固氮酶活性中心FeMo-Cofactor对N2活化方式的探讨

结合实验和理论计算的结果, 讨论了固氮酶的活性中心铁钼辅基(FeMo-co-facto r) 对N₂ 的各种活化方式, 并在此基础上提出了一种新模型, 即N₂ 在FeMo2cofacto r 的内部以“4Fe 端基配位+2Fe 侧基配位”的方式被活化,N₂ 的三重键完全断裂, 断裂产生的两个含N 的碎片分别偏向两侧的“窗口”, 再在H 的进攻下被还原为NH₃, 并分别从两侧的“窗口”离去。     

Enzymatic and catalytic reduction of dinitrogen to ammonia: Density functional theory characterization of alternative molybdenum active sites

We used density functional calculations to model dinitrogen reduction by a FeMo cofactor containing a central nitrogen atom and by a Mo‐based catalyst. Plausible intermediates, reaction pathways, and relative energetics in the enzymatic and catalytic reduction of N₂ to ammonia at a single Mo center are explored. Calculations indicate that the binding of N₂ to the Mo atom and the subsequent multiple proton–electron transfer to dinitrogen and its protonated species involved in the conversion of N₂ are feasible energetically. In the reduction of N₂ the Mo atom experiences a cycled oxidation state from Mo(IV) to Mo(VI) by nitrogenase and from Mo(III) to Mo(VI) by the molybdenum catalyst, respectively, tuning the gradual reduction of N₂. Such a wide range of oxidation states exhibited by the Mo center is crucial for the gradual reduction process via successive proton–electron transfer. Present results suggest that the Mo atom in the N‐centered FeMo cofactor is a likely alternative active site for dinitrogen binding and reduction under mild conditions once there is an empty site available at the Mo site. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

On the Synthesis of the FeMo Cofactor of Nitrogenase: Gene-Controlled in Nature versus Laboratory-Produced by Man

One of the primary challenges of chemistry is the controlled synthesis of compounds with tailor-made structures and properties. Natural products serve as inspiration in this quest, ranging from biocatalysts with optimal selectivity and activity to “inorganic materials” with exceptional properties, whose generation can be described by the term biomineralization. It is of fundamental importance to comprehend the courses of events at the interface between gene expression and the subsequent processes of epigenesis that are no longer under gene control. Chemistry has been able to achieve many goals; however, in the area of controlled syntheses of highly complex, tailor-made metal clusters, there is a lack of fundamental theories and principles. This is especially true for the fascinating metal–sulfur cluster of nitrogenase, which, in this enzyme, functions as the active center for the N₂ reduction and, so far, has eluded all attempts to be synthesized in the laboratory. To understand the biosynthesis of this cluster, information from genetics and chemistry must be combined.     

The Fe–V Cofactor of Vanadium Nitrogenase Contains an Interstitial Carbon Atom

The first direct evidence is provided for the presence of an interstitial carbide in the Fe? V cofactor of Azotobacter vinelandii vanadium nitrogenase. As for our identification of the central carbide in the Fe? Mo cofactor, we employed Fe Kβ valence‐to‐core X‐ray emission spectroscopy and density functional theory calculations, and herein report the highly similar spectra of both variants of the cofactor‐containing protein. The identification of an analogous carbide, and thus an atomically homologous active site in vanadium nitrogenase, highlights the importance and influence of both the interstitial carbide and the identity of the heteroatom on the electronic structure and catalytic activity of the enzyme.     

Substituting CF2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2′‐β or 2′‐α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF₂ group for the O4′ atom (O4′‐CF₂ modification) leads to a preference of the BI relative to AI DNA‐like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4′‐CF₂ derivative. Consequently, the O4′‐CF₂ modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.     

Carbon boronyls: species with higher viable possibility than boron carbonyls at the density functional theory

Density functional theory investigations indicate that carbon boronyls (CBO)n (n = 3-7) are considerably more stable in thermodynamics than their boron carbonyl isomers (BCO)n and exhibit aromaticity throughout the whole series. The extra stabilities of (CBO)n originate from their frontier pi molecular orbitals delocalized over the Dnh Cn central rings which are absent in (BCO)n. It is expected that experimental characterization of these (CBO)n species may open a new branch of chemistry on carbon boronyls.     

Influence of the protein and DFT method on the broken‐symmetry and spin states in nitrogenase

The enzyme nitrogenase contains a complicated MoFe₇CS₉ cofactor with 35 possible broken‐symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one‐electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single‐point energies calculated on a single geometry give a good correlation (R² = 0.92‐0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57‐0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the second most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism.     

