Hierarchical Equations of Motion for Quantum Chemical Dynamics: Recent Methodology Developments and Applications.

ConspectusQuantum effects are critical to understanding many chemical dynamical processes in condensed phases, where interactions between molecules and their environment are usually strong and non-Markovian. In this Account, we review recent progress from our group in development and application of the hierarchical equations of motion (HEOM) method, highlighting its ability to address some challenging problems in quantum chemical dynamics.In the HEOM method, the bath degrees of freedom are represented using effective modes from exponential decomposition of the bath correlation function. Complex spectral densities and low temperature simulations often require a larger number of modes, making the simulations very expensive. Recent advances, such as the barycentric spectral decomposition (BSD) technique, can significantly reduce the number of effective modes, allowing to handle complex spectral densities and enabling simulations at very low temperatures, including near-zero temperature dynamics.Another key improvement in the computational efficiency is the use of tensor network methods like matrix product states and hierarchical tensor networks. These techniques allow for efficient HEOM propagation with thousands of effective modes, crucial for simulating large molecular systems interacting with multiple baths. This combination enables simulations of excitation energy transfer (EET) in systems like the Fenna-Matthews-Olson (FMO) complex and even larger systems with experimentally determined spectral densities.The versatility of the HEOM method is demonstrated through applications to a wide range of chemical dynamics problems. Simulations of EET and related ultrafast spectroscopy are first briefly covered. Applications of the HEOM to quantum tunneling effects in proton transfer reactions are then presented. Early works have studied the non-Kramers dependence of the rate constant as a function of bath friction due to deep tunneling and revealed vibrationally nonadiabatic dynamics within the so-called nontraditional view of proton transfer reactions. A recent work on the large kinetic isotope effects in soybean lipoxygenase also indicated that many quantum correction approximations to classical transition-state theory may fall short in describing deep tunneling effects.Charge transport and separation dynamics in organic semiconductors are another area where the HEOM method has been instrumental. We first demonstrate that the HEOM provides a unified description of both band-like and thermally assisted charge carrier transport in organic materials. The effect of non-nearest neighbor transitions is then investigated by combining generalized master equations with exact memory kernels. The HEOM method also enables simulation of charge separation in organic photovoltaics (OPVs) and reveals how factors such as external electric fields, entropy, and charge delocalization influence the charge separation barrier and dynamics.Moreover, HEOM has been applied to investigate hydrogen atom scattering on the Au(111) surface and vibrational energy relaxation at molecule-metal interfaces. These studies provide deeper insights into how electron-hole pair excitations and temporary charge transfer states influence the nuclear motion, offering a new framework for simulating nonadiabatic dynamics on metal surfaces.In summary, the HEOM method has developed into a robust tool for simulating quantum effects in condensed phases. Future developments in algorithm efficiency and computational power will likely expand its applicability to even more complex systems.

Simulation of the Pump-Probe Spectra and Excitation Energy Relaxation of the B850 Band of the LH2 Complex in Purple Bacteria.

Ultrafast spectroscopic techniques have been vital in studying excitation energy transfer (EET) in photosynthetic light harvesting complexes. In this paper, we simulate the pump-probe spectra of the B850 band of the light harvesting complex 2 (LH2) of purple bacteria, by using the hierarchical equation of motion method and the optical response function approach. The ground state bleach, stimulated emission, and excited state absorption components of the pump-probe spectra are analyzed in detail. The laser pulse-induced population dynamics are also simulated to help understand the main features of the pump-probe spectra and the EET process. It is shown that the excitation energy relaxation is an ultrafast process with multiple time scales. The first 40 fs of the pump-probe spectra is dominated by the relaxation of the k = ±1 states to both the k = 0 and higher energy states. Dynamics on a longer time scale around 200 fs reflects the relaxation of higher energy states to the k = 0 state.

Ethyl Vanillin Rapid Crystallization from Carboxymethyl Chitosan Ion-Switchable Hydrogels.

