黑芥子苷生物合成中酶催化机理的QM/MM研究

黑芥子苷作为植物中硫代葡萄糖苷最为主要且丰富的类型,在促进健康和昆虫防御方面具有潜在的功能. 黑芥子苷核心结构生物合成的最后一步在硫代葡萄糖苷化合物中具有高度的代表性. 这一步是在硫转移酶的催化作用下,从3-(甲基硫代)丙基脱硫葡萄糖苷转化为3-(甲基硫代)丙基葡萄糖苷的过程. 由于硫转移酶与3-(甲基硫代)丙基葡萄糖苷复合物的晶体结构还未见报道,因此一直以来人们对该磺化反应的细节知之甚少. 幸运的是,黑芥子苷与3-(甲基硫代)丙基葡萄糖苷的结构十分相似,而且结合有黑芥子苷的拟南芥硫转移酶18的晶体结构已经确定. 为了了解此酶的作用机理,本文采用分子动力学模拟以及组合的量子力学和分子力学方法研究了拟南芥硫转移酶18催化脱硫-黑芥子苷转化为黑芥子苷的过程. 计算结果表明,该反应是通过协同解离机理发生的,而且在反应过程中,赖氨酸93、苏氨酸96、苏氨酸97、酪氨酸130、组氨酸155和酶的两条肽链(脯氨酸92-赖氨酸93肽链和谷氨酰胺95-苏氨酸96-苏氨酸97肽链)稳定了过渡态的结构,在定位底物和促进催化反应中发挥了重要的作用,其中,组氨酸155在反应过程中充当催化碱,赖氨酸93充当催化酸. 目前提出的协同解离机理解释了拟南芥硫转移酶18在黑芥子苷生物合成中的作用,并对其他硫转移酶催化葡萄糖苷生物合成的研究具有指导意义.     

New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach

Molecular Diversity - SARS-CoV-2 Mpro, also known as the main protease or 3C-like protease, is a key enzyme involved in the replication process of the virus that is causing the COVID-19 pandemic....     

Hydrogen bonding in liquid water: An ab initio QM/MM MD simulation study

Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.     

Metal-insulator transition in Ni-doped Na0.75CoO2: Insights from infrared studies

Nickel substitution at the cobalt site in Na_0.75CoO₂ induces an upturn in the resistivity on lowering the temperature, with the metal-to-insulator transition temperature (T _MIT) increasing with the Ni content. Low temperature far infrared measurements on polycrystalline samples of Na_0.75CoO₂ and Na_0.75Co_0.95Ni_0.05O₂, the latter having T _MIT ∼ 175 K, have been carried out. Dramatic changes in the Na mode frequencies, and relative intensities of the out-of-plane modes corresponding to the two Na sites are observed, coincident with the MIT in Na_0.75Co_0.95Ni_0.05O₂. It is argued that these changes are associated with a charge ordering of the CoO₂ layer, associated with the metal-insulator transition.     

Insights into fractal feature evolution from Au/Ge thin films after annealing

We report a perplexing behavior of fractal shape transition that results from a change in the annealing temperature and time or the film thickness ratio. We find that a compact-to-open fractal shape transition can be induced by increasing the annealing temperature and time or decreasing the thickness ratio of the Au and Ge films. This behavior is not completely consistent with what is predicted by theories based on diffusion-limited aggregation and previous experimental observations. In this new system, we find that fractal shape transitions are truly dominated by the random-successive nucleation and growth mechanism. PACS 61.43.Hv; 68.55.-a; 81.05.Gc     

Reactions of oxygen-containing molecules on transition metal carbides: Surface science insight into potential applications in catalysis and electrocatalysis

