Theoretical Study of One-electron Redox Potentials of Some NADH Model Compounds

Several 1‐benzyl‐1,4‐dihydronicotinamide derivatives, which are important NADH model compounds were studied theoretically in acetonitrile. The performances of various DFT methods including B3LYP, B1B95, B3PW91, MPW1B95, MPWKCIS, and M06 were tested to calculate the redox potentials. The first theoretical protocol to predict the redox potentials of these derivatives is B1B95, whose reliability has been tested against almost all the available experimental data. Strikingly, the mean absolute derivations (MAD) and root mean square (RMS) error of the current theoretical model equal 0.015 and 0.017, respectively. By using this method, the important thermodynamic properties of BNAHs were investigated and the mechanisms of hydride transfer progress were explained. Besides, para‐substituents that have a big effect on these redox potentials of BNAH were systematically studied and carefully demonstrated.     

Theoretical Study on the NO2＋NO2^— Electron Transfer Reaction

The NO2 NO2^- electron transfer reaction was studied with DFT-B3LYP method at 6-311 G^* basis set level for the eight selected structures:four species favor the structure of “head to head”.The geometry of transition state was obtained by the linear corrdinate method.Three parameters,non-adiabatic activation energy(Ead),coupling matrix element(Hif) and reorganization energy(λ) for electron transfer reaction can be calculated.According to the reorganization energy of the ET reaction,the values obtained from George-Griffith-Marcus (GGM) method(the contribution only from diagonal elements of force constant matrix) are larger than those obtained from Hessian matrix method(including the contribution from both diagonal and off-diagonal elements), which suggests that the coupling interactions between different vibrational modes are important to the inner-sphere reorganization energy for the ET reactions in gaseous phase.The value of rate constant was obtained by using above three activation parameters.     

Dicopper(II) Anthraquinophanes as Multielectron Reservoirs for Oxidation and Reduction: A Joint Experimental and Theoretical Study

Two new dinuclear copper(II) metallacyclophanes with 1,4‐disubstituted 9,10‐anthraquinonebis(oxamate) bridging ligands are reported that can reversibly take and release electrons at the redox‐active ligand and metal sites, respectively, to give the corresponding mono‐ and bis(semiquinonate and/or catecholate) Cu^II₂ species and mixed‐valent Cu^II/Cu^III and high‐valent Cu^III₂ ones. Density functional calculations allow us to give further insights on the dual ligand‐ and metal‐based character of the redox processes in this novel family of antiferromagnetically coupled di‐ copper(II) anthraquinophanes. This unique ability for charge storage could be the basis for the development of new kinds of molecular spintronic devices, referred to as molecular magnetic capacitors (MMCs).     

Theoretical investigation of the isomers photolysis reaction for chlorine nitrate

For the reactant ClONO₂ the equilibrium geometry and energy have been calculated by using various density functional (DFT) theory methods. The harmonic vibrational frequencies were computed using the B3LYP method for the ground state of the reactant; the results were in good agreement with those of the experiment. It was shown that the DFT methods were superior to other ab initio methods in optimizing geometry and predicting vibrational frequencies. In the process of forming the products from the dissociation reactions of ClONO₂, the results indicated it undergoes the TS₂, but not the TS₁ transition state. According to the relative energies of various species, the potential energy surface reflected intuitively the mechanisms of these dissociation reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 44–50, 2003     

Proton Catalysis in the Redox Responsivity of a Mini‐Sized Photochromic Diarylethene

A thermally irreversible dithienylethene (DTE) photochrom can be turned into a thermally reversible one in presence of Cu^II triflate. A ring opening (DTEC closed→DTEO open) occurs through the formation of a copper‐containing fast transient intermediate. Stopped‐flow experiments monitored at 410 and 780 nm have allowed to show that the stoichiometry of this intermediate is DTE/Cu=1:1. At longer monitoring times (i.e., several seconds after mixing), the intermediate undergoes a slow decay while the residual DTEC closed form opens. A joint detailed kinetic and electrochemical analysis has unveiled a proton catalysis scenario in which electron transfer between DTEC and Cu^II, ligand exchange, protonation‐deprotonation equilibria of the cation radicals and ring opening are embedded into two main reaction cycles. At the beginning of the reaction, Cu^II is reduced into Cu^I and DTE is degraded without ring opening. Then, as the reaction progresses, the triflic acid released from the Cu^II reduction switches‐on a propagation cycle during which ring opens without any more Cu^II consumption. Cyclic voltammetry, spectro‐electrochemical measurements, delayed photocoloration experiments in presence of Cu^II and acid–base additions have confirmed the main features of the proton catalysis.     

