The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems.

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Conformational preference analysis in C2H6 using orbital forces and non-covalent interactions; comparison with related systems.

Dynamic Orbital Forces (DOF) and Non-Covalent Interactions (NCIs) are used to analyze the attractive/repulsive interactions responsible of the conformational preference of ethane and some related compounds. In ethane, it is found that the stabilization of the staggered conformation with respect to the adiabatic eclipsed one arises from both attractive and repulsive interactions in CH3⋯CH3. Attractive ones are predominant in a ratio 2 : 1, with an important role of a σ MO. On the contrary, the stabilization of the staggered conformation with respect to the vertical eclipsed one arises almost only from repulsive π interactions. Weak long-range H⋯H repulsions also favour the staggered conformation. From the sum of DOFs, yielding intrinsic bond energies, the rotation barrier can be decomposed into a weakening of the C-C bond (ca. 7 kcal mol-1), moderated by a strengthening of C-H ones (ca. 4 kcal mol-1). This evidences the decrease of hyperconjugation in the eclipsed conformation with respect to the staggered one. In the compounds CH3-SiH3, SiH3-SiH3, CH3-CF3 and CF3-CF3, the conformational preference is predominantly or exclusively due to repulsive interactions, with respect as well to adiabatic as to vertical eclipsed structures.

Strong correlation between electronic bonding network and critical temperature in hydrogen-based superconductors.

By analyzing structural and electronic properties of more than a hundred predicted hydrogen-based superconductors, we determine that the capacity of creating an electronic bonding network between localized units is key to enhance the critical temperature in hydrogen-based superconductors. We define a magnitude named as the networking value, which correlates with the predicted critical temperature better than any other descriptor analyzed thus far. By classifying the studied compounds according to their bonding nature, we observe that such correlation is bonding-type independent, showing a broad scope and generality. Furthermore, combining the networking value with the hydrogen fraction in the system and the hydrogen contribution to the density of states at the Fermi level, we can predict the critical temperature of hydrogen-based compounds with an accuracy of about 60 K. Such correlation is useful to screen new superconducting compounds and offers a deeper understating of the chemical and physical properties of hydrogen-based superconductors, while setting clear paths for chemically engineering their critical temperatures.

The Pauli principle and the confinement of electron pairs in a double well: Aspects of electronic bonding under pressure.

It has become recently clear that chemical bonding under pressure is still lacking guiding principles for understanding the way electrons reorganize when their volume is constrained. As an example, it has recently been shown that simple metals can become insulators (aka electrides) when submitted to high enough pressures. This has lead to the general believe that "a fundamental yet empirically useful understanding of how pressure alters the chemistry of the elements is lacking" [R. J. Hemley, High Pressure Res. 30, 581 (2010)]. In this paper, we are interested in studying the role that the Pauli principle plays on the localization/delocalization of confined noninteracting electrons. To this end, we have considered the simple case of a 1-dimensional (1-D) double well as a confining potential, and the Electron Localization Function (ELF) has been used to characterize the degree localization/delocalization of the systems of noninteracting electrons. Then, we have systematically studied the topology of the ELF as a function of the double well parameters (barrier eight and wells distance) and of the number of electrons. We have found that the evolution of the ELF distributions has a good correspondence with the evolution of chemical bonding of atomic solids under pressure.