Multicomponent Molecular Orbital–Climbing Image–Nudged Elastic Band Method to Analyze Chemical Reactions Including Nuclear Quantum Effect

To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHY?XCHCHCHYH (X, Y=O, NH, or CH₂) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital‐climbing image‐nudged elastic band (MC_MO–CI–NEB) method. We obtain not only transition state structures but also minimum‐energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO–CI–NEB method. We find that nuclear quantum effect affects not only stationary‐point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (k_H/k_D).     

负载金属对MoO3-TiO2光催化剂结构与催化性能的影响

用溶胶-凝胶和浸渍-还原相结合的方法制得M/MoO3-TiO2 (M=Pd, Cu, Ni和Ag)光催化剂。利用X-射线衍射(XRD)、程序升温还原(TPR)、红外光谱(IR)、程序升温脱附(TPD)、紫外-可见漫反射光谱(UV-VisDRS)和光反应等技术,研究了负载金属复合半导体的物相结构、吸附性能、吸光性能和光催化反应性能。结果表明,金属M(M=Pd, Cu)负载在复合半导体上,延迟了TiO2由锐钛矿向金红石相的转化,增强了Mo与载体TiO2的相互作用,促进Mo物种由四面体配位向八面体配位转化,使TiO2光吸收限发生蓝移,对可见光部分的吸收明显增加,拓宽了催化剂的光响应范围;固体材料吸光性能强弱顺序Pd/MoO3-TiO2 >Cu/MoO3-TiO2>Ag/MoO3-TiO2>Ni/MoO3-TiO2;Pd对CO2吸附能力过强,卧式吸附态脱附温度高,光催化效率不高;金属Cu对CO2吸附能力适中,CO2与C3H6脱附温度较接近,实现了光-表面-热的协同作用,光量子效率最高。     

Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase

The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.     

复合半导体负载金属材料光催化性能研究

CO₂和烃类光催化直接合成烃类氧化物在合成化学、碳资源利用和环境保护等方面均有重大意义。用溶胶-凝胶和浸渍-还原相结合的方法制得M/V₂O₅-TiO₂(M=Pd、Cu、Ni和Ag)光催化剂。利用XRD、TPR、IR、TPD、UV-Vis DRS和光反应器等技术研究了负载金属复合半导体的物相结构、吸附性能、光吸收性能和光催化反应性能。结果表明：金属负载在复合半导体上延迟了TiO₂由锐钛矿向金红石相的转化,增强了V与载体TiO₂的相互作用,使TiO₂光吸收限发生蓝移,对可见光部分的吸收明显增加,拓宽了催化剂的光响应范围;材料吸光性能强弱顺序Pd/V₂O₅-TiO₂ >Cu/V₂O₅-TiO₂ >Ag/V₂O₅-TiO₂>Ni/V₂O₅-TiO₂;材料的吸附性能及反应物的吸附态是反应发生的关键,CO₂在Ag/V₂O₅-TiO₂表面无法形成卧式吸附态,没有目的产物甲基丙烯酸(MAA)生成,光量子效率低;光吸收性能较好的Pd/V₂O₅-TiO₂对CO₂吸附能力过强,卧式吸附态脱附温度高,光催化效率不高;Cu/V₂O₅-TiO₂对CO₂吸附能力适中,CO₂与C₃H₆脱附温度较接近,实现了“光-表面-热”的协同作用,光量子效率最高,达15.1%。     

Kinetic and geometric isotope effects originating from different adsorption potential energy surfaces: cyclohexane on Rh(111)

Novel isotope effects were observed in desorption kinetics and adsorption geometry of cyclohexane on Rh(111) by the use of infrared reflection absorption spectroscopy, temperature programmed desorption, photoelectron spectroscopy, and spot-profile-analysis low energy electron diffraction. The desorption energy of deuterated cyclohexane (C(6)D(12)) is lower than that of C(6)H(12). In addition, the work function change by adsorbed C(6)D(12) is smaller than that by adsorbed C(6)H(12). These results indicate that C(6)D(12) has a shallower adsorption potential than C(6)H(12) (vertical geometric isotope effect). The lateral geometric isotope effect was also observed in the two-dimensional cyclohexane superstructures as a result of the different repulsive interaction between interfacial dipoles. The observed isotope effects should be ascribed to the quantum nature of hydrogen involved in the C-H···metal interaction.     

