%0 Journal Article %1 doi:10.1021/ct100641a %A Contreras-García, Julia %A Johnson, Erin R. %A Keinan, Shahar %A Chaudret, Robin %A Piquemal, Jean-Philip %A Beratan, David N. %A Yang, Weitao %D 0 %J Journal of Chemical Theory and Computation %K vdw visualization %N 0 %R 10.1021/ct100641a %T NCIPLOT: A Program for Plotting Noncovalent Interaction Regions %U http://pubs.acs.org/doi/abs/10.1021/ct100641a %V 0 %X Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent 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 vdW 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 noncovalent 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 .

@article{doi:10.1021/ct100641a, abstract = { Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent 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 vdW 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 noncovalent 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 . }, added-at = {2011-03-03T19:28:18.000+0100}, author = {Contreras-García, Julia and Johnson, Erin R. and Keinan, Shahar and Chaudret, Robin and Piquemal, Jean-Philip and Beratan, David N. and Yang, Weitao}, biburl = {https://www.bibsonomy.org/bibtex/26481bc6488e24e0f3ece48bc015f22b9/fok}, description = {NCIPLOT: A Program for Plotting Noncovalent Interaction Regions - Journal of Chemical Theory and Computation (ACS Publications)}, doi = {10.1021/ct100641a}, eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct100641a}, interhash = {fb390eb644a1c6aedfe233d934bd5313}, intrahash = {6481bc6488e24e0f3ece48bc015f22b9}, journal = {Journal of Chemical Theory and Computation}, keywords = {vdw visualization}, number = 0, timestamp = {2011-03-03T23:17:45.000+0100}, title = {NCIPLOT: A Program for Plotting Noncovalent Interaction Regions}, url = {http://pubs.acs.org/doi/abs/10.1021/ct100641a}, volume = 0, year = 0 }