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    10 July 2021, Volume 42 Issue 7
    Content
    Cover and Content of Chemical Journal of Chinese Universities Vol.42 No.7(2021)#br#
    2021, 42(7):  2. 
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    Review
    Theory and Applications of Time Dependent Density Matrix Renormalization Group
    LI Weitang, REN Jiajun, SHUAI Zhigang
    2021, 42(7):  2085-2102.  doi:10.7503/cjcu20210151
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    Density matrix renormalization group(DMRG) is well known as a powerful method to study low- dimensional highly-correlated systems and has been widely used for electronic structure calculation in quantum chemistry. In recent years, the theory of time dependent DMRG(TD-DMRG) has developed rapidly and TD-DMRG has gradually emerged as one of the most important methods of quantum dynamics simulation for complex systems. This review briefly sketches the basic theory of DMRG in the language of matrix product states(MPS) and matrix product operators(MPO), and discusses several most common TD-DMRG time evolution algorithms at length, including the propagation and compression(P&C) algorithm, algorithms based on time dependent variational principle(TDVP), and the time step targeting(TST) algorithm. This review also introduces the purification algorithm and minimally entangled typical thermal states(METTS) algorithm that enable TD-DMRG to study the finite temperature effect and summarizes the recent applications of TD-DMRG in quantum dynamics of complex systems.

    Research Advances on Nonadiabatic Energy Transfer Dynamics for Triatomic Molecules
    AN Feng, HU Xixi, XIE Daiqian
    2021, 42(7):  2103-2110.  doi:10.7503/cjcu20210116
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    The collision energy transfer processes involving nonadiabatic transition play important roles in atmosphere, interstellar, combustion chemistry, and chemical lasers. Since such energy transfer processes usually involve a variety of nonadiabatic effects between multiple electronic states, theoretical studies on the diabatic potential energy surfaces and dynamics calculations are very challenging. In this paper, we review the calculation methods of the diabatic potential energy matrices, the diabatic potential energy surfaces, the conical intersections, and spin-orbit couplings in the nonadiabatic energy transfer dynamics, focused on two important nonadiabatic energy transfer processes of C(1D)+N2 and I(2P3/2)+O2a1Δg). The dynamics of both two nonadiabatic energy transfer processes are discussed and summarized. The importance of the nonadiabatic effects in these processes is also revealed.

    Research Progress of Silicone Supramolecular Materials
    WANG Linlin, LI Lei, FENG Shengyu
    2021, 42(7):  2111-2122.  doi:10.7503/cjcu20210093
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    Due to their unique organic-inorganic structures, silicone materials with excellent thermostability, biocompatibility, electrical insulation and gas permeability have been widely used in various fields. However, traditional silicone materials are mainly based on irreversible covalent cross-linking, thus lacking the ability of damage repair, reprocessing and recycling. In this context, silicone supramolecular materials have attracted extensive attention, and a variety of functional materials have been developed. This review outlines the recent research progress of silicone supramolecular materials with regard to their molecular design, superior properties and prospective applications. By combination with the research results of our group in this field, we summarized various types of silicone supramolecular materials, including the hydrogen bond type, metal coordination bond type, Lewis acid-base pair type, ionic bond type, and π-π stacking type silicone supramolecular materials. The future directions of this field are also commented.

    The PBFC-PI Quantum Dynamical Method and Its Applications
    BIAN Wensheng, CAO Jianwei
    2021, 42(7):  2123-2135.  doi:10.7503/cjcu20210129
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    Quantum dynamics(QD) calculations of polyatomic systems are very important, however, accurate QD calculations for molecular system with more than six atoms remain a challenge nowadays. The process-oriented basis function customization(PBFC)-parallelized iterative(PI) method is an e?cient QD method developed by Bian’s group, which has been applied in accurate QD calculations of H transfer rate in malonaldehyde, a nine-atom isomerization system. In this review, we ?rst present an explanation on the basic idea of PBFC, which may have general importance, and then focus on the details of the PBFC-PI method, its combination with other methods and the recent progresses in its applications. Using these methods, large-scale parallel calculations have been performed for three kinds of benchmark systems, featuring single H transfer, concerted double H transfer, and sequential double H transfer, respectively. These calculations are helpful for acquiring new insights into H transfer processes.