A mechanism for water splitting and hydrogen absorbing functions of metal–oxide layered hydrogen storage materials studied by means of ion beam analysis

This review describes a study of catalytic functions of water splitting at the surface and hydrogen gas emitting from the bulk of metal–oxide layered materials as well as hydrogen storage materials as its application by means of the ion beam analysis techniques. First are described a microscopic model for water splitting at the oxide surface and mass balance equations for hydrogen atoms in the bulk. The latter is a mathematical expression of a one‐way diffusion model proposed for an anomalous isotope effect in D–H and H–D replacements of both deuterium (D) implanted into perovskite oxide ceramics by protium (H) in H₂O vapour and the vise versa. The latter model brings about finding of catalytic functions of water splitting at the surface and hydrogen gas emitting from the bulk. Second, experimental results on the anomalous isotope effect are presented and the D–H replacement rates are described in detail. Subsequently are shown results on H₂ gas emission measured with a Bach method, which give a clear evidence for the water splitting and hydrogen gas emitting catalytic functions of the oxide surface. Finally, we present experimental data on the hydrogen absorption and emission characteristics of the metal–oxide layered hydrogen storage materials as an application of the water splitting and hydrogen absorbing catalysts. Copyright © 2014 John Wiley & Sons, Ltd.     

纳米钯膜电极的制备、结构表征和特殊反应性能

用循环伏安方法制备纳米钯膜电极,运用扫描隧道显微镜和原位红外光谱等方法研究其结构和反应性能.STM图像表明,制备的纳米钯膜具有特殊的层状结构,纳米级厚度的层状晶体由直径6nm左右的Pd微晶聚集而成.发现当钯膜厚度为几个纳米时,CO的吸附表现出异常红外效应,即红外谱峰反向和红外吸收显著增强(增强因子可达42.6).纳米钯膜电极对氢的反应也具有特殊的性能,与氢向钯晶格扩散吸收过程相比较,氢吸脱附的表面过程成为主要反应.研究结果还指出,纳米钯膜电极的异常红外效应和对氢反应的特殊性能与钯膜厚度密切关联,并可归结为钯膜材料的纳米尺度效应.     

DFT-based Machine Learning for Ensemble Effect of Pd@Au Electrocatalysts on CO2 Reduction Reaction

The ensemble effect due to variation of Pd content in Pd−Au alloys have been widely investigated for several important reactions, including CO₂ reduction reaction (CO₂RR), however, identifying the stable Pd arrangements on the alloyed surface and picking out the active sites are still challenging. Here we use a density functional theory (DFT) based machine-learning (ML) approach to efficiently find the low-energy configurations of Pd−Au(111) surface alloys and the potentially active sites for CO₂RR, fully covering the Pd content from 0 to 100 %. The ML model is actively learning process to improve the predicting accuracy for the configuration formation energy and to find the stable Pd−Au(111) alloyed surfaces, respectively. The local surface properties of adsorption sites are classified into two classes by the K-means clustering approach, which are closely related to the Pd content on Au surface. The classification is reflected in the variation of adsorption energy of CO and H: In the low Pd content range (0–60 %) the adsorption energies over the surface alloys can be tuned significantly, and in the medium Pd content (37-68 %), the catalytic activity of surface alloys for CO₂RR can be increased by increase the Pd content and attributed to the meta-stable active site over the surface. Thus, the active site-dependent reaction mechanism is elucidated based on the ensemble effect, which provides new physical insights to understand the surface-related properties of catalysts.     

