NCIPLOT: a program for plotting non-covalent interaction regions.
NCIPLOT: a program for plotting non-covalent interaction regions.
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DOI：
10.1021/ct100641a
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发表时间：
2011-03-08
影响因子：
5.5
通讯作者：
Yang, Weitao
中科院分区：
文献类型：
--
作者：
Contreras-Garcia, Julia;Johnson, Erin R.;Keinan, Shahar;Chaudret, Robin;Piquemal, Jean-Philip;Beratan, David N.;Yang, Weitao
非共价相互作用是理解许多化学、生物和技术问题的关键。准确地描述这些非共价相互作用，包括它们在真实的空间中的位置，构成了解耦定义非共价相互作用的复杂力平衡过程的第一步。由于大分子的尺寸，最常见的方法是根据原子之间的成对距离根据它们的货车德瓦尔斯半径来分配货车德瓦尔斯相互作用（vdW）、空间碰撞（SC）和氢键（HB）。我们最近开发了另一种观点，从电子密度：非共价相互作用（NCI）指数[J. Am. 2010，132，6498]。该指数具有双重优点，即通常可转移到不同的化学应用中，并且计算速度非常快，因为它可以从原分子密度计算出来。因此，NCI分析适用于大型系统，包括蛋白质和DNA，其中非共价相互作用的分析具有很大的潜在价值。在这里，我们描述了NCI计算算法和它们的实施弱相互作用的分析和可视化，使用自洽的完全量子力学，以及promolecular，密度。还提供了用于调整要绘制的相互作用范围的各种选项。为了证明我们的方法的能力，给出了几个例子，从有机，无机，固态和大分子化学，包括NCI分析的情况下，洞察到非常规的化学键合。NCI代码及其手册可从http://www.chem.duke.edu/~yang/software.htm下载
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
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影响因子：
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通讯作者：
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