首页 > 期刊 > 物理化学学报
前言
表面物理化学
吴凯
2018, 34(12): 1299-1301  doi: 10.3866/PKU.WHXB201804192
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亮点
Au单原子的制备及其在CO氧化反应中荷电状态的表征
张涛
2018, 34(12): 1302-1303  doi: 10.3866/PKU.WHXB201801192
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Re(0001)上强界面相互作用诱导的石墨烯-碳化物新奇的转变行为
吴凯
2018, 34(12): 1304-1305  doi: 10.3866/PKU.WHXB201712061
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Au(110)面上烷烃C―H键活化的构效关系研究
吴凯
2018, 34(12): 1306-1307  doi: 10.3866/PKU.WHXB201803021
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氧空位依赖的氯氧化铋光催化反应
杨金龙
2018, 34(12): 1308-1309  doi: 10.3866/PKU.WHXB201712082
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利用金属有机框架铆钉分子催化剂在气液固界面上催化二氧化碳氢化
韩布兴
2018, 34(12): 1310-1311  doi: 10.3866/PKU.WHXB201712142
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通讯
衬底对N@C60分子电子自旋共振谱的影响
赵烨梁, 王兵
2018, 34(12): 1312-1320  doi: 10.3866/PKU.WHXB201803011
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N@C60内嵌富勒烯是一种在量子科技领域有较高应用前景的分子。科学家们设计了一系列以内嵌富勒烯分子为基本量子单元的量子计算机模型,而构筑这样的模型具有极高的挑战。其中,由于内嵌富勒烯分子阵列的制备通常需要合适的衬底,而衬底与分子之间的相互作用会影响甚至破坏内嵌N原子的自旋信号。因此研究和理解衬底与内嵌富勒烯分子的相互作用具有重要的意义。本文制备了高质量的N@C60分子,并采用扫描隧道显微镜对其在Au(111)表面的结构及电子态进行表征。通过对比N@C60分子在Au(111)、Si(111)、SiO2表面的电子自旋共振(ESR)信号随时间及其抽真空处理的变化,表明Au原子的核自旋与内嵌N原子的电子自旋的耦合作用是Au(111)表面N@C60单分子层的ESR谱中内嵌N原子的信号衰减的主要原因。
综述
超高真空条件下碱基与金属在Au(111)表面的相互作用
王心怡, 谢磊, 丁元琪, 姚心仪, 张弛, 孔惠慧, 王利坤, 许维
2018, 34(12): 1321-1333  doi: 10.3866/PKU.WHXB201802081
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碱基是生命体中核酸的重要组成部分,用以携带遗传信息。碱基之间的互补配对行为在DNA和RNA的高保真复制过程中起到重要作用。除了碱基间的特异性识别,碱基分子与金属,盐类和一些小分子也可发生相互作用,特别是与某些金属原子或离子的相互作用会造成核酸的损伤,并可能进一步导致基因突变甚至诱发细胞的癌变。同时,基于DNA金属化形成的纳米器件逐渐成为纳米科技领域的研究热点。因此研究碱基与金属作用的现象和机制对于生物化学和纳米科学都十分重要。扫描隧道显微镜可以在实空间原子尺度下揭示纳米结构,密度泛函理论计算可以帮助确定反应机理。本文对近年来报道的利用以上两种方法在超高真空环境下碱基及其衍生物与碱金属、碱土金属和过渡金属的相互作用进行了介绍,总结了碱基与金属的作用位点及反应发生的机理,并进一步提出单原子尺度下的结构模型、可能的反应路径,进而揭示相互作用的本质。
REVIEW
Atomic Layer Deposition: A Gas Phase Route to Bottom-up Precise Synthesis of Heterogeneous Catalyst
Hengwei WANG, Junling LU
2018, 34(12): 1334-1357  doi: 10.3866/PKU.WHXB201804201
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Heterogeneous catalysts are usually synthesized by the conventional wet-chemistry methods, including wet-impregnation, ion exchange, and deposition-precipitation. With the development of catalyst synthesis, great progress has been made in many industrially important catalytic processes. However, these catalytic materials often have very complex structures along with poor uniformity of active sites. Such heterogeneity of active site structures significantly decreases catalytic performance, especially in terms of selectivity, and hinders atomic-level understanding of structure-activity relationships. Moreover, loss of exposed active components by sintering or leaching under harsh reaction conditions causes considerable catalyst deactivation. It is desirable to develop a facile method to tune catalyst active site structures, as well as their local chemical environments on the atomic level, thereby facilitating reaction mechanisms understanding and rational design of catalysts with high stability. Atomic layer deposition (ALD), a gas-phase technique for thin film growth, has emerged as an alternative method to synthesize heterogeneous catalysts. Like chemical vapor deposition (CVD), ALD relies on a sequence of molecular-level, self-limiting surface reactions between the vapors of precursor molecules and a substrate. This unique character makes it possible to deposit various catalytic materials uniformly on a high-surface-area support with nearly atomic precision. By tuning the number, sequence, and types of ALD cycles, bottom-up precise construction of catalytic architectures on a support can be achieved. In this review, we focus on the design and synthesis of supported metal catalysts using ALD. We first review strategies developed to precisely tailor the size, composition, and structures of metal nanoparticles (NPs) using ALD. Catalytic performances of these ALD metal catalysts are also discussed and compared to conventional catalysts. We highlight synthetic strategies for synthesis of metal single-atom catalysts and bottom-up precise synthesis of dimeric metal catalysts. Their impact on catalysis is discussed. We demonstrate that metal oxide ALD on metal NPs can enhance catalytic activity, selectivity, and especially stability. In particular, we show that site-selective blocking of metal NPs with an oxide overcoat improves selectivity and contributes to an understanding of the distinct functionalities of the low-and high-coordination sites in catalytic reactions on the atomic level. Next, we discuss an effective method to construct bifunctional catalysts via precisely-controlled addition of a secondary functionality using ALD. Finally, we summarize the advantages of ALD for the advanced design and synthesis of catalysts and discuss the challenges and opportunities of scaling up ALD catalyst synthesis for practical applications.
论文
O2和CO在Ni(111)表面的吸附活化
段园, 陈明树, 万惠霖
2018, 34(12): 1358-1365  doi: 10.3866/PKU.WHXB201803071
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采用高分辨电子能量损失谱(HREELS)、俄歇电子能谱(AES)和低能电子衍射(LEED)研究镍单晶表面氧物种及CO与O2的共吸附。实验结果表明,Ni(111)表面氧化后存在两种氧物种,位于54 meV能量损失峰的表面化学吸附氧物种和位于69 meV能量损失峰的表面氧化镍。首先,随着暴露氧量的增加,表面化学吸附氧物种的能量损失峰蓝移至58 meV;其次,通过真空退火及与CO相互作用考察,发现表面化学吸附氧物种较不稳定。在室温条件下,表面预吸附形成的表面化学吸附氧物种与CO共吸附,导致端位吸附CO增多,表明氧优先吸附在穴位上,随着CO暴露量的增加化学吸附氧物种与CO反应脱去;而表面氧化镍需在较高温度和较高CO分压下才能被CO还原。预吸附CO可被氧逐渐移去。
利用原位APXPS与STM研究H2在ZnO(1010)表面的活化
刘强, 韩永, 曹云君, 李小宝, 黄武根, 余毅, 杨帆, 包信和, 李毅敏, 刘志
2018, 34(12): 1366-1372  doi: 10.3866/PKU.WHXB201804161
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Cu/ZnO/Al2O3是工业中最广泛使用的甲醇合成催化剂。然而该催化反应的活性位点和机理目前仍存争议。H2作为反应物之一,研究其在ZnO表面的活化和解离对于弄清甲醇合成反应的催化机理具有重要的帮助。本工作利用近常压光电子能谱(APXPS)和扫描隧道显微镜(STM)原位研究了H2在ZnO(1010)表面上的活化和解离。APXPS结果表明:在0.3 mbar (1 mbar = 100 Pa)的H2气氛中,室温下ZnO表面形成羟基(OH)吸附物种。STM实验发现通入H2后ZnO表面发生了(1×1)到(2×1)的重构。上述结果和原子H在ZnO(1010)表面的吸附结果一致。然而吸附H2O可以导致同样的现象。因此,我们还开展了H2O在ZnO(1010)表面吸附的对比实验。结果表明:H2气氛中ZnO表面发生0.3 eV的能带弯曲,而H2O吸附实验中几乎观察不到能带弯曲发生。同时,热稳定性实验表明H2气氛中ZnO表面的OH不同于H2O解离吸附产生的OH,前者具有更高的脱附温度。因此,本工作的结果表明常温和常压下H2在ZnO(1010)表面发生解离吸附。这一结果和以往超高真空下未发现H2在ZnO(1010)表面上的解离不同,说明H2的活化是一个压力依赖过程。
