Model Dimer System Research Articles

Coarse-Grained Approach to Simulate Signatures of Excitation Energy Transfer in Two-Dimensional Electronic Spectroscopy of Large Molecular Systems.

Two-dimensional electronic spectroscopy (2DES) has proven to be a highly effective technique in studying the properties of excited states and the process of excitation energy transfer in complex molecular assemblies, particularly in biological light-harvesting systems. However, the accurate simulation of 2DES for large systems still poses a challenge because of the heavy computational demands it entails. In an effort to overcome this limitation, we devised a coarse-grained 2DES method. This method encompasses the treatment of the entire system by dividing it into distinct weakly coupled segments, which are assumed to communicate predominantly through incoherent exciton transfer. We first demonstrate the efficiency of this method through simulation on a model dimer system, which demonstrates a marked improvement in calculation efficiency, with results that exhibit good concordance with reference spectra calculated with less approximate methods. Additionally, the application of this method to the light-harvesting antenna 2 (LH2) complex of purple bacteria showcases its advantages, accuracy, and limitations. Furthermore, simulating the anisotropy decay in LH2 induced by energy transfer and its comparison with experiments confirm that the method is capable of accurately describing dynamical processes in a biologically relevant system. This method presented lends itself to an extension that accounts for the effect of intrasegment relaxation processes on the 2DES spectra, which for computational efficiency are ignored in the implementation reported here. It is envisioned that the method will be employed in the future to accurately and efficiently calculate 2D spectra of more extensive systems, such as photosynthetic supercomplexes.

Transient chiral dynamics revealed by two-dimensional circular dichroism spectroscopy.

Chirality has been considered as one of the key factors in the evolution of life in nature. It is important to uncover how chiral potentials of molecular systems play vital role in fundamental photochemical processes. Here, we investigate the role of chirality in photoinduced energy transfer in a model dimeric system, where the monomers are excitonically coupled. To observe transient chiral dynamics and energy transfer, we employ circularly polarized laser pulses in two-dimensional electronic spectroscopy to construct the two-dimensional circular dichroism (2DCD) spectral maps. Tracking time-resolved peak magnitudes in 2DCD spectra allows one to identify chirality induced population dynamics. The dynamics of energy transfer is revealed by the time-resolved kinetics of cross peaks. However, the differential signal of 2DCD spectra shows the magnitude of cross peaks is dramatically reduced at initial waiting time, which indicates the weak chiral interactions between two monomers. The downhill energy transfer is resolved by presenting a strong magnitude of cross peak in 2DCD spectra after long waiting time. The chiral contribution towards coherent and incoherent energy-transfer pathways in the model dimer system is further examined via control of excitonic couplings between two monomers. Applications are made to study the energy-transfer process in the Fenna-Matthews-Olson complex. Our work uncovers the potential of 2DCD spectroscopy to resolve the chiral-induced interactions and population transfers in excitonically coupled systems.

Correlated driving‐and‐dissipation equation for non‐Condon spectroscopy with the Herzberg–Teller vibronic coupling

AbstractCorrelated driving‐and‐dissipation equation (CODDE) is an optimized complete second‐order quantum dissipation approach, which is originally concerned with the reduced system dynamics only. However, one can actually extract the hybridized bath dynamics from CODDE with the aid of dissipaton‐equation‐of‐motion theory, a statistical quasi‐particle quantum dissipation formalism. Treated as a one–dissipaton theory, CODDE is successfully extended to deal with the Herzberg–Teller vibronic couplings in dipole–field interactions. Demonstrations will be carried out on the non‐Condon spectroscopies of a model dimer system.

Charge transfer via spin flip configuration interaction: Benchmarks and application to singlet fission.

Charge transfer and multi-exciton states are among the most difficult to characterize using electronic structure theories. Previously, restricted active space-spin flip (RAS-SF) methods have been applied to describe multi-exciton states, but these have not yet been shown to be useful for charge-transfer states. Herein, a variant of RAS-SF is introduced to treat charge-transfer states and electronic couplings. This approach relies on partitioning of the full RAS-SF Hamiltonian into charge-transfer and non-charge-transfer blocks, allowing the different types of diabatic states to be resolved in a straightforward fashion. To demonstrate this approach in practice, model dimer systems, intramolecular charge-transfer dyads, and an intramolecular singlet fission system were examined. Being low-cost and relatively accurate, RAS-SF provides important insight into electron transfer pathways in conventional donor-acceptor systems, as well as characterizations of charge transfer mechanisms involving strongly correlated multi-exciton states. Studies of electron transfer from an intramolecular singlet fission chromophore to an anthraquinone acceptor demonstrate the unique capabilities of the proposed RAS-SF method.