    Article
    Theoretical Study on the Excited State Properties and Photophysical Mechanism of Selenothymine and Adenine Base Pairs in DNA Environment
    PENG Qin, FANG Yeguang, ZHANG Tengshuo, CUI Ganglong, FANG Weihai
    2021, 42(7):  2136-2145.  doi:10.7503/cjcu20210117
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    Multi-state second-order perturbation approach was applied, the combination of quantum mecha-nics/molecular mechanics methods, under the theoretical framework of the QM(MS-CASPT2//CASSCF)/MM, to study the relevant minima, conical intersections, crossing points, and excited-state relaxation paths in the lowest five electronic states(i.e., S0, S1, S2, T2, and T1) of 2- and 4-selenothymine and adenine bases(2SeT-A and 4SeT-A) in DNA. Although 2SeT-A and 4SeT-A share similar electron excitation states, their electron structural characteristics are different due to the different n and π orbitals involved, resulting in a higher vertical and adiabatic excitation energy for 2SeT-A than for 4SeT-A. In addition, both 2SeT-A and 4SeT-A have different minimum energy structures and inactivation pathways in the DNA environment. For 2SeT-A, after excitation, the system first reaches the S2(ππ*) state in the Franck-Condon region, then relaxes to the S2 state minimal energy structure, and finally to the S1nπ*) state. Next, the S1→T1 process with a large S1/T1 spin-orbit coupling reaches the T1(ππ*) state, which can be arrived to the S0 state again through the T1/S0 intersection. But the minimum energy structure of T1 and the barrier of 22.6 kJ/mol between T1/S0 intersection make the system stay in the lowest T1 triplet state for a period of time. 4SeT-A has similar photophysical process of S2→S1→T1, but its S2→S1 internal transformation process needs to overcome the energy barrier of 60.7 kJ/mol. The results reveals the different sources of the excitation state properties and photophysical mechanisms of 2SeT-A and 4SeT-A base pairs in DNA environment, and provides insight into the mechanism, which will help to understand the excitation state properties and photophysical mechanisms of bases substi- tuted by selenium atoms in complex environment.

    Analytical Gradient Method for Fundamental Invariant Neural Networks
    SHANG Chenyao, ZHANG Donghui
    2021, 42(7):  2146-2154.  doi:10.7503/cjcu20210294
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    It is very important for dynamic simulation to improve the running speed of the potential energy surface. Compared with the numerical gradient calculation, which is simple but time-consuming, the direct analytical formula to solve the gradient of the potential energy surface can greatly improve the running efficiency of the potential energy surface. In this work, a method for generating analytic gradients for fundamental invariant neural networks was developed. The code to calculate the analytic gradient can be generated automatically by program. After testing a large number of data points, it was found that this method can get the correct output of the gradient of potential energy surface. By measuring the calculation time of different potential energy surfaces, it was found that the analytical gradient method can bring more than a ten-fold improvement in performance. The larger the system, the more significant the performance improvement will be.

    Nonequilibrium System-Bath Entanglement Theorem Versus Heat Transport
    DU Pengli, CHEN Zihao, SU Yu, WANG Yao, XU Ruixue, YAN Yijing
    2021, 42(7):  2155-2160.  doi:10.7503/cjcu20210317
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    In this work, we extend the recently established system-bath entanglement theorem(SBET) to the nonequilibrium scenario, in which an arbitrary system couples to multiple Gaussian bath environments at different temperatures. The existing SBET connects the entangled system-bath response functions to those of local systems, while the extended theory is concerned with the nonequilibrium steady-state quantum transport current through molecular junctions. The new theory is established on the basis of the generalized Langevin equation, with a close relation to nonequilibrium thermodynamics in the quantum regime.