Polymer gels are usually used for crystal growth as the recovered crystals have better properties. Fast crystallization under nanoscale confinement holds great benefits, especially in polymer microgels as its tunable microstructures. This study demonstrated that ethyl vanillin can be quickly crystallized from carboxymethyl chitosan/ethyl vanillin co-mixture gels via classical swift cooling method and supersaturation. It found that EVA appeared with bulk filament crystals accelerated by a large quantity of nanoconfinement microregions resulted from space-formatted hydrogen network between EVA and CMCS when their concentration exceeds 1:1.4 and may occasionally arise when the concentration less than 1:0.8. It was observed that EVA crystal growth has two models involving hang-wall growth at the air-liquid interface at the contact line, as well as extrude-bubble growth at any sites on the liquid surface. Further investigations found that EVA crystals can be recovered from as-prepared ion-switchable CMCS gels by 0.1 M hydrochloric acid or acetic acid without defects. Consequently, the proposed method may offer an available scheme for a large-scale preparation of API analogs.

A Novel Distributed Fault Detection Approach Based on the Variational Autoencoder Model.

In large-scale industrial fault detection, a distributed model is typically established on the basis of blocked units. However, blocked distributed methods consider units as independent of one another and disregard the relationship between units, thus leading to incomplete information on local units. In fact, the operation status of a unit is affected by a local unit and its surrounding neighboring units. In addition, the fault detection performance of a system is seriously reduced once data are missing from the data source. Variational autoencoder (VAE) is not only a popular deep generative model but also has a powerful nonlinear feature extraction capability. In this study, VAE is extended to the distributed case. In this study, a distributed fault detection method DVAE based on VAE is proposed. This method can not only describe local and neighboring information, but it can also reconstruct missing data. First, system variables are divided into local and neighboring units in accordance with the system mechanism. Second, for each local unit, a DVAE model is established to map the multivariable data onto the latent variable space. The obtained latent variable contains the information on a local unit and can reflect the complex relationship with its neighboring units. Lastly, Euclidean distance is used to detect system faults. When applied on the Tennessee Eastman process for verification, the proposed method shows good performance in fault detection and missing data reconstruction.

Silver-mediated trifluoromethoxylation of aryl stannanes and arylboronic acids.

A silver-mediated cross-coupling of trifluoromethoxide with aryl stannanes and arylboronic acids to give aryl trifluoromethyl ethers is reported. This is the first report of a transition-metal-mediated C(aryl)-OCF(3) bond formation.

pH responsive release of paclitaxel by self-assembling Chitosan-ethyl vanillin@GNRs nanocomposites.

Carboxylation chitosan achieved by alkalization linked with ethyl vanillin to obtain Chitosan-ethyl vanillin (EV-CMCS) compound through Schiff base reaction and confirmed by FT-IR, UV, XRD, TG and NMR. EV-CMCS refluxed with GNRs for acquisition of EV-CMCS@GNRs nanocomposites for PTX Loading and release. Results demonstrated that both EV-CMCS and EV-CMCS@GNRs are nanoscale composites with excellent solubilization due to their micelle structure taking CMC values of 0.06683 mg/mL and 0.06537 mg/mL. It was found that the loading and encapsulation rate of EV-CMCS and EV-CMCS@GNRs for PTX are 19.59~37.64% and 60.36~80.79% as well as 20.99~37.02% and 58.78~79.77%. Compared with only the delayed release of EV-CMCS that it have 11.5% and 18.7% accumulative release amount for 24 h and 14.9% and 23.7% for 48 h under both pH 6.8 and 7.4, the EV-CMCS@GNRs represent sudden release that it have an accumulative release amount of 90.2% for 24 h and 96.0% for 48 h at pH 6.8. It deduced that the broken Schiff base under acidic condition can increase CMC of EV-CMCS@GNRs, which offered an alternative way for paclitaxel delivery for tumor therapy.

Predicting the structure of supramolecular dendrimers via the analysis of libraries of AB3 and constitutional isomeric AB2 biphenylpropyl ether self-assembling dendrons.

