In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations （70°, 30°, 140°） and （110°, 340°, 100°） for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as （10°, 280°, 210°）. Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.
采用半经验Austin Model 1(AM1)方法,计算了齐分子吡咯聚合物(PPy)的中性态和带电态的几何结构性质.与中性态相比,带电态下其分子结构表现在C-C键长发生显著改变,单电荷掺杂导致极化子元激发;当掺杂的双电荷随机放置时,出现了两种情况:一种情况下产生双极化子,另一种情况下会产生两个分立的极化子.通过控制链的长度,可实现极化子与双极化子之间的相变,从而揭示出在有机半导体材料中实现自旋极化输运的可能性.
