Intramolecular Vibrations Research Articles

Exciton transfer using rates extracted from the "hierarchical equations of motion".

Frenkel exciton population dynamics of an excitonic dimer is studied by comparing the results from a quantum master equation involving rates from second-order perturbative treatment with respect to the excitonic coupling with the non-perturbative results from "Hierarchical Equations of Motion" (HEOM). By formulating generic Liouville-space expressions for the rates, we can choose to evaluate them either via HEOM propagations or by applying the cumulant expansion. The coupling of electronic transitions to bath modes is modeled either as overdamped oscillators for the description of thermal bath components or as underdamped oscillators to account for intramolecular vibrations. Cases of initial nonequilibrium and equilibrium vibrations are discussed. In the case of HEOM, initial equilibration enters via a polaron transformation. Pointing out the differences between the nonequilibrium and equilibrium approach in the context of the projection operator formalism, we identify a further description, where the transfer dynamics is driven only by fluctuations without involvement of dissipation. Despite this approximation, this approach can also yield meaningful results in certain parameter regimes. While for the chosen model, HEOM has no technical advantage for evaluation of the rate expressions compared to cumulant expansion, there are situations where only evaluation with HEOM is applicable. For instance, a separation of reference and interaction Hamiltonian via a polaron transformation to account for the interplay between Coulomb coupling and vibrational oscillations of the bath at the level of a second-order treatment can be adjusted for a treatment with HEOM.

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5–18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Ultrafast investigation of intramolecular proton transfer dynamics and vibration relaxation in 1,8-dihydroxyanthraquinone

Photoinduced dynamics of excited-state intramolecular proton transfer (ESIPT) and vibration relaxation (VR) of 1,8-DHAQ in ethanol are investigated by time-resolved transient absorption spectroscopy combined with the quantum chemical calculations. Experimental and calculated results show dual fluorescence is obtained from the S1 state of the normal form of 9,10-quinone and the tautomer form of 1,10-quinone. Three characteristic bands of excited state absorption and stimulated emission are observed in transient absorption spectroscopy upon excitation with ultrafast laser pulses at 390 nm. ESIPT process happens within 96.8 fs from the normal S1 state to the tautomer S1 state, and the VR process is observed in the time constant of 4.1 ps. Ultimately, the tautomer S1 state decays within 269.1 ps for a deactivation pathway of emitting fluorescence. The mechanism of ESIPT dynamics and ultrafast excited-state dynamics in 1,8-DHAQ in ethanol is concluded by a schematic diagram of four electronic states and vibrational energy levels.

Real-Time Path Integral Simulation of Exciton-Vibration Dynamics in Light-Harvesting Bacteriochlorophyll Aggregates.

The mechanism of excitation energy transfer in photoexcited bacteriochlorophyll (BChl) aggregates poses intriguing questions, which have important implications for the observed efficiency of photosynthesis. We investigate this process through fully quantum mechanical calculations of exciton-vibration dynamics in chains and rings of BChl a molecules, with parameters characterizing the B850 ring of the LH2 complex of photosynthetic bacteria. The calculations are performed using the modular path integral methodology, which allows the exact treatment of 50 intramolecular vibrations on each pigment using parameters obtained from spectroscopic Huang-Rhys factors with computational effort that scales linearly with aggregate length. Our results indicate that the interplay between electronic and vibrational time scales leads to the rapid suppression but not the overdamping of electronic coherence, which facilitates the spreading of excitation energy throughout the aggregate.

INFLUENCE OF PRESSURE ON STRUCTURAL, ELECTRONIC, AND OPTICAL PROPERTIES OF CHOLINE IODIDE

The influence of pressure on structural, electronic, and optical properties of choline iodide is studied within the density functional theory approach using the РВЕ gradient functional, the D3(BJ) dispersion correction, and a basis set of localized orbitals. Elastic constants, parameters of the Birch–Murnaghan equation of state, density of electronic states, and frequencies of normal longwave vibrations are calculated. It is shown that the immediate environment of the iodine atom contains 12 carbon atoms with the shortest O–H⋯I distance equal to 2.486 A. The О–H distance increases slightly together with pressure, and the I–H distance decreases while its linear modulus is an order of magnitude smaller than the bulk modulus under 97 GPa. In contrast to intramolecular vibrations, the pressure shifts of lattice vibrations exceed 10 cm–1/GPa, and their modal Gruneisen parameters are an order of magnitude larger.