    Residue Specific Binding Mechanisms of PD-1 to Its Monoclonal Antibodies by Computational Alanine Scanning
    WEN Wei, HUANG Dading, BAO Jingxiao, ZHANG John Z. H.
    2021, 42(7):  2161-2169.  doi:10.7503/cjcu20210245
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    Molecular dynamics simulations were conducted on two PD-1/monoclonal antibody(pembrolizu-mab, nivolumab) complexes separately. The binding hotspots of the monoclonal antibody(mAb) and PD-1 were predicted by using efficient computational alanine scanning method. The comparation between the predicted hotspots and the important residues in PD-1/PD-L1 complex shows that pembrolizumab combines with PD-1 in a way similar to PD-L1, while nivolumab combines with PD-1 in a more different way by N-loop. PD-1K131 is the only hotspot shared by the two PD-1/mAb complexes. It is also found that key residues of mAbs binding to D-1K131 are similarly dominated by van der Waals(vdW) energy. Furthermore, hotspots on both the monoclonal antibodies are dominated by vdW energy, indicating a demand to improve the contributions of electrostatic energy. The present work provides important insights for the design of new mAbs targeting PD-1.

    Molecular Dynamics Simulation of Pulsed Electric Field O/W Emulsion Demulsification
    LIU Shasha, ZHANG Heng, YUAN Shiling, LIU Chengbu
    2021, 42(7):  2170-2177.  doi:10.7503/cjcu20210139
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    The aggregation behavior of two heavy oil droplets in an O/W emulsion system in a pulsed electric field was studied by molecular dynamics method. By changing the simulation parameters of duty cycle, the aggregation of oil droplets under certain electric field intensity and the relation between electric field intensity parameters and duty cycle parameters during electric field demulsification were discussed. At the same time, the charge distribution and the accumulation mechanism of oil droplets in the electric field were explained from the microscopic point of view by analysis methods of electrostatic potential distribution, interaction potential energy and adsorption structure statistics. The simulation results showed that: (1) the duty cycle could be adjusted to control the applied time of electric field. Oil droplets accumulate at electric field in the range of 0.40—0.75 V/nm, and the duty cycle decreases with the increase of electric field intensity; (2) the oil droplets deforme and the charge is polarized in the electric field, and the negatively charged asphaltene molecules guid the droplet to move in the opposite direction of the electric field; (3) the asphaltenes are at the interface of two oil droplets in the process of aggregation without electric field, and van der Waals action is the main force for oil droplets' aggregation. Meanwhile, asphaltenes at the interface of oil droplets form π-π binding conformation with surrounding molecules, which enhances the interaction between oil droplets.

    Surface and Size Effects of Nitrogen-vacancy Centers in Diamond Nanowires
    HU Wei, LIU Xiaofeng, LI Zhenyu, YANG Jinlong
    2021, 42(7):  2178-2186.  doi:10.7503/cjcu20210135
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    To control the electronic structures and stability of nitrogen-vacancy(NV) center in diamond is crucial for their practical applications. The surface and size effects on the structural, electronic, magnetic properties and stability of NV centers doped in diamond nanowires(DNs) were systematically investigated via large-scale spin-polarized density functional theory calculations. We theoretically design several types of DNs with different surface modifications(clean, hydrogenated and fluorinated) and the diameter sizes up to hundreds of atoms. It demonstrated that the electronic structures of neutral NV0 and negative NV- centers are not affected by semiconducting surface modifications and diameter sizes of DNs, but the stability are sensitive to these two effects. Furthermore, we find that the surface modifications induce a size-independent and long-range effect on the stability of the NV-center doped in DNs due to the cylindrical surface electric dipole layer in DNs. In particular, the NV- center doped in DNs can be stabilized for n-type fluorinated diamond surfaces, while NV0 is relatively more stable for p-type hydrogenated surfaces. Therefore, surface modification provides a precise and effective way to control the electronic structures and stability of charged defects in semiconductors.