ARTICLE
Growth of Ordered ZnO Structures on Au(111) and Cu(111)
Xinfei ZHAO, Hao CHEN, Hao WU, Rui WANG, Yi CUI, Qiang FU, Fan YANG, Xinhe BAO
2018, 34(12): 1373-1380  doi: 10.3866/PKU.WHXB201804131
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The growth and structural properties of ZnO thin films on both Au(111) and Cu(111) surfaces were studied using either NO2 or O2 as oxidizing agent. The results indicate that NO2 promotes the formation of well-ordered ZnO thin films on both Au(111) and Cu(111). The stoichiometric ZnO thin films obtained on these two surfaces exhibit a flattened and non-polar ZnO(0001) structure. It is shown that on Au(111), the growth of bilayer ZnO nanostructures (NSs) is favored during the deposition of Zn in presence of NO2 at 300 K, whereas both monolayer and bilayer ZnO NSs could be observed when Zn is deposited at elevated temperatures under a NO2 atmosphere. The growth of bilayer ZnO NSs is caused by the stronger interaction between two ZnO layers than between ZnO and Au(111) surface. In contrast, the growth of monolayer ZnO NSs involves a kinetically controlled process. ZnO thin films covering the Au(111) surface exhibits a multilayer thickness, which is consistent with the growth kinetics of ZnO NSs. Besides, the use of O2 as oxidizing agent could lead to the formation of sub-stoichiometric ZnOx structures. The growth of full layers of ZnO on Cu(111) has been a difficult task, mainly because of the interdiffusion of Zn promoted by the strong interaction between Cu and Zn and the formation of Cu surface oxides by the oxidation of Cu(111). We overcome this problem by using NO2 as oxidizing agent to form well-ordered ZnO thin films covering the Cu(111) surface. The surface of the well-ordered ZnO thin films on Cu(111) displays mainly a moiré pattern, which suggests a (3 × 3) ZnO superlattice supported on a (4 × 4) supercell of Cu(111). The observation of this superstructure provides a direct experimental evidence for the recently proposed structural model of ZnO on Cu(111), which suggests that this superstructure exhibits the minimal strain. Our studies suggested that the surface structures of ZnO thin films could change depending on the oxidation level or the oxidant used. The oxidation of Cu(111) could also become a key factor for the growth of ZnO. When Cu(111) is pre-oxidized to form copper surface oxides, the growth mode of ZnOx is altered and single-site Zn could be confined into the lattice of copper surface oxides. Our studies show that the growth of ZnO is promoted by inhibiting the diffusion of Zn into metal substrates and preventing the formation of sub-stoichiometric ZnOx. In short, the use of an atomic oxygen source is advantageous to the growth of ZnO thin films on Au(111) and Cu(111) surfaces.
Morphologies and Electronic Structures of Calcium-Doped Ceria Model Catalysts and Their Interaction with CO2
Yan WANG, Xiong LI, Shanwei HU, Qian XU, Huanxin JU, Junfa ZHU
2018, 34(12): 1381-1389  doi: 10.3866/PKU.WHXB201804092
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CeO2-based catalysts are promising for use in various important chemical reactions involving CO2, such as the dry reforming of methane to produce synthesis gas and methanol. CeO2 has a superior ability to store and release oxygen, which can improve the catalytic performance by suppressing the formation of coke. Although the adsorption and activation behavior of CO2 on the CeO2 surface has been extensively investigated in recent years, the intermediate species formed from CO2 on ceria has not been clearly identified. The reactivity of the ceria surface to CO2 has been reported to be tuned by introducing CaO, which increases the number of basic sites for the ceria-based catalysts. However, the mechanism by which Ca2+ ions affect CO2 decomposition is still debated. In this study, the morphologies and electronic properties of stoichiometric CeO2(111), partially reduced CeO2-x(111) (0 < x < 0.5), and calcium-doped ceria model catalysts, as well as their interactions with CO2, were investigated by scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, and synchrotron radiation photoemission spectroscopy. Stoichiometric CeO2(111) and partially reduced CeO2-x(111) films were epitaxially grown on a Cu(111) surface. STM images show that the stoichiometric CeO2 film exhibits large, flat terraces that completely cover the Cu(111) surface. The reduced CeO2-x film also has a flat surface and an ordered structure, but dark spaces are observed on the film. Different Ca-doped ceria films were prepared by physical vapor deposition of metallic Ca on CeO2(111) at room temperature and subsequent annealing to 600 or 800 K in ultrahigh vacuum. The different preparation procedures produce samples with various surface components, oxidation states, and structures. Our results indicate that the deposition of metallic Ca on CeO2 at room temperature leads to a partial reduction of Ce from the +4 to the +3 state, accompanied by the oxidation of Ca to Ca2+. Large CaO nanofilms are observed on CeO2 upon annealing to 600 K. However, small CaO nanoislands appear near the step edges and more Ca2+ ions migrate into the subsurface of CeO2 upon annealing to 800 K. In addition, different surface-adsorbed species are identified after CO2 adsorption on ceria (CeO2 and reduced CeO2-x) and Ca-doped ceria films. CO2 adsorption on the stoichiometric CeO2 and partially reduced CeO2-x surfaces leads to the formation of surface carboxylate. Moreover, the surface carboxylate species is more easily formed on reduced CeO2-x with enhanced thermal stability than on stoichiometric CeO2. On Ca-doped ceria films, the presence of Ca2+ ions is observed to be beneficial for CO2 adsorption; further, the carbonate species is identified.