The synthesis of 4'-hydroxy-4-biphenylpropionic, 3',4'-dihydroxy-4-biphenylpropionic, 3',5'-dihydroxy-4-biphenylpropionic, and 3',4',5'-trihydroxy-4-biphenylpropionic methyl esters via three efficient and modular strategies including one based on Ni-catalyzed borylation and sequential cross-coupling is reported. These building blocks were employed in a convergent iterative approach to the synthesis of one library of 3,4,5-trisubstituted and two libraries of constitutional isomeric 3,4- and 3,5-disubstituted biphenylpropyl ether dendrons. Structural and retrostructural analysis of supramolecular dendrimers revealed that biphenylpropyl ether dendrons self-assemble and self-organize into the same periodic lattices and quasi-periodic arrays observed in previously reported libraries, but with larger dimensions, different mechanisms of self-assembly, and improved solubility, thermal, acidic, and oxidative stability. The different mechanisms of self-assembly led to the discovery of two new supramolecular structures. The first represents a new banana-like lamellar crystal with a four layer repeat. The second is a giant vesicular sphere self-assembled from 770 dendrons that exhibits an ultrahigh molar mass of 1.73 x 10(6) g/mol. Thus, the enhanced size of the self-assembled structures constructed from biphenylpropyl ether dendrons permitted for the first time discrimination of various molecular mechanisms of spherical self-assembly and elaborated a continuum between small filled spheres and very large hollow spheres that is dictated by the primary structure of the dendron. The comparative analysis of libraries of biphenylpropyl ether dendrons with the previously reported libraries of benzyl-, phenylpropyl-, and biphenyl-4-methyl ether dendrons demonstrated biomimetic self-assembly wherein the primary structure of the dendron and to a lesser extent the structure of its repeat unit determines the supramolecular tertiary structure. A "nanoperiodic table" of self-assembling dendrons and supramolecular dendrimers that allows the prediction of the general features of tertiary structures from primary structures was elaborated.

Sequential Ni-catalyzed borylation and cross-coupling of aryl halides via in situ prepared neopentylglycolborane.

A procedure for NiCl(2)(dppp)-catalyzed pinacolborylation and neopentylglycolborylation that utilizes in situ prepared inexpensive pinacolborane and neopentylglycolborane is reported. The scope of this reaction was demonstrated with a variety of aryl bromides and iodides. The resulting aryl neopentylglycolboronic esters undergo a NiCl(2)(dppe)-catalyzed cross-coupling with aryl halides, resulting in an extremely efficient and cost-effective method for the synthesis of functional biaryls, dendritic building blocks, and other complex architectures.

A one-step immunoassay for carbohydrate antigen 19-9 by biosensor based on imaging ellipsometry.

Cancer markers can offer much more information for developing or developed cancers. Simple and short-time assay of cancer biomarker is essential for clinic diagnosis and management. In this study, a one-step immunoassay for carbohydrate antigen 19-9 (CA19-9) by biosensor based on imaging ellipsometry (BIE) is described and its analysis performances are evaluated. Anti-CA19-9 monoclonal antibody as ligand covalently immobilized on carboxyl-modified silicon substrate and its immobilization concentration concurrently screened. Then, bovine serum albumin (BSA) is used to block for acquisition of sensing layer. The detection linear range is from 15.0 to 120.0 U/mL with a minimum limit of 10.0 U/mL (S/N=3). The intra-slide and inter-slide reproducibility, expressed as coefficient variation (CV%), are 9.9, 5.9, 5.4% and 9.6, 7.6, 5.3% for 31.9, 57.4, and 99.2 U/mL of CA19-9, respectively. Accuracy determined by spiked-recovery is among 95.1-106.7%. Specificity expressed as cross-reaction rate are all below 5.8% evaluated by three analogous biomarkers alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA), and carbohydrate antigen 242 (CA242). Application of BIE to 25 clinic samples demonstrated that the results are in high correlate with electrochemiluminescent immunoassay (ECLIA, R2=0.997). The proposed immunoassay has the potential for clinic application.

The octadecanoid signaling pathway participates in the chilling-induced transcription of ω-3 fatty acid desaturases in Arabidopsis.

