Kinetic study of the oxidation of L-threonine by MnO4? ions

A self-catalytic effect attributed to Mn²⁺ ions was observed when studying the oxidation of L-threonine by permanganate ions. The process obeys the rate equation:

Identification of exchange-coupled V4+ and Cu2+ ions in Cu?V?Mo oxide systems

ESR studies of X(CuO)·V₂O₅·8.3 MoO₃ (X=1–2) calcined in flowing nitrogen at 250–350 °C have revealed the exchange interaction of Cu²⁺ and V⁴⁺ ions that form a paramagnetic system.

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X(CuO) V₂O₅·8,3 MoO₃, X=1–2, , 250–350°C, Cu²⁺ V⁴⁺, .

     

Spectroscopic Parameters of X3∑-, a1△, and A'3△ Electronic States of SO Radical

The potential energy curves (PECs) of three low-lying electronic states (X³∑^-, a¹△, and A^'3△) of SO radical have been studied by ab initio quantum chemical method. The calcula-tions were carried out with the full valence complete active space self-consistent field method followed by the highly accurate valence internally contracted multireference configuration in-teraction (MRCI) approach in combination with correlation-consistent basis sets. Effects of the core-valence correlation and relativistic corrections on the PECs are taken into account. The core-valence correlation correction is carried out with the cc-pCVDZ basis set. The way to consider the relativistic correction is to use the second-order Douglas-Kroll Hamiltonian approximation, and the correction is performed at the level of cc-pV5Z basis set. To obtain more reliable results, the PECs determined by the MRCI calculations are also corrected for size-extensivity errors by means of the Davidson modification (MRCI+Q). These PECs are extrapolated to the complete basis set limit by the two-point energy extrapolation scheme. With these PECs, the spectroscopic parameters are determined.     

Rotational Mechanism of Ammonium Ion in Water and Methanol?

Dynamics of ammonium and ammonia in solutions is closely related to the metabolism of ammoniac compounds, therefore plays an important role in various biological processes. NMR measurements indicated that the reorientation dynamics of NH₄⁺ is faster in its aqueous solution than in methanol, which deviates from the Stokes-Einstein-Debye rule since water has higher viscosity than methanol. To address this intriguing issue, we herein study the reorientation dynamics of ammonium ion in both solutions using numerical simulation and an extended cyclic Markov chain model. An evident decoupling between translation and rotation of methanol is observed in simulation, which results in the deviation of reorientation from the Stokes-Einstein-Debye rule. Slower hydrogen bond (HB) switchings of ammonium with methanol comparing to that with water, due to the steric effect of the methyl group, remarkably retards the jump rotation of ammonium. The observations herein provide useful insights into the dynamic behavior of ammonium in the heterogeneous environments including the protein surface or protein channels.     

Absorption Spectroscopy of (8,1) Band in d3△-a3ПSystem of CS Radical

The CS radical was generated by discharging the mixture gas of CS₂ and Helium. The Doppler limited spectra of CS were recorded in the region of 12350～12950 cm^-1 using optical heterodyne concentration modulation absorption spectroscopy. Three hundred and twenty-six lines were recorded and assigned to the d³△-a³П(8,1) band, in which eighty-three transitions were first observed. A set of improved molecular constants for the d³△(v=8) and a³П(8,1)(v=1) levels were determined by a non-linear least-squares fitting of all the lines to the effective Hamiltonian.     

Evaluation of the Reactivity of Cyclohexanone СН Bonds in Reactions with tert-Butylperoxy Radical by Quantum Chemical Methods

Kinetics and Catalysis - The effective charges on hydrogen and carbon atoms and the Fukui functions for the electrophilic and radical attacks for the hydrogen atoms of the chair and boat...     

Polyatomic anion versus acetonitrile in coordinating ability: structural properties of AgX-bearing 1,4-bis(2-isonicotinoyloxyethyl)piperazine (X??=?NO3?, CF3SO3?, ClO4?, BF4?, and PF6?)

