細胞受到氧化破壞後，DNA (deoxyribonucleic acid) 鹼基中的鳥糞嘌呤 (guanine) 及腺嘌呤 (adenine) 會分別形成黃嘌呤 (xanthine) 與次黃嘌呤 (hypoxanthine)，與正常鹼基配對之後會導致點突變。鹼基對的分子間氫鍵會影響整個核酸的結構和穩定，因此本文利用密度泛涵理論計算 (DFT) 研究黃嘌呤二聚物 (XX) 、胸線嘧啶二聚物(TT) 和兩者的配對錯合物 (XT) 之能量與芳香性，並進一步分析次黃嘌呤與正常鹼基的配對情形 (HT、TC) 作為比對。
藉由各種鹼基之氫鍵錯合物的天然鍵結軌域 (NBO) 分析結果，我們發現氫鍵若由相同原子所形成，則分子間的距離、E(2) 値和 Δs% 可以有效的判斷氫鍵的強弱及錯合物的穩定性，其中E(2) 値更包含了二級靜電效應的影響。
除此之外，本研究引進芳香性的簡諧振動模型 (Harmonic Oscillator Model of Aromaticity，HOMA) 以及核獨立化學位移 (Nucleus Independent Chemical Shifts，NICS) 方法分析錯合物的芳香性，證實外環雙鍵取代基會減弱分子的芳香性。鹼基使用羰基配對後，氫鍵的干擾使得鹼基分子的環上芳香性特徵受到改變，增加作用環的電子極化能力，若此羰基位在環的主要貢獻區域上，則整體的芳香性會增加較多。

The noncanonical nucleobases xanthine and hypoxanthine are important lesions that are formed from the canonical bases guanine and adenine by nitrogen loss when a cell is under oxidative stress. It is known that they lead to point mutations. Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. Our purpose is to understand the interaction between nucleotide bases. We have studied numerous model systems for dimers and mismatched pairs involving xanthine (X), thymine (T), hypoxanthine (H), and cytosine (C) at density functional theory (DFT).
The wavefunctions were analyzed by the Natural Bond Orbitals (NBO). If those two-dentate pairing modes were formed by the same functional groups, we can use E(2) (the second order perturbation energy), Δs% (the change of s-orbital contents) and the average intermolecular distances to describe the H-bonding strengths and stability of complexes. Among which, E(2) may show great correlation with secondary electrostatic interactions.
Furthermore, aromaticity of the ring of four compounds and their complexes was analyzed by the aromaticity index HOMA (Harmonic Oscillator Model of Aromacity) and NICS (Nucleus Independent Chemical Shifts). Aromaticity of the bases decreases with an increase of the number of double-bond substituents at the rings. Even if hydrogen bonding is much weaker perturbation than the substituent effect, H-bonds involving C=O groups in mismatched pairs may cause an increase of the aromatic character of the rings, but the increasing value is not identical in the pairs which build of the same compound, such as six thymine dimers. It is regard as whether H-bonds contribute to increasing the ring resonance.

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