Absorption and Circular Dichroism Spectra of Molecular Aggregates With the Full Cumulant Expansion.

The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic techniques such as linear absorption and circular dichroism. To compare calculated Hamiltonians to experiments, a lineshape theory is needed, which takes into account the coupling of the excitons with inter- and intramolecular vibrations. This coupling is normally introduced in a perturbative way through the cumulant expansion formalism and further approximated by assuming a Markovian exciton dynamics, for example with the modified Redfield theory. Here, we present the implementation of the full cumulant expansion (FCE) formalism (J. Chem. Phys.142, 2015, 09410625747060) to efficiently compute absorption and circular dichroism spectra of molecular aggregates beyond the Markov approximation, without restrictions on the form of exciton–phonon coupling. By employing the LH2 system of purple bacteria as a challenging test case, we compare the FCE lineshapes with the Markovian lineshapes obtained with the modified Redfield theory, showing that the latter presents a less satisfying agreement with experiments. The FCE approach instead accurately describes the lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the FCE approach will become a valuable tool for accurately comparing model exciton Hamiltonians with optical spectroscopy experiments.

In Situ Controllable Generation of Copper Nanoclusters Confined in a Poly-l-Cysteine Porous Film with Enhanced Electrochemiluminescence for Alkaline Phosphatase Detection.

Copper nanoclusters (Cu NCs) as emerging luminescent metal NCs are gaining increasing attention owing to the comparatively low cost and high abundance of the Cu element in nature. However, it remains challenging to manipulate the optical properties of Cu NCs. Unlike most dispersed Cu NCs, whose luminescence efficiency was restricted by nonexcited relaxation, the Cu NCs confined in a porous poly-l-cysteine (poly-l-Cys) film were generated controllably with enhanced electrochemiluminescence (ECL) by in situ electrochemical reduction. Specifically, poly-l-Cys provided a porous structure to regulate the generation of Cu NCs within its holes, which not only increased the restriction on the intramolecular vibration and rotation of the ligands but also expedited the electron transfer near the electrode surface, reflecting in an enhancement of the ECL signal and efficiency. As an application of the confined Cu NCs, an ECL biosensor with high performance was constructed skillfully for highly sensitive detection of alkaline phosphatase (ALP), which adopted Cu NCs as the ECL luminophore and poly-l-Cys as a coreaction accelerator in a novel ECL ternary system (Cu NCs/S2O82-/poly-l-Cys). Furthermore, an ingenious target amplification based on the combination of a DNA walker and click chemistry was developed to convert ALP to DNA strands efficiently, achieving great improvement in the recognition efficiency. As a result, the biosensor had a low detection limit (9.5 × 10-7 U·L-1) and a wide linear range (10-8-10-2 U·L-1) for ALP detection, which showed great promise for the detection of non-nucleic acid targets and the diagnosis of diseases.

Primary Electronic and Vibrational Dynamics of Cytochrome c Observed by Sub-10 fs NUV Laser Pulses.

The primary reaction mechanism of cytochrome c (Cyt c) was elucidated for two redox forms of ferric (oxidized) and ferrous (reduced) Cyt c by measuring their transient absorption (TA) spectra using a homemade sub-10 fs broadband NUV laser pulses system. The TA traces measured in the broad probe wavelength region were analyzed by the global analysis method to study the electronic dynamics. The difference of relaxation dynamics dependent on the excitation bandwidth enabled us to elucidate that the 2.5 ps component in ferrous Cyt c can be assigned to intramolecular vibration energy redistribution and not to vibrational cooling, which was not clear until this work. The temporal resolution of 10 fs observes TA signal modulation caused by the molecular vibration in the time domain, which can be used to calculate the instantaneous frequency of the molecular vibration mode. The observed vibrational dynamics has visualized that the heme structure changes in 0.8 ps for ferric Cyt c and in >1.0 ps for ferrous Cyt c. These estimated lifetimes of vibrational dynamics reflect vibrational relaxation in the ground state of ferric Cyt c and electronic transition from the S2 state to the S1 state in ferrous Cyt c, respectively.

