2018 Vol. 31, No. 4

Content
Contents
2018, 31(4): 0-0.
Chinese abstract
Chinese Abstracts
2018, 31(4): I-Ⅳ.
Editorial
Letter
In this letter, we report a quantitative analysis of how a Pt(Ⅱ) precursor is reduced to atoms at different temperatures for the formation of Pt nanocrystals with different morphologies and sizes. Our results suggest that in the early stage of a synthesis, the Pt(Ⅱ) precursor is reduced to atoms exclusively in the solution phase, followed by homogeneous nucleation to generate nuclei and then seeds. At a relatively low reaction temperature such as 22℃, the growth of the seeds is dominated by autocatalytic surface reduction that involves the adsorption and then reduction of the Pt(Ⅱ) precursor on the surface of the just-formed seeds. This particular growth pathway results in relatively large assemblies of Pt nanocrystals. When the reaction temperature is increased to 100℃, the dominant reduction pathway will be switched from surface to solution phase, producing much smaller assemblies of Pt nanocrystals. Our results also demonstrate that a similar trend applies to the seed-mediated growth of Pt nanocrystals in the presence of Pd nanocubes.
Review
Cells are crowded microenvironments filled with macromolecules undergoing constant physical and chemical interactions. The physicochemical makeup of the cells affects various cellular responses, determines cell-cell interactions and influences cell decisions. Chemical and physical properties differ between cells and within cells. Moreover, these properties are subject to dynamic changes in response to environmental signals, which often demand adjustments in the chemical or physical states of intracellular molecules. Indeed, cellular responses such as gene expression rely on the faithful relay of information from the outside to the inside of the cell, a process termed signal transduction. The signal often traverses a complex path across subcellular spaces with variable physical chemistry, sometimes even influencing it. Understanding the molecular states of such signaling molecules and their intracellular environments is vital to our understanding of the cell. Exploring such intricate spaces is possible today largely because of experimental and theoretical tools. Here, we focus on one tool that is commonly used in chemical physics studies-light. We summarize recent work which uses light to both visualize the cellular environment and also control intracellular processes along the axis of signal transduction. We highlight recent accomplishments in optical microscopy and optogenetics, an emerging experimental strategy which utilizes light to control the molecular processes in live cells. We believe that optogenetics lends unprecedented spatiotemporal precision to the manipulation of physicochemical properties in biological contexts. We hope to use this work to demonstrate new opportunities for chemical physicists who are interested in pursuing biological and biomedical questions.
Capsule catalysts composed of pre-shaped core catalysts and layer zeolites have been widely used in the tandem reactions where multiple continuous reactions are combined into one process. They show excellent catalytic performance in heterogeneous catalysis, including the direct synthesis of middle isoparaffins or dimethyl ether from syngas, as compared to the conventional hybrid catalysts. The present review highlights the recent development in the design of capsule catalysts and their catalytic applications in heterogeneous catalysis. The capsule catalyst preparation methods are introduced in detail, such as hydrothermal synthesis method, dual-layer method, physically adhesive method and single crystal crystallization method. Furthermore, several new applications of capsule catalysts in heterogeneous catalytic processes are presented such as in the direct synthesis of liquefied petroleum gas from syngas, the direct synthesis of para-xylene from syngas and methane dehydroaromatization. In addition, the development in the design of multifunctional capsule catalysts is discussed, which makes the capsule catalyst not just a simple combination of two different catalysts, but has some special functions such as changing the surface hydrophobic or acid properties of the core catalysts. Finally, the future perspectives of the design and applications of capsule catalysts in heterogeneous catalysis are provided.
Molecular dynamics (MD) simulation has become a powerful tool to investigate the structurefunction relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets containing millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape (geometric clustering) and kinetics (kinetic clustering). In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, agglomerative algorithms (single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage), center-based algorithms (K-Means, K-Medoids, K-Centers, and APM), density-based algorithms (neighbor-based, DBSCAN, density-peaks, and Robust-DB), and spectral-based algorithms (PCCA and PCCA+). In particular, differences between geometric and kinetic clustering metrics will be discussed along with the performances of different clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algorithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.