Kinetics of localized adsorption of colloid particles

Methods of analyzing localized adsorption of colloid particles at solid/liquid interfaces were extensively reviewed. First, the initial adsorption fluxes calculated using the Levich-Smoluchowski approximation were discussed. The uniformly, and nonuniformly accessible interfaces were distinguished and the superiority of the former in experimental studies was pointed out. A criterion was introduced for estimating the relative significance of the bulk transfer and surface adsorption steps. It was shown that for the majority of experimental and practical situations the surface mass balance equation can be decoupled from the bulk continuity equation. Thus, in due course attention was focused on theoretical and experimental methods of determining the surface blocking parameter B. It was shown that for low and moderate surface concentration range the statistical mechanic approach can be effectively used for predicting B. By introducing the equivalent hard sphere radius r¹ it became possible to analyze quantitatively blocking effects of interacting as well as nonspherical particles. The analytical solutions were compared with numerical simulation methods valid for the entire range of surface concentrations. The Monte-Carlo algorithm based on the random sequential adsorption (RSA) concept was compared with the sequential Brownian-Dynamics (SBD) method. Theoretical results obtained using these approaches were extensively discussed especially the role of repulsive electrostatic interaction among adsorbing particles. It was shown that these interactions diminish profoundly both the particle adsorption rate and the maximum surface concentration of particles forming “random” monolayers. When the electrostatic forces were operating (lower ionic strength) two distinctive adsorption regimes were predicted (i) fast Langmuir-type adsorption for short times and then (ii) very slow RSA-type approach to the maximum surface concentrations. As discussed such long lasting transient adsorption states could erroneously be interpreted as equilibrium adsorption isotherms. Then, the indirect and direct experimental methods aimed at a quantitative determination of particle adsorption kinetics were described. Illustrative experimental results performed for model latex suspensions were evoked. A satisfactory agreement with theoretical predictions was found for a variety of important physicochemical parameters studied. The RSA approach was found useful for describing particle adsorption kinetics for low and moderate surface concentrations in the case when the flow induced effects could be neglected. On the other hand, the SBD method was found of general validity especially in describing the hydrodynamic scattering effect observed experimentally for higher shear rates. Finally, the theoretical and experimental results concerning structure formation in adsorption processes were presented. The experimentally measured two-dimensional (2D) pair correlation function g12 of adsorbed particles suggested a liquid-like short range ordering occurring for larger surface concentrations. The extent of the 2D ordering was influenced by the adsorption mechanisms of particles, especially the presence of external field of forces.     

Combined plane wave and localized orbital electronic structure calculation: Adsorption energy of hydrogen on Pd(111)

To achieve the necessary accuracy when calculating the electronic structures of materials, for example, for surface or bulk models, we propose a combined plane wave (PW) and localized orbital (LO) electronic structure calculation approach. A high level theory calculation based on the LO approach can be used to describe chemical reactions and other electronic processes using a cluster model. Conversely, the electronic structure of a surface or bulk model is best calculated using a PW approach. In this study, we analyzed the potential energy surface of a hydrogen atom adsorption on a Pd(111) surface using our proposed combined PW and LO approach. We clearly demonstrate that the combined PW and LO approach is both effective and necessary to determine local surface phenomena. We expect that the proposed approach will be effective for a broad range of applications in the material science field.     

Quantum dynamics of dissociative adsorption of H_2 and D_2:The time-dependent wave packet method

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Phenomenological aspects related to the electrochemical behaviour of smooth palladium electrodes in alkaline solutions

