光化学反应作为最重要且最基本的反应之一，早已渗透于人类生活的方方面面，例如生物领域的光动力学治疗，环境领域的光催化降解，以及材料领域的分子光开关等。其如此广泛的应用一直吸引着实验与理论科研工作者的不断探究。本论文采用完全活化空间自洽场(CASSCF)和多参考态二级微扰(CASPT2)等理论计算方法研究了非天然碱基dTPT3在水溶液中的光物理机理、4-2'-对羟基苯吡啶分子的激发态分子内质子转移过程，以及邻羟基绿色荧光蛋白发色团的光物理机理。这些工作为实验提供理论参考的同时，也为下一步的实验设计指明方向。本论文的概况如下： (1)通过引入非天然碱基对，比如dNaM:d5SICS和dTPT3:dNaM，能够大幅度增加基因信息的存储量；但是，目前尚不明确这些非天然碱基对是否和天然碱基对一样具有很高的光稳定性。最近实验研究表明，dTPT3经光激发后会弛豫到最低三重态并产生高量子产率的单线态氧，导致基因突变和DNA光损伤。由于其光物理机理并不清楚，因此我们采用QM(MS-CASPT2//CASSCF)/MM方法研究了dTPT3在水溶液中的光谱性质和激发态弛豫机理。计算结果表明，dTPT3经光激发后，可以通过两条主要的激发态弛豫通道有效地失活到最低三重态T1(3ππ*)。其中，S2/S1/T2交叉区域在激发态弛豫通道中起着至关重要的作用。本研究将为我们理解非天然碱基的光物理机理、设计光稳定的非天然碱基提供重要的理论参考。 (2)激发态分子内或分子间的质子转移过程存在于许多生物体系和材料体系中；其中，发生在电负性较强的两个原子之间的激发态质子转移过程已得到实验和理论的广泛研究，而激发态质子转移至碳原子等中性原子的理论计算工作相对较少。因此，我们采用激发态电子结构计算(CASSCF/CASPT2)和非绝热动力学模拟(OM2/MRCI)相结合的方法系统地研究了4-2'-对羟基苯吡啶分子(HPP)的激发态性质及失活途径。计算结果表明，HPP分子存在两条激发态失活通道：(i) 94%的轨迹通过超快的激发态分子内质子转移(ESIPT)过程到达酮式S1极小点，再经酮式交叉点失活到电子基态；(ii) 剩余6%直接经过醇式的交叉点失活到电子基态。当体系到达S0态后，酮式结构会通过基态的氢转移过程返回至醇式结构。本工作为激发态质子转移至中性原子的反应提供了重要的理论参考。 (3)绿色荧光蛋白发色团(GFP)在生物领域中有着广泛的应用，例如可以作为生物成像工具。最近，实验上新合成了三种邻羟基绿色荧光蛋白发色团(OHIM，CHBDI和MHBDI)，具有奇特的光物理现象，但是其微观机制并不清楚。我们采用高精度的电子结构计算方法(MS-CASPT2和CASSCF)系统地研究了三者的激发态分子内质子转移过程和激发态失活机理。计算结果表明，OHIM和CHBDI的ESIPT过程需要分别克服3.4和4.2 kcal/mol的能垒，但是MHBDI中的ESIPT则是无垒的。此外，我们在这三个体系中发现了两条高效的S1激发态失活通道。第一条是直接经过醇式的圆锥交叉点失活到电子基态；第二条则是先通过S1 ESIPT到达酮式S1极小点，再经酮式S1/S0圆锥交叉点失活到电子基态。最后，我们讨论了不同取代基对邻羟基绿色荧光蛋白发色团的光物理过程的影响，为下阶段设计性能更加优越的绿色荧光蛋白发色团提供了重要的理论参考。

Photochemical reaction, as one of the most important and basic reactions, has already penetrated into every aspect of human life. Such as photodynamic therapy in the biological field, photocatalytic degradation in the environmental field, and photoswitches in the material field. Such wide applications have always attracted the constant researches of experimental and theoretical researchers. In this dissertation, we have employed complete active space self-consistent field (CASSCF) method and other theoretical calculation methods to explore three systems. (1) Excited-state relaxation mechanism of a semisynthetic dTPT3 base in aqueous solution. (2) Excited-state proton transfer process of 4-(2’-hydroxyphenyl)pyridine. (3) Mechanistic insights into the photophysics of ortho-hydroxyl GFP core chromophores. These works provide theoretical reference for experiments, and guide the design of the next step. The main contents are summarized as follows: (1)Semisynthetic alphabet can potentially increase the genetic information stored in DNA through the formation of unusual base pairs, such as dNaM:d5SICS and dTPT3:dNaM. However, it is not clear whether these unnatural base pairs have high photostability as natural base pairs. Recent experiments show that near-visible-light irradiation on the dTPT3 chromophore could lead to the formation of a reactive triplet state and of singlet oxygen in high quantum yields. However, the detailed excited-state relaxation paths that populate the lowest triplet state are unclear. Herein we have for the first time employed the QM(MS-CASPT2//CASSCF)/MM method to explore the spectroscopic properties and excited-state relaxation mechanism of the aqueous dTPT3 chromophore. On the basis of the results, we have found two main excited-state relaxation pathways that efficiently populate the lowest triplet state. Morover, an S2/S1/T2 intersection region is found to play a vital role in the excited-state relaxation. These new mechanistic insights help understand the photophysics and photochemistry of unusual base pairs. (2)Excited-state intramolecular or intermolecular proton transfers exist in a lot of molecular and biochemical systems and material devices. Most of previous studies mainly focus on excited-state proton transfer between two highly electronegative atoms, whereas there has been much less theoretical work on ESIPT to other atoms such as carbon. We have employed combined electronic structure calculations (CASPT2 and CASSCF) and trajectory-based surface-hopping dynamics simulations (OM2/MRCI) to explore the excited-state properties and decay dynamics of 4-(2’-hydroxyphenyl)- pyridine. We have found two S1 excited-state radiationless channels. (i) 94% trajectories undertake a dynamically ultrafast and thermodynamically favorable ESIPT process to generate the S1 keto species, then, it decays to the S0 state via the keto S1/S0 conical intersection. (ii) the remaining 6% ones jump to the S0 state via the enol S1/S0 conical intersections. Once arrival on the S0 state, the keto species will return to the enol one by an efficient ground-state reverse hydrogen transfer reaction. This work provides a theoretical reference for the ESIPT to neutral atoms. (3)Green fluorescent proteins (GFPs) have a lot of ubiquitous applications in molecular biology, for example, as powerful bio-imaging tools. Herein we have employed the MS-CASPT2//CASSCF method to study the S1 excited-state intramolecular proton transfers (ESIPTs) of recently synthesized ortho-hydroxyl GFP core chromophores, i.e. OHIM, CHBDI, and MHBID, and their excited-state relaxation pathways. We have found that in OHIM and CHBDI, the ESIPT process is associated with small barriers of 3.4 and 4.2 kcal/mol; while, in MHBDI, it becomes essentially barrierless. Moreover, we have found two main S1 excited-state radiationless channels. In the first one, the enol S1 species decays to the S0 state via the enol S1/S0 conical intersection. In the second one, the keto S1 species is first generated through the ESIPT event; then, it is de-excited into the S0 state in the vicinity of the keto S1/S0 conical intersection. Finally, we have discussed the effects of different functional groups at the ortho-hydroxyl GFP chromophores on their photophysics. The insights gained from the present work may help guide the design of new ortho-hydroxyl GFP core chromophores with improved fluorescence emission and brightness.