Vibrational decoherence induced by ultrafast intramolecular charge separation of an asymmetric bianthryl derivative.

Coherent wavepacket oscillation accompanying the ultrafast photoexcited intramolecular charge separation (CS) of 9,9'-bianthryl (BA) and 10-cyano-9,9'-bianthryl (CBA) in a room temperature ionic liquid, N,N-diethyl-N-methyl-N-(methoxyethyl)ammonium tetrafluoroborate (DemeBF4), was investigated by femtosecond time-resolved transient absorption spectroscopy. The frequency of the coherent oscillation observed for CBA in nonpolar n-hexane solution (Hex) was 377 cm-1, while this oscillation was undetectable in DemeBF4. For BA in DemeBF4, coherent oscillation with a frequency of 394 cm-1 was observed, which is similar to that for CBA in Hex. CS of CBA occurs in the ultrashort time range of ≤100 fs, while that of BA occurs in a few picosecond range [E. Takeuchi et al., J. Phys. Chem. C 120, 14502-14512 (2016)]. Hence, the oscillation of CBA in Hex and that of BA in DemeBF4 are assigned to the molecular vibration in the locally excited state, while this oscillation dephases instantaneously for CBA in DemeBF4 due to the ultrafast CS and no oscillation was generated in the CS state. This result suggests that the CS reaction is not mediated by a specific intramolecular vibration in the CS state but occurs incoherently through higher levels of multiple vibrational modes.

Molecule-photon interactions in phononic environments

Molecules constitute compact hybrid quantum optical systems that can interface photons, electronic degrees of freedom, localized mechanical vibrations and phonons. In particular, the strong vibronic interaction between electrons and nuclear motion in a molecule resembles the optomechanical radiation pressure Hamiltonian. While molecular vibrations are often in the ground state even at elevated temperatures, one still needs to get a handle on decoherence channels associated with phonons before an efficient quantum optical network based on opto-vibrational interactions in solid-state molecular systems could be realized. As a step towards a better understanding of decoherence in phononic environments, we take here an open quantum system approach to the non-equilibrium dynamics of guest molecules embedded in a crystal, identifying regimes of Markovian versus non-Markovian vibrational relaxation. A stochastic treatment based on quantum Langevin equations predicts collective vibron-vibron dynamics that resembles processes of sub- and superradiance for radiative transitions. This in turn leads to the possibility of decoupling intramolecular vibrations from the phononic bath, allowing for enhanced coherence times of collective vibrations. For molecular polaritonics in strongly confined geometries, we also show that the imprint of opto-vibrational couplings onto the emerging output field results in effective polariton cross-talk rates for finite bath occupancies.

Sub-picosecond to Sub-nanosecond Vibrational Energy Transfer Dynamics in Pentaerythritol Tetranitrate.

The time scale associated with shock-induced detonation is a key property of energetic materials that remains poorly understood. Herein, we test aspects of one potential mechanism, the phonon up-pumping mechanism, where shock compression excites lattice phonon modes, transferring energy to intramolecular vibrations leading to chemical bond cleavage and reaction. Using ultrafast infrared pump-probe spectroscopy on pentaerythritol tetranitrate (PETN), we reveal sub-picosecond vibrational energy transfer (VET) from the photoexcited band at 1660 cm-1 into every other infrared-active mode in the probed frequency range 800-1800 cm-1. Energy transfer processes remain incomplete at 150 ps. Computational predictions from density functional theory are used in tandem to elucidate VET pathways in PETN.

Coupling of three intramolecular vibration modes of liquid H2O molecules in the framework of the fluctuation theory of hydrogen bonding.

