自由電子雷射器和傅裡葉變換質譜儀的組合使之成為一種研究生物分子和一些水和離子的溶解動力學的有力工具。而理論方法作為實驗的輔助手段常用于判斷一些分子的結構。在本論文中，我運用密度泛函理論和第一性分子動力學方法研究了陽離子化的氨基酸和一些水合陰離子的實驗紅外多光子吸收譜。 / 第二章研究了氫離子和鹼金屬離子化的天冬醯胺酸的紅外多光子吸收譜。以前有文獻用簡諧近似的方法研究過這個團簇，不過這種方法忽略了分子的動力學和非諧效應。我用第一性分子動力學方法重新研究了這個體系，結果顯示這種陽離子化的氨基酸的分子結構非常柔軟，在有限溫度下可以通過二面角的轉動和離子與氨基酸中的氧和氮原子距離的振動可以相互的轉化。而這些構型的相互轉化可以解釋實驗紅外吸收峰的展寬和相對強度變化趨勢。 / 第三章研究了水合碳酸氫根陰離子的紅外多光子吸收譜。以前的文獻指出，對於這種團簇，僅通過對比實驗和簡諧近似的紅外譜圖不能夠判斷是否只有一種異構體存在。應用第一性分子動力學方法，我發現簡諧近似紅外譜和實驗譜的不吻合之處，特別是水分子個數小於等於5時，水分子中氫原子的左右搖擺振動和來回搖擺振動吸收峰在實驗譜中的缺失。通過計算一系列異構體的熱能，我發現一些含量較少的異構體仍然對吸收峰有比較大的貢獻，考慮了這些結構的貢獻我們就可以理解為什麼隨著團簇尺寸的增加，一些吸收峰的強度有一定的變化趨勢。 / 最後兩章研究了水合磷酸二氫根的紅外多光子吸收譜。這是第一次我們和實驗組合作成果。在這個專案裡，我負責分析和全部的理論計算。對於這種團簇，實驗上測量了紅外譜的低頻和高頻區(n=1-4)。有趣的是，特別是體系只包含一個水分子時，兩個穩定的異構體均不能單獨解釋低頻和高頻的實驗結果。基於分子動力學的研究發現，有一個過渡態的吸收峰出現在了高頻區。其原因是氫原子的零點能和隧穿效應。與n=1類似,對於存在多個水分子的體系，實驗譜也揭示了低溫下的異構體效應，而這個效應使得簡諧效應完全失效。 / The combination of the FEL with FTICR makes it a powerful tool in researching the biochemical molecules and solvation dynamics of small hydrated ions. And theoretical methods are often employed in the determination of the molecular structures as auxiliary tools. In this thesis, density functional theory and ab initio molecular dynamics method have been applied to study the experimental infrared multiphoton dissociation (IRMPD) processes for cationized amino acids and hydrated anions. / The second Chapter is the AIMD simulated IR spectra for Asparagine cationized by H⁺, Li⁺, Na⁺, K⁺, and Cs⁺. The previous work simulated these type clusters with harmonic approximation in which the dynamics and anharmonicity effects were missed. My result shows that M⁺(Asn) complexes are very flexible and they could convert into each other at finite temperatures by torsional rotation and stretching the distances between the ion and N, O atoms in Asn. The broaden features and shift of the relative intensities of the vibrational profiles for these conformers are dependent on the structural flexibility of the complexes. / The third Chapter is the IRMPD spectra of the hydrated bicarbonate anion clusters for n=1-7. For some clusters, as mentions in the former harmonic results, comparing the experimental and calculated spectra does not always identify a single isomer as being responsible for the spectrum. By using AIMD technique, I found discrepancies between the harmonic and experimental spectra, especially for the absence of water wagging and rocking mode in the experimental result for n=1-5. By calculating the thermal energies of various isomers of each cluster, I found that the less dominate conformer also shows its large contributions to the vibrational profiles and this could explain the peak intensity trend as the cluster size increase. / The vibrational spectra for (HO)₂PO₂⁻(H₂O)n=1-4, 6, and 8 are presented in the last two chapters. It is the first time we collaborate with experiment group. In these works, I have done all the theoretical simulations. For these clusters, both the low and high (n=1-4) frequency regions of IRMPD spectra are measured. Interestingly for n=1, both the two stable isomer cannot alone represent both the low and high frequency profiles. Base on the AIMD simulations, I found that the existence of an unstable transient state shows it absorption profile in the high frequency region due to the zero point energy and tunneling effect of hydrogen atom. Similar to n=1, the IRMPD spectra of larger clusters (n>1) also show evidence for isomerization at cryogenic temperatures which leads to a complete breakdown of the harmonic approximation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Sun, Shoutian. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references. / Abstracts also in Chinese. / Sun, Shoutian.