Article
For an energy transfer network, the irreversible depletion of excited electron energy occurs through either an efficient flow into an outer energy sink or an inefficient decay. With a small decay rate, the energy transfer efficiency is quantitatively reflected by the average life time of excitation energy before being trapped in the sink where the decay process is omitted. In the weak dissipation regime, the trapping time is analyzed within the exciton population subspace based on the secular Redfield equation. The requirement of the noise-enhanced energy transfer is obtained, where the trapping time follows an exact or approximate 1/Γ-scaling of the dissipation strength Γ. On the opposite side, optimal initial system states are conceptually constructed to suppress the 1/Γ-scaling of the trapping time and maximize the coherent transfer efficiency. Our theory is numerically testified in four models, including a biased two-site system, a symmetric three-site branching system, a homogeneous onedimensional chain, and an 8-chromophore FMO protein complex.
Intraparticle charge delocalization occurs when metal nanoparticles are functionalized with organic capping ligands through conjugated metal-ligand interfacial bonds. In this study, metal nanoparticles of 5d metals (Ir, Pt, and Au) and 4d metals (Ru, Rh, and Pd) were prepared and capped with ethynylphenylacetylene and the impacts of the number of metal d electrons on the nanoparticle optoelectronic properties were examined. Both FTIR and photoluminescence measurements indicate that intraparticle charge delocalization was enhanced with the increase of the number of d electrons in the same period with palladium being an exception.
The ultraviolet (UV) photodissociation of jet-cooled 1-pentyl radical is investigated in the wavelength region of 236-254 nm using the high-n Rydberg-atom time-of-flight (HRTOF) technique. The H-atom photofragment yield spectrum of the 1-pentyl radical shows a broad UV absorption feature peaking near 245 nm, similar to the 2pz→3s absorption bands of ethyl and n-propyl. The center-of-mass translational energy distribution, P(ET), of the H+C5H10 product channel is bimodal, with a slow peak at~5 kcal/mol and a fast peak at~50 kcal/mol. The fraction of the average translational energy release in the total available energy, 〈fT〉, is 0.30, with those of the slow and fast components being 0.13 and 0.58, respectively. The slow component has an isotropic product angular distribution, while the fast component is anisotropic with an anisotropy parameter~0.4. The bimodal translational energy and angular distributions of the H+C5H10 products indicate two H-atom elimination channels in the photodissociation of 1-pentyl:(i) a direct, prompt dissociation from the electronic excited state and/or the repulsive part of the ground electronic state potential energy surface; and (ii) a unimolecular dissociation of internally hot radical in the ground electronic state after internal conversion from the electronic excited state.
An efficient and accurate method for computing the equilibrium reduced density matrix is presented for treating open quantum systems characterized by the system-bath model. The method employs the multilayer multiconfiguration time-dependent Hartree theory for imaginary time propagation and an importance sampling procedure for calculating the quantum mechanical trace. The method is applied to the spin-boson Hamiltonian, which leads to accurate results in agreement with those produced by the multi-electronic-state path integral molecular dynamics method.
Dissociation of molecular hydrogen (H2) is extensively studied to understand the mechanism of hydrogenation reactions. In this study, H2 dissociation by Au1-doped closed-shell titanium oxide cluster anions AuTi3O7- and AuTi3O8- has been identified by mass spectrometry and quantum chemistry calculations. The clusters were generated by laser ablation and massselected to react with H2 in an ion trap reactor. In the reaction of AuTi3O8- with H2, the ion pair Au+-O22- rather than Au+-O2- is the active site to promote H2 dissociation. This finding is in contrast with the previous result that the lattice oxygen is usually the reactive oxygen species in H2 dissociation. The higher reactivity of the peroxide species is further supported by frontier molecular orbital analysis. This study provides new insights into gold catalysis involving H2 activation and dissociation.
Gaseous dibenzo-7-phosphanorbornadiene P-sulfide anions APS-(A=C14H10 or anthracene) were generated via electrospray ionization, and characterized by magnetic-bottle photoelectron spectroscopy, velocity-map imaging (VMI) photoelectron spectroscopy, and quantum chemical calculations. The electron affinity (EA) and spin-orbit (SO) splitting of the APS· radical are determined from the photoelectron spectra and Franck-Condon factor simulations to be EA=(2.62±0.05) eV and SO splitting=(43±7) meV. VMI photoelectron images show strong and sharp peaks near the detachment threshold with an identical electron kinetic energy (eKE) of 17.9 meV at three different detachment wavelengths, which are therefore assigned to autodetachment from dipole-bound anion states. The B3LYP/6-31++G(d,p) calculations indicate APS· has a dipole moment of 3.31 Debye, large enough to support a dipole-bound electron.
