## Current Issue 2021, Volume 34,  Issue 4

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2021, 34(4): i-ii.
2021, 34(4): iii-iv.
2021, 34(4): 373-380. doi: 10.1063/1674-0068/cjcp2103045
Fast and accurate quantitative detection of 14CO2 has important applications in many fields. The optical detection method based on the sensitive cavity ring-down spectroscopy technology has great potential. But currently it has difficulties of insufficient sensitivity and susceptibility to absorption of other isotopes/impurity molecules. We propose a stepped double-resonance spectroscopy method to excite 14CO2 molecules to an intermediate vibrationally excited state, and use cavity ring-down spectroscopy to probe them. The two-photon process significantly improves the selectivity of detection. We derive the quantitative measurement capability of double-resonance absorption spectroscopy. The simulation results show that the double-resonance spectroscopy measurement is Doppler-free, thereby reducing the effect of other molecular absorption. It is expected that this method can achieve high-selectivity detection of 14CO2 at the sub-ppt level.
2021, 34(4): 381-385. doi: 10.1063/1674-0068/cjcp2102033
A slow and clean fluorine atom beam source is one of the essential components for the low-collision energy scattering experiment involving fluorine atom. In this work, we describe a simple but effective photolysis fluorine atom beam source based on ultraviolet laser photolysis, the performance of which was demonstrated by high-resolution time-of-flight spectra from the reactive scattering of F+HD. This beam source paved the way for studies of low energy collisions with fluorine atoms.
2021, 34(4): 386-392. doi: 10.1063/1674-0068/cjcp2104060
N-ethylpyrrole is one of ethyl-substituted derivatives of pyrrole and its excited-state decay dynamics has never been explored. In this work, we investigate ultrafast decay dynamics of N-ethylpyrrole excited to the S1 electronic state using a femtosecond time-resolved photoelectron imaging method. Two pump wavelengths of 241.9 and 237.7 nm are employed. At 241.9 nm, three time constants, 5.0±0.7 ps, 66.4±15.6 ps and 1.3±0.1 ns, are derived. For 237.7 nm, two time constants of 2.1±0.1 ps and 13.1±1.2 ps are derived. We assign all these time constants to be associated with different vibrational states in the S1 state. The possible decay mechanisms of different S1 vibrational states are briefly discussed.
2021, 34(4): 393-405. doi: 10.1063/1674-0068/cjcp2104069
Understanding the influence of nanoparticles on the formation of protein amyloid fibrillation is crucial to extend their application in related biological diagnosis and nanomedicines. In this work, Raman spectroscopy was used to probe the amyloid fibrillation of hen egg-white lysozyme in the presence of silver nanoparticles (AgNPs) at different concentrations, combined with atomic force microscopy and thioflavin T (ThT) fluorescence assays. Four representative Raman indicators were utilized to monitor transformation of the protein tertiary and secondary structures at the molecular level: the Trp doublet bands at 1340 and 1360 cm-1, the disulfide stretching vibrational peak at 507 cm-1, the N-C$\alpha$-C stretching vibration at 933 cm-1, and the amide Ⅰ band. All experimental results confirmed the concentration-dependent influence of AgNPs on the hen egg-white lysozyme amyloid fibrillation kinetics. In the presence of AgNPs at low concentration (17 μg/mL), electrostatic interaction of the nanoparticles stabilizes disulfide bonds, and protects the Trp residues from exposure to hydrophilic environment, thus leading to formation of amorphous aggregates rather than fibrils. However, with the action of AgNPs at high concentration (1700 μg/mL), the native disulfide bonds of hen egg-white lysozyme are broken to form Ag-S bonds owing to the competition of electrostatic interaction from a great deal of nanoparticles. As for providing functional surfaces for protein to interact with, AgNPs play a bridge role in direct transformation from $\alpha$-helices to organized $\beta$-sheets. The present investigation sheds light on the controversial effects of AgNPs on the kinetics of hen egg-white lysozyme amyloid fibrillation.
