光合释氧机理的ABEEM/MM/MD和BS-DFT理论研究

建立了S₂态光合释氧络合物（OEC）的原子-键电负性均衡模型（ABEEMσπ）的电荷参数,并使用ABEEM/MM/MD可极化力场的分子动力学模拟和对称性破损的DFT研究了光合作用制造氧气的微观机制.HF/STO-3G（采用此基组的原因请见引用文献）水平下的电荷拟合结果证明了ABEEMσπ模型计算电荷分布的合理性和高效性.MD模拟显示,S₂态Mn₄CaO₅的双向异构化过程伴随Ca上的水分子W3转移至Mn1（III）/Mn4（III）,它很可能作为底物水之一,与O5在S₄态结合产生O₂.基于此,考察了全自旋态下两种异构体形式中O－O键形成的自由基耦合机理.BS-DFT计算结果表明,开立方结构的释氧活性大大优于闭立方结构,金属锰和氧自由基的自旋耦合方式也是反应性的决定性因素,同时,OEC的结构灵活性对于S态循环和光合水分解至关重要.     

S掺杂促进Fe/N/C催化剂氧还原活性的实验与理论研究

向Fe/N/C非贵金属催化剂中再引入S掺杂是进一步提高其氧还原催化活性的有效方法。为了探究活性提高的原因,本文以三聚氰胺-甲醛树脂为前驱体,氯化钙为模板,氯化铁为铁源,通过添加硫氰化钾(KSCN)来控制热解催化剂的S掺杂量。通过对比分析催化剂的物化性质,结合密度泛函理论(DFT)计算,分析S掺杂促进Fe/N/C催化剂氧还原活性的原因。透射电子显微镜(TEM)和N_2吸脱附等温线测试结果表明,S元素可抑制含铁纳米粒子的形成,促使形成多孔碳结构,提高比表面积。X射线光电子能谱(XPS)结果表明,适量S前驱体可实现较高的S掺杂含量,得到最优的活性,过量的S反而会导致Fe和S的掺杂量同时降低,影响活性。DFT计算结果表明在Fe-N_4大环中引入S掺杂,可增强O_2分子和中间体OOH与Fe-N_4结构中的Fe的相互作用,促进形成Fe―O键,从而导致O―O键的键能显著降低,为后续反应O―O键的断裂提供可能,促进ORR反应的进行。     

Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution,Nominal S3 State Crystal Structures of Photosystem II

Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S₃ intermediate state of its Mn₄Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S₃ structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S₁ structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5−O6 separation of ∼1.5 Å. In the latest S₃ variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S₃, closely ligating one Mn, with O5−Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017 ) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a ‘low’ Mn oxidation paradigm (mean S₁ Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015 ), rather than a ‘high’ oxidation model (mean S₁ oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018 ) this oxidation state assumption predicted two energetically close S₃ structural forms, one with the metal centres and O5 (as OH⁻) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H₂O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S₃ structure is also a likely superposition of forms, but with O5 (as OH⁻) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural ‘lability’ of the WOC centre in the S₃ state, which is likely catalytically relevant to its water splitting function.     

一种非血红素四氮杂轮烯配合物[Fe(III)TMTAA]催化过氧化氢歧化反应机理的理论研究

采用密度泛函理论B3LYP方法计算了一种非血红素四氮杂轮烯配合物[Fe(III)TMTAA]催化H₂O₂歧化的反应机理. 对二重态、四重态和六重态势能面上各驻点进行了全优化, 发现反应易于沿四重态势能面发生. 整个反应分两阶段进行, 第一阶段通过氧氧均裂形成中间体IM6和第一个水, 第二阶段经两次氢转移形成第二个水. 反应决速步骤为 O—O均裂步骤, 能垒为63.9 kJ•mol^－1, 相对于自由H₂O₂均裂所需能垒226.7 kJ•mol^－1有较大的降低. 这表明标题配合物可有效地降低标题反应的能垒, 有可能作为一种潜在的过氧化氢仿酶.     

Theoretical insight into the photodeactivation pathway of the tetradentate Pt(II) complex: The π‐conjugation effect

In this work, density functional theory and time‐dependent density functional theory were used to investigate the effects of π‐conjugation of the ligand on the photophysical properties, radiative/nonradiative processes and phosphorescence quantum efficiency of tetradentate cyclometalated Pt (II) complex with carbazolyl‐pyridine ligands PtNON . By simulating the absorption spectra and emission wavelengths, increasing the π‐conjugation of the ligand could cause the absorption and emission wavelengths to red‐shift. The results of the computation of key parameters in the radiative decay process, such as singlet‐triplet splitting energy, transition dipole moment and spin‐coupled matrix element between the lowest triplet and singlet excited states, showed that the expansion of π‐conjugation on the carbazole ligand of PtNON resulted in reduction of these parameters, thereby reducing the radiation rate constant. The analyses of the PtNON nonradiative pathway also found that the high activation energy of PtNON made it one of the reasons for the high phosphorescence quantum yield. At the same time, enhancing the molecular orbital delocalization of the ligand further enlarged the energy barrier of the nonradiative pathway, and was conducive to the improvement of phosphorescence quantum yield.     

