QM/MM Study on the Light Emitters of Aequorin Chemiluminescence,Bioluminescence, and Fluorescence: A General Understanding of the Bioluminescence of Several Marine Organisms

Aequorea victoria is a type of jellyfish that is known by its famous protein, green fluorescent protein (GFP), which has been widely used as a probe in many fields. Aequorea has another important protein, aequorin, which is one of the members of the EF‐hand calcium‐binding protein family. Aequorin has been used for intracellular calcium measurements for three decades, but its bioluminescence mechanism remains largely unknown. One of the important reasons is the lack of clear and reliable knowledge about the light emitters, which are complex. Several neutral and anionic forms exist in chemiexcited, bioluminescent, and fluorescent states and are connected with the H‐bond network of the binding cavity in the protein. We first theoretically investigated aequorin chemiluminescence, bioluminescence, and fluorescence in real proteins by performing hybrid quantum mechanics and molecular mechanics methods combined with a molecular dynamics method. For the first time, this study reported the origin and clear differences in the chemiluminescence, bioluminescence and fluorescence of aequorin, which is important for understanding the bioluminescence not only of jellyfish, but also of many other marine organisms (that have the same coelenterazine caved in different coelenterazine‐type luciferases).     

氮混杂金属卟啉吸收光谱性质的理论研究

采用密度泛函理论在B3LYP/6-31+G(d)水平上研究了4种金属Mg, Ni, Cu, Zn配位的自由卟啉(FBP)及氮混杂卟啉(NECP)的几何结构及分子轨道能级. 采用含时密度泛函理论(TD-DFT)方法计算了金属与2种卟啉配位后在气体条件下的电子吸收光谱, 包括激发能、 吸收波长、 跃迁组成和振子强度.计算结果表明, 与金属配位的FBP(M-FBP)具有D_4h对称性, 分子轨道能级HOMO/HOMO-1和LUMO/LUMO+1因能级相近发生简并, HOMO-LUMO轨道能级差大约3.0 eV, 在Soret带出现较强吸收峰.由于C/N原子位置的改变, 非对称性结构的M-NECP前线轨道组成发生改变, 轨道能级差(HOMO-LUMO)减小至2.6 eV左右, 且能级发生分裂, Soret带出现多个电子吸收谱峰, Q带也出现吸收峰. 本文研究了水、 氯仿和苯3种不同极性溶剂对M-FBP和M-NECP的分子轨道及电子吸收光谱的影响, 结果表明, 随溶剂极性减弱金属配合物的电子吸收光谱发生红移, 并且吸收峰强度增强.     

一类五核平面开口型过渡金属原子簇电子吸收光谱和二阶非线性光学性质的TDDFT研究

运用TDDFT B3LYP/LanL2DZ方法, 研究了一类具有非中心对称的五核平面开口构型过渡金属原子簇化合物[MoS₄Cu₄(py)₆X₂] (X＝Br, I)的电子吸收光谱和静态二阶非线性极化率, 估算了晶体的宏观二阶非线性光学系数. 电子吸收光谱的计算结果与实验测量结果比较符合; 碘系簇合物的静态二阶非线性极化率大于溴系. 详细讨论了该类金属簇合物电子吸收光谱的归属及其相关联的电子跃迁方式; 在微观水平上阐述了其二阶非线性光学性质的起源. 研究结果表明外围无机卤素配体4p/5p轨道到簇芯[MoS₄]杂化轨道的电子转移对静态二阶非线性极化率的贡献大于有机配体的贡献; 而过渡金属簇芯内的电子转移也有较大的贡献. 这对于理解过渡金属原子簇化合物内的电子转移对光学激发的作用以及用来设计新的无机-有机杂化二阶非线性光学材料有较大的帮助.     

含氯不对称配体8-羟基喹啉铝配合物电子和光谱性质的TDDFT研究

以含时密度泛函理论(TDDFT) B3LYP方法通过电子结构计算研究了含氯不对称配体8-羟基喹啉铝配合物AlQ(ClQ)₂的吸收和发射光谱性质. 计算表明, 第一激发态与基态结构变化主要集中在单一含氯配体中, 与mer-AlQ₃相比, 前线占有轨道离域程度变大而未占据轨道则定域化程度提高. 最大吸收主要来自配体内电荷转移跃迁, 电荷从苯酚环和氯向含氮的吡啶环跃迁. 电子陷入态计算表明, 抽取电子能量比AlQ₃相应值略大, 与实验结果一致.     

