NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

Abstract

Non-covalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these non-covalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define non-covalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their van der Waals radii. We recently developed an alternative perspective, derived from the electronic density: the Non-Covalent Interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of non-covalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both selfconsistent fully quantum-mechanical, as well as promolecular, densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at

Density-decomposed orbital-free density functional theory for covalently bonded molecules and materials

“…We introduced a scale function dependent on the local density to identify localized electrons and further decompose the total density into localized and Recent studies probing the relation between density distributions and bonding properties could prove useful. 79,80 Moreover, the models to describe the localized, interaction, and delocalized kinetic energies are also flexible and improvable. The optimal scale function parameter m and the coordination number (c.n.)…”

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

“…Interestingly, NCI is capable of revealing weak interactions, including pure London dispersion, even when the density is derived from a method that poorly describes van der Waals forces. 185 Usually, 5,182 although not always, 186 NCI correctly identifies these interactions even when promolecular densities (i.e., sums of atomic densities) are used. In turn, that allows the treatment of very large systems such as DNA fragments 187,188 and proteins.…”

“…NCI is able to handle also the covalent interactions, 5,182,190 but to obtain a clear and intuitive picture of both strong and weak interactions at the same time the combination of NCI with ELF is needed. 191 This is a significant nuisance as a huge advantage of the original NCI is its simple, nearly "black-box" use.…”

Electron density analysis of large (molecular and periodic) systems: A parallel implementation

“…Several schemes have been proposed in the last decades to extract from ρ(r) as much chemical information as possible, which involve its visualization (profiles, 2D maps, 3D graphical representations), partition according to different schemes, topological analysis, etc. [4][5][6][7][8][9][10][11][12][13][14][15] In this respect, one of the most powerful and popular techniques is represented by Bader's quantum theory of atoms in molecules (QTAIM), which relies on the topological analysis of ρ(r). 16 If a routine analysis of the wave-function |Ψ of a small system is a non particularly demanding task from a computational point of view (when compared to the convergence of the self-consistent field, SCF, procedure or to the analytical evaluation of energy gradients), this is clearly no more the case either when rather sophisticated techniques are adopted (such as QTAIM) or when large systems are studied.…”