Vibrational spectra of liquid water contain a wealth of information about its structure and dynamics but there are no generally acknowledged interpretation of their band profiles, unfortunately. We have tried to calculate them taking into account only the coupling of three intramolecular vibrations in the set of H2O molecules with different initial oscillator frequencies and intensities. The matter is that each water molecule forms hydrogen bonds of different strengths; thus the OH stretching band spans several hundreds of wave numbers (the fluctuation theory of hydrogen bonding). This distribution overlaps with the similar band of the first overtone of the HOH bending frequencies thus triggering a Fermi resonance between three vibrations. There were some problems causing some simplifications in previous theoretical modeling of vibrational transitions in condensed water. To solve them we extract the statistical distribution of OH frequencies of H2O molecules directly from the experimental spectra of HOD molecules at the same conditions instead of defining it theoretically. Also the bending overtone is allowed to have non-zero intrinsic intensity when calculating the Fermi resonance. The test calculation of the isotropic component of the Raman spectrum which is most critical for interpretation shows that our algorithm can reproduces the characteristic peculiarities of the experiment. The spectrum consists of three non-Gaussian contours. The overtone of bending vibration, being strengthened by Fermi resonance, makes the greatest contribution to the dominating low-frequency spectrum component that was previously attributed to intermolecular coupling of adjacent OH oscillators by some authors. Further we plan to calculate similar band profiles in the IR and also Raman isotropic and anisotropic spectra of Н2О and D2О molecules within a wide temperature range for their quantitative comparison with experiment.

Effects of intramolecular vibrations on excitation energy transfer dynamics of the Fenna-Matthews-Olson complex

The role of vibrational coherence in photosynthetic pigment-proteins has been controversial. The present article investigates theoretically how the intramolecular vibrations of bacteriochlorophyll (BChl) influence the excitation energy transfer (EET) dynamics in the Fenna-Matthews-Olson complex (FMO). To this end, we use an exciton model incorporating recent experimental data and treat the vibrations as both coherent and incoherent. We simulate the transfer phenomena numerically with non-Markovian quantum dynamics. Our results at 300 K indicate that incoherent vibrations can moderately improve the efficiency of EET between FMO and a reaction center. With a vibronic model, we show that the coherent vibrations in either strongly or resonantly coupled BChl pairs can generate characteristic oscillations in their electronic populations which persist for several picoseconds even at 300 K. Despite such robust coherences, no significant improvement in the efficiency of EET is observed.

Modular path integral for finite-temperature dynamics of extended systems with intramolecular vibrations.

The modular decomposition of the path integral is a linear-scaling, numerically exact algorithm for calculating dynamical properties of extended systems composed of multilevel units with local couplings. In a recent article, we generalized the method to wavefunction propagation in aggregates characterized by non-diagonal couplings between adjacent units. Here, we extend the method to the calculation of reduced density matrices in aggregates where each unit includes an arbitrary number of coupled harmonic bath modes, which may describe intramolecular normal mode vibrations, at finite temperature. The effects of harmonic modes are included through influence functional factors, which involve analytical expressions that we derive. Representative applications to spin arrays described by the Heisenberg Hamiltonian with dissipative interactions and to J-aggregates of perylene bisimide, where all coupled normal modes are treated explicitly, are presented.

Raman spectroscopy of captopril crystals under low-temperature conditions.

The polymorphism is a characteristic of several active principles, and can affect the bioavailability of a drug. Among the drugs used in the treatment of heart diseases, captopril is one of the most widely used in the world. Despite the knowledge of vibrational properties of captopril under high temperature and under high pressure, a lack of information impedes the understanding of the substance in the crystal form at low temperatures. In this research, we investigated the vibrational properties of captopril crystals under cryogenic conditions in the 300-8K interval using Raman spectroscopy. By observing the behavior of the inter- and intra-molecular vibrations it was possible to infer that the captopril molecules suffered a rearranging into the unit cell due slight orientational changes mainly involving CH⋯O hydrogen bonds. The phenomenon occurs in a large temperature range. However, the observed changes do not suggest the occurrence of a structural phase transition and the Raman spectra indicate that the trans conformation is recorded down to the lowest temperature available in the experiments.

Quantum yield and energy efficiency of photoinduced intramolecular charge separation.

Kinetics of photoinduced intramolecular charge separation (CS) and the ensuing ultrafast charge recombination (CR) in electron-donor-acceptor dyads are studied numerically, taking into account the excitation of charge-transfer active intramolecular vibrations and multiple relaxation time scales of the surrounding polar solvent. Both energetic and dynamic properties of intramolecular and solvent reorganization are considered, and their influence on the CS/CR kinetics and quantum yield of ultrafast CS is explored. Particular attention is paid to the energy efficiency of CS, as one of the most important parameters indicating the promise of using a molecular compound as a basis for emerging optoelectronic devices. The CS quantum yield and the energy efficiency of CS are shown to depend differently on the key model parameters. Necessary conditions for the highly efficient CS are evaluated using analytic formulae for the electron transfer rates and derived from numerical simulation data. The reasons why low-exergonic CS taking place in the Marcus normal region can be much slower than CR in the deep inverted region are discussed.

