Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details.
Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details.
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DNA 中电子转移的微秒模拟：基于原子细节的高效电子转移模型的自下而上参数化
DOI：
10.1021/acs.jpcb.6b11384
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
T. Kubař
中科院分区：
文献类型：
--
作者：
M. Wolter;M. Elstner;U. Kleinekathöfer;T. Kubař
电子在复杂分子系统中的长距离转移是生物化学和技术中的重要现象。近年来，我们一直在开发有效的模型来研究复杂系统中的ET，包括DNA作为一个突出的例子。从头算和模型的方法已被结合在一个“上的飞行”计算的ET参数，它可以用来传播核和电子的自由度同时。这些以前的努力，旨在获得一个有效的非绝热量子力学分子力学（QM/MM）模拟计划ET，使纳秒模拟ET在现实系统中成为可能。然而，这仍然不足以处理大型供体-桥-受体系统，如DNA中的ET，克服长腺嘌呤桥。因此，我们以自下而上的方式构建了一个理论模型。所有的量子化学以及力场的计算都被分子水平上所涉及的现象的理论模型所取代，包括分子环境的极化和弛豫，这在其他最近开发的ET理论模型中经常被忽略。采用非绝热模拟方案，不需要关于ET机制的假设。因此，保留了模拟的预测能力，同时将可访问的时间尺度的限制推到微秒以上。这种基于模型的模拟方案适用于ET在各种DNA物种。对于原型DNA ET系统、polyA序列以及包含腺嘌呤作为桥位点的序列GTnGGG，观察到与“完全”原子非绝热QM/MM方案的良好一致性。此外，ET在更大，更复杂的DNA序列进行了模拟，并对结果进行了讨论。
The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an “on-the-fly” calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical–molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor–bridge–acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the “full” atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.
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影响因子：
56.9
作者：
MURPHY, CJ;ARKIN, MR;BARTON, JK
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15
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