靛蓝及其取代物的密度泛函理论研究

运用量子化学中密度泛函理论(DFT)方法,在B3LYP／6-31G^ 水平上对靛蓝及其芳环4,4′-,5,5′-,6,6′-,7,7′-取代衍生物进行理论计算．探讨了F,Cl,Br,NO2,CH3O,CH3在不同位置的取代对分子的几何构型、电子结构和电子光谱的影响,获得与实验结果相一致的结论．还用含时密度泛函理论(TD-DFT)方法在相同水平计算其电子光谱．结果表明靛蓝及其芳环取代衍生物的最低激发单重态(S1)均源自HOMO-LUMO(π-π^*)跃迁．     

Understanding Bacterial Bioluminescence: A Theoretical Study of the Entire Process,from Reduced Flavin to Light Emission

Bacterial bioluminescence (BL) has been successfully applied in water‐quality monitoring and in vivo imaging. The attention of researchers has been attracted for several decades, but the mechanism of bacterial BL is still largely unknown due to the complexity of the multistep reaction process. Debates mainly focus on three key questions: How is the bioluminophore produced? What is the exact chemical form of the bioluminophore? How does the protein environment affect the light emission? Using quantum mechanics (QM), combined QM and molecular mechanics (QM/MM) and molecular dynamic (MD) calculations in gas‐phase, solvent and protein environments, the entire process of bacterial BL was investigated, from flavin reduction to light emission. This investigation revealed that: 1) the chemiluminescent decomposition of flavin peroxyhemiacetal does not occur through the intramolecular chemical initiated electron exchange luminescence (CIEEL) or the “dioxirane” mechanism, as suggested in the literature. Instead, the decomposition occurs according to the charge‐transfer initiated luminescence (CTIL) mechanism for the thermolysis of dioxetanone. 2) The first excited state of 4a‐hydroxy‐4a,5‐dihydroFMN (HFOH) was affirmed to be the bioluminophore of bacterial BL. This study provides details regarding the mechanism by which bacterial BL is produced and is helpful in understanding bacterial BL in general.     

Effects of Electron Donating Ability of Substituents and Molecular Conjugation on the Electronic Structures of Organic Radicals

The geometries and electronic structures of a series of electron donor-acceptor radical molecules have been studied theoretically. The computational results show that the introduction of substituents with strong electron donating ability into tri-(2,4,6-trichlorophenyl) methyl(TTM) radicals enables the radical molecules to form the non-Aufbau electronic structure. The difficulty of forming the non-Aufbau electronic structure decreases with the enhancement of the electron donating ability of the substituent, but the expansion of the molecular conjugated system is not conducive to the formation. The hybridization of different fragments in molecular orbitals results in the disproportionation of orbital energy level and forms a staggered energy level structure. The electronic structure of radical molecules can be adjusted by substituents and molecular skeleton profoundly, which is a very effective means for molecular design.     

4-硝基-1,3-丁二烯基胺分子的氢键效应

在从头计算的水平上, 利用杂化密度泛函理论研究了溶剂对4-硝基-1,3-丁二烯基胺分子的几何结构、分子内的电荷分布和电荷转移态的能量漂移的影响. 在四种极性溶剂中, 我们构造了包括氢键作用的超分子结构. 分别研究了由极化连续模型模拟的溶剂和溶质分子的长程相互作用, 溶剂和溶质分子的氢键作用, 以及溶剂和溶质分子的整体作用对分子结构和性质的影响. 研究结果表明氢键作用引起了溶质分子结构和性质的较大变化, 从而将明显地影响该类分子的非线性光学性质. 因此, 在模拟溶剂效应时需要考虑氢键作用.     

Ni2＋与双甘氨肽相互作用的理论研究

使用密度泛函的B3PW91方法研究了Ni^2＋离子与二肽的相互作用, 优化了各种可能复合物的三重态、五重态和单重态. 研究结果表明所得配合物的基态为三重态, 基态复合物基本上是以二肽分子中碳链上的两个O原子和末端N原子形成的二齿或三齿配合物. 在气相中基态的最稳定复合物构型为三配位的³I, 而在溶液中为两性离子配合物³VIII. 在配合过程中, 静电相互作用占主导地位. 三重态的配位过程中配体的电子主要转移到空3d轨道和4s4p上而五重态中配体的电子主要转移到单占据d轨道上, 导致自旋密度转移到配体上去. 溶剂化过程中, 溶剂与溶质间的静电相互作用起主导作用.     