2021, 34(4): 406-412. doi: 10.1063/1674-0068/cjcp2103037
The pharmaceutically active compound atenolol, a kind of $\beta$-blockers, may result in adverse effects both for human health and ecosystems if it is excreted to the surface water resources. To effectively remove atenolol in the environment, both direct and indirect photodegradation, driven by sunlight play an important role. Among indirect photodegradation, singlet oxygen (1O2), as a pivotal reactive species, is likely to determine the fates of atenolol. Nevertheless, the kinetic information on the reaction of atenolol with singlet oxygen has not been well investigated and the reaction rate constant is still ambiguous. Herein, the reaction rate constant of atenolol with singlet oxygen is investigated directly through observing the decay of the 1O2 phosphorescence at 1270 nm. It is determined that the reaction rate constant between atenolol and 1O2 is 7.0×105 (mol/L)$^{-1}\cdot$s-1 in D2O, 8.0×106 (mol/L)$^{-1}\cdot$s-1 in acetonitrile, and 8.4×105 (mol/L)$^{-1}\cdot$s-1 in EtOH, respectively. Furthermore, the solvent effects on the title reaction were also investigated. It is revealed that the solvents with strong polarity and weak hydrogen donating ability are suitable to achieve high rate constant values. These kinetics information on the reaction of atenolol with singlet oxygen may provide fundamental knowledge to the indirect photodegradation of $\beta$-blockers.
2021, 34(4): 413-418. doi: 10.1063/1674-0068/cjcp2105088
Photocatalytic N2 fixation has attracted substantial attention in recent years, as it represents a green and sustainable development route toward efficiently converting N2 to NH3 for industrial applications. How to rationally design catalysts in this regard remains a challenge. Here we propose a strategy that uses plasmonic hot electrons in the highly doped TiO2 to activate the inert N2 molecules. The synthesized semiconductor catalyst Mo-doped TiO2 shows a NH3 production efficiency as high as 134 μmol·g-1·h-1 under ambient conditions, which is comparable to that achieved by the conventional plasmonic gold metal. By means of ultrafast spectroscopy we reveal that the plasmonic hot electrons in the system are responsible for the activation of N2 molecules, enabling improvement the catalytic activity of TiO2. This work opens a new avenue toward semiconductor plasmon-based photocatalytic N2 fixation.
2021, 34(4): 419-428. doi: 10.1063/1674-0068/cjcp2105098
Metalation reaction of metal-free phthalocyanine molecule with Co atom adsorbed on Au(111) surface has been studied in situ at single atom/molecule scale by low-temperature scanning tunneling microscopy (STM) experiment combined with simulations based on density function theory calculations. Through manipulations using STM tip, we showed a controlled manner to have a single metal-free phthalocyanine molecule react with a Co atom to form Co phthalocyanine molecule. In this reaction process, an intermediate state originating from $\pi$-d interaction between the metal-free phthalocyanine molecule and Co atom has been identified. Moreover, we also revealed that the redox reaction represented as bond breaking and bond forming relative to the Co and pyrrolic N atoms, not pyrrolic H atoms, is a key process for dehydrogenation and metalation reaction. Our DFT calculations provided theoretical supporting for the above conclusions, and further understanding of the related mechanisms.
