## Current Issue 2021, Volume 34,  Issue 3

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2021, 34(3): i-ii.
2021, 34(3): iii-iv.
2021, 34(3): 249-255. doi: 10.1063/1674-0068/cjcp2012221
The interaction of reactants with catalysts has always been an important subject for catalytic reactions. As a promising catalyst with versatile applications, titania has been intensively studied for decades. In this work we have investigated the role of bridge bonded oxygen vacancy (O$_\textrm{v}$) in methyl groups and carbon monoxide (CO) adsorption on rutile TiO$_2$(110) (R-TiO$_2$(110)) with the temperature programmed desorption technique. The results show a clear different tendency of the desorption of methyl groups adsorbed on bridge bonded oxygen (O$_\textrm{b}$), and CO molecules on the five coordinate Ti$^{4+}$ sites (Ti$_{5\textrm{c}}$) as the O$_\textrm{v}$ concentration changes, suggesting that the surface defects may have crucial influence on the absorption of species on different sites of R-TiO$_2$(110).
2021, 34(3): 256-262. doi: 10.1063/1674-0068/cjcp2009173
Laser flash photolysis was used to investigate the photoinduced reactions of excited triplet bioquinone molecule duroquinone (DQ) with tryptophan (Trp) and tyrosine (Tyr) in acetonitrile-water (MeCN-H$_2$O) and ethylene glycol-water (EG-H$_2$O) solutions. The reaction mechanisms were analyzed and the reaction rate constants were measured based on Stern-Volmer equation. The H-atom transfer reaction from Trp (Tyr) to $^3$DQ$^*$ is dominant after the formation of $^3$DQ$^*$ during the laser photolysis. For DQ and Trp in MeCN-H$_2$O and EG-H$_2$O solutions, $^3$DQ$^*$ captures H-atom from Trp to generate duroquinone neutral radical DQH$^\bullet$, carbon-centered tryptophan neutral radical Trp$^\bullet$/NH and nitrogen-centered tryptophan neutral radical Trp/N$^\bullet$. For DQ and Tyr in MeCN-H$_2$O and EG-H$_2$O solutions, $^3$DQ$^*$ captures H-atom from Tyr to generate duroquinone neutral radical DQH$^\bullet$ and tyrosine neutral radical Tyr/O$^\bullet$. The H-atom transfer reaction rate constant of $^3$DQ$^*$ with Trp (Tyr) is on the level of 10$^9$ L$\cdot$mol$^{-1}$$\cdot$s$^{-1}$, nearly controlled by diffusion. The reaction rate constant of $^3$DQ$^*$ with Trp (Tyr) in MeCN/H$_2$O solution is larger than that in EG/H$_2$O solution, which agrees with Stokes-Einstein relationship qualitatively.
2021, 34(3): 263-272. doi: 10.1063/1674-0068/cjcp2009171
Ruthenium (Ru) serves as a promising catalyst for ammonia synthesis via the Haber-Bosch process, identification of the structure sensitivity to improve the activity of Ru is important but not fully explored yet. We present here density functional theory calculations combined with micro-kinetic simulations on nitrogen molecule activation, a crucial step in ammonia synthesis, over a variety of hexagonal close-packed (hcp) and face-center cubic (fcc) Ru facets. Hcp $\left\{ {21\overline 3 0} \right\}$ facet exhibits the highest activity toward N$_2$ dissociation in hcp Ru, followed by the (0001) monatomic step sites. The other hcp Ru facets have N$_2$ dissociation rates at least three orders lower. Fcc $\{211\}$ facet shows the best performance for N$_2$ activation in fcc Ru, followed by $\{311\}$, which indicates stepped surfaces make great contributions to the overall reactivity. Although hcp Ru $\left\{ {21\overline 3 0} \right\}$ facet and (0001) monatomic step sites have lower or comparable activation barriers compared with fcc Ru $\{211\}$ facet, fcc Ru is proposed to be more active than hcp Ru for N$_2$ conversion due to the exposure of the more favorable active sites over step surfaces in fcc Ru. This work provides new insights into the crystal structure sensitivity of N$_2$ activation for mechanistic understanding and rational design of ammonia synthesis over Ru catalysts.
2021, 34(3): 273-280. doi: 10.1063/1674-0068/cjcp2009170
Magnetic tunnel junction with a large tunneling magnetoresistance has attracted great attention due to its importance in the spintronics applications. By performing extensive density functional theory calculations combined with the nonequilibrium Green's function method, we explore the spin-dependent transport properties of a magnetic tunnel junction, in which a non-polar SrTiO$_{3}$ barrier layer is sandwiched between two Heusler alloy Co$_{2}$MnSi electrodes. Theoretical results clearly reveal that the near perfect spin-filtering effect appears in the parallel magnetization configuration. The transmission coefficient in the parallel magnetization configuration at the Fermi level is several orders of magnitude larger than that in the antiparallel magnetization configuration, resulting in a huge tunneling magnetoresistance (i.e. $>10^6$), which originates from the coherent spin-polarized tunneling, due to the half-metallic nature of Co$_{2}$MnSi electrodes and the significant spin-polarization of the interfacial Ti 3d orbital.