Influence of Solvent Polarity and Hydrogen Bonding on the Electronic Transition of Coumarin 120: A TDDFT Study

The characteristics of the electronic transition energy of Coumarin 120 (C120) and its H‐bonded complexes in various solvents have been examined by time‐dependent density functional theory (TDDFT) in combination with a polarizable continuum solvent model (PCM). Molecular structures of C120 and its H‐bonded complexes are optimized with the B3LYP method in PCM solution, and the dihedral angle H14? N13? C7? H15 is dependent on solvent polarity and the type of H‐bond. A linear correlation of the absorption maximum of C120 with the solvent polarity function is revealed with the PCM model for all solvents except DMSO. The experimental absorption maximum of C120 in nine solvents is well described by a PCM–TDDFT scheme augmented with explicit inclusion of a few H‐bonded solvent molecules, and quantitative agreement between our calculated results and experimental measurements is obtained with an average error of less than 2 nm. H‐bonding at three different sites shifts the absorption wavelength of C120 either to the blue or to the red, that is, a significant role is played by solvent molecules in the first solvation shell in determining the electronic transition energy of C120. The dependence on the H‐bonding site and solvent polarity is examined by using the Kamlet–Taft equation for solvatochromism.     

Theoretical investigations on the carbazole‐based conjugated polymers containing electron‐donating divinylaryl

The polycarbazoles have been proved to efficiently suppress the keto defect emission. Three carbazole‐based conjugated polymers, poly[9‐methyl‐3‐(4‐vinylstyryl)‐9H‐carbazole] (PBC), poly[9‐methyl‐3‐(2‐(5‐vinylthiophen‐2‐yl)vinyl)‐9H‐carbazole] (PBT) and poly[9‐methyl‐3‐(2‐(5‐vinylfuran‐2‐yl)vinyl)‐9H‐carbazole] (PBF), were investigated by quantum‐chemical techniques, and gain a detailed understanding of the influence of carbazole units and the introduction of electron‐donating on the electronic and optical properties. The electronic properties of the neutral molecules, HOMO‐LUMO gaps (ΔE), in addition to ionization potential (I_p) and electron affinity (E_a), are studied using B3LYP density functional theory. The lowest excitation energies (E_g) and the absorption wavelength are studied using the time dependent density functional theory (TDDFT). The calculated results show that all three series of polymers have good planarity. And the highest‐occupied molecular orbital (HOMO) energies lift about 0.36–0.61 eV and thus the I_P decrease about 0.01–0.19 eV compared to polycarbazole, suggesting the significant improved hole‐accepting and transporting abilities. By introducing the electron‐donating 1,4‐divinylphenylene or 2,5‐divinylthiophene or 2,5‐divinylfuran units in the backbone, and the lowest‐unoccupied molecular orbital (LUMO) energies decrease 0.20–0.39 eV. In addition, PBC, PBT and PBF have longer maximal absorption wavelengths than polycarbazole. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 706–714, 2009     

Re_2(edt)_4的电子结构和电子吸收光谱的从头算研究

用密度泛函理论中的B3LYP/CEP-4G方法对Re2（edt）4进行了结构优化和自然键轨道计算,并用单电子激发组态相互作用方法（CIS）计算了Re2（edt）4的分子轨道和激发态。结果表明Re-Re之间不存在明显的三重键,进而很好地解释了Re2（edt）4分子的电子吸收光谱。     

一系列水合和非水合铀酰卤族(F,Cl,Br)配合物在水溶液中的结构和紫外吸收光谱性质的密度泛函理论研究

本文考虑相对论效应并应用密度泛函理论(DFT)研究水溶液中UO2Xn(H2O)5-n(X=F,Cl,Br;n=1～4)和UO2Xn(X=F,Cl,Br;n=1～6)一系列水合和非水合铀酰化合物的结构和紫外吸收光谱性质。将这一系列物质命名为Xnm(X为F,Cl,和Br;n为卤素配体个数,m为水分子配体的个数)。在水溶液中,溶剂化效应采用类导体屏蔽模型(COSMO)并采用SAS溶剂接触曲面构造空穴模拟水溶剂对配合物的作用。配合物的紫外光谱性质采用考虑旋-轨耦合相对论效应的含时密度泛函(SO-TD-DFT)进行计算。U=O键随着F配体数目的增加而明显伸长,然而随Cl和Br配体数目的增加变化较小。随X配体数目的增加和水分子参与配位,铀与X的结合能逐渐减弱。配合物的紫外光谱计算表明铀酰氟的各种配合物并不出现特征吸收峰,而铀酰氯和铀酰溴的各种配合物均有特征吸收光谱。通过分子轨道分析可以很好解释光谱所体现的特征。     

Quantum Chemical Study Aimed at Modeling Efficient Aza-BODIPY NIR Dyes: Molecular and Electronic Structure,Absorption, and Emission Spectra

