2021 Vol. 34, No. 5
2021, 34(5): 497-524.
doi: 10.1063/1674-0068/cjcp2109157
The generalized quantum master equation (GQME) provides a general and exact approach for simulating the reduced dynamics in open quantum systems where a quantum system is embedded in a quantum environment. Dynamics of open quantum systems is important in excitation energy, charge, and quantum coherence transfer as well as reactive photochemistry. The system is usually chosen to be the interested degrees of freedom such as the electronic states in light-harvesting molecules or tagged vibrational modes in a condensed-phase system. The environment is also called the bath, whose influence on the system has to be considered, and for instance can be described by the GQME formalisms using the projection operator technique. In this review, we provide a heuristic description of the development of two canonical forms of GQME, namely the time-convoluted Nakajima-Zwanzig form (NZ-GQME) and the time-convolutionless form (TCL-GQME). In the more popular NZ-GQME form, the memory kernel serves as the essential part that reflects the non-Markovian and non-perturbative effects, which gives formally exact dynamics of the reduced density matrix. We summarize several schemes to express the projection-based memory kernel of NZ-GQME in terms of projection-free time correlation function inputs that contain molecular information. In particular, the recently proposed modified GQME approach based on NZ-GQME partitions the Hamiltonian into a more general diagonal and off-diagonal parts. The projection-free inputs in the above-mentioned schemes expressed in terms of different system-dependent time correlation functions can be calculated via numerically exact or approximate dynamical methods. We hope this contribution would help lower the barrier of understanding the theoretical pillars for GQME-based quantum dynamics methods and also envisage that their combination with the quantum computing techniques will pave the way for solving complex problems related to quantum dynamics and quantum information that are currently intractable even with today's state-of-the-art classical supercomputers.
2021, 34(5): 525-531.
doi: 10.1063/1674-0068/cjcp2107119
In (relativistic) electronic structure methods, the quaternion matrix eigenvalue problem and the linear response (Bethe-Salpeter) eigenvalue problem for excitation energies are two frequently encountered structured eigenvalue problems. While the former problem was thoroughly studied, the later problem in its most general form, namely, the complex case without assuming the positive definiteness of the electronic Hessian, was not fully understood. In view of their very similar mathematical structures, we examined these two problems from a unified point of view. We showed that the identification of Lie group structures for their eigenvectors provides a framework to design diagonalization algorithms as well as numerical optimizations techniques on the corresponding manifolds. By using the same reduction algorithm for the quaternion matrix eigenvalue problem, we provided a necessary and sufficient condition to characterize the different scenarios, where the eigenvalues of the original linear response eigenvalue problem are real, purely imaginary, or complex. The result can be viewed as a natural generalization of the well-known condition for the real matrix case.
2021, 34(5): 532-540.
doi: 10.1063/1674-0068/cjcp2108134
[4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins are a superfamily of oxidoreductases that can catalyze a series of challenging transformations using the common 5-dAdo radical intermediate. Although the structures and functions of radical SAM enzymes have been extensively studied, the electronic state-dependent reactions of the [4Fe-4S] clusters in these enzymes are still elusive. Herein we performed QM/MM calculations to elucidate the electronic state-dependent reactivity of the [4Fe-4S] cluster in pyruvate-formate lyase activating enzyme. Our calculations show that the electronic state-dependent SAM activation by the [4Fe-4S] clusters in radical SAM enzyme is determined by both the super-exchange and exchange-enhanced reactivities. The super-exchange coupling in the [4Fe-4S] cluster favors the antiferromagnetic coupling between two neighbouring pairs, which results in the $\alpha$-electron rather than the $\beta$-electron donation from the [4Fe-4S]$^{1+}$ cluster toward the SAM activation. Meanwhile, in the most favorable electronic state for the reductive cleavage of S$-$C5$'$, Fe4 would donate its $\alpha$-electron to gain the maximum exchange interactions in the Fe4-block. Such super-exchange and exchange-enhanced reactivity could be the general principles for reactivities of [4Fe-4S] cluster in RS enzymes.
The formation and migration of polarons have important influences on physical and chemical properties of transition metal oxides. Density functional theory plus the Hubbard $U$ correction (DFT+$U$) and constrained density functional theory (cDFT) are often used to obtain the transfer properties for small polarons. In this work we have implemented the cDFT plus the Hubbard $U$ correction method in the projector augmented wave (PAW) framework, and applied it to study polaron transfer in the bulk phases of TiO$_2$. We have confirmed that the parameter $U$ can have significant impact on theoretical prediction of polaronic properties. It was found that using the Hubbard $U$ calculated by the cDFT method with the same orbital projection as used in DFT+$U$, one can obtain theoretical prediction of polaronic properties of rutile and anatase phases of TiO$_2$ in good agreement with experiment. This work indicates that the cDFT+$U$ method with consistently evaluated $U$ is a promising first-principles approach to polaronic properties of transition metal oxides without empirical input.