    Molecular Face Guiding the Proton Transfer Reactions of Hydroxyl Carbene and Its Derivatives
    ZHAO Dongxia, ZHANG Haixia, FENG Wenjuan, YANG Zhongzhi
    2021, 42(7):  2187-2196.  doi:10.7503/cjcu20210211
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    Molecular face(MF) is a molecular intrinsic characteristic contour(MICC) with calculating and describing the electron density(ED) on it. MF not only gives the molecular boundary surface, but also shows the interaction sites and reactivity indicators, including the frontier ED(MFED). M06-2X/6-311G(dp) level of theory was employed to study proton transfer reactions of the singlet and triplet hydroxyl carbene molecules and their derivatives and to calculate their respective activation energies. It is shown that the substitutes with the strong electron?withdrawing and electron?donating groups make the activation energies of the singlet hydroxyl carbene reaction increase, whereas the substituent ─CN with the biggest electron?withdrawing group makes the activation energy of the triplet hydroxyl carbene reaction increase. Moreover, other substitutes with the strong electron-donating group make the activation energies of the singlet hydroxyl carbene reaction increase, whereas they make the activation energies of the triplet hydroxyl carbene reaction decrease. The strong electron-withdrawing groups make the activation energies of these reactions decrease. MF was used to explore the reactions mentioned above. Their MFs represent the changes of the molecular faces, and connect the reactive sites and change trend of the involved physical properties. There is a linear correlation of the difference between the maximum electron density around the C atom and the minimum electron density around the H atom of the singlet hydro-xyl carbene reactants and their corresponding reaction activation energies.

    An In-depth Theoretical Study of Ligand Field and Charge Transfer Effects on Co2+2pL2,3-edges X-ray Absorption Spectra
    CHENG Xiao, K BORA Debajeet, GLANS Per⁃Anders, GUO Jinghua, LUO Yi
    2021, 42(7):  2197-2209.  doi:10.7503/cjcu20210130
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    The 2p L2,3-edges X-ray absorption spectrum of Co2+ in octahedral(Oh) symmetric ligand field is studied theoretically via the multiplet calculation method. The octahedral symmetric crystal field and corresponding charge transfer effect between ligands and Co2+ cation have been investigated. All the parameters used in the multiplet calculation are discussed systematically in regards to their specific effect on X-ray absorption features and related mechanisms. The calculated results are compared with the L-edge X-ray absorption spectra of CoO and CoCl2, both with the same Oh symmetrical local structure of the Co2+ cation. The experimentally observed multiplet spectra features are assigned to different spin states and their intensity change is rela-ted to the crystal field strength. The underlying charge transfer effect has also been revealed. This study provides a fundamental basis for multiplet calculations of complex systems with lower symmetry associated with cobalt and other transition metals.

    Development and Benchmark of Lower Scaling Doubly Hybrid Density Functional XYG3
    ZHENG Ruoxin, ZHANG Igor Ying, XU Xin
    2021, 42(7):  2210-2217.  doi:10.7503/cjcu20210308
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    Doubly hybrid density functional XYG3 is one of the most accurate density functional approximations currently available. XYG3 introduces the unoccupied orbital information in the form of the second-order perturbation theory(PT2), and therefore suffers the same computational costs as the standard PT2 method. The formal computational scaling of the canonical XYG3 is N to the fifth power[ON5], where N denotes the system size, and the memory consumption scales in the fourth power[ON4], which significantly limit the applicability of XYG3 to complex large systems. In this work, we introduce a local-scaling XYG3 method, LT-XYG3, which is based on the local variant of Resolution-of-Identity technique(RI-LVL) and the Laplace-Transformed PT2(LT-PT2). The use of an OpenMP/MPI hybrid parallel design guarantees the parallel efficiency of LT-XYG3 for different kinds of chemical environment. Systematic benchmark on a serial of water clusters with various system sizes and the ISOL22 test set demonstrates that LT-XYG3 holds the same accuracy as the canonical XYG3 and brings a great advantage in both time and memory consumptions, suggesting a tremendous potential of applying lower scaling doubly hybrid density functionals to complex large systems.