The jasmonate signaling pathway is known to be involved in various stress responses in plants, but little is known specifically on the role of the octadecanoid pathway in the regulation of ω-3 fatty acid desaturase (FAD) genes in response to low temperature. To uncover this problem, the expression level of three ω-3 FAD genes (AtFAD3, AtFAD7, and AtFAD8) and the content of linolenic acid (C18:3) in both wild type (WT) and mutant (or WT suppressed) plants disrupted in the octadecanoid pathway were analyzed under normal conditions and the chilling treatment (4 °C), respectively. As compared with WT plants, chilling-induced organ-specific expressions of ω-3 FAD genes significantly changed when the octadecanoid pathway was blocked or suppressed, and presented either the "suppressed increase" or the "enhanced decrease" tendency. Meanwhile, chilling-induced increases in the content of C18:3 found in WT plants, obviously reduced in both leaves and roots, and even turned to a decrease in stems when the octadecanoid pathway was disrupted. Overall, the transcription of ω-3 FAD genes and the proportion of C18:3 in the whole plant both of aos mutants and salicylic acid (SA)-treated plants under chilling stress were evidently lower than those of WT plants, except the expression of AtFAD3 gene in leaves. All these findings indicate that the octadecanoid pathway does participate in the chilling-induced transcription of ω-3 FAD genes in Arabidopsis.

Isolation of high-quality RNA from Reaumuria soongorica, a desert plant rich in secondary metabolites.

RNA isolation is a prerequisite for the study of the molecular mechanisms of stress tolerance in the desert plant Reaumuria soongorica, an extreme xeric semi-shrub. However, R. soongorica that contains high levels of secondary metabolites that co-precipitate with RNA, making RNA isolation difficult. Here the authors propose a new protocol suitable for isolating high-quality RNA from the leaves of R. soongorica. Based on a CTAB method described by Liu et al., the protocol has been improved as follows: the samples were ground with PVPP to effectively inhibit the oxidation of phenolics, contaminating DNA was removed with DNase I, and NaAc was used along with ethanol for precipitation to enhance the RNA yield and shorten the precipitation time. Gel electrophoresis and spectrophotometric analysis indicated that this isolation method provides RNA with no DNA contamination. Moreover, the yield (183.79 ± 40.36 µg/g) and quality were superior to those using the method of Liu et al., which yields RNA with significant DNA contamination at 126.30 ± 29.43 µg/g. Gene amplification showed that the RNA obtained using this protocol is suitable for use in downstream molecular procedures. This method was found to work equally well for isolating RNA from other desert plants. Thus, it is likely to be widely applicable.

Involvement of glucose-6-phosphate dehydrogenase in reduced glutathione maintenance and hydrogen peroxide signal under salt stress.

Cellular redox homeostasis is essential for plant growth, development as well as for the resistance to biotic and abiotic stresses, which is governed by the complex network of prooxidant and antioxidant systems. Recently, new evidence has been published that NADPH, produced by glucose-6-phosephate dehydrogenase enzyme (G6PDH), not only acted as the reducing potential for the output of reduced glutathione (GSH), but was involved in the activity of plasma membrane (PM) NADPH oxidase under salt stress, which resulted in hydrogen peroxide (H(2)O(2)) accumulation. H(2)O(2) acts as a signal in regulating G6PDH activity and expression, and the activities of the enzymes in the glutathione cycle as well, through which the ability of GSH regeneration was increased under salt stress. Thus, G6PDH plays a critical role in maintaining cellular GSH levels under long-term salt stress. In this addendum, a hypothetical model for the roles of G6PDH in modulating the intracellular redox homeostasis under salt stress is presented.

Glucose-6-phosphate dehydrogenase plays a central role in modulating reduced glutathione levels in reed callus under salt stress.

