Ozkanlar Abdullah, Clark Aurora E
Department of Chemistry, Washington State University, Pullman, Washington, 99164.
J Comput Chem. 2014 Mar 5;35(6):495-505. doi: 10.1002/jcc.23506. Epub 2013 Dec 5.
Many intermolecular chemical interactions persist across length and timescales and can be considered to form a "network" or "graph." Obvious examples include the hydrogen bond networks formed by polar solvents such as water or alcohols. In fact, there are many similarities between intermolecular chemical networks like those formed by hydrogen bonding and the complex and distributed networks found in computer science. Contemporary network analyses are able to dissect the complex local and global changes that occur within the network over multiple time and length scales. This work discusses the ChemNetworks software, whose purpose is to process Cartesian coordinates of chemical systems into a network/graph formalism and apply topological network analyses that include network neighborhood, the determination of geodesic paths, the degree census, direct structural searches, and the distribution of defect states of network. These properties can help to understand the network patterns and organization that may influence physical properties and chemical reactivity. The focus of ChemNetworks is to quantitatively describe intermolecular chemical networks of entire systems at both the local and global levels and as a function of time. The code is highly general, capable of converting a wide variety of systems into a chemical network formalism, including complex solutions, liquid interfaces, or even self-assemblies.
许多分子间的化学相互作用在长度和时间尺度上持续存在，可被视为形成了一个“网络”或“图”。明显的例子包括由极性溶剂（如水或醇）形成的氢键网络。事实上，像由氢键形成的分子间化学网络与计算机科学中发现的复杂分布式网络之间存在许多相似之处。当代网络分析能够剖析网络在多个时间和长度尺度上发生的复杂局部和全局变化。这项工作讨论了ChemNetworks软件，其目的是将化学系统的笛卡尔坐标处理成网络/图形式，并应用拓扑网络分析，包括网络邻域、测地线路径的确定、度普查、直接结构搜索以及网络缺陷状态的分布。这些性质有助于理解可能影响物理性质和化学反应性的网络模式和组织。ChemNetworks的重点是在局部和全局层面定量描述整个系统的分子间化学网络，并将其作为时间的函数。该代码具有高度通用性，能够将各种系统转化为化学网络形式，包括复杂溶液、液体界面甚至自组装体。