    λ-DFCAS: A Hybrid Density Functional Complete Active Space Self Consistent Field Method
    YING Fuming, JI Chenru, SU Peifeng, WU Wei
    2021, 42(7):  2218-2226.  doi:10.7503/cjcu20210119
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    A multireference density functional theory method, named λ-DFCAS, is presented in this paper. Based on the strategy used in λ-DFVB method, the λ-DFCAS method divides electronic correlation into two parts: the static correlation is covered by multi-reference wave function method, complete active space self-consistent field(CASSCF), while the dynamic correlation is provided by Kohn-Sham density functional theory(KS-DFT). The parameter λ in λ-DFCAS, controlling the hybrid extent of dynamic and static correlations, varies according to the multireference character of a given molecular system. The λ-DFCAS method provides a multireference density functional theory with size-consistency. Test examples show that the accuracy of λ-DFCAS is close to the complete active space second perturbation theory(CASPT2) method, while its computational cost is roughly the same as CASSCF.

    Generalized Energy-based Fragmentation Clustering Algorithm for Localized Excited States
    DU Jiahui, LIAO Kang, HONG Benkun, WANG Zhongye, MA Jing, LI Wei, LI Shuhua
    2021, 42(7):  2227-2237.  doi:10.7503/cjcu20210314
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    Generalized energy-based fragmentation(GEBF) approach can approximately express the local excitation(LE) energy of large system as a linear combination of the excitation energies of a series of active subsystems. Thus, it reduces the computational scaling of the excited-state calculations for large systems. Howe-ver, it is still a challenge to effectively identify the excitation characteristics of all active subsystems and combine the excitation energies when the total system has multiple localized excitations. Here, a clustering algorithm for localized excited states was proposed. This scheme is based on hole-electron analysis and density-based spatial clustering of applications with noise(DBSCAN) algorithm in machine learning, which can automatically collect the excited states with maximum similarity in different subsystems and combine the corresponding localized excited-state energies or excitation energies. With this algorithm, the improved LE-GEBF approach has shown satisfactory results in various systems including derivatives of fluorescent molecules, fluorescent dye-water clusters, and green fluorescent protein models. This algorithm is expected to greatly improve the stabilities and accuracies of the LE-GEBF approach for calculating localized excitations, and can effectively treat large systems with multiple peaks in the absorption spectrum.

    Binding Selectivity Between Diazobenzene and Different Nucleophilic Reagents: Covalent and Noncovalent Interactions
    WANG Gaobo, MA Jing
    2021, 42(7):  2238-2244.  doi:10.7503/cjcu20210237
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    The specific interaction and reaction mechanism between aromatic diazonium salts and nucleophi-lic reagents have not been fully clarified yet. Within the framework of density functional theory, we calculated the binding sites and reaction coordinates of six different nucleophiles with diazobenzene. Chemical hardness of the attacking atom is the main descriptor for describing the binding site. Moreover, a quantitative descriptor is proposed to predict the activation energy barrier in terms of local ionization energy and charge distribution. These results are useful to gain insight for understanding the reaction mechanism of reactions involving aroma-tic diazonium salts and to explore better reaction conditions.

    Theoretical Study on the Structural-photophysical Relationships of Tetra-Pt Phosphorescent Emitters
    WANG Jian, ZHANG Hongxing
    2021, 42(7):  2245-2253.  doi:10.7503/cjcu20210175
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    Quantitative comprehension of the photophysical process is essential for developing novel highly efficient emitters. Improving the photoluminescence quantum efficiency of Pt(Ⅱ) complexes is the key to their application as emitters in organic light-emitting diodes(OLEDs). With the help of density functional theory(DFT) calculation, the current contribution addresses the microscopic mechanisms of phosphorescence for Pt(Ⅱ) complexes including calculations of the spin-orbit couplings integrals, radiative lifetime, rate constants, transition dipole moments, and intersystem crossing(ISC) channels. We found that pushing electrons in N→Pt direction can effectively shield the non-radiative decay process, thereby improving the phosphorescence emission efficiency. This work would provide useful insight into the molecular engineering for high- efficient emitters.