We perform an experimental study on high-order harmonic generation (HHG) of aligned acetylene molecules induced by a 35-fs 800-nm strong laser field, by using a home-built HHG spectrometer. It is observed that the molecular HHG probability declines with increasing the laser ellipticity, which is in consistence with the deduction from the well-known tunneling-plus-rescattering scenario. By introducing a weak femtosecond laser pulse to nonadiabatically align the molecules, we investigated the molecular orbital effect on the HHG in both linearly and elliptically polarized driving laser fields. The results show that the harmonic intensity is maximum for the molecular axis aligned perpendicularly to the laser electric field. It indicates that both the highest occupied molecular orbitals (HOMO) and HOMO-1 contribute to the strong-field HHG of acetylene molecules. Our study should pave the way for understanding the interaction of molecules with ultrafast strong laser fields.
Tryptophan derivatives have long been used as site-specific biological probes. 4-Cyanotryptophan emits in the visible region and is the smallest blue fluorescent amino acid probe for biological applications. Other indole or tryptophan analogs may emit at even longer wavelengths than 4-cyanotryptophan. We performed FTIR, UV-Vis, and steady-state and time-resolved fluorescence spectroscopy on six ester-derivatized indoles in different solvents. Methyl indole-4-carboxylate emits at 450 nm with a long fluorescence lifetime, and is a promising candidate for a fluorescent probe. The ester-derivatized indoles could be used as spectroscopic probes to study local protein environments. Our measurements provide a guide for choosing esterderivatized indoles to use in practice and data for computational modeling of the effect of substitution on the electronic transitions of indole.
Adsorption and dehydrogenation of ethylene on Cu(410) surface are investigated with firstprinciples calculations and micro-kinetics analysis. Ethylene dehydrogenation is found to start from the most stable π-bonded state instead of the previously proposed di-σ-bonded state. Our vibrational frequencies calculations verify the π-bonded adsorption at step sites at low coverage and low surface temperature and di-σ-bonded ethylene on C-C dimer (C2H4-CC) is proposed to be the species contributing to the vibrational peaks experimentally observed at high coverage at 193 K. The presence of C2H4-CC indicates that the dehydrogenation of ethylene on Cu(410) can proceed at temperature as low as 193 K.
Resonance enhancement has been increasingly employed in the emergent femtosecond stimulated Raman spectroscopy (FSRS) to selectively monitor molecular structure and dynamics with improved spectral and temporal resolutions and signal-to-noise ratios. Such joint efforts by the technique-and application-oriented scientists and engineers have laid the foundation for exploiting the tunable FSRS methodology to investigate a great variety of photosensitive systems and elucidate the underlying functional mechanisms on molecular time scales. During spectral analysis, peak line shapes remain a major concern with an intricate dependence on resonance conditions. Here, we present a comprehensive study of line shapes by tuning the Raman pump wavelength from red to blue side of the ground-state absorption band of the fluorescent dye rhodamine 6G in solution. Distinct line shape patterns in Stokes and anti-Stokes FSRS as well as from the low to high-frequency modes highlight the competition between multiple third-order and higher-order nonlinear pathways, governed by different resonance conditions achieved by Raman pump and probe pulses. In particular, the resonance condition of probe wavelength is revealed to play an important role in generating circular line shape changes through oppositely phased dispersion via hot luminescence (HL) pathways. Meanwhile, on-resonance conditions of the Raman pump could promote excited-state vibrational modes which are broadened and red-shifted from the coincident ground-state vibrational modes, posing challenges for spectral analysis. Certain strategies in tuning the Raman pump and probe to characteristic regions across an electronic transition band are discussed to improve the FSRS usability and versatility as a powerful structural dynamics toolset to advance chemical, physical, materials, and biological sciences.