2021, 34(3): 281-286. doi: 10.1063/1674-0068/cjcp2010187
The binding energy spectrum and electron momentum profiles of the inner orbitals of methyl iodide have been measured using an electron momentum spectrometer at the impact energy of 1200 eV plus binding energy. Two peaks in the binding energy spectrum, arising from the spin-orbit splitting, are observed and the corresponding electron momentum profiles are obtained. Relativistic density functional calculations are performed to elucidate the experimental electron momentum profiles of two spin-orbit splitting components, showing agreement with each other except for the intensity in low momentum region. The measured high intensity in the low momentum region can be further explained by the distorted wave calculation.
2021, 34(3): 287-296. doi: 10.1063/1674-0068/cjcp2008144
The potential energy landscape of the neutral Ni$_2$(CO)$_5$ complex was re-examined. A new $C_{\rm{2v}}$ structure with double bridging carbonyls is found to compete with the previously proposed triply carbonyl-bridged $D_{\rm{3h}}$ isomer for the global minimum of Ni$_2$(CO)$_5$. Despite that the tri-bridged isomer possesses the more favored (18, 18) configuration, where both metal centers satisfy the 18-electron rule, the neutral Ni$_2$(CO)$_5$ complex prefers the di-bridged geometry with (18, 16) configuration. The isomerization energy decomposition analysis reveals that the structural preference is a consequence of the maximization of electrostatic and orbital interactions.
2021, 34(3): 297-308. doi: 10.1063/1674-0068/cjcp2009174
The structure and stability of the compounds MRg$^+$ and MRgF (Rg=Ar, Kr, and Xe; M=Co, Rh, and Ir) were investigated using the B3LYP, MP2, MP4(SDQ) and CCSD(T) methods. We reported the geometry, vibrational frequencies and thermodynamics properties of these compounds. A series of theoretical methods on the basis of wavefunction analysis, including natural bond orbitals, atoms in molecules, electron localization function, and energy decomposition analysis, were performed to explore bonding nature of the M$-$Rg and Rg$-$F bonds. These bonds are mainly noncovalent, the metal weakly interacts with Rg in MRg$^+$, but their interaction is much stronger in MRgF. The neutral molecule MRgF can be well described by the Lewis structure [MRg]$^+$F$^-$.
2021, 34(3): 309-322. doi: 10.1063/1674-0068/cjcp2005063
The natural attapulgite (NAPT) was disaggregated by high-pressure homogenization technology combined with extrusion process to prepare the attapulgite with disaggregated rod crystal bundles (DAPT) and large specific surface area of 133.7 m2/g. NAPT and DAPT were incorporated into the silicone rubber to obtain the composite NAPT-SR and DAPT-SR by mechanical blending method, respectively. After thermal oxidative ageing at 300 ℃ for 0.5 h, temperature for the 5% weight loss increased greatly from 385 ℃ of the neat silicone rubber to 396℃ - 399 ℃ with addition of NAPT and DAPT. NAPT and DAPT enhanced the interaction between the filler nanoparticles and rubber matrix thus inhibited the nanoparticle agglomeration. The conservation rate of the side methyl group in NAPT-SR and DAPT-SR was greatly improved after ageing. Therefore, the thermal oxidative degradation and ageing performance of the silicone rubber composites was significantly reinforced. Moreover, DAPT could greatly restrain the growth of nanoparticles after ageing. Therefore, DAPT-SR showed the better retention of tensile strength (40.6%), elongation at break (34.9%) and tear strength (30.1%) compared with the corresponding mechanical properties of the neat silicone rubber (10.6%, 7.4%, and 5.0%) after ageing.
2021, 34(3): 323-333. doi: 10.1063/1674-0068/cjcp2008150
The interaction between Amyloid β (Aβ) peptide and acetylcholine receptor is the key for our understanding of how Aβ fragments block the ion channels within the synapses and thus induce Alzheimer's disease. Here, molecular docking and molecular dynamics (MD) simulations were performed for the structural dynamics of the docking complex consisting of Aβ and α7-nAChR (α7 nicotinic acetylcholine receptor), and the inter-molecular interactions between ligand and receptor were revealed. The results show that A$\beta_{25-35}$ is bound to α7-nAChR through hydrogen bonds and complementary shape, and the A$\beta_{25-35}$ fragments would easily assemble in the ion channel of $\alpha$7-nAChR, then block the ion transfer process and induce neuronal apoptosis. The simulated amide-I band of A$\beta_{25-35}$ in the complex is located at 1650.5 cm$^{-1}$, indicating the backbone of A$\beta_{25-35}$ tends to present random coil conformation, which is consistent with the result obtained from cluster analysis. Currently existing drugs were used as templates for virtual screening, eight new drugs were designed and semi-flexible docking was performed for their performance. The results show that, the interactions between new drugs and $\alpha$7-nAChR are strong enough to inhibit the aggregation of A$\beta_{25-35}$ fragments in the ion channel, and also be of great potential in the treatment of Alzheimer's disease.