The voltammetric behaviour of smooth palladium electrodes in 1 M NaOH is studied in the potential range related to the thermodynamic stability of water. The electrosorption of H atoms on bulk Pd appears as a reversible reaction coupled to a diffusion process which occurs within bulk Pd. The voltammetric electrodesorption of H from bulk Pd is a process under mixed control, i.e. the diffusion from the bulk and the surface oxidation of H atoms. Fast pseudocapacitive reactions are detected in the range 0.2–0.4 V associated with the adsorption of H atoms at the submonolayer level. The initial stages of Pd oxide layer formation, at ca. 0.68 V, involves two reversible stages. The Pd oxide monolayer formation is achieved at 1.25 V/RHE and is followed by the formation of a third reversible system. This system is enhanced by an excursion in the potential range of the oxygen evolution reaction. This reversible system is probably a redox system involving Pd(II)/Pd(IV) species. The voltammetric electroreduction of the Pd oxide film shows rather irreversible behaviour. Inhibition effects on the reversible adsorption of H atoms due to residual oxide species were observed as well as inhibition on loading the Pd electrode with hydrogen to form the (α + β)-PdH phase. Rotating ring-disc experiments demonstrate that Pd electrodissolution in basic solutions is much smaller than in acid solutions. However, soluble palladium species are detected, especially during the formation of the fast redox systems, in the potential range related to Pd oxide layer growth.     

Correlations between hydrogen electrosorption properties and composition of Pd-noble metal alloys

Hydrogen adsorption on and absorption into Pd alloys with other noble metals was studied in acidic solutions (0.5 M H₂SO₄) using cyclic voltammetry. Correlations were found between the potentials of adsorbed/absorbed hydrogen oxidation peaks and surface/bulk compositions of Pd–Rh alloys. The potential of the α–β-phase transition depends linearly on Pd bulk content in Pd–Au, Pd–Rh, Pd–Pt and Pd–Pt–Rh alloys. The obtained relationships can be utilized for the determination of the composition of homogeneous Pd-noble alloys from hydrogen electrosorption experiments.     

Multicomponent QM study on the reaction of HOSO + NO2 with H2O: Nuclear quantum effect on structure and reaction energy profile

The hydrogen transfer reaction in the reaction of HOSO + NO₂ with and without H₂O have been investigated using multicomponent quantum-mechanics method, which can directly take nuclear quantum effect (NQE) of light nuclei into account. For the case of the reaction without H₂O, our calculation reveals that the reaction leading to trans-HONO is preferred. For the reaction with H₂O, water-non-mediated and water-mediated (hydrogen-relay) hydrogen transfer mechanism are investigated. The NQE of hydrogen nucleus lowers the relative energy of the stationary point structures and reduces the activation barrier of the reactions. The largest stabilization is found in the transition state structure of the hydrogen-relay type reaction. H/D isotope effects for the reactions are also analyzed. In particular, H/D isotope effect on the activation barrier is analyzed in detail with the aid of the active strain model.     

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.     

Pd(510)台阶面对氢分子解离吸附的影响

本文应用对势方法构造了Ｈ２－Ｐｄ（１００）和Ｈ２－Ｐｄ（５１０）体系相互作用的ＬＥＰＳ势能面．考察了氢分子在Ｐｄ（１００）面上的非活化前驱态解离吸附特性，理论结果和实验符合得很好．对氢分子在Ｐｄ（５１０）台阶面上的解离吸附行为的研究表明，由于台阶的影响，在台阶下形成了非活化直接解离通道，在台阶上及台阶边棱处，主要存在非活化前驱态解离通道；在台阶面上发现了氢分子的活化吸附．     

氢在钯单晶表面的解离与在体相的扩散

氢分子在金属表面的解离吸附与氢原子在金属体相的扩散是个典型的表面过程.前者在甲烷化及合成氨等基础化工反应中起着关键作用;后者常常导致金属材料的脆化与断裂,但过渡金属及其合金是安全和优良的储氢材料.因此,研究氢分子在金属表面的解离吸附与氢原子在金属体相的扩散,是多相催化与金属物理广泛感兴趣的课题,具有重要的理论和应用价值.本文采用分子动力学方法初步探讨了二者之间的关联.分子催化动力学为从微观层次上研究上述课题提供了一种理论方法.本文采用经过我们改进的半经验LEPS方法,计算了氢分子在Pd(100)和(110)晶面的解离和氢原子在钯表面与体相扩散的相互作用位能面,并根据计算结果探讨了其微观机理.     

