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L7 和 S12L 中大分子非共价复合物以及 C 二聚体、DNA-椭圆黄素和 HIV-茚地那韦的耦合簇基准测试。

Coupled Cluster Benchmarking of Large Noncovalent Complexes in L7 and S12L as Well as the C Dimer, DNA-Ellipticine, and HIV-Indinavir.

机构信息

Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States.

出版信息

J Phys Chem A. 2022 Jul 14;126(27):4326-4341. doi: 10.1021/acs.jpca.2c01421. Epub 2022 Jun 29.

Abstract

In this work, we report the benchmark binding energies of the seven complexes within the L7 data set, six host-guest complexes from the S12L data set, a C dimer, the DNA-ellipticine intercalation complex, and the largest system of the study, the HIV-indinavir system, which contained 343 atoms or 139 heavy atoms. The high-quality values reported were obtained via a focal point method that relies on the canonical form of second-order Møller-Plesset theory and the domain-based local pair natural orbital scheme for the coupled cluster with single double and perturbative triple excitations [DLPNO-CCSD(T)] extrapolated to the complete basis set (CBS) limit. The results in this work not only corroborate but also improve upon some previous benchmark values for large noncovalent complexes albeit at a relatively steep cost. Although local CCSD(T) and the largely successful fixed-node diffusion Monte Carlo (FN-DMC) have been shown to generally agree for small- to medium-size systems, a discrepancy in their reported binding energy values arises for large complexes, where the magnitude of the disagreement is a definite cause for concern. For example, the largest deviation in the L7 data set was 2.8 kcal/mol (∼10%) on the low end in C3GC. Such a deviation only grows worse in the S12L set, which showed a difference of up to 10.4 kcal/mol (∼25%) by a conservative estimation in buckycatcher-C. The DNA-ellipticine complex also generated a disagreement of 4.4 kcal/mol (∼10%) between both state-of-the-art methods. The disagreement between local CCSD(T) and FN-DMC in large noncovalent complexes shows that it is urgently needed to have the canonical CCSD(T), the Monte Carlo CCSD(T), or the full configuration interaction quantum Monte Carlo approaches available to large systems on the hundred-atom scale to solve this dilemma. In addition, the performances of cheaper popular computational methods were assessed for the studied complexes with respect to DLPNO-CCSD(T)/CBS. rSCAN-3c, B97M-V, and PBE0+D4 work well in large noncovalent complexes in this work, and GFN2-xTB performs well in π-π stacking complexes. B97M-V is the most reliable computationally efficient approach to predicting noncovalent interactions for large complexes, being the only one to have binding errors within the so-called 1 kcal/mol "chemical accuracy". The benchmark interaction energies of these host-guest complexes, molecular materials, and biological systems with electronic and medicinal implications provide crucial reference data for the improvement of current and future lower-cost methods.

摘要

在这项工作中,我们报告了 L7 数据集内的七个配合物、S12L 数据集内的六个主体-客体配合物、C 二聚体、DNA-椭圆碱嵌入复合物以及研究中最大的系统 HIV-茚地那韦系统的基准结合能,这些系统包含 343 个原子或 139 个重原子。高质量的值是通过依赖于二阶 Møller-Plesset 理论的规范形式和基于域的局部对自然轨道方案的焦点方法获得的,该方法用于耦合簇与单双和微扰三激发[DLPNO-CCSD(T)]扩展到完全基组(CBS)极限。本工作的结果不仅证实了,而且改进了一些以前的大非共价复合物基准值,尽管成本相对较高。尽管局部 CCSD(T)和成功的固定节点扩散蒙特卡罗(FN-DMC)已被证明对于中小系统通常是一致的,但对于大复合物,它们报告的结合能值存在差异,而且这种差异的幅度确实令人担忧。例如,在 L7 数据集的 C3GC 中,低端的最大偏差为 2.8 千卡/摩尔(约 10%)。在 S12L 集合中,这种偏差变得更糟,保守估计在 buckycatcher-C 中最大偏差高达 10.4 千卡/摩尔(约 25%)。DNA-椭圆碱复合物也在两种最先进的方法之间产生了 4.4 千卡/摩尔(约 10%)的差异。局部 CCSD(T)和 FN-DMC 在大非共价复合物中的差异表明,迫切需要在百原子尺度上为大系统提供规范 CCSD(T)、蒙特卡罗 CCSD(T)或全组态相互作用量子蒙特卡罗方法来解决这一困境。此外,还评估了研究复合物中较便宜的流行计算方法相对于 DLPNO-CCSD(T)/CBS 的性能。在这项工作中,rSCAN-3c、B97M-V 和 PBE0+D4 在大非共价复合物中表现良好,而 GFN2-xTB 在π-π 堆积复合物中表现良好。B97M-V 是预测大复合物中非共价相互作用最可靠的计算效率方法,是唯一一种结合误差在所谓的 1 千卡/摩尔“化学精度”范围内的方法。这些主体-客体配合物、分子材料和具有电子和医学意义的生物系统的基准相互作用能为改进当前和未来的低成本方法提供了关键的参考数据。

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