Type studies on competitive polyatomic anion versus acetonitrile coordination in the self-assembly of a series of [Ag₂(X) _m (bip)(NCCH₃) _n ](X)_2−m (X⁻ = NO₃ ⁻, CF₃SO₃ ⁻, ClO₄ ⁻, BF₄ ⁻, and PF₆ ⁻; m = 0, 2; n = 0, 2, 4; bip = 1,4-bis(2-isonicotinoyloxyethyl)piperazine) were carried out. Each bip spacer acts as an N₄ tetradentate ligand and is linked to four silver(I) centers through two pyridine and two piperazine moieties, producing a double strand consisting of two 20-membered ring units. The coordinating environment around the silver(I) center is subtly determined by the competition of the polyatomic anions with acetonitrile, that is, by the Ag···NCCH₃ versus Ag···X interactions. The coordinating ability of acetonitrile is inversely proportional to the order of the coordination ability of the Hoffmeister series of polyatomic anions, NO₃ ⁻ ≫ CF₃SO₃ ⁻ > ClO₄ ⁻ > BF₄ ⁻ ≫ PF₆ ⁻.     

Structure and thermal properties of [RhPy4Cl2]X complex salts (X = Cl?, ReO 4? , ClO 4? )

[RhPy₄Cl₂]Cl·4H₂O (I), [RhPy₄Cl₂]ReO₄ (II), [RhPy₄Cl₂]ClO₄ (III), and [RhPy₄Cl₂]ReO₄·2H₂O complex salts were synthesized. The crystal structure of compounds II (P4/ncc, a = 25.5655(3) ?, c = 14.3521(4) ?), III (P2₁/n, a = 13.5308(3) ?, b = 15.1044(5) ?, c = 23.3457(8) ?, β = 93.327°), and dyhydrate of II (Pbcm, a = 10.6199(9) ?, b = 10.4964(9) ?, c = 22.9834(16)?) was determined by X-ray diffraction analysis. The thermal transformations of the complexes were studied by differential thermal analysis. The substances were characterized by IR spectroscopy, XRPA, and element analysis Original Russian Text Copyright ? 2009 by D. B. Vasilchenko, I. A. Baidina, E. Yu. Filatov, and S. V. Korenev __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 50, No. 2, pp. 349–356, March–April, 2009.     

镁二次电池正极材料纳米Fe3S4的电化学性能

首次将尖晶石相的纳米Fe₃S₄材料用作镁二次电池的正极材料。采用水热法一步合成了具有纳米结构的Fe₃S₄材料, 并采用XRD、SEM测试手段对产物的物相、形貌进行了表征。实验结果表明, 在160 ℃能够合成纯相的Fe₃S₄材料, 该材料具有银耳状纳米结构。电化学测试结果显示, 水热法合成的纳米Fe₃S₄材料能够在镁二次电池体系中进行有效的可逆充放电, 放电平台电压为0.9 V, 首次放电容量高达267 mAh·g^-1, 50次循环后衰减至110 mAh·g^-1。电化学交流阻抗测试结果表明镁离子能够在Fe₃S₄晶格中扩散。     

Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics

Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.     

Concerted Asynchronous Hula‐Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein

Fluorescence emission of wild‐type green fluorescent protein (GFP) is lost in the S65T mutant, but partly recovered in the S65T/H148D double mutant. These experimental findings are rationalized by a combined quantum mechanics/molecular mechanics (QM/MM) study at the QM(CASPT2//CASSCF)/AMBER level. A barrierless excited‐state proton transfer, which is exclusively driven by the Asp148 residue introduced in the double mutant, is responsible for the ultrafast formation of the anionic fluorescent state, which can be deactivated through a concerted asynchronous hula‐twist photoisomerization. This causes the lower fluorescence quantum yield in S65T/H148D compared to wild‐type GFP. Hydrogen out‐of‐plane motion plays an important role in the deactivation of the S65T/H148D fluorescent state.     