CO Induced Single and Multiple Au Adatoms Trapped by Melem Self-Assembly
Lili HUANG, Xiang SHAO
2018, 34(12): 1390-1396  doi: 10.3866/PKU.WHXB201804191
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The controllability of metal adatoms has been attracting ever-growing attention because the metal species in particular single-atom metals can play an important role in various surface processes, including heterogeneous catalytic reactions. On the other hand, organic self-assembly films have been regarded as an efficient and versatile bottom-up method to fabricate surface nanostructures, whose functionality and periodicity can be highly designable. In this work, we have developed a novel strategy to steer the generation and distribution of metal adatoms by combining the surface self-assemblies with exposure to small inorganic gaseous molecules. More specifically, we have prepared a honeycomb structure of melem (triamino-s-heptazine) on the Au(111) surface based on a well-structured hydrogen bonding network. The achieved melem self-assembly contains periodic hexagonal pores having diameters as large as around 1 nm. More importantly, the peripheries of the nanopores are decorated with heterocyclic N atoms that can probably form strong interactions with the metal species. Upon exposing the melem self-assembly to a CO atmosphere at room temperature, a fair number of Au adatoms were produced and trapped inside the nanopores encircled by the melem molecules. Single or clustered Au vacancies were concomitantly formed that were also trapped by the melem pores and stabilized by the surrounding molecules, as confirmed by high-resolution scanning tunneling microscopy (STM) images. Both types of added species showed positive correlations with the CO exposure and saturated at around 0.01 monolayer. In addition, owing to the large pore size, as well as the presence of multiple docking sites inside the nanopores, more than one Au adatom can reside in a melem nanopore; they can be distributed in a variety of configurations for bi-Au (two Au adatoms) and tri-Au (three Au adatoms) species, whose population can be manipulated with the CO exposure. Moreover, control experiments demonstrated that these CO-induced Au species, including the adatoms and vacancies, can survive annealing treatments up to the temperature at which the melem molecules start to desorb, indicating a substantial thermal stability. The formed Au species may hold great potential for serving as active sites for surface reactions. More interestingly, the bi-Au and tri-Au species have moderate Au-Au intervals, and can be potentially active for certain structurally sensitive bimolecular reactions. Considering all these aspects, we believe that this work presents a fresh approach to utilizing organic self-assembly films and has demonstrated a rather novel strategy for preparing various single-atom metal species on substrate surfaces.
Article
Tree-Like NiS-Ni3S2/NF Heterostructure Array and Its Application in Oxygen Evolution Reaction
Pan LUO, Fang SUN, Ju DENG, Haitao XU, Huijuan ZHANG, Yu WANG
2018, 34(12): 1397-1404  doi: 10.3866/PKU.WHXB201804022
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In the past decade, fossil fuel resources have been exploited and utilized extensively, which could lead to increasing environmental crises, like greenhouse effect, water pollution, etc. Accordingly, many coping strategies have been put forward, such as water electrolysis, metal-air batteries, fuel cell, etc. Among the strategies mentioned above, water electrolysis is one of the most promising. Water splitting, which can achieve sustainable hydrogen production, is a favorable strategy due to the abundance of water resources. Splitting of water includes two half reactions integral to its operation: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). However, its practical application is mainly impeded by the sluggish anode reaction. Simultaneously, noble metal oxides (IrO2 and RuO2) and Pt-based catalysts have been recognized as typical OER catalysts; however, the scarcity of noble metals greatly limits their development. Hence, designing an alternative electrocatalyst plays a vital role in the development of OER. However, exploring a highly active electrocatalyst for OER is still difficult. Herein, a miraculous construction of a tree-like array of NiS/Ni3S2 heterostructure, which is directly grown on Ni foam substrate, is synthesized via one-step hydrothermal process. Since NiS and Ni3S2 have shown great OER performance in previous investigations, this novel NiS-Ni3S2/Nikel foam (NF) heterostructure array has tremendous potential as a practical OER catalyst. Upon application in OER, the NiS-Ni3S2/NF heterostructure array catalyst exhibits excellent activity and stability. More specifically, this novel tree-like NiS-Ni3S2 heterostructure array shows extremely low overpotential (269 mV to achieve a current density of 10 mA·cm-2) and small Tafel slope for OER. It also shows extraordinary stability in alkaline electrolytes. Compared with the Ni3S2 nanorods array, the NiS-Ni3S2 heterostructure array has a synergistic effect that can improve the OER performance. Due to the secondary structure (Ni3S2 nanosheets), the tree-like NiS-Ni3S2 array provides more active sites could have higher specific surface area. The greater activity of the NiS/Ni3S2 heterostructure may also stem from the tight conjunction between tree-like NiS/Ni3S2 and the Ni foam substrate, which is beneficial for electronic transmission. Hydroxy groups can accumulate in large amounts on the surface of the tree-like array, and it also generates some Ni-based oxides that are favorable to OER. Moreover, the synergistic effect of such heterostructure can intrinsically improve the OER activity. The unique tree-like NiS-Ni3S2 heterostructure array has great potential as an alternative OER electrocatalyst.