B掺杂SWCNT表面吸附DNA碱基的理论研究

采用基于密度泛函理论的LDA (PWC)方法对比研究了纯单壁纳米碳管(SWCNT)和B掺杂单壁碳纳米管(B doped SWCNT)表面吸附DNA碱基(腺嘌呤)A、(胸腺嘧啶)T、(胞嘧啶)C、(鸟嘌呤)G的吸附特性和本质, 计算研究了最佳吸附位点, 吸附能, 以及稳定吸附模型的电子结构. 结果表明掺杂元素B的引入不会造成SWCNT的结构畸变, 可以局部影响碳纳米管的电子结构, 有效增强SWCNT与DNA碱基之间的电子相互作用, DNA碱基以化学吸附的形式修饰在B掺杂SWCNT的表面. 研究结果预示B掺杂SWCNT表面修饰DNA碱基有潜力成为DNA生物传感器生物识别界面的主要成分.     

Theoretical Study on the Structures,Spectra and Thermodynamic Property of Herbicidal Monosulfuron

The structure optimization and frequency calculation have been carried out at the B3LYP/6-31G* level towards herbicidal monosulfuron using density functional theory.The computed results showed that the intramolecular hydrogen bond N-H…N can stabilize the molecule.IR spectra,Raman spectra and thermodynamic properties under different temperatures were also obtained.The first vertical excited state electronic transition energy was calculated by time-dependent density function theory,and absorption wavelength of the lowest energy excitation was obtained at 339.59 nm,belonging to the near UV.These results provided the basis for studies on compound's structure-activity relationship.     

Theoretical study on the ring-opening isomerization reaction mechanism of the ring isomers of N8H8

Ring-opening isomerization from ring-shaped isomers to chain-shaped isomers of N(8)H(8) has been studied by a density function B3LYP method at 6-311+ +G** level. 20 ring-shaped isomers have been found to be able to transform into chain-shaped isomers, with 20 possible transition states got by ring-opening structure optimization. Furthermore, the ring-openings have been found in the longer N-N single bond by analyzing the length change of N-N bond of ring-shaped isomers in ring-opening processes. In addition, with the activation energies in ring-opening processes, the differences of the activation energies in isomerization between the isomers have been found according to the classification of rings. The activation energies in ring-opening isomerization of six-membered ring-shaped isomers are higher than that of the four-membered ring-shaped isomers. It indicates that six-membered ring-shaped isomers difficult in ring-opening in the isomerization are the steadiest ring-shaped isomers of N(8)H(8) while four-membered ring-shaped isomers easy in ring-opening are the most unstable.     

氟硼二吡咯类pH荧光探针PET光谱特性的理论计算

氟硼二吡咯(BODIPY)类pH荧光探针分子是基于光诱导电子转移(PET)的荧光探针分子, 识别基团氮原子上引入不同取代基可呈现不同的光学灵敏度. 本文应用密度泛函理论(DFT)及含时密度泛函理论(TD-DFT)方法对六种含不同取代基的探针分子进行了几何构型优化及激发态计算, 探讨了不同取代基对PET效应影响. 计算结果表明: 基态时这些探针分子的最高占有分子轨道(HOMO)和最低未占有分子轨道(LUMO)都在荧光母体BODIPY的π, π^*轨道, 而识别基团上氮原子孤对电子所在的轨道为HOMO-1轨道. 但是在激发态, 当氮原子上有两个取代基时, HOMO-1→LUMO跃迁的激发能都小于荧光团的HOMO→LUMO跃迁, 这将有可能产生PET效应并导致荧光熄灭, 而当氮原子上有一个取代基时不会出现这种现象. 通过激发态结构优化可以发现, 无论识别基团氮原子上有一个还是两个取代基, N原子的轨道对称性都发生变化, 由sp³→sp², 孤对电子占据在p轨道上, 其轨道能级升高至荧光团的HOMO和LUMO轨道之间, 将导致不同程度的PET效应, 与实验结果一致.     

