Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality

Wei Qichao; Zhao Weilong; Yang Yang; Cui Beiliang; Xu Zhijun; Yang Xiaoning

摘要

Abstract >Considerable interest in characterizing protein/peptide–surface interactions has prompted extensive computational studies on calculations of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calculations to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well‐established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small molecules on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calculations. For the hydrophobic surface, steered molecular dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calculation methods, especially at the region close to the surface. Therefore, a general principle of how to discriminate between methodological and sampling issues based on the interfacial characteristics of the system under investigation is proposed. </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</标题> >表征蛋白质/肽表面相互作用的相当兴趣促使广泛的计算研究对吸附的计算自由能。然而，在许多情况下，每个单独的研究都集中在将自由能量计算应用于特定系统;因此，难以将结果结合成一个广播图片，以选择感兴趣系统的适当策略。这里，系统地比较了三种良好的计算算法，并评估了在两个代表性表面上计算小分子的吸附自由能。结果清楚地表明研究的界面系统的特点对吸附无能量计算的准确性和效率具有重要影响。对于疏水性表面，转向分子动力学表现出最高效率，这似乎是增强采样模拟的有利选择方法。然而，对于带电的表面，只有伞采样方法具有准确探索吸附自由能表面的能力。水层与表面的亲和力显着影响自由能量计算方法的性能，尤其是在靠近表面的区域。因此，提出了一种基于调查中系统的界面特征来区分方法学和采样问题的一般原则。</ 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-16300/'>《Chemphyschem: A European journal of chemical physics and physical chemistry》</a> <b style="margin: 0 2px;">|</b><span>2018年第6期</span><b style="margin: 0 2px;">|</b><span>共13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=Wei Qichao&option=202" target="_blank" rel="nofollow">Wei Qichao;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Zhao Weilong&option=202" target="_blank" rel="nofollow">Zhao Weilong;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Yang Yang&option=202" target="_blank" rel="nofollow">Yang Yang;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Cui Beiliang&option=202" target="_blank" rel="nofollow">Cui Beiliang;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Xu Zhijun&option=202" target="_blank" rel="nofollow">Xu Zhijun;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Yang Xiaoning&option=202" target="_blank" rel="nofollow">Yang Xiaoning;</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>College of Chemical EngineeringNanjing Tech UniversityNanjing 210009 P.R. China;</p> <p>Department of Polymer ScienceUniversity of AkronAkron OH 44325-3909 USA;</p> <p>Department of ChemistryHaverford CollegeHaverford PA 19041 USA;</p> <p>Network Information CenterNanjing Tech UniversityNanjing 210009 P.R. China;</p> <p>College of Chemical EngineeringNanjing Tech UniversityNanjing 210009 P.R. China;</p> <p>College of Chemical EngineeringNanjing Tech UniversityNanjing 210009 P.R. China;</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=adsorption&option=203" rel="nofollow">adsorption;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=free energy calculations&option=203" rel="nofollow">free energy calculations;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=molecular dynamics&option=203" rel="nofollow">molecular dynamics;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=surface analysis&option=203" rel="nofollow">surface analysis;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=water chemistry&option=203" rel="nofollow">water chemistry;</a> </p> <div class="translation"> 机译：吸附;自由能量计算;分子动力学;表面分析;水化学; 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