栏目

  

Preface
Molecular Simulations in Materials Science
Huai SUN
2018, 34(10): 1095-1096  doi: 10.3866/PKU.WHXB201803291
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Article
Simple Ligand Modifications to Modulate the Activity of Ruthenium Catalysts for CO2 Hydrogenation: Trans Influence of Boryl Ligands and Nature of Ru―H Bond
Tian LIU, Jun LI, Weijia LIU, Yudan ZHU, Xiaohua LU
2018, 34(10): 1097-1105  doi: 10.3866/PKU.WHXB201712131
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The development of efficient catalysts for the hydrogenation of CO2 to formic acid (FA) or formate has attracted significant interest as it can address the increasingly severe energy crisis and environmental problems. One of the most efficient methods to transform CO2 to FA is catalytic homogeneous hydrogenation using noble metal catalysts based on Ir, Ru, and Rh. In our previous work, we demonstrated that the activity of CO2 hydrogenation via direct addition of hydride to CO2 on Ir(Ⅲ) and Ru(Ⅱ) complexes was determined by the nature of the metal-hydride bond. These complexes could react with the highly stable CO2 molecule because they contain the same distinct metal-hydride bond formed from the mixing of the sd2 hybrid orbital of metal with the 1s orbital of H, and evidently, this property can be influenced by the trans ligand. Since boryl ligands exhibit a strong trans influence, we proposed that introducing such ligands may enhance the activity of the Ru―H bond by weakening it as a result of the trans influence. In this work, we designed two potential catalysts, namely, Ru-PNP-HBcat and Ru-PNP-HBpin, which were based on the Ru(PNP)(CO)H2 (PNP = 2, 6-bis(dialkylphosphinomethyl)pyridine) complex, and computationally investigated their reactivity toward CO2 hydrogenation. Bcat and Bpin (cat = catecholate, pin = pinacolate) are among the most popular boryl ligands in transition metal boryl complexes and have been widely applied in catalytic reactions. Our optimization results revealed that the complexes modified by boryl ligands possessed a longer Ru―H bond. Similarly, natural bond orbital (NBO) charge analysis indicated that the nucleophilic character of the hydride in Ru-PNP-HBcat and Ru-PNP-HBpin was higher as compared to that in Ru-PNP-H2. NBO analysis of the nature of Ru―H bond indicated that these complexes also followed the law of the bonding of Ru―H bond proved in the previous works (Bull. Chem. Soc. Jpn. 2011, 84 (10), 1039; Bull. Chem. Soc. Jpn. 2016, 89 (8), 905), and the d orbital contribution of the Ru atom in Ru-PNP-HBcat and Ru-PNP-HBpin was smaller than that in Ru-PNP-H2. Consequently, the Ru-PNP-HBcat and Ru-PNP-HBpin complexes were more active than Ru-PNP-H2 for the direct hydride addition to CO2 because of the lower activation energy barrier, i.e., from 29.3 kJ∙mol-1 down to 24.7 and 23.4 kJ∙mol-1, respectively. In order to further verify our proposed catalyst-design strategy for CO2 hydrogenation, the free energy barriers of the complete pathway for the hydrogenation of CO2 to formate catalyzed by complexes Ru-PNP-H2, Ru-PNP-HBcat, and Ru-PNP-HBpin were calculated to be 76.2, 67.8, and 54.4 kJ∙mol-1, respectively, indicating the highest activity of Ru-PNP-HBpin. Thus, the reactivity of Ru catalysts for CO2 hydrogenation could be tailored by the strong trans influence of the boryl ligands and the nature of the Ru―H bond.
Efficient Calculation of Absorption Spectra in Solution: Approaches for Selecting Representative Solvent Configurations and for Reducing the Number of Explicit Solvent Molecules
Bai XUE, Tiannan CHEN, J. Ilja SIEPMANN
2018, 34(10): 1106-1115  doi: 10.3866/PKU.WHXB201701083
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Dye-sensitized solar cells (DSSCs) are one of the most promising renewable energy technologies. Charge transfer and charge transport are pivotal processes in DSSCs, which govern solar energy capture and conversion. These processes can be probed using modern electronic structure methods. Because of the heterogeneity and complexity of the local environment of a chromophore in DSSCs (such as solvatochromism and chromophore aggregation), a part of the solvation environment should be treated explicitly during the calculation. However, because of the high computational cost and unfavorable scaling with the number of electrons of high-level quantum mechanical methods, approaches to explicitly treat the local environment need careful consideration. Two problems must be tackled to reduce computational cost. First, the number of configurations representing the solvent distribution should be limited as much as possible. Second, the size of the explicit region should be kept relatively small. The purpose of this study is to develop efficient computational approaches to select representative configurations and to limit the explicit solvent region to reduce the computational cost for later (higher-level) quantum mechanical calculations. For this purpose, an ensemble of solvent configurations around a 1-methyl-8-oxyquinolinium betaine (QB) dye molecule was generated using Monte Carlo simulations and molecular mechanics force fields. Then, a fitness function was developed using data from inexpensive electronic structure calculations to reduce the number of configurations. Specific solvent molecules were also selected for explicit treatment based on a distance criterion, and those not selected were treated as background charges. The configurations and solvent molecules selected proved to be good representatives of the entire ensemble; thus, expensive electronic structure calculations need to be performed only on this subset of the system, which significantly reduces the computational cost.
A Molecular Dynamics Study of Carbon Dimerization on Cu(111) Surface with Optimized DFTB Parameters
Di YIN, Zongyang QIU, Pai LI, Zhenyu LI
2018, 34(10): 1116-1123  doi: 10.3866/PKU.WHXB201801151
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摘要:
Cu has been widely used as a substrate material for graphene growth. To understand the atomistic mechanism of growth, an efficient and accurate method for describing Cu-C interactions is necessary, which is the prerequisite of any possible large-scale molecular simulation studies. The semi-empirical density-functional tight-binding (DFTB) method has a solid basis from the density functional theory (DFT) and is believed to be a good tool for achieving a balance between efficiency and accuracy. However, existing DFTB parameters cannot provide a reasonable description of the Cu surface structure. At the same time, DFTB parameters for Cu-C interactions are not available. Therefore, it is highly desirable to develop a set of DFTB parameters that can describe the Cu-C system, especially for surface reactions. In this study, a parametrization for Cu-C systems within the self-consistent-charge DFTB (SCC-DFTB) framework is performed. One-center parameters, including on-site energy, Hubbard, and spin parameters, are obtained from DFT calculations on free atoms. Two-center parameters can be calculated based on