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Register a new userStatistical Analysis of $sigma$-Holes: A Novel Complementary View on Halogen Bonding
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Added by
Michal H. Kol\\'a\\v{r}
Publication date
2017
fields
Physics
and research's language is
English
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To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP, called $sigma$-hole, is a concept of central importance for halogen bonding. We aim at simplifying the view on $sigma$-holes and provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as of biomolecular complexes and attempt to improve the intuition of chemists when dealing with halogenated compounds.
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A new measure of the crystal-field strength, complementary to the conventional one, is defined. It is based on the rotational invariants |B_{k0}|_{av} or |sum_{k}B_{k0}|_{av}, k=2,4,6, of the crystal-(ligand)-field (CF) Hamiltonian H_{CF} parametrizations, i.e. on the axial CF parameters modules averaged over all reference frame orientations. They turn out to be equal to |H_{CF}^{(k)}|_{av} and |H_{CF}|_{av}, respectively. While the traditional measure is established on the parametrization modules or on the second moment of the CF energy levels, the introduced scale employs rather the first moment of the energy modules and has better resolving power. The new scale is able to differentiate the strength of various iso-modular parametrizations according to the classes of rotationally equivalent parametrizations. Using both the compatible CF strength measures one may draw more accurate conclusions about the Stark levels arrays and particularly their total splitting magnitudes.
Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure calculations on isolated molecules and/or crystal structures that are not readily transferable to liquids and disordered phases. To address this issue, we present a first-principles simulation-based approach for quantifying halogen bonds in molecular systems rooted in an understanding of nuclei-nuclei and electron-nuclei spatial correlations. We then demonstrate how this approach can be used to quantify the structure and dynamics of halogen bonds in condensed phases, using solid and liquid molecular chlorine as prototypical examples with high concentrations of halogen bonds. We close with a discussion of how the knowledge generated by our first-principles approach may inform the development of classical empirical models, with a consistent representation of halogen bonding.
The high energy evolution equations that describe the evolution of hadronic amplitudes with energy are derived assuming eikonal interaction of the evolved hadronic wave function with the target. In this note we remark that this derivation allows a different interpretation, whereby the hadronic wave function is not evolved, but instead the evolution acts on the S - matrix operator. In this approach, analogous to the Heisenberg picture of Quantum mechanics, the scattering is not eikonal and additional boost provides for radiation of more gluons in the final state.
In this paper I propose a new way for counting the microstates of a system out of equilibrium. As, according to quantum mechanics, things happen as if a given particle can be found in more than one state at once, I extend this concept to propose the coherent access by a particle to the available states of a system. By coherent access I mean the possibility for the particle to act as if it is populating more than one microstate at once. This hypothesis has experimental implications, since the thermodynamical probability and, as a consequence, the Bose-Einstein distribution as well as the argument of the Boltzmann factor is modified.
We have experimentally determined the lateral registry and geometric structure of free-base porphine (2H-P) and copper-metalated porphine (Cu-P) adsorbed on Cu(111), by means of energy-scanned photoelectron diffraction (PhD), and compared the experimental results to density functional theory (DFT) calculations that included van der Waals corrections within the Tkatchenko-Scheffler approach. Both 2H-P and Cu-P adsorb with their center above a surface bridge site. Consistency is obtained between the experimental and DFT-predicted structural models, with a characteristic change in the corrugation of the four N atoms of the molecules macrocycle following metalation. Interestingly, comparison with previously published data for cobalt porphine adsorbed on the same surface evidences a distinct increase in the average height of the N atoms above the surface through the series 2H-P, Cu-P, cobalt porphine. Such an increase strikingly anti-correlates the DFT-predicted adsorption strength, with 2H-P having the smallest adsorption height despite the weakest calculated adsorption energy. In addition, our findings suggest that for these macrocyclic compounds, substrate-to-molecule charge transfer and adsorption strength may not be univocally correlated.
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