Investigation of the pathways of excess electron transfer in DNA with flavin-donor and oxetane-acceptor modified DNA hairpins

Oxetane is a potential intermediate that is enzymatically formed during the repair of (6-4) DNA lesions by special repair enzymes (6-4 DNA photolyases). These enzymes use a reduced and deprotonated flavin to cleave the oxetane by single electron donation. Herein we report synthesis of DNA hairpin model compounds containing a flavin as the hairpin head and two different oxetanes in the stem structure of the hairpin. The data show that the electron moves through the duplex even over distances of 17 A. Attempts to trap the moving electron with N2O showed no reduction of the cleavage efficiency showing that the electron moves through the duplex and not through solution. The electron transfer is sequence dependent. The efficiency is reduced by a factor of 2 in GC rich DNA hairpins.     

木质素二聚体模型物裂解历程的理论研究

木质素作为生物质的主要成分之一, 是生物油的重要组分, 在工业生产中有着重要的应用. 生物质高温裂解液化制备生物油的过程伴随着木质素的裂解, 因此研究木质素高温裂解历程, 对生物油的制备有很大的帮助. 利用密度泛函方法对木质素在高温条件下的裂解历程进行理论研究, 并通过对各步反应的热力学焓变计算, 确定了初次裂解的路径为Cα—Cβ和β-O-4热裂解路径. 根据进一步的研究预测了裂解反应的主要产物.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Experimental and Theoretical Study of Enhanced Photocatalytic Activity of Mg‐Doped ZnO NPs and ZnO/rGO Nanocomposites

A systematic experimental and theoretical study of the origin of the enhanced photocatalytic performance of Mg‐doped ZnO nanoparticles (NPs) and Mg‐doped ZnO/reduced graphene oxide (rGO) nanocomposites has been performed. In addition to Mg, Cd was chosen as a doping material for the bandgap engineering of ZnO NPs, and its effects were compared with that of Mg in the photocatalytic performance of ZnO nanostructures. The experimental results revealed that Mg, as a doping material, recognizably ameliorates the photocatalytic performance of ZnO NPs and ZnO/graphene nanocomposites. Transmission electron microscopy (TEM) images showed that the Mg‐doped and Cd‐doped ZnO NPs had the same size. The optical properties of the samples indicated that Cd narrowed the bandgap, whereas Mg widened the bandgap of the ZnO NPs and the oxygen vacancy concentration was similar for both samples. Based on the experimental results, the narrowing of the bandgap, the particle size, and the oxygen vacancy did not enhance the photocatalytic performance. However, Brunauer–Emmett–Teller (BET) and Barret–Joyner–Halenda (BJH) models showed that Mg caused increased textural properties of the samples, whereas rGO played an opposite role. A theoretical study, conducted by using DFT methods, showed that the improvement in the photocatalytic performance of Mg‐doped ZnO NPs was due to a higher electron transfer from the Mg‐doped ZnO NPs to the dye molecules compared with pristine ZnO and Cd‐doped ZnO NPs. Moreover, according to the experimental results, along with Mg, graphene also played an important role in the photocatalytic performance of ZnO.     

Theoretical determination of electron affinity and ionization potential of DNA and RNA bases

The ionization potentials and electron affinities of thymine, cytosine, adenine, guanine, and uracil were determined at density functional level using different exchange‐correlation functionals and basis sets. Results showed that the computed ionization potentials are very close to the experimental counterparts. The sign of adiabatic electron affinities of adenine, thymine, and uracil is unaffected by the used level of theory while that for guanine and cytosine depends on both the used potential and basis set. Vertical electron affinities are always negative in agreement with the experimental indications. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1243–1250, 2000     

Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

纤维素二聚体模型物热裂解的热力学性质研究

纤维素是生产生物质燃料,精细化工品的重要原料. 热解是由纤维素解聚的重要手段之一. 了解纤维素热解的反应机理对发展高效的生物质转化技术具有重要意义. 我们利用密度泛函理论方法,以纤维素二聚体为模型,详细研究了其发生键均裂过程的热力学能量变化. 发现糖苷键和侧链C—C键的均裂相对于C—OH键和O—H键均裂在热力学上更优. 此外,我们发现不同物种的热力学稳定性与其在纤维素快速热解实验产物中的比例无关. 最后我们发现温度对反应能否自发发生具有重要的影响,为通过调节温度来改变不同类型反应的选择性提供了一条思路.