碳源对鱼骨式纳米碳纤维及其负载的钯催化剂性能的影响

分别以甲烷、一氧化碳和乙烯为碳源合成了3种鱼骨式结构的纳米碳纤维(FCNF-C1,FCNF-CO和FCNF-C2),并作为载体制备了3种钯催化剂(Pd0.5%),考察了在对苯二甲酸加氢精制中的催化活性,通过N2吸附-脱附、X射线衍射、程序升温脱附、电子透射显微镜及CO化学吸附等方法对载体以及催化剂的结构进行了表征.结果表明,从不同碳源合成的纳米碳纤维(CNF)具有相似的直径和鱼骨式石墨层排列方式,但其物理化学性能差异较大,其中CO作为碳源得到的CNF具有最大的比表面积,最高的石墨化程度和最多的表面含氧基团;不同碳源的鱼骨式CNF负载的钯催化剂的活性为:Pd/FCNF-CO>Pd/FCNF-C1>Pd/FCNF-C2,与Pd分散度的顺序一致.CNF的织构、晶体结构和表面化学等协同载体效应,决定了Pd金属在CNF上的分散状态以及催化性能,而CNF的石墨层排列方式对其影响很小.     

Nuclear quantum and H/D isotope effects on three-centered bonding diborane: Path integral molecular dynamics simulations

Nuclear quantum and H/D isotope effects of bridging and terminal hydrogen atoms of diborane (B₂H₆) molecules were systematically studied by classical ab initio molecular dynamics (CLMD) and ab initio path integral molecular dynamics (PIMD) simulations with BHandHLYP/6-31++G** level of theory at room temperature (298.15 K). Calculated results clearly show that H/D isotope effect appears in the distribution of hydrogen (deuterium) of B₂H₆ (B₂D₆). Geometry of B₂H₆ also plays a significant role in the nuclear quantum effect proved by PIMD simulations, but slightly deviated from its equilibrium structure when simulated via CLMD simulation. The bond lengths between boron atoms R (B1 … B2) and the bridging hydrogen atoms R_HH (H_B1 … H_B2) of the B₂H₆ molecule obtained from PIMD simulations are slightly longer than those of the deuterated form of the diborane (B₂D₆) molecule. The principal component analysis (PCA) was also employed to distinguish the important modes of bridging hydrogen as related to the nuclear quantum and H/D isotope effects. The highest level of contribution obtained from PCA of PIMD simulations is bending, while various mixed vibrations with less contribution were also found. Therefore, the nuclear quantum and H/D isotope effects need to be taken into account for a better understanding of diborane geometry.     

Modeling of nucleic acid adsorption on 3D prisms in microchannels

Understanding nucleic acid adsorption in microchannels is critical to improve the efficiency of purifying and extracting nucleic acid (NA) from sample solutions by microfluidic technologies. Using a microchannel with 3D prismatic silica elements on the wall can dramatically increase the surface area-to-volume ratio, and hence facilitate the nucleic acid adsorption on the wall. In this study a theoretical model for modeling adsorption in a microchannel with a designed 3D surface structure was developed, and five dimensionless numbers were found to be the key parameters in the adsorption process. Extensive numerical simulations were conducted. Two flow modes, the electroosmotic flow (EOF) and pressure-driven flow (PDF), were investigated for their effect on the adsorption. It was found that the EOF is more desirable than PDF. The 3D prismatic elements can increases the NA molecule adsorption not only by providing more surface areas, but also by the induced pressure resisting the central bulk electroosmotic flow. Finally, the effects of adsorption kinetic parameters (i.e., the kinetic association/dissociation constants, the diffusion coefficient, the total site density, the loading concentration, and the channel height), on the adsorption process were discussed in detail.