atomic wavefunctions. The remaining repulsive potential is obtained as the best compromise to describe different kinds of systems. Test calculations on Cu surfaces and Cu-or C atom-adsorbed Cu surfaces indicate that the obtained parameters can generate reasonable geometric structures and energetics. Based on this parameter set, carbon dimerization on the Cu(111) surface has been investigated via molecular dynamics simulations. Since they are the feeding species for graphene growth, it is important to understand how carbon dimers are formed on the Cu surface. It is difficult to observe carbon dimerization in brute-force MD simulations even at high temperatures, because of the surface structure distortion. To study the dimerization mechanism, metadynamics simulations are performed. Our simulations suggest that carbon atoms will rotate around the bridging Cu atom after a bridging metal structure is formed, which eventually leads to the dimer formation. The free energy barrier for dimerization at 1300 K is about 0.9 eV. The results presented here provide useful insights for understanding graphene growth.
Microscopic Investigation of Ethylene Carbonate Interface: A Molecular Dynamics and Vibrational Spectroscopic Study
Lin WANG, Liang XIN, Tatsuya ISHIYAMA, Qiling PENG, Shen YE, Akihiro MORITA
2018, 34(10): 1124-1135  doi: 10.3866/PKU.WHXB201801291
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摘要:
Ethylene carbonate (EC) liquid and its vapor-liquid interface were investigated using a combination of molecular dynamics (MD) simulation and vibrational IR, Raman and sum frequency generation (SFG) spectroscopies. The MD simulation was performed with a flexible and polarizable model of the EC molecule newly developed for the computation of vibrational spectra. The internal vibration of the model was described on the basis of the harmonic couplings of vibrational modes, including the anharmonicity and Fermi resonance coupling of C=O stretching. The polarizable model was represented by the charge response kernel (CRK), which is based on ab initio molecular orbital calculations and can be readily applied to other systems. The flexible and polarizable model can also accurately reproduce the structural and thermodynamic properties of EC liquid. Meanwhile, a comprehensive set of vibrational spectra of EC liquid, including the IR and Raman spectra of the bulk liquid as well as the SFG spectra of the liquid interface, were experimentally measured and reported. The set of experimental vibrational spectra provided valuable information for validating the model, and the MD simulation using the model comprehensively elucidates the observed vibrational IR, Raman, and SFG spectra of EC liquid. Further MD analysis of the interface region revealed that EC molecules tend to orientate themselves with the C=O bond parallel to the interface. The MD simulation explains the positive Im[\begin{document}$ \chi ^{(2)}$\end{document}](ssp) band of the C=O stretching region in the SFG spectrum in terms of the preferential orientation of EC molecules at the interface. This work also elucidates the distinct lineshapes of the C=O stretching band in the IR, Raman, and SFG spectra. The lineshapes of the C=O band are split by the Fermi resonance of the C=O fundamental and the overtone of skeletal stretching. The Fermi resonance of C=O stretching was fully analyzed using the empirical potential parameter shift analysis (EPSA) method. The apparently different lineshapes of the C=O stretching band in the IR, Raman, and SFG spectra were attributed to the frequency shift of the C=O fundamental in different solvation environments in the bulk liquid and at the interface. This work proposes a systematic procedure for investigating the interface structure and SFG spectra, including general modeling procedure based on ab initio calculations, validation of the model using available experimental data, and simultaneous analysis of molecular orientation and SFG spectra through MD trajectories. The proposed procedure provides microscopic information on the EC interface in this study, and can be further applied to investigate other interface systems, such as liquid-liquid and solid-liquid interfaces.
Selective Permeation of Gas Molecules through a Two-Dimensional Graphene Nanopore
Chengzhen SUN, Bofeng BAI
2018, 34(10): 1136-1143  doi: 10.3866/PKU.WHXB201801301
[摘要]  (10) [HTML全文] (10) [PDF 1142KB] (10)
摘要:
Selective molecular permeation through two-dimensional nanopores is of great importance for nanoporous graphene membranes. In this study, we investigate the selective permeation characteristics of gas molecules through a nitrogen-and hydrogen-modified graphene nanopore using molecular dynamics simulations. We reveal the mechanisms of selective molecular permeation from the aspects of molecular size and structure, pore configuration, and interactions between gas molecules and graphene. The results show that the permeances of different molecules are different, and the following order is observed in our study: H2O > H2S > CO2 > N2 > CH4. Molecular permeance is related to the molecular size, mass, and molecular density on the graphene surface. The molecular permeation rate is inversely proportional to the molecular mass based on gas kinetic theory, while the molecular density on the graphene surface exerts a positive effect on molecular permeation. The permeance of H2O molecules is the highest owing to their smallest diameter, while the permeance of CH4 molecules is the lowest owing to their biggest diameter; in these cases, the molecular size is a dominating factor. For H2S and CO2 molecules, the diameters of H2S molecules are larger than those of CO2 molecules, but the interactions between H2S molecules and graphene are stronger, resulting in a stronger permeation ability of H2S molecules. Between CO2 and N2 molecules, CO2 molecules show higher permeation rates owing to smaller diameters and stronger interactions with graphene. The graphene surface also shows nonuniform molecular density distribution owing to molecular permeation through graphene nanopores. Because of the doped nitrogen atoms, the CH4 molecules prefer to permeate from the left and right sides of the graphene nanopore, while the other molecules prefer to permeate from the center of the nanopore owing to their small diameters. For the molecules that show stronger interactions with graphene, the molecular density on the graphene surface is higher; accordingly, the residence time on the graphene surface is longer and the experience time period during permeation is also longer. The mechanisms identified in this study can provide theoretical guidelines for the application of graphene-based membranes. In addition, the permeance of gas molecules in the graphene nanopore adopted in this study is on the order of 10-3 mol·s-1·m-2·Pa-1, and the selectivity of other molecules relative to CH4 molecules is also high, showing that the membranes based on this type of nanopore can be employed in natural gas processing and other separation industries.