    Application of New Nonequilibrium Solvation Theory in Electronic Spectra of Organic Dyes
    SU Yingli, REN Haisheng, LI Xiangyuan
    2021, 42(7):  2254-2262.  doi:10.7503/cjcu20200805
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    Dye sensitized solar cells(DSSCs) are the new-type photovoltaic devices with the advantages of low cost, easy manufacture and environmental friendliness. Solvation can improve the photoelectric conversion efficiency of DSSCs through changing the electronic structures and spectroscopic properties of organic dyes. The novel nonequilibrium solvation theory and the numerical solutions for calculating the electronic absorption and emission spectra in solution based on time-dependent density functional theory(TD-DFT) in the quantum chemistry software Q-Chem were summarized. Then, the electronic structures and spectral properties of orga-nic dyes TPA??CH=CH??CA(n=0—4) in gas phase and acetonitrile solvent were calculated by this method. It was found that the number of ??CH=CH?? in π-conjugated bridge and the solvent effects are able to improve the photoelectric conversion efficiency. This study will provide new ideas on the design of organic dye molecules in DSSCs.

    Density Functional Theory Study of NH3 Adsorption on Boron Nanotubes
    LIU Changhui, LIANG Guojun, LI Yanlu, CHENG Xiufeng, ZHAO Xian
    2021, 42(7):  2263-2270.  doi:10.7503/cjcu20200862
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    The adsorption behavior and related electronic properties of NH3 on perfect and defective boron nanotubes were investigated via density functional theory. The results show that for α-type boron nanotubes, NH3 is more likely to be adsorbed at the top position with the coordination number of 6 under different diametral and chiral conditions. The electronic structure calculation results show that the strong interaction between N and B atoms is the dominant reason for the stably adsorption of NH3 on the surface of boron nanotubes. It indicates that boron nanotubes are one of the potential NH3 gas sensitive materials.

    Direct Synthesis of Graphene on AlN Substrates via Ga Remote Catalyzation
    LIU Yang, LI Qingbo, SUN Jie, ZHAO Xian
    2021, 42(7):  2271-2278.  doi:10.7503/cjcu20210210
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    Graphene films were directly grown on AlN substrates by chemical vapor deposition(CVD) via Ga remote catalyzation. The effects of growth temperature and catalyst distance on the growth, optical and electrical properties of graphene were studied. The results show that graphene films with thickness of about 5 layers can be prepared at 1070 ℃ and uniform thickness can be obtained within 1.4 cm around Ga. The optical and electrical properties of graphene were characterized by transmittance and square resistance. The results show that the transmittance of graphene film can reach more than 90% in the wavelength range of 400—800 nm, and the square resistance is about 230 Ω/□. First principles calculations results show that graphene remains metallic, and AlN substrate has adsorption doping effect on graphene, which can effectively reduce the square resistance of graphene and improve the electrical contact between graphene and substrate.

    Effect of Collision Energy on the Stereodynamics of the Reaction K(2S)+HF(X1Σ+)→KF(X1Σ+)+H(2S)
    CHEN Hailiang, ZHANG Zhihong, LYU Wencai
    2021, 42(7):  2279-2285.  doi:10.7503/cjcu20210198
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    The stereodynamics of the atom-molecule reaction K(2S) +HF(X1+)→KF(X1+) +H(2S) was studied using quasi-classical trajectory method based on the potential energy surface constructed by Sayós et al. Four generalized polarization-dependent differential cross-sections[(2π)(dσ00/dωt), (2π)· (dσ20/dωt), (2π)(dσ22+/dωt), (2π)(dσ21-/dωt)], the distributions functionPθr)], the dihedral angle distribution function[P?r)] and the polar distriloution function[Pθr?r)]are studied in detail. The results show that the rotational angular momentum j′of the product KF is not only strongly aligned along the direction perpendicular to k, but also oriented along the negative direction of the y axis. The orientation of j′depends very sensitively on the collision energy.

