Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

机译：从分子动力学建模嵌入式系统的吸收线φ：教程评论

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Abstract >In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton–phonon coupling computed from a Born–Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects. </abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><Abstract Type =“main”XML：lang =“en”> <标题类型=“main”>抽象</ title> >在本教程审查中，我们专注于多尺度方法来计算电子吸收线形状嵌入在生物环境中的分子染料。为了用系统的核自由度对电子激发的耦合，我们使用从出生的oppenheimer分子动力学计算的激子 - 声子耦合的光谱密度（SD），这考虑了生物学的效果染料核和电子自由度的环境。给出了方法的理论基础，以及对沿着经典轨迹的电子激发来提取能量隙自相关函数的计算协议的综合描述。此外，来自最近公布的研究的基准应用是如何用衍生的SD如何在计算光谱中使用以准确模拟吸收线φ的示例，包括振动和温度效应。</ p> </摘要> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" >著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-21753/'>《International Journal of Quantum Chemistry》</a> <b style="margin: 0 2px;">|</b><span>2019年第1期</span><b style="margin: 0 2px;">|</b><span>共14页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Loco Daniele&option=202" target="_blank" rel="nofollow">Loco Daniele;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Cupellini Lorenzo&option=202" target="_blank" rel="nofollow">Cupellini Lorenzo;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>Laboratoire de Chimie ThéoriqueSorbonne Université CNRSParis France;</p> <p>Department Chemistry and Industrial ChemistryUniversity of PisaPisa Italy;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li > <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span><a href="https://www.zhangqiaokeyan.com/clc/1186.html" title="物理化学（理论化学）、化学物理学">物理化学（理论化学）、化学物理学;</a></span> </li> <li class="antistop"> <span class="lefttit">关键词</span> <p style="width: 86%;vertical-align: text-top;"> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=absorption lineshape&option=203" rel="nofollow">absorption lineshape;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=spectral density&option=203" rel="nofollow">spectral density;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=QM/MM molecular dynamics&option=203" rel="nofollow">QM/MM molecular dynamics;</a> </p> <div class="translation"> 机译：吸收线;光谱密度;qm / mm分子动力学; 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