Deformation of Polymer-Grafted Janus Nanosheet: A Dissipative Particle Dynamic Simulations Study
Teng LU, Yongxiang ZHOU, Hongxia GUO
2018, 34(10): 1144-1150  doi: 10.3866/PKU.WHXB201802122
[摘要]  (9) [HTML全文] (9) [PDF 2356KB] (9)
摘要:
Because of broad potential applications in sensing, drug delivery, and molecular motors, two-dimensional (2D), flexible, responsive Janus materials have attracted considerable interest recently in many fields. Unfortunately, the molecular-level responsive deformation of these 2D Janus nanomaterials is still not clearly understood. Hence, investigating the influence factor and responsiveness of the deformation of the 2D flexible responsive Janus nanomaterials should be helpful to deepen our understanding of the deformation mechanism and may provide valuable information in the design and synthesis of novel functional 2D Janus nanomaterials. Therefore, a mesoscopic simulation method, dissipative particle dynamics simulation, based on coarse-grained models, is employed in this work to systematically investigate the effect of the chain length difference between grafted polymers within two compartments of each individual Janus nanosheet and the effect of solvent selectivity difference of these two compartments on the deformation of the polymer-grafted Janus nanosheet. Although the coarse-grained model within this simulation is relatively crude, it is still valid to provide a qualitative image of the deformation of the polymer-grafted Janus nanosheet. Furthermore, we find two basic principles: (1) with increasing length difference between grafted polymers on the two opposite surfaces, the nanosheet will bear an entropy-driven deformation with increasing curvature; (2) the solvent will preferentially wet the polymer layer with better compatibility, and such a swelling effect may also provide a driving force for the deformation process. Owing to the interplay of conformational entropy and mixing enthalpy, the equilibrium structures of the polymer-grafted Janus nanosheet result in several interesting structures, such as a tube-like structure with a hydrophobic outer surface, an envelope-like structure, and a bowl-like structure, with tuning of the chain length and solvent compatibility of grafted polymers. Additionally, an unusually tube-like structure with a hydrophobic outer surface has been observed for a relatively weak solvent selectivity, which may provide us a novel method to transfer materials into the incompatible environment and therefore has potential applications in many areas, such as controllable drug delivery and release, and industrial and medical detection. Our theoretical results first provide a fundamental insight into the controllable deformation of the flexible Janus nanosheet, which can then help in the design and synthesis of novel Janus nanodevices for potential applications in pharmaceuticals and biomedicine. Bearing the limited of the computational capabilities, our model Janus nanosheets are relatively small, which are not direct mappings from real system. We hope that a systematic simulation study on this topic would be possible soon with the rapid developments in computer technology and simulation methods, and this would provide an exhaustive and universal methodology to guide experimental studies and applications.
Reaction Mechanisms in the Thermal Decomposition of CL-20 Revealed by ReaxFF Molecular Dynamics Simulations
Chunxing REN, Xiaoxia LI, Li GUO
2018, 34(10): 1151-1162  doi: 10.3866/PKU.WHXB201802261
[摘要]  (12) [HTML全文] (12) [PDF 897KB] (12)
摘要:
The thermal decomposition of condensed CL-20 was investigated using reactive force field molecular dynamics (ReaxFF MD) simulations of a super cell containing 128 CL-20 molecules at 800–3000 K. The VARxMD code previously developed by our group is used for detailed reaction analysis. Various intermediates and comprehensive reaction pathways in the thermal decomposition of CL-20 were obtained. Nitrogen oxides are the major initial decomposition products, generated in a sequence of NO2, NO3, NO, and N2O. NO2 is the most abundant primary product and is gradually consumed in subsequent secondary reactions to form other nitrogen oxides. NO3 is the second most abundant intermediate in the early stages of CL-20 thermolysis. However, it is unstable and quickly decomposes at high temperatures, while other nitrogen oxides remain. At all temperatures, the unimolecular pathways of N―NO2 bond cleavage and ring-opening C―N bond scission dominate the initial decomposition of condensed CL-20. The cleavage of the N―NO2 bond is greatly enhanced at high temperatures, but scission of the C―N bond is not as favorable. A bimolecular pathway of oxygen-abstraction by NO2 to generate NO3 is observed in the initial decomposition steps of CL-20, which should be considered as one of the major pathways for CL-20 decomposition at low temperatures. After the initiation of CL-20 decomposition, fragments with different ring structures are formed from a series of bond-breaking reactions. Analysis of the ring structure evolution indicates that the pyrazine derivatives of fused tricycles and bicycles are early intermediates in the decomposition process, which further decompose to single ring pyrazine. Pyrazine is the most stable ring structure obtained in the simulations of CL-20 thermolysis, supporting the proposed existence of pyrazine in Py-GC/MS experiments. The single imidazole ring is unstable and decomposes quickly in the early stages of CL-20 thermolysis. Many C4 and C2 intermediates are observed after the initial fragmentation, but eventually convert into stable products. The distribution of the final products (N2, H2O, CO2, and H2) obtained in ReaxFF MD simulation of CL-20 thermolysis at 3000 K quantitatively agrees with the results of the CL-20 detonation experiment. The comprehensive understanding of CL-20 thermolysis obtained through this study suggests that ReaxFF MD simulation, combined with the reaction analysis capability of VARxMD, would be a promising method for obtaining deeper insight into the complex chemistry of energetic materials exposed to thermal stimuli.
Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations
Noriyuki YOSHII, Mika KOMORI, Shinji KAWADA, Hiroaki TAKABAYASHI, Kazushi FUJIMOTO, Susumu OKAZAKI
2018, 34(10): 1163-1170  doi: 10.3866/PKU.WHXB201802271
[摘要]  (12) [HTML全文] (12) [PDF 1772KB] (12)
摘要:
Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ΔGi+j, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, Gi, which was obtained through MD calculations. The calculated ΔGi+j was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy \begin{document}$\sum\limits_i {{n_i}\left( {l, k} \right)G_i^\dagger } $\end{document} and the free energy of mixing \begin{document}$\sum\limits_i {{n_i}(l, k){k_B}Tln({n_i}(l, k)/n(l, k))} $\end{document}, where ni(l, k) is the number of i-mer in the system at the l-th aggregation path and k-th state, with \begin{document}$n\left( {l, k} \right) = \sum\limits_i {{n_i}\left( {l, k} \right)} $\end{document}. All the aggregation pathways were obtained from the initial state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, tFPT. The calculated tFPT was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.
