Effective Ion Mobility Calculations for Macromolecules by Scattering on Electron Clouds
Effective Ion Mobility Calculations for Macromolecules by Scattering on Electron Clouds
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DOI：
10.1021/jp505012c
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发表时间：
2014-08-28
影响因子：
2.9
通讯作者：
Shvartsburg, Alexandre A.
中科院分区：
文献类型：
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作者：
Alexeev, Yuri;Fedorov, Dmitri G.;Shvartsburg, Alexandre A.
离子迁移谱/质谱（IMS/MS）平台的广泛商业化和不断提高的分辨率已经导致IMS在气相生物分子结构表征中的应用激增。这重新引起了人们对更准确和快速的离子迁移率计算的兴趣，这些计算需要从测量中得出离子的几何形状。一种基于电子密度等值面散射（SEDI）的方法反映了分子碰撞的物理过程，在十年前被证明比涉及原子坐标的常用方法优越上级，但由于极端的计算需求，对于大离子仍然不切实际。在这里，我们加速SEDI高达500倍，使用碎片分子轨道方法的表面生成和多路复用散射算法结合新的网格外推程序的横截面评估。超级计算机上代码的并行化进一步提高了速度，允许对蛋白质（由超过一百万个表面点定义）进行SEDI计算，精度为
Broad commercialization and increasing resolving power of ion mobility spectrometry/mass spectrometry (IMS/MS) platforms have engendered an explosion of IMS applications to structural characterization of gas-phase biomolecules. That has renewed interest in more accurate and rapid ion mobility calculations that are needed to elicit ion geometries from the measurements. An approach based on scattering on electron density isosurfaces (SEDI) that mirrors the physics of molecular collisions was proven superior to the common methods involving atomic coordinates a decade ago but has remained impractical for large ions because of extreme computational demands. Here, we accelerate SEDI by up to similar to 500 times using the fragment molecular orbital approach for surface generation and the multiplexed scattering algorithm in conjunction with the new grid extrapolation procedure for cross section evaluations. Parallelization of the code on a supercomputer has produced major further speed gains, allowing SEDI calculations for proteins (defined by over a million surface points) with a precision of