    Solutions of Atomic and Molecular Schrödinger Equations with One-dimensional Function Approach
    SARWONO Yanoar Pribadi, UR RAHMAN Faiz, ZHAO Rundong, ZHANG Ruiqin
    2021, 42(7):  2286-2298.  doi:10.7503/cjcu20210138
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    Rigorous numerical techniques to solve the Schr?dinger equation are both interesting and desirable, particularly with one that can include new features beyond the standard methods. In this article, we review one-dimensional function(1D function) approach developed recently by us to obtain the solutions of the Schr?dinger equations of atomic and molecular systems where one-dimensional basis functions have been applied to separate components. A uniform real-space grid representation of the electronic wavefunctions is employed; hence, a refinement technique of residual vector correction can be implemented. The 1D function approach facilitates such convenient numerical integrations that many problems related with the many-electron multi-center potential molecular integrals are circumvented. The converged energy is obtained from a strictly upper bound one, while the obtained two-electron Schr?dinger wavefunction exhibits the electron correlation effect on one-electron distribution. Different from density functional theory or Hartree-Fock with the assumed particle-separability, the obtained solution treats more accurately many-body effect of electron correlation found in the electron-electron repulsion energy.

    Theoretical Study on Gold-catalyzed Cyclization of Alkynyl Benzodioxin to 8-Hydroxy-isocoumarin
    YANG Yiying, ZHU Rongxiu, ZHANG Dongju, LIU Chengbu
    2021, 42(7):  2299-2305.  doi:10.7503/cjcu20210157
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    Density functional theory(DFT) calculations were carried out on the gold-catalyzed cyclization of alkynyl benzodioxin to 8-hydroxy-isocoumarin reaction to show the molecular mechanism of the reaction. The conclusions obtained from this work are different from those in the previous experimental study. The results show that water molecule acts as both the reactant and the proton shuttle, and promotes the reaction with gold complexes under mild conditions. The nucleophilic addition site of water on the substrate is the C(sp3) atom on the side of the substrate far away from the oxabenzene ring, resulting in C(sp3)—O bond breaking in the substrate. The formation of new C—O bond and the cleavage of C—O bond in the substrate follow a step-by-step mechanism. The oxygen in the side-product acetone comes from the contribution of water in the reaction system. The regioselectivity of the reaction originates from the polarization of alkynyl π-electrons induced by substituents.

    Theoretical Insights into the Cleavage of β-Hydroxy Ketone Catalyzed by Artificial Retro-aldolase RA95.5-8F
    LI Xinyi, LIU Yongjun
    2021, 42(7):  2306-2312.  doi:10.7503/cjcu20210125
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    The mechanism of the cleavage of β-hydroxy ketone catalyzed by the artificial retro-aldolase RA95.5-8F was studied by the combined quantum mechanics and molecular mechanics(QM/MM) method. The results show that the cleavage reaction includes the nucleophilic attack of Lys1083 on the substrate, formation of Schiff base intermediate, hydrolysis of enamine, C—N cleavage and so on. The final step of the cleavage of C—N bond to generate acetone is the rate-limiting step with the energy barrier of 106.27 kJ/mol. Lys1083, Tyr1051, Asn1110 and Tyr1180 form a catalytic tetrad, in which Lys1083 and Tyr1051 act as nucleophile and catalytic acid-base, respectively. The hydrogen bond network of the catalytic tetrad stabilizes the reaction transition states and makes it easier for R-configuration substrate to bind to the active site, resul?ting in the high selectivity and reactivity of RA95.5-8F for R-configuration substrate.