Data set for the article "Refining Protein Amide I Spectrum Simulations with Simple yet Effective Electrostatic Models for Local Wavenumbers and Dipole Derivative Magnitudes" published by Baronio & Barth in Physical Chemistry Chemical Physics

Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the C=O bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.

对蛋白质酰胺I带的剖析或许是生物分析红外光谱应用最为广泛的技术之一。尽管在更细致的结构解析方面极具需求，但对该吸收带的定量描述仍然存在难度。本研究旨在通过优化数种静电模型，以再现蛋白质环境对局部酰胺I振子的固有波数的效应。我们考虑了主要的二级结构——α螺旋、平行和反平行β片层——并纳入最多21个酰胺基团。这些模型基于沿酰胺基团中C=O键的电势以及/或电场分量，该分量在最多四个原子上进行了研究。它们通过与基于BPW91、6-31G**水平密度泛函理论计算的Hessian矩阵重建进行比较而进行了基准测试。静电模型的表现取决于用于计算电场和电势的电荷集。在常见的力场中使用的Gromos和DSSP电荷集对于表现更佳的模型并非最优。通过考虑所考虑酰胺基团中氧、氮和氢原子的电场，我们实现了一个在性能和模型参数稳定性之间取得良好平衡的模型。该模型不仅描述了局部构象效应的一些方面，而且其单独的性能与结合显式局部构象效应的实现相仿。它优于局部氢键模型与局部构象效应的结合。尽管短程氢键模型的表现较差，但它捕捉了局部波数对分子环境的敏感性等重要方面。此外，我们还通过开发一个电静模型来描述局部酰胺I振子之间耦合的依赖性，从而改善了对其的描述。