KSSOLV (Kohn-Sham Solver) is a MATLAB (Matrix Laboratory) toolbox for solving the Kohn-Sham density functional theory (KS-DFT) with the plane-wave basis set. In the KS-DFT calculations, the most expensive part is commonly the diagonalization of Kohn-Sham Hamiltonian in the self-consistent field (SCF) scheme. To enable a personal computer to perform medium-sized KS-DFT calculations that contain hundreds of atoms, we present a hybrid CPU-GPU implementation to accelerate the iterative diagonalization algorithms implemented in KSSOLV by using the MATLAB built-in Parallel Computing Toolbox. We compare the performance of KSSOLV-GPU on three types of GPU, including RTX3090, V100, and A100, with conventional CPU implementation of KSSOLV respectively and numerical results demonstrate that hybrid CPU-GPU implementation can achieve a speedup of about 10 times compared with sequential CPU calculations for bulk silicon systems containing up to 128 atoms.
2021, 34(5): 565-582.
doi: 10.1063/1674-0068/cjcp2108138
We propose a method for calculating the nonradiative decay rates for polyatomic molecules including anharmonic effects of the potential energy surface (PES) in the Franck-Condon region. The method combines the n-mode representation method to construct the ab initio PES and the nearly exact time-dependent density matrix renormalization group method (TD-DMRG) to simulate quantum dynamics. In addition, in the framework of TD-DMRG, we further develop an algorithm to calculate the final-state-resolved rate coefficient which is very useful to analyze the contribution from each vibrational mode to the transition process. We use this method to study the internal conversion (IC) process of azulene after taking into account the anharmonicity of the ground state PES. The results show that even for this semi-rigid molecule, the intramode anharmonicity enhances the IC rate significantly, and after considering the two-mode coupling effect, the rate increases even further. The reason is that the anharmonicity enables the C-H vibrations to receive electronic energy while C-H vibrations do not contribute on the harmonic PES as the Huang-Rhys factor is close to 0.
2021, 34(5): 583-590.
doi: 10.1063/1674-0068/cjcp2108145
LASP (large-scale atomistic simulation with neural network potential) software developed by our group since 2018 is a powerful platform (www.lasphub.com) for performing atomic simulation of complex materials. The software integrates the neural network (NN) potential technique with the global potential energy surface exploration method, and thus can be utilized widely for structure prediction and reaction mechanism exploration. Here we introduce our recent update on the LASP program version 3.0, focusing on the new functionalities including the advanced neural network training based on the multi-network framework, the newly-introduced $ S^7 $ and $ S^8 $ power type structure descriptor (PTSD). These new functionalities are designed to further improve the accuracy of potentials and accelerate the neural network training for multiple-element systems. Taking Cu$ - $C$ - $H$ - $O neural network potential and a heterogeneous catalytic model as the example, we show that these new functionalities can accelerate the training of multi-element neural network potential by using the existing single-network potential as the input. The obtained double-network potential CuCHO is robust in simulation and the introduction of $ S^7 $ and $ S^8 $ PTSDs can reduce the root-mean-square errors of energy by a factor of two.
2021, 34(5): 598-604.
doi: 10.1063/1674-0068/cjcp2108132
Coherent vibrational dynamics can be observed in atomically precise gold nanoclusters using femtosecond time-resolved pump-probe spectroscopy. It can not only reveal the coupling between electrons and vibrations, but also reflect the mechanical and electronic properties of metal nanoclusters, which holds potential applications in biological sensing and mass detection. Here, we investigated the coherent vibrational dynamics of [Au25(SR)18]- nanoclusters by ultrafast spectroscopy and revealed the origins of these coherent vibrations by analyzing their frequency, phase and probe wavelength distributions. Strong coherent oscillations with frequency of 40 cm-1 and 80 cm-1 can be reproduced in the excited state dynamics of [Au25(SR)18]-, which should originate from acoustic vibrations of the Au13 metal core. Phase analysis on the oscillations indicates that the 80 cm-1 mode should arise from the frequency modulation of the electronic states while the 40 cm-1 mode should originate from the amplitude modulation of the dynamic spectrum. Moreover, it is found that the vibration frequencies of [Au25(SR)18]- obtained in pump-probe measurements are independent of the surface ligands so that they are intrinsic properties of the metal core. These results are of great value to understand the electron-vibration coupling of metal nanoclusters.
2021, 34(5): 605-612.
doi: 10.1063/1674-0068/cjcp2108135
MXenes, a new family of two-dimensional (2D) materials, have received extensive interest due to their fascinating physicochemical properties, such as outstanding light-to-heat conversion efficiency. However, the photothermal conversion mechanism of MXenes is still poorly understood. Here, by using femtosecond visible and mid-infrared transient absorption spectroscopy, the electronic energy dissipation dynamics of MXene (Ti3C2Tx) nanosheets dispersed in various solvents are carefully studied. Our results indicate that the lifetime of photoexcited MXene is strongly dependent on the surrounding environment. Especially, the interfacial electron-vibration coupling between the MXene nanosheets and the adjacent solvent molecules is directly observed following the ultrafast photoexcitation of MXene. It suggests that the interfacial interactions at the MXene-solvent interface play a critical role in the ultrafast energy transport dynamics of MXene, which offers a potentially feasible route for tailoring the light conversion properties of 2D systems.