Giant Conductance Enhancement of Intramolecular Circuits through Interchannel Gating

Summary For neutral intramolecular circuits with two constitutionally identical branches, a maximum 4-fold increase in total conductance can be obtained according to constructive quantum interference (CQI). For charged intramolecular circuits, however, the strong electrostatic interactions entangle the quantum states of these two parallel pathways, thus introducing complicated transport behavior that warrants experimental investigation of the intramolecular circuit rules. Here, we report that a tetracationic cyclophane with parallel channels exhibits a 50-fold conductance enhancement compared with that of a single-channel control, an observation that supplements intramolecular circuit law in systems with strong Coulombic interactions. Flicker noise measurements and theoretical calculations show that strong electrostatic interactions between charged parallel channels—serving as the chemical gate to promote the effective conductance of each channel—and CQI boosts the total conductance of the two-channel circuit. The molecular design presented herein constitutes a proof-of-principle approach to charged intramolecular circuits that are desirable for quantum circuits and devices.

A 2-D π–π dimer model system to investigate structure-charge transfer relationships in rubrene

A two dimensional π–π model dimer system that will enable researchers to predict charge transport properties for rubrene-based materials using their single crystal π-stacking data.

Excited states and excitonic interactions in prototypic polycyclic aromatic hydrocarbon dimers as models for graphitic interactions in carbon dots.

The study of electronically excited states of stacked polycyclic aromatic hydrocarbons (PAHs) is of great interest due to promising applications of these compounds as luminescent carbon nanomaterials such as graphene quantum dots (GQDs) and carbon dots (CDs). In this study, the excited states and excitonic interactions are described in detail based on four CD model dimer systems of pyrene, coronene, circum-1-pyrene and circum-1-coronene. Two multi-reference methods, DFT/MRCI and SC-NEVPT2, and two single-reference methods, ADC(2) and CAM-B3LYP, have been used for excited state calculations. The DFT/MRCI method has been used as a benchmark method to evaluate the performance of the other ones. All methods produce useful lists of excited states. However, an overestimation of excitation energies and an inverted ordering of states, especially concerning the bright HOMO-LUMO excitation, are observed. In the pyrene-based systems, the first bright state appears among the first four states, whereas the number of dark states is significantly larger for the coronene-based systems. Fluorescence emission properties are addressed by means of geometry optimization in the S1 state. The inter sheet distances for the S1 state decrease in comparison to the corresponding ground-state values. These reductions are largest for the pyrene dimer and decrease significantly for the larger dimers. Several minima have been determined on the S1 energy surface for most of the dimers. The largest variability in emission energies is found for the pyrene dimer, whereas in the other cases a more regular behavior of the emission spectra is observed.

Dissipaton dynamics theory versus quantum master equations

In this review article we present first a comprehensive account on the recently developed the dissipaton-equation-of-motion (DEOM) theory. This is a statistical quasi-particle theory for open quantum systems. It treats not only the quantum dissipative systems of primary interest, but also the hybrid environment dynamics that could be experimentally measurable. On the basis of the exact and nonperturbative DEOM theory, we then revisit some commonly used quantum master equations (QMEs). Traditionally, QMEs are concerned with the reduced system dynamics only. We will elaborate the fact that one can extract the hybridization bath dynamics, even from the second-order QMEs that are actually one-dissipaton theories. Illustrations will be carried out on the Fano interference spectroscopies of a model dimer system, in both the strong and weak optical response regimes.

Signatures of spatially correlated noise and non-secular effects in two-dimensional electronic spectroscopy.

We investigate how correlated fluctuations affect oscillatory features in rephasing and non-rephasing two-dimensional (2D) electronic spectra of a model dimer system. Based on a beating map analysis, we show that non-secular environmental couplings induced by uncorrelated fluctuations lead to oscillations centered at both cross- and diagonal-peaks in rephasing spectra as well as in non-rephasing spectra. Using an analytical approach, we provide a quantitative description of the non-secular effects in terms of the Feynman diagrams and show that the environment-induced mixing of different inter-excitonic coherences leads to oscillations in the rephasing diagonal-peaks and non-rephasing cross-peaks. We demonstrate that as correlations in the noise increase, the lifetime of oscillatory 2D signals is enhanced at rephasing cross-peaks and non-rephasing diagonal-peaks, while the other non-secular oscillatory signals are suppressed. We discuss that the asymmetry of 2D lineshapes in the beating map provides information on the degree of correlations in environmental fluctuations. Finally we investigate how the oscillatory features in 2D spectra are affected by inhomogeneous broadening.