Historically the interest in the catalytic properties of transition metal carbides (TMC) has been inspired by their “Pt-like” properties in the transformation reactions of hydrocarbon molecules. Recent studies, however, have revealed that the reaction pathways of oxygen-containing molecules are significantly different between TMCs and Pt-group metals. Nonetheless, TMCs demonstrate intriguing catalytic properties toward oxygen-containing molecules, either as the catalyst or as the catalytically active substrate to support metal catalysts, in several important catalytic and electrocatalytic applications, including water electrolysis, alcohol electrooxidation, biomass conversion, and water gas shift reactions. In the current review we provide a summary of theoretical and experimental studies of the interaction of TMC surfaces with oxygen-containing molecules, including both inorganic (O₂, H₂O, CO and CO₂) and organic (alcohols, aldehydes, acids and esters) molecules. We will discuss the general trends in the reaction pathways, as well as future research opportunities in surface science studies that would facilitate the utilization of TMCs as catalysts and electrocatalysts.     

Investigation of the transition of acrylate cation exchangers from solidlike into highly elastic state under hydration

The transition from solid-like (glassy) state into the (elastic) state with high intramolecular mobility under hydration was investigated for two⁵⁷Fe³⁺-substituted cation exchangers (SGK ?7 and SG ?1 m with acrylic and methacrylic nature of chains). The transition was observed as sharp change of Mössbauer lineshape (appearance of quasielastic components) and decrease of Mössbauer effect probability. The region of hydration degrees in which the transition occurs in both systems varies from 1 to 3–4 H₂O molecules per ?COOH group depending on cross-linkage concentration in a nonmonotonous way.     

Insights into homonuclear decoupling from efficient numerical simulation: techniques and examples

A combination of techniques, including rational number synchronisation and pre-diagonalisation of the time-dependent periodic Hamiltonian, are described which allow the efficient simulation of NMR experiments involving both magic-angle spinning (MAS) and RF irradiation, particularly in the important special case of phase-modulated decoupling sequences. Chebyshev and conventional diagonalisation approaches to calculating propagators under MAS are also compared, with Chebyshev methods offering significant advantages in cases where the Hamiltonian is large and time-dependent but not block-diagonal (as is the case for problems involving combined MAS and RF). The ability to simulate extended coupled spin systems efficiently allows 1H spectra under homonuclear decoupling to be calculated directly and compared to experimental results. Reasonable agreement is found for the conditions under which homonuclear decoupling is typically applied for rigid solids (although the increasing deviation of experimental results from the predictions of theory and simulation at higher RF powers is still unexplained). Numerical simulations are used to explore three features of these experiments: the interaction between the magic-angle spinning and RF decoupling, the effects of tilt pulses in acquisition windows and the effects of "phase propagation delays" on tilted axis precession. In each case, the results reveal features that are not readily anticipated by previous analytical studies and shed light on previous empirical observations.     

Kinetics of a phase transition into an inhomogeneous state in a ferroelectric plate

The kinetics of the emergence of a polarization vector field after a ferroelectric sample is rapidly cooled is investigated in two cases, in which the rate of growth of the polarization vector is determined by viscous forces of phonon origin or by the diffusion of charged particles. Analytic expressions are obtained for the rate of growth of the polarization vector and the period of the inhomogeneous phase as a function of the degree of supercooling of the sample. The existence of a slow relaxation process in the domain structure is established and the time dependence of this process is found. Zh. éksp. Teor. Fiz. 114, 2238–2245 (December 1998)     

Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values

The rate-determining proton transfer step in the amine reduction reaction catalysed by the enzyme methylamine dehydrogenase has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. Variational transition state theory, combined with multidimensional tunnelling corrections, has been employed to calculate reaction rate constants, and hence deuterium kinetic isotope effects (KIE). To render these calculations computationally feasible, the electronic structure was described using a PM3 method with specific reaction parameters obtained by a fit to energetics obtained at a high level for a small model system. Compared to the use of standard parameters, these revised parameters result in a considerable improvement in the predicted KIE values and activation energy. For both methylamine and ethanolamine substrates, through-barrier, rather than over-barrier, motion is found to dominate with KIE values that are large and close to the experimental values. A major difference between the two substrates is that, for ethanolamine, different hydrogen bonding structures involving the substrate hydroxyl are possible, leading to very different potential energy surfaces with KIE values covering a considerable range. We speculate that this is the origin of the differing temperature behaviour observed for the KIEs of the two substrates.     