The Limit of Spin Lifetime in Solid-State Electronic Spins.

The development of spin qubits for quantum technologies requires their protection from the main source of finite-temperature decoherence: atomic vibrations. Here we eliminate one of the main barriers to the progress in this field by providing a complete first-principles picture of spin relaxation that includes up to two-phonon processes. Our method is based on machine learning and electronic structure theory and makes the prediction of spin lifetime in realistic systems feasible. We study a prototypical vanadium-based molecular qubit and reveal that the spin lifetime at high temperature is limited by Raman processes due to a small number of THz intramolecular vibrations. These findings effectively change the conventional understanding of spin relaxation in this class of materials and open new avenues for the rational design of long-living spin systems.

2D Inorganic Bimolecular Crystals with Strong In-Plane Anisotropy for Second-Order Nonlinear Optics.

2D inorganic bimolecular crystals, consisting of two different inorganic molecules, are expected to possess novel physical and chemical properties due to the synergistic effect of the individual components. However, 2D inorganic bimolecular crystals remain unexploited because of the difficulties in preparation arising from non-typical layered structures and intricate intermolecular interactions. Here, the synthesis of 2D inorganic bimolecular crystal SbI3 ·3S8 nanobelts via a facile vertical microspacing sublimation strategy is reported. The as-synthesized SbI3 ·3S8 nanobelts exhibit strong in-plane anisotropy of phonon vibrations and intramolecular vibrations as well as show anisotropic light absorption with a high dichroism ratio of 3.9. Furthermore, it is revealed that the second harmonic generation intensity of SbI3 ·3S8 nanobelts is highly dependent on the excitation wavelength and crystallographic orientation. This work can inspire the growth of more 2D inorganic bimolecular crystals and excite potential applications for bimolecular optoelectronic devices.

Effect of Fe (III) on L-asparagine monohydrate investigated under low- and high-temperature conditions.

Raman spectra of Fe-doped L-asparagine monohydrate (LAM:Fe) crystal were studied under several temperatures varying from 17 to 490K. The effect of Fe (III) ion on the stability of the crystal in changing temperature through the vibrational spectra was discussed. The behavior of inter and intra-molecular vibration modes has indicated two phase transitions and an amorphous transformation. These effects were also clarified by X-ray powder diffraction measurements which corroborate very well the Raman data. In addition, we have determinated the lattice parameters of all phases and verified that under low temperature conditions the crystal undergoes a conformational transition whereas under high temperatures its structure transforms from the orthorhombic (P212121-space group) to the monoclinic (P21-space group) symmetry and, after this process, it goes to an amorphous phase due to the start of the decomposition. Finally, differential scanning calorimetry analysis was utilized as complementary technique to investigate the structural stability of LAM:Fe and results are in a good agreement with the Raman and the X-ray diffraction data.

Transformation of terahertz vibrational modes of cytosine under hydration

Cytosine and cytosine monohydrate are representative biomolecules for investigating the effect of hydrogen bonds in deoxyribonucleic acid. To better understand intermolecular interactions, such as hydrogen bonds, between nucleobases it is necessary to identify the low-frequency vibrational modes associated with intermolecular interactions and crystalline structures. In this study, we investigated the characteristic low-frequency vibrational modes of cytosine and cytosine monohydrate using terahertz time-domain spectroscopy (THz-TDS). The crystal geometry was obtained by the powder X-ray diffraction technique. The optimized atomic positions and the normal modes in the terahertz region were calculated using density functional theory (DFT), which agreed well with the experimental results. We found that overall terahertz absorption peaks of cytosine and cytosine monohydrate consist of collective vibrations mixed with intermolecular and intramolecular vibrations in mode character analysis, and that the most intense peaks of both samples involve remarkable intermolecular translational vibration. These results indicate that THz-TDS combined with DFT calculations including mode character analysis can be an effective method for understanding how water molecules contribute to the characteristics of the low-frequency vibrational modes by intermolecular vibrations with hydrogen bonding in biological and biomedical applications.