2021, 34(3): 334-342. doi: 10.1063/1674-0068/cjcp2010181
Binding and releasing ligands are critical for the biological functions of many proteins, so it is important to determine these highly dynamic processes. Although there are experimental techniques to determine the structure of a protein-ligand complex, it only provides a static picture of the system. With the rapid increase of computing power and improved algorithms, molecular dynamics (MD) simulations have diverse of superiority in probing the binding and release process. However, it remains a great challenge to overcome the time and length scales when the system becomes large. This work presents an enhanced sampling tool for ligand binding and release, which is based on iterative multiple independent MD simulations guided by contacts formed between the ligand and the protein. From the simulation results on adenylate kinase, we observe the process of ligand binding and release while the conventional MD simulations at the same time scale cannot.
Three kinds of thermochromic materials (DC8, DC12, DC16) were synthesized by linking the rigid 1, 4-bis[2-(4-pyridyl)ethenyl]-benzene (bpeb) with different lengths of alkyl chains. They exhibit remarkable fluorescent color changes under the irradiation of 365 nm light with elevating temperature, which is supposed to be caused by the transition between the crystal state and the amorphous state. Interestingly, the DC16 solid also has a photochromic character. It should be noticed that the phase transition temperatures of three materials measured by differential scanning calorimetry are higher than those of the fluorescence color changes during the heating process. Thus, the allochroic effect is attributed to the synergistic effect of both heating and photo-inducement (365 nm). Ethanol can turn the heated powder into the initial crystal again which indicates that their thermochromic behavior is reversible and makes the fluorescence recover.
2021, 34(3): 350-355. doi: 10.1063/1674-0068/cjcp2010186
Photocatalytic water splitting to generate hydrogen gas is an ideal solution for environmental pollution and unsustainable energy issues. In the past few decades, many efforts have been made to increase the efficiency of hydrogen production. One of the most important ways is to achieve light absorption in the visible range to improve the conversion efficiency of solar energy into chemical energy, but it still presents great challenges. We here predicted a novel organic film, which can be obtained by polymerizing HTAP molecules, as an ideal material for photocatalytic water splitting. Based on first-principles calculations and Born-Oppenheimer quantum molecular dynamic simulations, the metal-free two-dimensional nanomaterial has been proven to be structurally stable, with a direct band gap of 2.12 eV, which satisfies the requirement of light absorption in the visible range. More importantly, the conduction bands and valence bands completely engulf the redox potentials of water, making the film be a promising photocatalyst for water splitting. This construction method through the topological periodicity of organic molecules provides a design scheme for the photocatalyst for water splitting.
2021, 34(3): 356-364. doi: 10.1063/1674-0068/cjcp2004059
Langevin dynamics simulations were conducted to study the collapse of grafted partially charged 4-arm star chains onto the oppositely charged grafting electrode in the presence of trivalent salt coions. Simulation results reveal that the average charge fraction of the grafted star chains and the salt concentration play critical roles in the competitive adsorption of charged monomers and trivalent salt coions onto the oppositely charged electrode. For grafted star chains with relatively high charge fraction, charged monomers are the dominant species collapsing on the oppositely charged electrode with the emergence of charge reversal on the grafting electrode. At a low charge fraction such that the total amount of charges on a grafted star molecule is comparable to that of a trivalent salt coion, trivalent salt coions absorb more strongly onto the electrode than grafted stars even at very low salt concentration. It is found that at relatively low charge fraction of star chains, the addition of trivalent salt coions does not lead to charge overcompensation of the surface charges on the grafting electrode. The stretching of star brushes under an electric field in the presence of trivalent salt coions was also briefly investigated.
2021, 34(3): 365-372. doi: 10.1063/1674-0068/cjcp2006090
Stimuli-responsive polymer gels have recently attracted great attention due to their heat/solvent resistance, dimensional stability, and unique sensitivity to external stimuli. In this work, we synthesized thiol-functionalized tetraphenylethylene (TPE) and constructed polymer gels through thiol-ene click reaction. The synthetic process of the polymer gels could be monitored by fluorescence emission of TPE moieties based on aggregation-induced emission mechanism. In addition, due to the dual redox- and acid responsiveness of the polymer gels, in the presence of dithiothreitol and trifluoroacetic acid, fluorescence quenching of the polymer gels can be observed. This stimuli-responsive characteristics endows the polymer gels with potential applications in fluorescent sensing and imaging, cancer diagnosis and selfhealing materials.