2021, 34(5): 613-620.
doi: 10.1063/1674-0068/cjcp2109154
Mixed halide perovskites (MHPs) are a class of semiconductor materials with great promise for many optoelectronic applications due to their outstanding photophysical properties. Understanding and tailoring the photogenerated carrier dynamics is essential for further improvement of perovskite performance. Herein, we report a study about the carrier transport and interfacial charge transfer dynamics in Br-gradient MAPbI3-xBrx perovskite thin films prepared by surface ion-exchange method. Driven by the bandgap gradient in MAPbI3-xBrx films, the accelerated internal hole transport and enhanced interfacial extraction efficiency were both observed. Meanwhile, the interfacial electron transfer was also found to be evidently facilitated due to the surface modification during post-treatment. Our findings suggest the possibility of simultaneous acceleration of interfacial electron and hole transfer processes in halide perovskite films via surface post-treatment technique, which is of great importance in further improving the power conversion efficiency of perovskite solar cells.
2021, 34(5): 621-627.
doi: 10.1063/1674-0068/cjcp2012220
After binding to human serum albumin, bilirubin could undergo photo-isomerization and photo-induced cyclization process. The latter process would result the formation of a product, named as lumirubin. These photo induced behaviors are the fundamental of clinical therapy for neonatal jaundice. Previous studies have reported that the addition of long chain fatty acids is beneficial to the generation of lumirubin, yet no kinetic study has revealed the mechanism behind. In this study, how palmitic acid affects the photochemical reaction process of bilirubin in Human serum albumin (HSA) is studied by using femtosecond transient absorption and fluorescence up-conversion techniques. With the addition of palmitic acid, the excited population of bilirubin prefers to return to its hot ground state (S0) through a 4 ps decay channel rather than the intrinsic ultrafast decay pathways (< 1 ps). This effect prompts the Z-Z to E-Z isomerization at the S$_0$ state and then further increases the production yield of lumirubin. This is the first time to characterize the promoting effect of long chain fatty acid in the process of phototherapy with femtosecond time resolution spectroscopy and the results can provide useful information to benefit the relevant clinical study.
2021, 34(5): 628-638.
doi: 10.1063/1674-0068/cjcp2011192
Consistency between density functional theory calculations and X-ray photoelectron spectroscopy measurements confirms our predications on the undercoordination-induced local bond relaxation and core level shift of alkali metal, which determine the surface, size and thermal properties of materials. Zone-resolved photoelectron spectroscopy analysis method and bond order-length-strength theory can be utilized to quantify the physical parameters regarding bonding identities and electronic property of metal surfaces, which allows for the study of the core-electron binding-energy shifts in alkali metals. By employing these methods and first principle calculation in this work, we can obtain the information of bond and atomic cohesive energy of under-coordinated atoms at the alkali metal surface. In addition, the effect of size and temperature towards the binding-energy in the surface region can be seen from the view point of Hamiltonian perturbation by atomic relaxation with atomic bonding.
2021, 34(5): 639-648.
doi: 10.1063/1674-0068/cjcp2009169
Owing to the unique structural, electronic, and physico-chemical properties, molybdenum clusters are expected to play an important role in future nanotechnologies. However, their ground states are still under debate. In this study, the crystal structure analysis by particle swarm optimization (CALYPSO) approach is used for the global minimum search, which is followed by first-principles calculations, to detect an obvious dimerization tendency in Mo$ _n $ ($ n $ = 2$ - $18) clusters when the 4s and 4p semicore states are not regarded as the valence states. Further, the clusters with even number of atoms are usually magic clusters with high stability. However, after including the 4s and 4p electrons as valence electrons, the dimerization tendency exhibits a drastic reduction because the average hybridization indices $ H_{ \rm{sp}} $, $ H_{ \rm{sd}} $, and $ H_{ \rm{pd}} $ are reduced significantly. Overall, this work reports new ground states of Mo$ _n $ ($ n $ = 11, 14, 15) clusters and proves that semicore states are essential for Mo$ _n $
2021, 34(5): 591-597.
doi: 10.1063/1674-0068/cjcp2109169
The intermolecular interaction determines the photophysical properties of the organic aggregates, which are critical to the performance of organic photovoltaics. Here, excitonic coupling, an important intermolecular interaction in organic aggregates, between the π-stacking graphene quantum dots is studied by using transient absorption spectroscopy. We find that the spectral evolution of the ground state bleach arises from the dynamic variation of the excitonic coupling in the excited π-stacks. According to the spectral simulations, we demonstrate that the kinetics of the vibronic peak can be exploited as a probe to measure the dynamics of excitonic coupling in the excited π-stacks.