A new potential energy surface (PES) for the atmospheric formation of sulfuric acid from OH+SO2 is investigated using density functional theory and high-level ab initio molecular orbital theory. A pathway focused on the new PES assumes the reaction to take place between the radical complex SO3·HO2 and H2O. The unusual stability of SO3·HO2 is the principal basis of the new pathway, which has the same final outcome as the current reaction mechanism in the literature but it avoids the production and complete release of SO3. The entire reaction pathway is composed of three consecutive elementary steps:(1) HOSO2+O2→SO3·HO2, (2) SO3·HO2+H2O→SO3·H2O·HO2, (3) SO3·H2O·HO2→H2SO4+HO2. All three steps have small energy barriers, under 10 kcal/mol, and are exothermic, and the new pathway is therefore favorable both kinetically and thermodynamically. As a key step of the reactions, step (3), HO2 serves as a bridge molecule for low-barrier hydrogen transfer in the hydrolysis of SO3. Two significant atmospheric implications are expected from the present study. First, SO3 is not released from the oxidation of SO2 by OH radical in the atmosphere. Second, the conversion of SO2 into sulfuric acid is weakly dependent on the humidity of air.
Quantum dots comprise a type of quantum impurity system. The entanglement and coherence of quantum states are significantly influenced by the strong electron-electron interactions among impurities and their dissipative coupling with the surrounding environment. Competition between many-body effects and transfer couplings plays an important role in determining the entanglement among localized impurity spins. In this work, we employ the hierarchical-equations-of-motion approach to explore the entanglement of a strongly correlated double quantum dots system. The relation between the total system entropy and those of subsystems is also investigated.
Electrochemical water splitting requires efficient water oxidation catalysts to accelerate the sluggish kinetics of water oxidation reaction. Here, we designed an efficient Co3O4 electrocatalyst using a pyrolysis strategy for oxygen evolution reaction (OER). Morphological characterization confirmed the ultra-thin structure of nanosheet. Further, the existence of oxygen vacancies was obviously evidenced by the X-ray photoelectron spectroscopy and electron spin resonance spectroscopy. The increased surface area of Co3O4 ensures more exposed sites, whereas generated oxygen vacancies on Co3O4 surface create more active defects. The two scenarios were beneficial for accelerating the OER across the interface between the anode and electrolyte. As expected, the optimized Co3O4 nanosheets can catalyze the OER efficiently with a low overpotential of 310 mV at current density of 10 mA/cm2 and remarkable long-term stability in 1.0 mol/L KOH.
Characterization of conformation kinetics of proteins at the interfaces is crucial for understanding the biomolecular functions and the mechanisms of interfacial biological action. But it requires to capture the dynamic structures of proteins at the interfaces with sufficient structural and temporal resolutions. Here, we demonstrate that a femtosecond sum frequency generation vibrational spectroscopy (SFG-VS) system developed by our group provides a powerful tool for monitoring the real-time peptide transport across the membranes with time resolution of less than one second. By probing the real-time SFG signals in the amide I and amide A bands as WALP23 interacts with DMPG lipid bilayer, it is found that WALP23 is initially absorbed at the gel-phase DMPG bilayer with a random coil structure. The absorption of WALP23 on the surface leads to the surface charge reversal and thus changes the orientation of membrane-bound water. As the DMPG bilayer changes from gel phase into fluid phase, WALP23 inserts into the fluid-phase bilayer with its N-terminal end moving across the membrane, which causes the membrane dehydration and the transition of WALP23 conformation from random coil to mixed helix/loop structure and then to pure α-helical structure. The established system is ready to be employed in characterizing other interfacial fast processes, which will be certainly helpful for providing a clear physical picture of the interfacial phenomena.
Although discovered more than 100 years ago, X-ray source technology has evolved rather slowly. The recent invention of the carbon nanotube (CNT) X-ray source technology holds great promise to revolutionize the field of biomedical X-ray imaging. CNT X-ray sources have been successfully adapted to several biomedical imaging applications including dynamic micro-CT of small animals and stationary breast tomosynthesis of breast cancers. Yet their more important biomedical imaging applications still lie ahead in the future, with the development of stationary multi-source CT as a noteworthy example.