Influence of Photoisomerization on Binding Energy and Conformation of Azobenzene-Containing Host-Guest Complex
Pingying LIU, Chunyan LIU, Qian LIU, Jing MA
2018, 34(10): 1171-1178  doi: 10.3866/PKU.WHXB201803024
[摘要]  (12) [HTML全文] (12) [PDF 1633KB] (12)
摘要:
The construction of a photo-controllable artificial molecular machine capable of realizing the light-driven motion on a molecular scale and of performing a specific function is a fascinating topic in supramolecular chemistry. The bistable switchable molecule, azobenzene (AZO), has been introduced into the supramolecular architecture as a key building block, owing to its efficient and reversible trans (E)-cis (Z) photoisomerization. The binding strength of the dibenzo[24]crown-8 (DB24C8) host and dialkylammonium-based rod-like guest consisting of an AZO moiety and the Z\begin{document}$\to $\end{document}E photoisomerization process in an interlocked host-guest complex have been investigated by the density functional theory (DFT) calculations and the reactive molecular dynamics (RMD) simulations by considering both torsion and inversion paths. The strong host-guest binding strength provides a necessary premise to stabilize the complex during the E-Z photoisomerization of the AZO unit, which is a terminal stopper to control the directional motion of the guest. A stronger binding strength for the Z isomer can be induced by the stronger hydrogen-bonding interaction. The steric effect is introduced into the Z isomer to force the ring slipping exclusively over the cyclopentyl terminal (pseudostopper). The host-guest complexation has a slight effect on the conformation of the AZO functional subunit for the two isomers. The faster Z\begin{document}$\to $\end{document}E photoisomerization process within the picosecond timescale is kinetically more favored than the dethreading of the ring through the pseudostopper subunit of the rod. After isomerization, a structure relaxation is observed for the crown ether ring within 500 ps. The flexible backbone of the crown ether ring is helpful in realizing steady and stable host-guest recognition during photoisomerization. Moreover, the orthogonality of the site-specific binding interaction is revealed by the similar binding energies obtained at similar hydrogen bonding recognition sites for various interlocked host-guest supramolecular systems although the constituents of the guests are different from each other. The introduction of two stereoisomers of the AZO subunit has little influence on the other conformations of guest subunits. These results are useful for the rational design of more sophisticated stimuli-controlled artificial molecular machines.
On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)
Liang XIN, Huai SUN
2018, 34(10): 1179-1188  doi: 10.3866/PKU.WHXB201803161
[摘要]  (13) [HTML全文] (13) [PDF 2346KB] (13)
摘要:
A complex reaction, such as combustion, polymerization, and zeolite synthesis, involves a large number of elementary reactions and chemical species. Given a set of elementary reactions, the apparent reaction rates, population of chemical species, and energy distribution as functions of time can be derived using deterministic or stochastic kinetic models. However, for many complex reactions, the corresponding elementary reactions are unknown. Molecular dynamics (MD) simulation, which is based on forces calculated by using either quantum mechanical methods or pre-parameterized reactive force fields, offers a possibility to probe the reaction mechanism from the first principles. Unfortunately, most reactions take place on timescales far above that of molecular simulation, which is considered to be a well-known rare event problem. The molecules may undergo numerous collisions and follow many pathways to find a favorable route to react. Often, the simulation trajectory can be trapped in a local minimum separated from others by high free-energy barriers; thus, crossing these barriers requires prohibitively long simulation times. Due to this timescale limitation, simulations are often conducted on very small systems or at unrealistically high temperatures, which might hinder their validity. In order to model complex reactions under conditions comparable with those of the experiments, enhanced sampling techniques are required. The replica exchange molecular dynamics (REMD) is one of the most popular enhance sampling techniques. By running multiple replicas of a simulation system using one or several controlling variables and exchanging the replicas according to the Metropolis acceptance rule, the phase space can be explored more efficiently. However, most published work on the REMD method focuses on the conformational changes of biological molecules or simple reactions that can be described by a reaction coordinate. The optimized parameters of such simulations may not be suitable for simulations of complex reactions, in which the energy changes are much more dramatic than those associated with conformational changes and the hundreds elementary reactions through numerous pathways are unknown prior to the simulations. Therefore, it is necessary to investigate how to use the REMD method efficiently for the simulation of complex reactions. In this work, we examined the REMD method using temperature (T-REMD) and Hamiltonian (H-REMD) as the controlling variable respectively. In order to quantitatively validate the simulation results against direct simulations and analytic solutions, we performed the study based on a simple replacement reaction (A + BC = AB + C) with variable energy barrier heights and reaction energies described using the ReaxFF functional forms. The aim was to optimize the simulation parameters including number, sequence, and swap frequency of the replicas. The T-REMD method was found to be efficient for modeling exothermic reactions of modest reaction energy (< 3 kcal∙mol-1) or activation energy (ca. < 20 kcal∙mol-1). The efficiency was severely impaired for reactions with high activation and reaction energies. The analysis of the simulation trajectory revealed that the problem was intrinsic and could not be solved by adjusting the simulation parameters since the phase space sampled using T-REMD was localized in the region favored by high (artificial for speed-up) temperatures, which is different from the region favored by low (experimental) temperatures. This issue was aggravated in the case of endothermic reactions. On the other hand, the H-REMD run on a series of potential surfaces having different activation energies was demonstrated to be remarkably robust. Since the energy barrier only reduces the reaction rates, while the phase space controlled by the reaction energy differences remains unchanged at a fixed temperature, excellent results were obtained with fewer replicas by using H-REMD. It is evident that H-REMD is a more suitable method for the simulation of complex reactions.

