Vemparala Satyavani, Ivanov Ivaylo, Pophristic Vojislava, Spiegel Katrin, Klein Michael L
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
J Comput Chem. 2006 Apr 30;27(6):693-700. doi: 10.1002/jcc.20382.
Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers.
使用密度泛函理论（DFT）方法，我们确定了一类具有抗菌和抗凝血抑制特性的重要芳基酰胺聚合物的分子内参数。这些功能与聚合物在溶液中和脂质双层界面所采用的构象之间已建立了紧密联系。因此，对于旨在探究这些系统构象行为的分子动力学模拟而言，准确描述扭转自由度至关重要。结果表明，标准力场在这方面存在不足。因此，我们通过一系列受限几何优化计算了相关的扭转能分布。我们还结合标准RESP电荷优化，利用我们的结果确定了静电参数。通过蒙特卡罗方案迭代匹配量子和经典正常模式，计算了键和角势能的力常数。由此得到的一组新参数准确地描述了芳基酰胺聚合物的构象和动力学行为。
