Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.

中文翻译：

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利用碎片分子轨道方法计算出的蛋白质分子电子的隧穿矩阵元素和隧穿路径。

提出了实用的方法来计算隧道基质元素，并使用片段分子轨道（FMO）方法分析蛋白质电子转移（ET）反应的隧道途径。仅针对FMO中共价键分离所涉及的原子直接使用最小基集可以通过具有成本效益的两体校正（FMO2）的蛋白质主链正确描述ET，而不会损失双zeta的质量基集。当前的FMO代码已与密度泛函理论，可极化连续体模型和模型核心电势接口，基于FMO的蛋白质ET计算可考虑电子相关性，溶剂化和过渡金属氧化还原中心的影响。α-螺旋和β-链构象，（2）在理想的α-螺旋和β-链构象中由聚丙氨酸接头共价桥接的两个质体醌之间的ET ，以及（3）钌（Ru）和铜（Cu）之间的空穴转移复合物通过一段聚甘氨酸接头共价桥接，作为金丝氨酸Ru修饰衍生物的模型。