Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine–alanine and glycine–glycine were used to extract functional groups such as CH₂, CHCH₃, NH₂, COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole–dipole interaction model were compared to those obtained from polarizable-continuum model calculations.

中文翻译：

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分布极化率和偶极矩的构建块数据库，用于估计孤立或显式溶剂化介质中生物大分子的光学特性

由于本体中的原子或官能团特性通常无法通过实验方法获得，因此基于分区方案的计算方法已成为一种快速而准确的途径，可以从具有化学意义的构​​建块中估计材料行为。在几个应用中，一个全面和系统地建立的原子或基团极化率和相关光电量的数据库将非常有用，不仅可以设想生物大分子的线性或非线性光学特性，而且可以提高致力于经典力场的准确性模拟生化过程。在这项工作中，我们提出了此类数据库的第一个条目，其中包含从肽片段中提取的分布式极化率和偶极矩。 CH ₂  ,  CHCH ₃  ,  NH ₂ ,  COOH,  CONH ，从而允许构建多种化学相关环境。为了评估我们数据库的准确性，在 M06-HF/aug-cc-pVDZ 理论水平上，针对密度泛函理论计算测试了包含多达六个丙氨酸和甘氨酸残基的较大肽的重建特性。该过程对于极化率张量的对角线分量特别准确，误差高达 15%。为了明确包括溶剂效应，肽还被一盒水分子包围，水分子的分布使用 CHARMM 力场进行了优化。将经典偶极-偶极相互作用模型引入的溶剂效应与从可极化连续介质模型计算获得的溶剂效应进行了比较。