2021, 34(4): 429-435. doi: 10.1063/1674-0068/cjcp2102024
Alkyl dinitrites have attracted attention as an important type of nitrosating agent and a pollution source in atmosphere. The reactivity and chemistry of alkyl dinitrites induced by the two ONO functional groups are relatively unknown. In this work, decompositions of 1, 3-cyclohexane dinitrite and 1, 4-cyclohexane dinitrite are studied by electron impact ionization mass spectroscopy (EI-MS). Apart from NO+ ($m/z$=30), fragment ions $m/z$=43 and 71 are the most abundant for the 1, 3-isomer. On the other hand, fragments $m/z$=29, 57, 85, and 97 stand out in the EI-MS spectrum of 1, 4-isomer. Possible dissociation mechanisms of the two dinitrites are proposed by theoretical calculations. The results reveal that the ring-opening of 1, 3-cyclohexane dinitrite mainly starts from the intermediate ion (M-NO)+ by cleavage of two $\alpha$C-$\beta$C bonds. For 1, 4-cyclohexane dinitrite, in addition to the decomposition via intermediate (M-NO)+, cleavage of $\beta$C-$\beta$C bonds can occur directly from the parent cation M+. The results will help to understand the structural related chemistry of alkyl dinitrites in atmosphere and in NO transfer process.
2021, 34(4): 436-442. doi: 10.1063/1674-0068/cjcp2104079
Chemical structure searching based on databases and machine learning has attracted great attention recently for fast screening materials with target functionalities. To this end, we established a high-performance chemical structure database based on MYSQL engines, named MYDB. More than 160000 metal-organic frameworks (MOFs) have been collected and stored by using new retrieval algorithms for efficient searching and recommendation. The evaluations results show that MYDB could realize fast and efficient keyword searching against millions of records and provide real-time recommendations for similar structures. Combining machine learning method and materials database, we developed an adsorption model to determine the adsorption capacitor of metal-organic frameworks toward argon and hydrogen under certain conditions. We expect that MYDB together with the developed machine learning techniques could support large-scale, low-cost, and highly convenient structural research towards accelerating discovery of materials with target functionalities in the field of computational materials research.
2021, 34(4): 443-452. doi: 10.1063/1674-0068/cjcp2104057
pH dependent fluorescence emission of a thioxanthone-based probe has been reported recently. The potential determinant factors of pH dependence may provide important clues to design novel thioxanthone-based probes in the future. pH dependence of photochemical kinetics of thioxanthone itself was investigated in this work using nanosecond time-resolved laser flash photolysis. The nanosecond time-resolved transient absorption spectra and kinetics of TX in aqueous acetonitrile were recorded, as well as for a model reaction system including TX with diphenylamine (DPA) as a co-initiator. Besides the well-known absorption peak of $^3$TX$^*$, other peaks at 417, 518, 673 and 780 nm, have been reliably attributed to major intermediates in the overall reaction between TX and DPA with photolysis, which has been confirmed to occur along a multistep process. In the strong acidic solution (pH$\approx$3.0), TX and protonated TX ions (TXH$^+$) coexist due to protonated equilibrium. Consequently, high proton concentration promotes the predominant decay pathway after photolysis from electron transfer to proton affinity. Subsequently, the different primary products, $^3$TXH$^{+*}$ or TX$^{\bullet-}$, proceed different secondary reaction channels. In addition, within the wide pH range from weak acid (pH = 5.0) to alkaline solution (pH = 13.0), the overall reaction mechanism and rates do not show visible changes.
2021, 34(4): 453-461. doi: 10.1063/1674-0068/cjcp2007117
The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients and kinetic isotope effects of the heavy-light-heavy abstract reaction Cl+XCl$\rightarrow$XCl+Cl (X = H, D, Mu). For the Cl+HCl reaction, the excellent agreement between the RPMD and experimental values provides a strong proof for the accuracy of the RPMD theory. And the RPMD results are also consistent with results from other theoretical methods including improved-canonical-variational-theory and quantum dynamics. The most novel finding is that there is a double peak in Cl+MuCl reaction near the transition state, leaving a free energy well. It comes from the mode softening of the reaction system at the peak of the potential energy surface. Such an explicit free energy well suggests strongly there is an observable resonance. And for the Cl+DCl reaction, the RPMD rate coefficient again gives very accurate results compared with experimental values. The only exception is at the temperature of 312.5 K, results from RPMD and all other theoretical methods are close to each other but slightly lower than the experimental value, which indicates experimental or potential energy surface deficiency.
