The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
复制标题
DOI：
10.1063/1.3597603
复制
发表时间：
2011-06-28
影响因子：
4.4
通讯作者：
Sprik, Michiel
中科院分区：
文献类型：
--
作者：
Costanzo, Francesca;Sulpizi, Marialore;Sprik, Michiel
应用最近发展的基于密度泛函理论（DFT）的质子和电子可逆消除分子动力学方法，计算了水溶液中质子耦合电子转移氧化酪氨酸和色氨酸的热化学常数。这种方法使我们能够从水合氢离子（h30 +）去质子化的自由能中估计出周期模型系统中质子（H+）的溶剂化自由能。以计算得到的H+的溶剂化自由能为参考，可以将水溶液的去质子化和氧化自由能转化为pK(a)和正常氢电极电位（NHE）。这种转化需要一定的热化学校正，这是在对氢苯醌氧化的类似研究中首次提出的[J]。Cheng， M. Sulpizi和M. Sprik， J. Chem。物理学报，2003,16(4):559 - 564。本文从不同的角度对水合氢离子的热力学状态进行了修正。与之前方案的关键区别在于，水合氢离子现在被当作质子从溶液到气相转移的中间物。通过对实验计算的pK(a)、NHE势和脱氢自由能的详细比较，评价了该方法的准确性。作为该技术的进一步应用，我们分析了溶剂在色氨酸自由基氧化酪氨酸中的作用。计算得到的氢原子转移反应的自由能变化与气相值非常接近，与实验结果一致。然而，分子动力学结果表明，溶剂对反应自由能的影响最小，同时伴随着溶剂的显著重组。(C) 2011年美国物理研究所。(doi: 10.1063/1.3597603)
The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3O+). Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3597603]