Spin-peierls systems in magnetic field: Phase transition from dimerized to soliton lattice state

The phase diagram for the spin-Peierls system in high magnetic field is studied. The line of transition from dimerized (D) to soliton lattice (SL) phase is found, and it is shown that the SL phase is stable in fields h;h_c. Magnetization vs h is calculated as well as the sound velocity u_s of the domain walls oscillations. The possible experimental verification of the proposed theory is discussed also.     

Thermodynamic model of the stabilization of an intermediate state in the region of the metamagnetic phase transition in erbium orthoferrite

The possible mechanisms of the thermodynamic stabilization of an intermediate state in the first-order metamagnetic phase transition in a magnetic field parallel to the Ising c axis of the Er³⁺ ions in erbium orthoferrite at T = 1.6 K have been analyzed. The model is chosen using the magneto-optical experimental data on the features of this state.     

Exchange interaction effects in the crossing of spin-polarized Landau levels in a silicon-germanium heterostructure: transition into a ferromagnetic state

The crossing of spin-split Landau levels in a Si/SiGe heterostructure is investigated by means of magneto-transport experiments in tilted magnetic fields. We observe a transition from a paramagnetic into a fully spin polarized state. During the transition strongly enhanced maxima in the transverse resistivity ρ_xx appear when the parallel field component is oriented along the Hall bar. We assign this effect to an energy level structure strongly modified by exchange interaction effects between different Landau levels. Surprisingly the maximum in ρ_xx totally disappears when the parallel field component is perpendicular to the Hall bar.     

First-order transition from superfluid to bose-metal state in systems with resonant pairing

Systems showing resonant superfluidity, driven by an exchange coupling of strength g between uncorrelated pairs of itinerant fermions and tightly bound ones, undergo a first-order phase transition as g increases beyond some critical value gc. The superfluid phase for ggc this state gives way to a phase-uncorrelated bosonic liquid with a q2 spectrum.     

Cr2O3催化合成气转化至甲醇的微观动力学研究

Cr₂O₃是双功能催化合成气转化的重要氧化物组分,其可将合成气转化为重要的中间物种甲醇. 结合密度泛函理论计算和微观动力学模拟,本文系统研究了干净Cr₂O₃(001)和(012)表面,以及氢覆盖或含有氧空位的还原(012)表面的结构及催化合成气转化至甲醇的活性. 本文探讨了合成气转化为甲醇的分步或协同反应路径,并确定CO或CHO氢化是决速步骤. 微观动力学分析表明,Cr₂O₃(001)表面难以催化合成气转化为甲醇,在673 K 时,两个还原性(012)表面的反应速率(25∽28 s^-1)比干净的(012)表面(4.3 s^-1)高出约五倍. 计算结果表明了Cr₂O₃表面还原性对催化活性的重要性,或许可以为双功能催化体系中氧化物组分的设计提供参考.     

Insights into phase stability of anhydrous/hydrate systems: a Raman‐based methodology

FT‐Raman spectroscopy turns out to be a powerful technique to evaluate the amount of polymorphic and pseudopolymorphic forms in crystalline samples—which is particularly relevant in pharmaceutical sciences. This paper presents a methodology that allows successful quantitative evaluation of the solid‐state hydration and dehydration processes, using FT‐Raman spectroscopy. All the steps required for a reliable evaluation of the hydration/dehydration process are illustrated for the caffeine system, a particularly challenging system presenting limited spectral differences between the pseudopolymorphs. The hydration process of caffeine was found to occur in a single‐step process with a half‐life time of ca 13 h, while the dehydration occurs through a two‐step mechanism. The critical relative humidity was found to be at ca 81 and 42% for anhydrous and hydrate caffeine forms, respectively. Copyright © 2009 John Wiley & Sons, Ltd.