2021, 34(4): 462-470. doi: 10.1063/1674-0068/cjcp2101004
In the pioneering work by R. A. Marcus, the solvation effect on electron transfer (ET) processes was investigated, giving rise to the celebrated nonadiabatic ET rate formula. In this work, on the basis of the thermodynamic solvation potentials analysis, we reexamine Marcus' formula with respect to the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Interestingly, the obtained RRKM analogue, which recovers the original Marcus' rate that is in a linear solvation scenario, is also applicable to the nonlinear solvation scenarios, where the multiple curve-crossing of solvation potentials exists. Parallelly, we revisit the corresponding Fermi's golden rule results, with some critical comments against the RRKM analogue proposed in this work. For illustration, we consider the quadratic solvation scenarios, on the basis of physically well-supported descriptors.
2021, 34(4): 471-479. doi: 10.1063/1674-0068/cjcp2103046
In studies of ion channel systems, due to the huge computational cost of polarizable force fields, classical force fields remain the most widely used for a long time. In this work, we used the AMOEBA polarizable atomic multipole force field in enhanced sampling simulations of single-channel gramicidin A (gA) and double-channel gA systems and investigated its reliability in characterizing ion-transport properties of the gA ion channel under dimerization. The influence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance, diffusion coefficient, and free energy profile. Results from the polarizable force field simulations show that the conductance of potassium and sodium ions passing through the single- and double-channel agrees well with experimental values. Further data analysis reveals that the molecular mechanism of protein dimerization affects the ion-transport properties of gA channels, i.e., protein dimerization accelerates the permeation of potassium and sodium ions passing through the double-channel by adjusting the environment around gA protein (the distribution of phospholipid head groups, ions outside the channel, and bulk water), rather than directly adjusting the conformation of gA protein.
2021, 34(4): 480-486. doi: 10.1063/1674-0068/cjcp1910172
The study of interactions between surfactant and salt in aqueous solutions has attracted significant interest in recent years because of their widespread applications and relatively complex behavior. This work reports the systematic study of surface phenomenon and self-aggregation behavior of cationic surfactant cetyltrimethyl ammonium bromide (CTAB) with ammonium nitrate (NH$_4$NO$_3$) salt. Surface and thermodynamic properties of cationic surfactant CTAB with NH$_4$NO$_3$ were investigated at different temperatures using different techniques such as conductometry and surface tensiometery. The surface tension measurement was carried out to find out the critical micelle concentration, free energy of adsorption, free energy of micellization, minimum area per molecule, and surface excess concentration. The study reveals that the process of micellization is spontaneous and exothermic in nature. Conductance measurement was carried out to determine critical micelle concentration, degree of ionization and degree of counter ion binding. Addition of NH$_4$NO$_3$ to the surfactant solutions increase the values of degree of ionization and degree of counter ion binding, although it lowers the values of critical micelle concentration showing that the process of micellization is more favorable and spontaneous. The study is very helpful to develop better understanding about interaction between electrolyte and surfactant, which are used in many applications and in different processes (e.g., pharmaceutical, industrial foaming, drug solubilization, oil recovery, and medium for metal nanoparticle formation).
2021, 34(4): 487-496. doi: 10.1063/1674-0068/cjcp2010184
A protein may exist as an ensemble of different conformations in solution, which cannot be represented by a single static structure. Molecular dynamics (MD) simulation has become a useful tool for sampling protein conformations in solution, but force fields and water models are important issues. This work presents a case study of the bacteriophage T4 lysozyme (T4L). We have found that MD simulations using a classic AMBER99SB force field and TIP4P water model cannot well describe hinge-bending domain motion of the wild-type T4L at the timescale of one microsecond. Other combinations, such as a residue-specific force field called RSFF2+ and a dispersion-corrected water model TIP4P-D, are able to sample reasonable solution conformations of T4L, which are in good agreement with experimental data. This primary study may provide candidates of force fields and water models for further investigating conformational transition of T4L.