Exploring structure based charge transport relationships in phenyl diketopyrrolopyrrole single crystals using a 2D π–π dimer model system

Two dimensional π–π model dimer system will enable researchers to predict charge transport properties for phenyl-based diketopyrrolopyrroles using their single crystal π-stacking data.

Intermolecular Interactions and Energetics in the Crystalline π–π Stacks and Associated Model Dimer Systems of Asymmetric Halogenated Diketopyrrolopyrroles

Four novel structurally analogous asymmetric, halogenated N-benzyl substituted diketopyrrolopyrroles (DPP) have been synthesized, and their crystal structures obtained. All four crystal structures exhibit π–π stacks with very small displacements along their short molecular axes, which based upon our previous studies involving symmetrical DPPs is a characteristic of N-benzyl substitution. Intermolecular interaction energies were computed for extracted crystal π–π dimer pairs by means of M06-2X density functional at the 6-311G(d) level to investigate the most energetically favored position of the halogen atoms in FBDPP and ClBDPP structures. In addition, effective stabilization energies arising from both benzyl and halogen substitution in these derivatives and in BrBDPP and IBDPP π–π dimer pairs were determined in order to probe the impact of these groups on the resulting dimer stability. Effects of the intermonomer displacements along the long molecular axis, which have been shown by us previously to signi...

Effects of Different Quantum Coherence on the Pump-Probe Polarization Anisotropy of Photosynthetic Light-Harvesting Complexes: A Computational Study.

Observations of oscillatory features in the 2D spectra of several photosynthetic complexes have led to diverged opinions on their origins, including electronic coherence, vibrational coherence, and vibronic coherence. In this work, effects of these different types of quantum coherence on ultrafast pump-probe polarization anisotropy are investigated and distinguished. We first simulate the isotropic pump-probe signal and anisotropy decay of the Fenna-Matthews-Olson (FMO) complex using a model with only electronic coherence at low temperature and obtain the same coherence time as in the previous experiment. Then, three model dimer systems with different prespecified quantum coherence are simulated, and the results show that their different spectral characteristics can be used to determine the type of coherence during the spectral process. Finally, we simulate model systems with different electronic-vibrational couplings and reveal the condition in which long time vibronic coherence can be observed in systems like the FMO complex.

Intramolecular radiationless transitions dominate exciton relaxation dynamics

Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems inevitably generate exciton superposition states observable by two-dimensional electronic spectroscopy. Here we report a careful photophysical characterization of a model dimer system, a diacetylene-linked perylenediimide dimer to examine that issue. The absorption spectrum of the dimer shows molecular exciton splitting, indicating that excitation is delocalized. The assignment of exciton states was supported by other photophysical measurements as well as theoretical calculations. Ultrafast two-dimensional electronic spectroscopy was employed to identify and characterize excitonic and vibrational features, as they evolve over time. Population transfer between the two exciton states is found to happen in <50fs, thus preventing the sustainment of exciton coherences. We show that such fast radiationless relaxation cannot be explained by coupling to a solvent spectral density and is therefore missed by standard approaches such as Redfield theory and the hierarchical equations of motion.

Coherent versus incoherent excitation energy transfer in molecular systems

We investigate the Markovian limit of a polaronic quantum master equation for coherent resonance energy transfer proposed recently by Jang et al. [J. Chem. Phys. 129, 101104 (2008)]. An expression for the rate of excitation energy transfer (EET) is derived and shown to exhibit both coherent and incoherent contributions. We then apply this theory to calculated EET rates for model dimer systems, and demonstrate that the small-polaron approach predicts a variety of dynamical behaviors. Notably, the results indicate that the EET dynamical behaviors can be understood by the interplay between noise-assisted EET and dynamical localization, while both are well captured by the polaron theory. Finally, we investigate bath correlation effects on the rate of EET and show that bath correlations (or anti-correlations) can either enhance or suppress EET rate depending on the strength of individual system-bath couplings. In summary, we introduce the small-polaron approach as an intuitive physical framework to consolidate our understanding of EET dynamics in the condensed phase.

