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.

蛋白质酰胺I带（amide I band）分析或许是生物分析红外光谱学（bioanalytical infrared spectroscopy）应用最为广泛的场景之一。尽管人们迫切希望通过该吸收带实现更精细的结构解析，对其进行定量描述仍颇具挑战。本研究优化了多款静电学模型，旨在复现蛋白质环境对局部酰胺I振子（amide I oscillator）本征波数的影响。我们选取了三类主要二级结构——α螺旋、平行与反平行β折叠——所对应的至多21个酰胺基团作为研究对象。这些模型基于酰胺基团内最多四个原子处沿C=O键方向的电势及/或电场分量构建。我们通过与BPW91、6-31G**级别密度泛函理论（density functional theory）计算重构得到的黑塞（Hessian）矩阵进行对比，完成了模型的基准测试。静电学模型的性能取决于计算电场与电势时所采用的电荷集（charge set）。常见分子力场（force field）中所采用的Gromos与DSSP电荷集，并非性能更优模型的最优选择。一款同时考量目标酰胺基团内氧、氮、氢原子处电场的模型，在模型性能与参数稳定性之间实现了良好平衡。该模型可描述局部构象效应的部分特征，且单独使用时的表现与结合局部构象效应显式实现方案时相当。其性能优于局部氢键模型与局部构象效应的组合方案。尽管短程氢键模型的表现稍逊，但它能够捕捉到局部波数对分子环境敏感性的关键特征。此外，我们还针对偶极导数幅值（dipole derivative magnitude）随蛋白质环境的变化关系构建了静电学模型，从而优化了局部酰胺I振子间耦合效应的描述方式。