WATLab, and Department of Chemistry University of Waterloo Waterloo, Ontario Canada N2L 3G1.
Langmuir. 2021 May 11;37(18):5540-5547. doi: 10.1021/acs.langmuir.1c00283. Epub 2021 Apr 21.
Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N-Si covalent bonding, while STM imaging reveals that such N-H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O-Si bonding configuration resulting from O-H dissociative adsorption is more thermodynamically favorable than the experimentally observed N-Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.
通过将扫描隧道显微镜（STM）和 X 射线光电子能谱（XPS）的结果与基于密度泛函理论（DFT）的从头算相结合，确定了丙氨酸在 Si（111）7×7 上的分子吸附键合构型和特定的界面化学。N 1s 区域的 XPS 光谱表明，丙氨酸分子通过 N-Si 共价键结合到 7×7 表面，而 STM 成像显示，丙氨酸发生了 N-H 离解吸附，在相邻的 Si adatoms 和 restatoms 对上，脱氢的丙氨酸部分和离解的 H 原子分别占据 Si adatoms 和 restatoms 位置。在样品偏压高于+2 V 时，脱氢的丙氨酸表现为一个明亮的圆形突起，略微偏离 Si adatoms 位置，向对面的 Si adatoms 倾斜，穿过二聚体壁。这种偏离中心的特征可以归因于脱氢的丙氨酸中富电子的羰基 O 与穿过二聚体壁的缺电子的最近 Si adatoms 之间的静电吸引。我们的 DFT 计算还表明，O-H 离解吸附导致的单齿 O-Si 键合构型比实验观察到的 N-Si 键合构型热力学上更有利，这表明界面离解吸附反应是动力学控制的，而不是热力学驱动的过程。在第二层（过渡层）中的丙氨酸分子被发现通过 N···HO 氢键附着在第一层（界面层）中的丙氨酸分子上，这得到了存在于 401.0 eV 的 N 1s 特征的支持。在 STM 中也观察到一个与第一层脱氢丙氨酸通过氢键结合的丙氨酸分子，它靠近脱氢第一层丙氨酸中游离 OH 基团的预期位置，是一个更亮更大的突起。在室温下，可能由于甲基的空间位阻，无法得到厚的两性离子丙氨酸膜。