In the present study, we investigated the role of glucose-6-phosphate dehydrogenase (G6PDH) in regulating the levels of reduced form of glutathione (GSH) to the tolerance of calli from two reed ecotypes, Phragmites communis Trin. dune reed (DR) and swamp reed (SR), in a long-term salt stress. G6PDH activity was higher in SR callus than that of DR callus under 50-150 mM NaCl treatments. In contrast, at higher NaCl concentrations (300-600 mM), G6PDH activity was lower in SR callus. A similar profile was observed in GSH contents, glutathione reductase (GR) and glutathione peroxidase (GPX) activities in both salt-stressed calli. After G6PDH activity and expression were reduced in glycerol treatments, GSH contents and GR and GPX activity decreased strongly in both calli. Simultaneously, NaCl-induced hydrogen peroxide (H2O2) accumulation was also abolished. Exogenous application of H2O2 increased G6PDH, GR, and GPX activities and GSH contents in the control conditions and glycerol treatment. Diphenylene iodonium (DPI), a plasma membrane (PM) NADPH oxidase inhibitor, which counteracted NaCl-induced H(2)O(2) accumulation, decreased these enzymes activities and GSH contents. Furthermore, exogenous application of H2O2 abolished the N-acetyl-L: -cysteine (NAC)-induced decrease in G6PDH activity, and DPI suppressed the effect of buthionine sulfoximine (BSO) on induction of G6PDH activity. Western-blot analyses showed that G6PDH expression was stimulated by NaCl and H2O2, and blocked by DPI in DR callus. Taken together, G6PDH activity involved in GSH maintenance and H2O2 accumulation under salt stress. And H2O2 regulated G6PDH, GR, and GPX activities to maintain GSH levels. In the process, G6PDH plays a central role.

Regulation of the plasma membrane during exposure to low temperatures in suspension-cultured cells from a cryophyte (Chorispora bungeana).

As the outermost boundary of the cell, the plasma membrane plays an important role in determining the stress resistance of organisms. To test this concept in a cryophyte, we analyzed alterations of several components in plasma membranes isolated from suspension-cultured cells of Chorispora bungeana Fisch. & C.A. Mey in response to treatment at 0 and -4 degrees C for 192 h. When compared with the controls growing at 25 degrees C, both the membrane permeability and fluidity showed recovery after the initial impairment. Linolenic acid and membrane lipid unsaturation increased by about 0.8-fold following cold treatments, although the kinetics of the increase varied with the temperatures examined. During the treatments, the plasma membrane H(+)-ATPase (EC 3.6.1.3) activity increased by 78.06% at 0 degrees C and 100.47% at -4 degrees C. However, the plasma membrane NADH oxidase (EC 1.6.99.3) activity only decreased when exposed to a lower temperature (-4 degrees C), and remained at 63.93% after being treated for 192 h. After the treatments, the physical properties of the plasma membranes of suspension-cultured cells, especially the -4 degrees C treated cells, were similar to those in the wild plants. These findings indicate that the specific mechanism of cold resistance of C. bungeana is tightly linked with the rapid and flexible regulation of membrane lipids and membrane-associated enzymes, which ensure the structural and functional integrity of the plasma membrane that is essential for withstanding low temperature.

Increased sensitivity to salt stress in an ascorbate-deficient Arabidopsis mutant.

The Arabidopsis thaliana ascorbate-deficient vtc-1 mutant has only 30% ascorbate contents of the wild type (WT). This ascorbate-deficient mutant was used here to study the physiological roles of ascorbate under salt stress in vivo. Salt stress resulted in a more significant decrease in CO2 assimilatory capacity in the vtc-1 mutant than in the WT. Photosystem II function in the Arabidopsis vtc-1 mutant also showed an increased sensitivity to salt stress. Oxidative stress, indicated by the hydrogen peroxide content, increased more dramatically in the vtc-1 mutant than in the WT under salt stress. To clarify the reason for the increased oxidative stress in the vtc-1 mutant, the contents of small antioxidant compounds and the activities of several antioxidant enzymes in the ascorbate-glutathione cycle were measured. Despite an elevated glutathione pool in the vtc-1 mutant, the ascorbate contents and the reduced form of ascorbate decreased very rapidly under salt stress. These results showed that the activities of MDAR and DHAR were lower in the vtc-1 mutant than in the WT under salt stress. Thus, low intrinsic ascorbate and an impaired ascorbate-glutathione cycle in the vtc-1 mutant under salt stress probably induced a dramatic decrease in the reduced form of ascorbate, which resulted in both enhanced ROS contents and decreased NPQ in the vtc-1 mutant.