An Efficient N(3)-Scaling Propagation Scheme for Simulating Two-Dimensional Infrared and Visible Spectra.

In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system. This is needed for calculating the third-order response functions governing the two-dimensional infrared and visible spectra. The method is tested on a model dimer system, the amide I spectrum of the Gramicidin A antimicrobial peptide, the spectrum of the OH stretching vibration of bulk water, and a homogeneous J-aggregate. Errors due to the approximation are hardly observable in the calculated spectra. Scaling simulations with different system sizes are used to demonstrate that the new scheme is indeed scaling with the system size to the third power, one order faster than the existing methods.

How Different Are Aromatic π Interactions from Aliphatic π Interactions and Non-π Stacking Interactions?

We compare aromatic π interactions with aliphatic π interactions of double- and triple-bonded π systems and non-π stacking interactions of single-bonded σ systems. The model dimer systems of acetylene (C2H2)2, ethylene (C2H4)2, ethane (C2H6)2, benzene (C6H6)2, and cyclohexane (C6H12)2 are investigated. The ethylene dimer has large dispersion energy, while the acetylene dimer has strong electrostatic energy. The aromatic π interactions are strong with particularly large dispersion and electrostatic energies, which would explain why aromatic compounds are frequently found in crystal packing and molecular self-engineering. It should be noted that the difference in binding energy between the benzene dimer (aromatic-aromatic interactions) and the cyclohexane dimer (aliphatic-aliphatic interactions) is not properly described in most density functionals.

Communication: Exciton–phonon information flow in the energy transfer process of photosynthetic complexes

Non-Markovian and nonequilibrium phonon effects are believed to be key ingredients in the energy transfer in photosynthetic complexes, especially in complexes which exhibit a regime of intermediate exciton-phonon coupling. In this work, we utilize a recently developed measure for non-Markovianity to elucidate the exciton-phonon dynamics in terms of the information flow between electronic and vibrational degrees of freedom. We study the measure in the hierarchical equation of motion approach which captures strong coupling effects and nonequilibrium molecular reorganization. We propose an additional trace distance measure for the information flow that could be extended to other master equations. We find that for a model dimer system and for the Fenna-Matthews-Olson complex the non-Markovianity is significant under physiological conditions.

Single-Molecule Spectroscopy of Intramolecular Electron Transfer in Donor-Bridge-Acceptor Systems

It is widely appreciated that single-molecule spectroscopy (SMS) can be used to measure properties of individual molecules which would normally be obscured in an ensemble-averaged measurement. In this article, we show how SMS can be used to investigate intramolecular electron transfer (IET) processes in model dimer systems composed of two perylene chromophores connected via an adjustable bridge. The fluorescence behaviors of a large number of molecules are cataloged and the results statistically analyzed to gauge information about the range of behaviors of the ensemble. Single-molecule fluorescence time trajectories reveal “blinks”, momentary losses in fluorescence (>20 ms to seconds in duration), which are attributed to discrete IET excursions to the charge-separated (CS) state. We find that fluorescence blinking behavior is dependent on bridge length and chromophore geometry, which affect the electronic coupling and therefore the IET. The statistical trends observed in this analysis are used to corroborate the assignment of the blinking behavior to IET. These results and methodology have implications for molecular electronics, where understanding and controlling the range of possible behaviors inherent to molecular systems will likely be as important as understanding the individual behavior of any given molecule.

A Study on Hydrogen-Bonded Network Structure of Polybenzoxazines

The hydrogen-bonded network structure for polybenzoxazines is investigated by Fourier Transform Infrared Spectroscopy (FT-IR) with model dimer systems. Comparing the FT-IR spectra of the polybenzoxazines and model dimers, it is shown that the simpler structures of asymmetric dimers well simulate the hydrogen-bonded network structure between polymer chains while the structures of symmetric dimers reflect the hydrogen bonding scheme related to the end-groups of polymer chains. It is confirmed that the amine functional group in the Mannich bridge is greatly responsible for the distribution of hydrogen bonding species. Bisphenol A/methylamine-based polymer (BA-m) mainly consists of −OH···N intramolecular hydrogen bonding while bisphenol A/aniline-based polymer (BA-a) has a large amount of intermolecular hydrogen bonding and relatively weak hydrogen bonding groups in the polymer network structure. The possible network structure, in the sense of hydrogen bonding, for BA-m and BA-a polymers is proposed and a gen...