The calculation of indirect nuclear spin-spin coupling constants in large molecules

We present calculations of indirect nuclear spin-spin coupling constants in large molecular systems, performed using density functional theory. Such calculations, which have become possible because of the use of linear-scaling techniques in the evaluation of the Coulomb and exchange-correlation contributions to the electronic energy, allow us to study indirect spin-spin couplings in molecules of biological interest, without having to construct artificial model systems. In addition to presenting a statistical analysis of the large number of short-range coupling constants in large molecular systems, we analyse the asymptotic dependence of the indirect nuclear spin-spin coupling constants on the internuclear separation. In particular, we demonstrate that, in a sufficiently large one-electron basis set, the indirect spin-spin coupling constants become proportional to the inverse cube of the internuclear separation, even though the diamagnetic and paramagnetic spin-orbit contributions to the spin-spin coupling constants separately decay as the inverse square of this separation. By contrast, the triplet Fermi contact and spin-dipole contributions to the indirect spin-spin coupling constants decay exponentially and as the inverse cube of the internuclear separation, respectively. Thus, whereas short-range indirect spin-spin coupling constants are usually dominated by the Fermi contact contribution, long-range coupling constants are always dominated by the negative diamagnetic spin-orbit contribution and by the positive paramagnetic spin-orbit contribution, with small spin-dipole and negligible Fermi contact contributions.     

椅型碳纳米管吸附氢原子电子结构的密度泛函研究

采用密度泛函方法对氢原子在(5,5)椅型碳纳米管上的吸附进行了研究, 分别考察了氢原子覆盖度为5%和10%时的构型和吸附能. 研究结果表明, H原子吸附在管外壁要比管内壁能量上更为有利, 同时第二个H原子倾向于吸附在前一个H原子的吸附位置邻近的碳原子上. 由能带计算结果得知, 吸附一个H原子时, 椅型碳纳米管将由导体转变为半导体; 当第二个H原子处在偶数位时, 纳米管仍保持较好的导电性能, 而吸附在奇数位时将使管的传输能力减弱. 本文进一步通过分析纳米管(共轭体系的分布情况对管传输性质的变化进行解释.     

The formulation of a self-consistent constricted variational density functional theory for the description of excited states

We outline here a self-consistent approach to the calculation of transition energies within density functional theory. The method is based on constricted variational theory (CV-DFT). It constitutes in the first place an improvement over a previous scheme [T. Ziegler, M. Seth, M. Krykunov, J. Autschbach, F. Wang, Chem. Phys. 130 (2009) 154102] in that it includes terms in the variational parameters to any desired order n including n = ∞. For n = 2, CV(n)-DFT is similar to TD-DFT. Adiabatic TD-DFT becomes identical to CV(2)-DFT after the Tamm-Dancoff approximation is applied to both theories. We have termed the new scheme CV(n)-DFT. In the second place, the scheme can be implemented self-consistently, SCF-CV(n)-DFT. The procedure outlined here could also be used to formulate a SCF-CV(n) Hartree-Fock theory. The approach is further kindred to the ΔSCF-DFT procedures predating TD-DFT and we describe how adiabatic TD-DFT and ΔSCF-DFT are related through different approximations to SCF-CV(n)-DFT.     

On the Energetics of Ions in Carbon and Gold Nanotubes

We investigate the insertion of halide and alkali atoms into narrow single‐walled carbon nanotubes with diameters <9 Å by density functional theory; both chiral and non‐chiral tubes are considered. The atoms are stored in the form of ions; the concomitant charge transfer affects the band structure and makes originally semiconducting tubes conducting. The electrostatic interaction between a charge and the walls of the tube is explicitly calculated. The insertion energies and the positions of the ions are determined by a competition between electrostatic energy and Pauli repulsion. For comparison, we consider ions in gold nanotubes. Alkali ions follow the same principles in gold as in carbon tubes, but chloride is specifically adsorbed inside gold tubes.     

硼氮掺杂的碳纳米管对硫化氢气敏性能的理论研究

应用密度泛函理论研究了纯(8, 0)单壁碳纳米管(SWCNT)和B原子、N原子以及BN原子对掺杂的(8, 0) SWCNTs对硫化氢气体分子的传感性质. 计算结果表明, 与纯碳纳米管相比, B原子掺杂的SWCNT显示了对H₂S分子的敏感性, 其几何结构和电子性质在吸附H₂S分子后发生了显著变化; 而N原子和BN原子对的掺杂没有改善SWCNT对H₂S分子的吸附性能, 因此我们建议B原子掺杂的SWCNT作为检测H₂S分子的新型气相传感器.     

A density functional study on the electronic structures of TiN solid

The electronic structures of TiN bulk have been studied by using different theoretical formalisms, and the DFT method, especially the BLYP method can produce reasonable results. The band structure of TiN (001) surface is also investigated and two a type surface states are presented in our results. The state located at 2.9 eV below EF in angle resolved photoemis-sion in (ARPES) is well reproduced in this work, which consists essentially of 2pz orbital of surface N atom. Another surface state is associated with the bands originated from 3d orbital of surface Ti atom. Furthermore, the elastic constants of TiN are also calculated by using BLYP method.