent dependent in the same manner as the un-esterified sample, indicating that minimal changes in the strength of interring hydrogen bonding result from such a substitution, and finally, as only subtle changes in the force-extension behavior of pectin resulted from changes in the degree of methylesterification, previous speculations about the role of force-induced transformations in vivo are supported.

Computational study of 1,3-dithiane 1,1-dioxide (1,3-dithiane sulfone). Description of the inversion process and manifestation of stereoelectronic effects on 1JC-H coupling constants

A theoretical study on the conformational interconversions in 1,3-dithiane 1,1-dioxide (1,3-dithiane sulfone) has been carried out. Nineteen conformations have been considered. Four minima and five transition states have been identified. A description of the inversion-topomerization process of 1,3-dithiane sulfone is presented. Calculations show that two transition states are associated with inversion and three more with topomerization. IGLO calculations of the (1)J(C-H) one-bond coupling constants in 1,3-dithiane sulfone have also been carried out. These constants are compared with those obtained for 1,3-dithiane, thiane, and thiane sulfone and their magnitude is explained in terms of stereoelectronic interactions.

Theoretical Study of Inversion and Topomerization Processes of Substituted Cyclohexanes: The Relevance of the Energy 3D Hypersurface

Although the potential energy surface of highly symmetric cyclohexane has been extensively reviewed, no attention has been paid to the study of the effect of substitution of a methylene group by a heteroatom. The substitution may cause changes in molecular symmetry as well as the dipole moment, and the unshared electron pairs associated with the heteroatom may also introduce changes in molecular reactivity. However, these phenomena are not yet completely understood. To address these issues, a rigorous description of the inversion-topomerization process of methylcyclohexane and a revision of the conformational potential energy of oxane and thiane are presented. Moreover, the usefulness of providing a three-dimensional representation of these processes is discussed. In the case of methylcyclohexane, calculations show that three transition states are associated with inversion and four more with topomerization. In contrast, for oxane and thiane, only two transition states are involved with inversion and two with topomerization. Two fundamental conclusions can be drawn from this study. The first is that the inversion process occurs through elementary, stages that we have denoted "conformational elemental stages", which is an analogous term to that used for reaction mechanism description (minima-transition state-minima) where several elemental steps take place. The second conclusion is that two independent processes, inversion and topomerization, are connected by some common conformers. The inversion process controls the ring interchange, while topomerization allows exchange between skewed boats.