A comprehensive study of the molecular structure of aza-BODIPY and its derivatives, obtained by introduction of one or more substituents, was carried out. We considered the changes in the characteristics of the electronic and geometric structure of the unsubstituted aza-BODIPY introducing the following substituents into the dipyrrin core; phenyl, 2-thiophenyl, 2-furanyl, 3-pyridinyl, 4-pyridinyl, 2-pyridinyl, and ethyl groups. The ground-state geometries of the unsubstituted Aza-BODIPY and 27 derivatives were computed at the PBE/6-31G(d) and CAM-B3LYP/6-31+G(d,p) levels of theory. The time-dependent density-functional theory (TDDFT) together with FC vibronic couplings was used to investigate their absorption and emission spectra.     

西红花酸二甲酯电子吸收光谱与热力学性质的理论研究

使用密度泛函理论B3LYP方法,对西红花酸二甲酯的结构、电子吸收光谱、热力学性质进行理论计算研究,并基于Tomasi的极化统一场模型(PCM)讨论溶剂效应.结果显示,溶剂对西红花酸二甲酯的前线分子轨道特征几乎无影响,溶剂作用使该分子的最大吸收波长红移约42 nm,红移程度与溶剂极性无关.西红花酸二甲酯分子的气态热力学性质与温度的关系式分别为:Cm p=189.782+0.925T,S m=457.503+1.366T,H m=1164.899+0.195T+4.671×10-4T2,Gm=1164.899-0.263T-8.989×10-4T2.298 K时,西红花酸二甲酯分子的气态标准摩尔生成焓和标准摩尔生成自由能分别为-1180.67和-733.23 kJ·mol-1.     

酞菁基态和激发态的计算

采用DFT方法在B3LYP/6-31G水平上得到了H2Pc(酞菁)的优化结构,并在此基础上采用TDDFT方法计算了激发态.通过与H2P(卟吩)、H2Pz(四氮卟吩)和H2TBP(四苯并卟啉)的比较,研究了苯并取代以及氮杂取代对H2Pc的分子轨道和激发态的影响,上述取代效应使得H2Pc的HOMO-1(132 b1u)和HOMO-3(130 b1u)轨道发生了翻转,氮杂取代的影响尤其明显.这两种取代都使得Q带振子强度增大,在这四种化合物中,H2Pc的振子强度最大.TDDFT计算结果与实验值符合得较好.     

R2C＝GeH2和R2Ge＝CH2结构与成键特征的理论研究

用密度泛函理论(DFT), 在B3LYP/6-31＋G(d, p)水平上研究了取代基对二取代锗烯R₂Ge＝CH₂和R₂C＝GeH₂ [R＝H, OH, NH₂, SH, PH₂, F, Cl, Br, (NHCH)₂, CH₃, (CH)₂]的影响. 研究发现π供电子取代基在碳上时更能引起分子结构在锗端的锥型化. 碳原子上的π电子给予取代基的给电子效应越强, R₂C的单-三态能量差越大, π电子的反极化效应就越强, 使得化合物的结构在锗端发生的弯曲越明显, 从而使得弯曲结构更稳定. 和前人的计算相比, 碳上的给电子取代基对GeH₂结构影响大于它对SiH₂的影响.     

ChemInform Abstract: Electronic Structure,Vibrational Spectra and Thermodynamics of P4O8.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Molecular Association and Solvent Effects in the Electronic and NMR Spectra of the Tricyanoterpyridineruthenate(II) Complex

Solvent effects on the electronic structure and NMR spectra of the[Ru(terpy)(CN)₃] complex(terpy = 2,2,6,2-terpyridine) have beeninvestigated and interpreted using quantum mechanical semiempirical methods.A systematic splitting of the electronic bands in the visible is observed, in addition to theirbathochromic shifts depending on the acceptor number of the solvent. The solvent-inducedsplittings are rationalized in terms of the involvement of several charge—transfertransitions exhibiting distinct participation of the ruthenium (II), terpy, and CN^–orbitals. Direct evidence of solvent interaction at the cyanide ligands is observedin the [¹³C]NMR spectra. The most enhanced solvent effects are at the middle¹³C-4 and ¹H-4 atoms of terpy, in complete agreement with the theoreticalcalculations. In D₂O, stacking interactions involving the terpy ligands are detectedfrom the [¹H]NMR spectra, leading to a bimolecular association constant of90 mol^–1-dm³. In acetone—D₂O mixed solvents, the spectroscopic changes areindicative of preferential solvation departing from the ideal linear behavior.