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NCIPLOT: a program for plotting non-covalent 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 self-consistent 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 http://www.chem.duke.edu/~yang/software.htm.

SUBMITTER: Contreras-Garcia J

PROVIDER: S-EPMC3080048 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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NCIPLOT: a program for plotting non-covalent interaction regions.

Contreras-García Julia J Johnson Erin R ER Keinan Shahar S Chaudret Robin R Piquemal Jean-Philip JP Beratan David N DN Yang Weitao W

Journal of chemical theory and computation 20110301 3

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 o ...[more]

PMID: 21516178

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Project description:A vast number of non-covalent interaction energies at the counterpoise corrected CCSD(T) level have been collected from the literature to build a diverse new dataset. The whole dataset, which consists of 2027 CCSD(T) energies, includes most of the published data at this level. A large subset of the data was then used to train a novel, B3LYP specific, empirical correction scheme for non-covalent interactions and basis set superposition error (abbreviated as B3LYP-MM). Results obtained with our new correction scheme were directly compared to benchmark results obtained with B3LYP-D3(1) and M06-2X(2) (two popular density functions designed specifically to accurately model non-covalent interactions). For non-covalent complexes dominated by dispersion or dipole-dipole interactions all three tested methods give accurate results with the medium size aug-cc-pVDZ(3-6) basis set with MUE's of 0.27 (B3LYP-MM), 0.32 (B3LYP-D3) and 0.47 kcal/mol (M06-2X) (with explicit counterpoise corrections). These results validate both B3LYP-D3 and M06-2X for interactions of this type using a much larger data set than was presented in prior work. However, our new dispersion correction scheme shows some clear advantages for dispersion and dipole-dipole dominated complexes with the small LACVP* basis set, which is very popular in use due to its low associated computational cost: The MUE for B3LYP-MM with the LACVP* basis set for this subset of complexes (without explicit counterpoise corrections) is only 0.28 kcal/mol, compared to 0.65 kcal/mol for M06-2X or 1.16 kcal/mol for B3LYP-D3. Additionally, our new correction scheme also shows major improvements in accuracy for hydrogen-bonded systems and for systems involving ionic interactions, for example cation-π interactions. Compared to B3LYP-D3 and M06-2X, we also find that our new B3LYP-MM correction scheme gives results of higher or equal accuracy for a large dataset of conformer energies of di- and tripeptides, sugars, and cysteine.

Dataset Information

NCIPLOT: a program for plotting non-covalent interaction regions.

Publications

NCIPLOT: a program for plotting non-covalent interaction regions.

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