Associative versus dissociative binding of CO to 4d transition metal trimers: A density functional study

Density functional calculations were performed to determine equilibrium geometrical structures, transition states and relative energies for M(3) clusters (M = Nb, Mo, Tc, Ru, Rh, Pd, Ag) reacting with CO, leading to proposed reaction pathways. For the Nb(3), Mo(3), and Tc(3) clusters, the lowest energy structure correlates to dissociated CO, with the C and O atoms bound on opposite sides of the metal triangle. For all other trimers, the lowest energy structures maintain the CO moiety. In the case of Pd(3) and Ag(3) the dissociated geometries lie higher in energy than the sum of the separated reactants. In most cases, several multiplicities were found to be similar in energy and for Mo(3)CO and Pd(3)CO singlet-triplet minimum energy crossing points were identified. In the case of Rh(3)CO, minimum energy crossing points for the doublet, quartet, and sextet reaction pathways were determined and compared. The electron densities of pertinent M(3)CO species were investigated using Natural Bond Order calculations. It was found that the effect of the metal trimer on the energy of the pure p-type pi* antibonding orbital of carbon monoxide directly correlates with the occurrence of CO dissociation.     

A promiscuous dicopper(II) system promoting the hydrolysis of bis(2,4‐dinitrophenyl)phosphate: Gaining mechanistic insight by means of structural and spectroscopic DFT studies

Catechol oxidases (COs) are plant enzymes that belong to the oxidoreductases class. They contain a dinuclear copper center in their active site. In this article, we have investigated the dicopper(II) model complex [Cu₂(μ‐OH)(C₂₁H₃₃ON₆)]²⁺ (Complex‐A) under a computational perspective, using the DFT method, since this approach has been very useful in the treatment of bimetallic copper systems. The structural and spectroscopic study of Complex‐A as well as the structural analysis of the BDNPP/Complex‐A (Complex‐B) adduct have been carried out. The calculated parameters for Complex‐A are in good accordance with the experimental X‐ray data. Some remarkable points can be observed from the calculated UV–vis relative excitations. The Complex‐B computed structure verifies its identity as a key intermediate species in the BDNPP hydrolysis mechanism. The Cu^II···Cu^II calculated distance in Complex‐B (3.026 Å) is shorter than the calculated for Complex‐A (3.080 Å); one copper atom is bonded to the oxygen of phosphate [Cu (2)···O64–P] at 2.511 Å. These arguments clearly suggest a monodentate interaction and lead to a new mechanism involving terminal substrate coordination and subsequent intramolecular nucleophilic attack by a bridging hydroxide. Such a hypothesis is completely new in terms of homobimetallic copper systems, and may have important implications regarding the chemistry of several biological dinuclear catalytic sites. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

The Effects of Heteroatoms Si and S on Tuning the Optical Properties of Rhodamine‐ and Fluorescein‐Based Fluorescence Probes: A Theoretical Analysis

The effects of the incorporated heteroatoms Si and S on tuning the optical properties of rhodamine‐ and fluorescein‐based fluorescence probes is investigated using DFT and time‐dependent DFT with four different functionals. As previously proposed, the large redshift (90 nm) produced by a Si atom in both the absorption and emission spectra can be attributed to the σ*–π* conjugation between the σ* orbital of the Si atom and the π* orbital of the adjacent carbon atoms. However, the presence of a Si atom does not alter the fluorescence quenching mechanism of the nonfluorescent forms of the investigated compounds. For the first time, these theoretical results indicate that the n orbital of the S atom plays an important role in determining the optical properties of the nonfluorescent form of rhodamine‐based fluorescence probes. It alters the fluorescence quenching mechanism by lowering the energy of the dark nπ* state, which is due to breakage of the C10?S52 bond upon photoexcitation.     

Ab initio investigations on the stabilities of AuOnq− (q = 0 to 3; n = 1 to 4) species: Superhalogen behavior of AuOn (n ≥ 2) and their interactions with an alkali metal

Theoretical density functional calculations are performed on AuO_n^q? species for q = 0–3 and n = 1–4 in various spin states. AuO_n species are found to be relatively more stable in their mono‐anionic forms and behave as superhalogens for n ≥ 2. The maximum oxidation state of Au is found to be +7 in these species, but limited to +5. This fact is explained by considering interactions of AuO_n superhalogens with K atom and which leads to the formation of more stable KAuO_n complex up to n = 3, only. Thus, the present study is expected not only to motivate the synthesis of a new class of salts but also to assign the maximum oxidation state of gold. © 2013 Wiley Periodicals, Inc.     

Topological analysis of the charge density response of a Ni4 cluster to a probe H2 molecule

Local density self-consistent field (SCF) discrete variationalX calculations are performed on a Ni₄ tetrahedron interacting with a probe H₂ molecule in special geometries. Optimized basis functions generated from the spherically averaged SCF potential are used. Topological charge-density analyses and binding energy calculations are used to study a portion of the energy surface for the approach of the H₂ molecule toward the Ni₄ tetrahedron. The effect of the H₂ molecule on Ni-Ni, Ni-H bonds and changes in the H-H covalent bond are investigated with the help of the field and various data at its critical points. The qualitative relationship between these data and the calculated binding energies is exploited.