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《物理化学学报》第4届编委会

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名誉主编

唐有祺

北京大学

顾问编委

包信和

中国科学院大连化学物理研究所

段雪

北京化工大学

付贤智

福州大学

侯建国

中国科学技术大学

黄维

南京工业大学

LIEBER Charles M.

Harvard University

田中群

厦门大学

万立骏

中国科学院化学研究所

吴云东

北京大学

谢晓亮

Harvard University, 北京大学

杨伟涛

 Duke University

姚建年

中国科学院化学研究所

赵新生

北京大学

主编

刘忠范

北京大学

副主编

韩布兴

中国科学院化学研究所

刘鸣华

国家纳米科学中心

申文杰

中国科学院大连化学物理研究所

吴凯

北京大学

杨金龙

中国科学技术大学

庄林

武汉大学

迟力峰

苏州大学

编委

曹勇

复旦大学

陈经广

University of Delaware

陈军

南开大学

崔屹

Stanford University

邓风

中国科学院武汉物理与数学研究所

邓友全

中国科学院兰州化学物理研究所

樊卫斌

中国科学院山西煤炭化学研究所

房喻

陕西师范大学

付红兵

中国科学院化学研究所

傅强

中国科学院大连化学物理研究所

高毅勤

北京大学

郭林

北京航空航天大学

郝京诚

山东大学

侯文华

南京大学

金荣超

Carnegie Mellon University

来鲁华

北京大学

李朝军

McGill University

李隽

清华大学

李象远

四川大学

梁万珍

厦门大学

刘海超

北京大学

刘洪来

华东理工大学

刘述斌

University of North Carolina

刘义

武汉大学

刘志敏

中国科学院化学研究所

罗小民

中国科学院上海药物研究所

马晶

南京大学

孟庆波

中国科学院物理研究所

邵翔

中国科学技术大学

孙俊奇

吉林大学

谭蔚泓

湖南大学

唐智勇

国家纳米科学中心

王键吉

河南师范大学

王鹏

中国科学院长春应用化学研究所

王心晨

福州大学

王永锋

北京大学

魏子栋

重庆大学

翁羽翔

中国科学院物理研究所

吴鹏

华东师范大学

夏永姚

复旦大学

许国勤

National University of Singapore

杨俊林

国家自然科学基金委员会

余家国

武汉理工大学

尉志武

清华大学

占肖卫

北京大学

张东辉

中国科学院大连化学物理研究所

张浩力

兰州大学

张锦

北京大学

章俊良

上海交通大学

周永贵

中国科学院大连化学物理研究所

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发布时间: 2018-05-02


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