应用QM与ABEEM/MM结合的方法研究NAMI-A的结构性质

应用量子力学(QM)与ABEEM浮动电荷力场(ABEEM/MM)相结合的方法研究了抗癌药物NAMI-A在水溶液中的结构性质. 所有的结构优化都是在DFT的B3LYP方法下采用6-31G(d,p)和LanL2DZ基组完成的, 没有加入任何限制性条件. 结果表明, 优化得到的NAMI-A构型受不同环境及方法的影响均有变化. 与气相中得到的构型相比, QM/MM迭代优化得到构型要比PCM的构型变化更明显. QM/MM (ABEEM/MM)迭代优化得到的NAMI-A构型比QM/MM (OPLS-AA)的变化要小. 总之, 溶剂通过极化效应对NAMI-A结构、电荷分布及径向分布函数等性质均有影响, 客观地处理极化效应才能正确地反映QM区的性质.     

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects

We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to- xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1,2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step.     

Synergistic Substrate and Oxygen Activation in Salicylate Dioxygenase Revealed by QM/MM Simulations

Salicylate 1,2‐dioxygenase (SDO) is the first enzyme to be discovered to catalyze the oxidative cleavage of a monohydroxylated aromatic compound, namely salicylate, instead of the well‐known electron‐rich substrates. We have investigated the mechanism of dioxygen activation in SDO by QM/MM calculations. Our study reveals that the non‐heme Fe^II center in SDO activates salicylate and O₂ synergistically through a strong covalent interaction to facilitate the reductive cleavage of O₂. A covalent salicylate–Fe^II–O₂ complex is the reactive oxygen species in this case, and its electronic structure is best described as being between the two limiting cases, Fe^II?O₂ and Fe^II?O₂^.?, with partial electron transfer from the activated salicylate to O₂ via the Fe center. Thus SDO employs a synergistic strategy of substrate and oxygen activation to carry out the catalytic reaction, which is unprecedented in the family of iron dioxygenases. Moreover, O₂ activation in SDO happens without the assistance of a proton source. Our study essentially shows a new mechanistic possibility for O₂ activation.     

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x-ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures of phosphodiesterase-5 (PDE5) in solution. The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO- or H2O. It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+. It has been demonstrated that the results of the QM/MM geometry optimizations are remarkably affected by the solvent water molecules, the dynamics of the protein environment, and the electronic embedding charges of the MM region in the QM part of the QMM/MM calculation. The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors. It is interesting to note that the PDE5(BL2 = HO-) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors. These results suggest the overall effects of these three important factors on the optimized geometries can roughly cancel out. However, the QM/MM calculations that only account for some of these factors could lead to considerably different geometries. These results might be useful also in guiding future QM/MM geometry optimizations on other enzymes.     

Molecular Dynamics and Combined QM/MM Studies on the Deactivation of anti-Tubercular Drug Isoniazid by Arylamine N-Acetyltransferases

Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics(QM/MM) study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases(NATs) and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as 'general base' rather than 'general acid'.If all the residues(including H2O molecules) were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.     

Coexistence of Different Electron‐Transfer Mechanisms in the DNA Repair Process by Photolyase

DNA photolyase has been the topic of extensive studies due to its important role of repairing photodamaged DNA, and its unique feature of using light as an energy source. A crucial step in the repair by DNA photolyase is the forward electron transfer from its cofactor (FADH^?) to the damaged DNA, and the detailed mechanism of this process has been controversial. In the present study, we examine the forward electron transfer in DNA photolyase by carrying out high‐level ab initio calculations in combination with a quantum mechanical/molecular mechanical (QM/MM) approach, and by measuring fluorescence emission spectra at low temperature. On the basis of these computational and experimental results, we demonstrate that multiple decay pathways exist in DNA photolyase depending on the wavelength at excitation and the subsequent transition. This implies that the forward electron transfer in DNA photolyase occurs not only by superexchange mechanism but also by sequential electron transfer.     

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.     

Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review

The main concepts and important technical details of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) simulations are explained and illustrated with the intent of assisting newcomers in performing and gauging the accuracy of such simulations, focused on smaller molecules in solution. Beginners are advised on how to increase the reliability and accuracy of the simulations through benchmarking. Central considerations on methodologies for QM/MM Molecular Dynamics (MD) simulations are presented, alongside technical fundamentals regarding the construction and manipulation of simulation systems using the python-based Atomic Simulation Environment (ASE). A worked example of QM/MM Born–Oppenheimer MD is included, and a flowchart summarizing the most salient decisions and tasks within the methodology is presented.