We report the investigation on the low-temperature oxidation of cyclohexane in a jet-stirred reactor over 500-742 K. Synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) was used for identifying and quantifying the oxidation species. Major products, cyclic olefins, and oxygenated products including reactive hydroperoxides and high oxygen compounds were detected. Compared with n-alkanes, a narrow low-temperature window (~80 K) was observed in the low-temperature oxidation of cyclohexane. Besides, a kinetic model for cyclohexane oxidation was developed based on the CNRS model[Combust. Flame 160 , 2319 (2013)], which can better capture the experimental results than previous models. Based on the modeling analysis, the 1,5-H shift dominates the crucial isomerization steps of the first and second O2 addition products in the low-temperature chain branching process of cyclohexane. The negative temperature coefficient behavior of cyclohexane oxidation results from the reduced chain branching due to the competition from chain inhibition and propagation reactions, i.e. the reaction between cyclohexyl radical and O2 and the decomposition of cyclohexylperoxy radical, both producing cyclohexene and HO2 radical, as well as the decomposition of cyclohexylhydroperoxy radical producing hex-5-en-1-al and OH radical.
We have investigated the photoinduced decomposition of formaldehyde (CH2O) on a rutile TiO2(100)-(1×1) surface at 355 nm using temperature-programmed desorption. Products, formate (HCOO-), methyl radical (CH3·), ethylene (C2H4), and methanol (CH3OH) have been detected. The initial step in the decomposition of CH2O on the rutile TiO2(100)-(1×1) surface is the formation of a dioxymethylene intermediate in which the carbonyl O atom of CH2O is bound to a Ti atom at the five-fold-coordinated Ti4+ (Ti5c) site and its carbonyl C atom bound to a nearby bridge-bonded oxygen (Ob) atom, respectively. During 355 nm irradiation, the dioxymethylene intermediate can transfer an H atom to the Ob atom, thus forming HCOO- directly, which is considered as the main reaction channel. In addition, the dioxymethylene intermediate can also transfer methylene to the Ob row and break the C-O bond, thus leaving the original carbonyl O atom at the Ti5c site. After the transfer of methylene, several pathways to products are available. Thus, we have found that Ob atoms are intimately involved in the photoinduced decomposition of CH2O on the rutile TiO2(100)-(1×1) surface.
Gold(I) thiolate compounds (i.e. AuI-SR) are important precursors for the synthesis of atomically precise Aun(SR)m nanoclusters. However, the nature of the AuI-SR precursor remains elusive. Here, we report that the Au10(TBBT)10 complex is a universal precursor for the synthesis of Aun(TBBT)m nanoclusters (where TBBT=4-tertbutylbenzenethiol/thiolate). Interestingly, the Au10(TBBT)10 complex is also found to be re-generated through extended etching of the Aun(SR)m nanoclusters with excess of TBBT thiol and O2. The formation of well-defined Au10(TBBT)10 complex, instead of polymeric AuI-SR, is attributed to the bulkiness of the TBBT thiol. Through 1D and 2D NMR characterization, the structure of Au10(TBBT)10 is correlated with the previously reported X-ray structure, which contains two inter-penetrated Au5(TBBT)5 rings. The photophysical property of Au10(TBBT)10 complex is further probed by femtosecond transient absorption spectroscopy. The accessibility of the precise Au10(TBBT)10 precursor improves the efficiency of the synthesis of the Aun(TBBT)m nanoclusters and is expected to further facilitate excellent control and understanding of the reaction mechanisms of nanocluster synthesis.
The photodissociation dynamics of m-bromofluorobenzene has been experimentally investigated at around 240 nm using the DC-slice velocity map imaging technique. The kinetic energy release spectra and the recoiling angular distributions of fragmented Br(2P3/2) and Br(2P1/2) atoms from photodissociation of m-bromofluorobenzene have been measured at different photolysis wavelengths around 240 nm. The experimental results indicate that two dissociation pathways via (pre-)dissociation of the two low-lying 1ππ* excited states dominate the production process of the ground state Br(2P3/2) atoms. Because of the weak spin-orbit coupling effect among the low-lying triplet and singlet states, the spin-orbit excited Br(2P1/2) atoms are mainly produced via singlet-triplet state coupling in the dissociation step. The similarity between the present results and that recently reported for o-bromofluorobenzene indicates that the substitution position of the fluorine atom does not significantly affect the UV photodissociation dynamics of bromofluorobenzenes.
