在液態水中連接兩個氫鍵之氫氧鍵結的旋轉

Abstract

由分子動力模擬顯示，當一個水分子的氫氧鍵結將氫鍵的接受者從一分子轉換到另一分子時，就會發生水分子之氫氧鍵結旋轉的跳躍機制(jump mechanism)。水分子處於氫鍵替換反應的過渡狀態時，只有幾個飛秒的時間，氫氧鍵結會同時連結兩個氫鍵的接受者，分別屬於兩個不同的水分子。氫氧鍵結旋轉的跳躍機制在生物及化學反應的過程中皆扮演重要角色。 針對過渡態的氫氧鍵結之定向相關函數是由這些連結兩個氫鍵的氫氧鍵結所計算得到。其中我們選用TIP4P/2005水模型且使用分子動力模擬來產生水分子位置及速度組態。另外分別由角速度相關函數及穩態之瞬間正則模(stable-INM)兩者的頻譜來預測定向相關函數，結果顯示這兩個方法皆能對模擬的定向相關函數在短時間內有良好的預測；其中穩態之瞬間正則模方法具有更佳的表現。

Indicated by MD simulations, the jump mechanism of molecular reorientation in water occurs when an OH group of a molecule trades its H-bond acceptor from one molecule to a third one. At the transition state for the HB exchange reaction, the OH-bond connects two H-bond acceptors, which are the initial and the final partners of the OH group, within a few femto-seconds. The jump mechanism of OH-bond reorientation is essential to biologic and chemical processes. In this thesis, we used the instantaneous-normal-mode (INM) approach to investigate the reorientation of the OH group connecting two H-bond acceptors initially. The OH-bond orientational time correlation functions (TCFs) were generated for these specific OH groups via MD simulations, which were performed with the TIP4P/2005 water model. The OH-bond orientational TCFs were calculated, respectively, with the power spectra of angular velocity autocorrelation functions and the stable-INMs. The predictions of the normal-mode approach agree with the simulation results at short times; however, the stable-INM approach gives a better agreement.