Ligorio Raphael F, Rodrigues Jose L, Zuev Anatoly, Dos Santos Leonardo H R, Krawczuk Anna
Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil.
Phys Chem Chem Phys. 2022 Dec 14;24(48):29495-29504. doi: 10.1039/d2cp04052b.
The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.
凝聚相中官能团性质的提取对于预测包括生物材料在内的材料行为非常有用。因此，基于划分方案的计算方法已经被开发出来，旨在从具有化学意义的构建块快速准确地估计性质。一个全面的基团极化率和偶极矩数据库不仅有助于预测生物大分子的光学性质，还能改进专注于模拟生化过程的分子力场。在这项工作中，我们对从一系列多肽中提取的官能团的分布式极化率和偶极矩数据库进行了基准测试。这使得能够重建各种相关的化学环境。我们的数据库的准确性通过预测更大的肽以及更简单的氨基酸的电光性质来测试，对于这些肽和氨基酸，选择理论水平为M06-HF/aug-cc-pVDZ的密度泛函理论计算作为参考。这种方法对于极化率张量的对角分量相当准确，误差不大于15% - 20%。不过，极化率的各向异性预测效果较小。通过用一盒水分子包围数据库条目来明确包含溶剂效应，这些水分子的分布使用CHARMM力场进行了优化。