Dynamics of ammonium and ammonia in solutions is closely related to the metabolism of ammoniac compounds, therefore plays an important role in various biological processes. NMR measurements indicated that the reorientation dynamics of NH4+ is faster in its aqueous solution than in methanol, which deviates from the Stokes-Einstein-Debye rule since water has higher viscosity than methanol. To address this intriguing issue, we herein study the reorientation dynamics of ammonium ion in both solutions using numerical simulation and an extended cyclic Markov chain model. An evident decoupling between translation and rotation of methanol is observed in simulation, which results in the deviation of reorientation from the Stokes-Einstein-Debye rule. Slower hydrogen bond (HB) switchings of ammonium with methanol comparing to that with water, due to the steric effect of the methyl group, remarkably retards the jump rotation of ammonium. The observations herein provide useful insights into the dynamic behavior of ammonium in the heterogeneous environments including the protein surface or protein channels.
The time-convolutionless (TCL) quantum master equation provides a powerful tool to simulate reduced dynamics of a quantum system coupled to a bath. The key quantity in the TCL master equation is the so-called kernel or generator, which describes effects of the bath degrees of freedom. Since the exact TCL generators are usually hard to calculate analytically, most applications of the TCL generalized master equation have relied on approximate generators using second and fourth order perturbative expansions. By using the hierarchical equation of motion (HEOM) and extended HEOM methods, we present a new approach to calculating the exact TCL generator and its high order perturbative expansions. The new approach is applied to the spin-boson model with different sets of parameters, to investigate the convergence of the high order expansions of the TCL generator. We also discuss circumstances where the exact TCL generator becomes singular for the spin-boson model, and a model of excitation energy transfer in the Fenna-Matthews-Olson complex.
Collective behaviours of active particle systems have gained great research attentions in recent years. Here we present a mode-coupling theory (MCT) framework to study the glass transition of a mixture system of active and passive Brownian particles. The starting point is an effective Smoluchowski equation, which governs the dynamics of the probability distribution function in the position phase space. With the assumption of the existence of a nonequilibrium steady state, we are able to obtain dynamic equations for the intermediate scattering functions (ISFs), wherein an irreducible memory function is introduced which in turn can be written as functions of the ISFs based on standard mode-coupling approximations. The effect of particle activity is included through an effective diffusion coefficient which can be obtained via short time simulations. By calculating the long-time limit of the ISF, the Debye-Waller (DW) factor, one can determine the critical packing fraction ηc of glass transition. We find that for active-passive (AP) mixtures with the same particle sizes, ηc increases as the partial fraction of active particle xA increases, which is in agreement with previous simulation works. For system with different active/passive particle sizes, we find an interesting reentrance behaviour of glass transition, i.e., ηc shows a non-monotonic dependence on xA. In addition, such a reentrance behaviour would disappear if the particle activity is large enough. Our results thus provide a useful theoretical scheme to study glass transition behaviour of active-passive mixture systems in a promising way.
Due to photoluminescence intermittency of single colloidal quantum dots (QDs), the traditional exponential fluorescence lifetime analysis is not perfect to characterize QDs' fluorescent emission behavior. In this work we used the time-tagged time-resolved (TTTR) mode to record the fluorescent photons from single QDs. We showed that this method is compatible with the traditional lifetime analysis. In addition, by constructing the trajectory over time and the distribution of average arrival time (AAT) of the fluorescent photons, more details about the emission behavior of QDs were revealed.
Chromophore structures inspired by natural green fluorescent protein (GFP) play an important role in the field of bio-imaging. In this work, photochemical properties of a new class of GFP-like chromophores are investigated using computational approaches. Thermodynamically stable isomers are identified in vacuum and in solvent. Spectral Stokes shifts are computed and compared to experiments. An inverted solvatochromic shift between absorption and emission emerging in this new class of GFP-like chromophores is observed, and attributed to the stabilized charge transfer and inhibited rotational structural reorganization in solvent.
We present a semiclassical (SC) approach for quantum dissipative dynamics, constructed on basis of the hierarchical-equation-of-motion (HEOM) formalism. The dynamical components considered in the developed SC-HEOM are wavepackets' phase-space moments of not only the primary reduced system density operator but also the auxiliary density operators (ADOs) of HEOM. It is a highly numerically efficient method, meanwhile taking into account the high-order effects of system-bath couplings. The SC-HEOM methodology is exemplified in this work on the hierarchical quantum master equation[J. Chem. Phys. 131 , 214111 (2009)] and numerically demonstrated on linear spectra of anharmonic oscillators.