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     

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。     

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.     

固氮酶的固氮机理和其人工模拟问题的探讨

固氮酶将N₂ 还原为NH₃ 的过程是自然界实现氮循环的重要环节。本文着重对固氮酶的固氮机理和其活性中心FeMo 辅基的人工模拟合成进行探讨, 其中包括FeMo蛋白中的质子和电子的传递, FeMo 辅基对N₂ 的活化方式,Mo 原子的作用, 固氮活性的测试。最后还就固氮酶的活性中心FeMo 辅基的人工模拟合成进行了探讨。     

On the reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase

Reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase are examined theoretically within the intermediate neglect of differential overlap model. The results obtained favor one of the experimentally suggested modes of contraction of the metal system which results in an expansion of the central cavity of the cofactor. The bond index analysis indicates marked changes in the Mo coordination upon electron addition which may contribute to an opening of the Mo atom as a possible binding site at the advanced stages of the reduction process. In this work we also compare the 39- and 41-electron [MoFe₇] core as possible native resting states, both compatible with known spin and M?ssbauer spectroscopies. Received: 19 March 1997 / Accepted: 8 May 1997     

Dissociation constants of 2‐azidoethanamines in aqueous solution

Aqueous‐phase dissociation constants (K_a) for the conjugate acids of a series of 2‐azidoethanamine bases: R¹N(R²)CH₂CH₂N₃ ( 1 , R¹ = CH₃, R² = H; 2 , R¹ = CH₃, R² = CH₃; 3 , R¹ = CH₂CH₃, R² = CH₂CH₃; 4 , R¹/R² =  CH₂CH₂CH₂CH₂ ; 5 , R¹/R² =  CH₂CH₂OCH₂CH₂ ; 6 , R¹ = CH₂CH₃, R² = CH₂CH₂N₃) were measured and found to fall between those for analogous unfunctionalized and cyano‐functionalized ethanamines. To explore the possibility of a relationship existing between the constants and molecular geometry, a theoretically based study was conducted. In it, the Gibbs free energies of aqueous‐phase (equilibrium) conformers of the bases and their conjugate acids were determined via a density functional theory/polarizable continuum model method. The results indicate that an attractive interaction between the amine and azide groups that underlies the lowest‐energy gas‐phase conformer of 2 is negated in an aqueous environment by solvent–solute interactions. The magnitudes of the free energy changes of solvation and −TS (entropic) energies of the conformers of the 2‐azidoethanamines and their conjugate acids are observed to correlate with the magnitude of the separation between the conformers' amine and azide groups. However, those correlations are not by themselves sufficient to predict the relative free energies of a molecule's conformers in an aqueous environment. That insufficiency is due to the influence of the correlations being mitigated by three other parameters that arise within the thermodynamic framework employed to compute the observable. The nature of those parameters is discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Catalytic reduction of molecular nitrogen in solutions

Reports on nitrogen fixation in solution are reviewed. The optimum catalyst is the polynuclear complex. The reaction proceeds as a multielectron process, and the limiting step involves the electron transfer from a reducing agent.     

Effect of the potential of an external electron donor on C<Subscript>2</Subscript>H<Subscript>2</Subscript> reduction catalyzed by the nitrogenase active center (FeMoco) isolated from the enzyme

The effect of potential value and chemical properties of an external electron donor on C₂H₂ reduction catalyzed by nitrogenase active center (cluster [(₆-N)Fe₇MoS₉·homocitrate] FeMoco isolated from the enzyme) has been investigated in the presence of proton donors of different acidity. The temperature—reaction rate dependences of these reactions have been studied. It has been shown that the rate-limiting steps of the reactions differ depending on the proton donor used. When thiophenol or water are used as proton donors, and electrochemical step — the electron transfer from cathode to adsorbed catalytic cluster — has been found to be a rate-limiting one. The effective activation energy of ethane formation as a product of four-electron C₂H₂ reduction is found to be 1.5 times lower than that of ethylene, namely, 13 kcal mol^–1. When stronger acid, pentafluorothiophenol, is used as a proton donor, the chemical step of intramolecular rearrangement of the catalyst—substrate complex taking place in solution becomes a rate-limiting one. The effective activation energies of both ethylene and ethane become equal to 32 kcal mol^–1.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1583–1591, August, 2004.     

Scrutinizing “Invisible” astatine: A challenge for modern density functionals

The main‐group 6p elements did not receive much attention in the development of recent density functionals. In many cases it is still difficult to choose among the modern ones a relevant functional for various applications. Here, we illustrate the case of astatine species (At, Z = 85) and we report the first, and quite complete, benchmark study on several properties concerning such species. Insights on geometries, transition energies and thermodynamic properties of a set of 19 astatine species, for which reference experimental or theoretical data has been reported, are obtained with relativistic (two‐component) density functional theory calculations. An extensive set of widely used functionals is employed. The hybrid meta‐generalized gradient approximation (meta‐GGA) PW6B95 functional is overall the best choice. It is worth noting that the range‐separated HSE06 functional as well as the old and very popular B3LYP and PBE0 hybrid‐GGAs appear to perform quite well too. Moreover, we found that astatine chemistry in solution can accurately be predicted using implicit solvent models, provided that specific parameters are used to build At cavities. © 2016 Wiley Periodicals, Inc.