Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way

Switchable Coupling of Vibrations to Two-Electron Carbon-Nanotube Quantum Dot States

We report transport measurements on a quantum dot in a partly suspended carbon nanotube. Electrostatic tuning allows us to modify and even switch 'on' and 'off' the coupling to the quantized stretching vibration across several charge states. The magnetic-field dependence indicates that only the two-electron spin-triplet excited state couples to the mechanical motion, indicating mechanical coupling to both the valley degree of freedom and the exchange interaction, in contrast to standard models

Structure energy relationship of biological halogen bonds

2012 Summer.Includes bibliographical references.The primary goal of the studies in this thesis is to derive a set of mathematical models to describe the anisotropic atomic nature of covalent bound halogens and by extension their molecular interactions. We use a DNA Holliday junctions as a experimental model system to assay the structure energy relationship of halogen bonds (X-bonds) in a complex biological environment. The first chapter of this dissertation is reserved for a review on DNA structure and the Holliday Junction in context of other DNA conformations. The conformational isomerization of engineered Holliday junctions will be established as a means to assay the energies of bromine X-bonds both in crystal and in solution. The experimental data are then used in the development of anisotropic force fields for use in the mathematical modeling of bromine halogen bonds, serving as a foundation to model all biological halogen interactions. The DNA Holliday junction experimental system is expanded to compare and contrast halogens from fluorine to iodine. This comprehensive study is used to determine the effects of polarization on the structure-energy relationship of biological X-bonds in solid state and solution phase. The culmination of the work in this thesis, in addition to previously published studies, provides a growing set of principles to guide knowledge-based application of halogens in drug design. These principles are applied to the selection of X-bond acceptors in a protein binding pocket, optimal placement of the halogen on the lead compound, and which halogen is best suited for a particular interaction

Spectrum of an open disordered quasi-two-dimensional electron system: strong orbital effect of the weak in-plane magnetic field

The effect of an in-plane magnetic field upon open quasi-two-dimensional electron and hole systems is investigated in terms of the carrier ground-state spectrum. The magnetic field, classified as weak from the viewpoint of correlation between size parameters of classical electron motion and the gate potential spatial profile is shown to efficiently cut off extended modes from the spectrum and to change singularly the mode density of states (MDOS). The reduction in the number of current-carrying modes, right up to zero in magnetic fields of moderate strength, can be viewed as the cause of magnetic-field-driven metal-to-insulator transition widely observed in two-dimensional systems. Both the mode number reduction and the MDOS singularity appear to be most pronounced in the mode states dephasing associated with their scattering by quenched-disorder potential. This sort of dephasing is proven to dominate the dephasing which involves solely the magnetic field whatever level of the disorder.Comment: RevTeX-4 class, 12 pages, 5 eps figure

Enantioseparation of 5,5'-Dibromo-2,2'-Dichloro-3-Selanyl-4,4'-Bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography

he chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantiosepa-ration of three 5,5-dibromo-2,2-dichloro-3-selanyl-4,4-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van't Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed