Excited-state Dynamics Simulations Research Articles

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications.

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

Self-trapping of excitons, violation of Condon approximation, and efficient fluorescence in conjugated cycloparaphenylenes.

Cycloparaphenylenes, the simplest structural unit of armchair carbon nanotubes, have unique optoelectronic properties counterintuitive in the class of conjugated organic materials. Our time-dependent density functional theory study and excited state dynamics simulations of cycloparaphenylene chromophores provide a simple and conceptually appealing physical picture explaining experimentally observed trends in optical properties in this family of molecules. Fully delocalized degenerate second and third excitonic states define linear absorption spectra. Self-trapping of the lowest excitonic state due to electron-phonon coupling leads to the formation of spatially localized excitation in large cycloparaphenylenes within 100 fs. This invalidates the commonly used Condon approximation and breaks optical selection rules, making these materials superior fluorophores. This process does not occur in the small molecules, which remain inefficient emitters. A complex interplay of symmetry, π-conjugation, conformational distortion and bending strain controls all photophysics of cycloparaphenylenes.

New developments in first-principles excited-state dynamics simulations: unveiling the solvent specificity of excited anionic cluster relaxation and electron solvation

Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I− (Solv)n]*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I− (Solv)n]* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I− (Solv)n]* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I− (Solv)n]* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.

Photorelaxation induced by water-chromophore electron transfer.

Relaxation of photoexcited chromophores is a key factor determining diverse molecular properties, from luminescence to photostability. Radiationless relaxation usually occurs through state intersections caused by distortions in the nuclear geometry of the chromophore. Using excited-state nonadiabatic dynamics simulations based on algebraic diagrammatic construction, it is shown that this is the case of 9H-adenine in water cluster, but not of 7H-adenine in water cluster. 7H-adenine in water cluster relaxes via a state intersection induced by electron transfer from water to the chromophore. This result reveals an unknown reaction pathway, with implications for the assignment of relaxation mechanisms of exciton relaxation in organic electronics. The observation of photorelaxation of 7H-adenine induced by water-chromophore electron transfer is a proof of principle calling for further computational and experimental investigations to determine how common this effect is.

Dynamics simulations of photoinduced proton transfer reactions of 2-(2′-hydroxyphenyl)benzoxazole in the gas phase and its hydrated clusters

The excited-state dynamics simulations of 2-(2′-hydroxyphenyl)benzoxazole (HBO) and hydrated HBO were performed on their lowest energy structures using RI-ADC(2)/SVP-SV(P). For free HBO, only syn-HBO can undergo tautomerization in the excited state. For HBO(H2O), two different pathways (A) the excited-state intramolecular proton transfer (PT) and (B) the excited-state intermolecular PT through hydrogen-bonded network occur. PT time of free HBO is ultrafast at 28fs, whereas, the PT time of HBO(H2O) takes longer with time range of 43–193fs depending on the initial structure. The slow PT process of HBO(H2O) is caused by competition between formations of intra- and intermolecular hydrogen bonds.

Steering the excited state dynamics of a photoactive yellow protein chromophore analogue with external electric fields

The first excited state of the Photoactive Yellow Protein chromophore exhibits a strong charge transfer character and the dipole moments of the excited and ground states differ significantly. Furthermore, the excited state charge distribution changes during the isomerization of this chromophore. These observations suggest that external electric fields can be used to control photo-isomerization, providing a new concept for developing photochromic devices, such as e-paper or optical memory. To test this idea, we performed excited state dynamics simulations and static calculations of a PYP chromophore analogue (pCK−) in an external electric field. By adjusting direction and strength of the field, we were able to control both selectivity (i.e., which bond isomerizes) and efficiency (excited state lifetime) of the isomerization process. Simulations like these could potentially be useful in validating whether a given chromophore could be suitable for electrochromic applications.

Direct Simulation of Excited-State Intramolecular Proton Transfer and Vibrational Coherence of 10-Hydroxybenzo[h]quinoline in Solution

We investigate an ultrafast excited-state intramolecular proton transfer (ESIPT) reaction and the subsequent coherent vibrational motion of 10-hydroxybenzo[h]quinoline in cyclohexane by the electronically embedded multiconfiguration Shepard interpolation method, which enables us to generate the potential energy surface of the reaction effectively and thus carry out a direct excited-state dynamics simulation with low computational costs. The calculated time scale of the ESIPT and the frequencies and lifetimes of coherent motions are in good agreement with the experimental results. The present study reveals that the coherent motions are caused by not only the proton transfer itself but also the backbone displacement induced by the ESIPT. We also discuss the effects of the solvent on the dynamics of the coherent vibrational modes.

Observation of breather excitons and soliton in a substituted polythiophene with a degenerate ground state

We investigated the ultrafast dynamics of a unique polythiophene derivative that has a degenerate ground state due to an alternating benzenoid-quinoid resonance. We probed 128 different wavelengths at the same time by using a sub-5-fs pulse laser and a detection system composed of a polychromator and a multichannel lock-in amplifier. The method allowed us to study the electronic relaxation and vibrational dynamics in completely same conditions at the same time. Because the polythiophene derivative has degenerate ground state, solitons are expected to be generated after photoexcitation. The dynamics of a breather composed of a dynamic bound state of solitons generated immediately after photoexcitation was time-resolved to reveal coupling between the vibrational modes and the solitons. The $\text{C}\text{C}$ and $\text{C}\text{C}$ stretching modes were found to be modulated by the breather, whose lifetime was determined to be 30--50 fs. The results of quantum-chemical excited-state molecular dynamics simulation are consistent with experimental results. Our modeling results allow to identify related vibrational normal modes strongly coupled to the electronic degrees of freedom. Moreover, analysis of calculated trajectories of excited state shows appearance of short-lived breather excitation decaying due to intramolecular vibrational energy equilibration on a time scale of hundreds of femtoseconds, which also agrees well with the experimental results.

Chemical bond elongation following core-excitation of ammonia: resonant Auger spectra calculation

Theoretical resonant Auger decay spectra of ammonia with core-hole excited state dynamics simulation were investigated and some specific features of the experiment, except for a vibrational structure, were reproduced. A power spectral analysis with short-time maximum entropy method has been applied, and an obtained vibrational spacing assigned to the NH stretching mode was 340 meV, which was consistent with the experiment of 390 ± 10 meV. Proton dynamics of ammonia on the first core-excited state was discussed.

Hydrogen Bonding Controls Excited-State Decay of the Photoactive Yellow Protein Chromophore

We have performed excited-state dynamics simulations of a Photoactive Yellow Protein chromophore analogue in water. The results of the simulations demonstrate that in water the chromophore predominantly undergoes single-bond photoisomerization, rather than double-bond photoisomerization. Despite opposite charge distributions in the chromophore, excited-state decay takes place very efficiently from both single- and double-bond twisted minima in water. Radiationless decay is facilitated by ultrafast solvent reorganization, which stabilizes both minima by specific hydrogen bond interactions. Changing the solvent to the slightly more viscous D2O leads to an increase of the excited-state lifetime. Together with previous simulations, the present results provide a complete picture of the effect of the protein on the photoisomerization of the chromophore in PYP: the positive guanidinium group of Arg52 favors double-bond isomerization over single-bond isomerization by lowering the barrier for double-bond isomerization, while the hydrogen bonds with Tyr42 and Glu46 enhance deactivation from the double-bond twisted minimum.

Wave Packet Simulation of Nonadiabatic Dynamics in Highly Excited 1,3-Dibromopropane

We have conducted wave packet simulations of excited-state dynamics of 1,3-dibromopropane (DBP) with the aim of reproducing the experimental results of the gas-phase pump-probe experiment by Kotting et al. [ Kotting, C. ; Diau, E. W.-G. ; Sølling, T. I. ; Zewail, A. H. J. Phys. Chem. A 2002, 106, 7530 ]. In the experiment, DBP is excited to a Rydberg state 8 eV above the ground state. The interpretation of the results is that a torsional motion of the bromomethylene groups with a vibrational period of 680 fs is activated upon excitation. The Rydberg state decays to a valence state, causing a dissociation of one of the carbon bromine bonds on a time scale of 2.5 ps. Building the theoretical framework for the wave packet propagation around this model of the reaction dynamics, the simulations reproduce, to a good extent, the time scales observed in the experiment. Furthermore, the simulations provide insight into how the torsion motion influences the bond breakage, and we can conclude that the mechanism that delays the dissociation is solely the electronic transition from the Rydberg state to the valence state and does not involve, for example, intramolecular vibrational energy redistribution (IVR).

Real-time, local basis-set implementation of time-dependent density functional theory for excited state dynamics simulations

We present a method suitable for large-scale accurate simulations of excited state dynamics within the framework of time-dependent density functional theory (DFT). This is achieved by employing a local atomic basis-set representation and real-time propagation of excited state wave functions. We implement the method within SIESTA, a standard ground-state DFT package with local atomic basis, and demonstrate its potential for realistic and accurate excited state dynamics simulations using small and medium-sized molecules as examples (H(2), CO, O(3), and indolequinone). The method can be readily applied to problems involving nanostructures and large biomolecules.

Arginine52 Controls the Photoisomerization Process in Photoactive Yellow Protein

We have performed excited-state dynamics simulations of the Arg52Gln (R52Q) mutant of photoactive yellow protein (PYP). The results of these simulations demonstrate that in the mutant the primary events after photoexcitation are different from those in the wild-type. In the mutant, the chromophore predominantly undergoes single bond photoisomerization, whereas in the wild-type, photoisomerization of the double bond occurs. Furthermore, the excited-state lifetime is around three times longer than in wild-type PYP, which agrees well with recent transient absorption measurements. In 20% of the trajectories, we observe the formation of a photoproduct that has the carbonyl oxygen atom of the chromophore flipped by almost 180°, disrupting the hydrogen bond between the chromophore and the backbone amino group of Cys69. This observation, in combination with the fact that the mutant is photoactive, suggests that the break of the hydrogen bond is the key step in the photoactivation process rather than the double bo...

The MP/SOFT methodology for simulations of quantum dynamics: Model study of the photoisomerization of the retinyl chromophore in visual rhodopsin

Rigorous simulations of excited-state nonadiabatic quantum dynamics in polyatomic chromophores are particularly challenging since they require solving the multichannel time-dependent Schrödinger equation describing nuclear wavepackets evolving on electronically coupled potential energy surfaces. This paper presents an overview of the matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method for simulations of nonadiabatic quantum dynamics [X. Chen, V.S. Batista, Matching-pursuit split operator Fourier transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine. J. Chem. Phys., 125 (2006) Art. No. 124313] and its application to the description of the 11- cis/all- trans photoisomerization of the retinyl chromophore in rhodopsin. The underlying nonadiabatic dynamics is described by a 2-state 25-dimensional wave-packet evolving according to an empirical model Hamiltonian with frequencies and excited-state gradients parameterized to reproduce the observed resonance Raman excitations of rhodopsin. The reported results show that the MP/SOFT method is a valuable tool to simulate nonadiabatic dynamics in polyatomic systems and to assess the validity of mixed quantum-classical approaches as applied to simulations of complex (nonintegrable) quantum dynamics in multidimensional systems.

The on-the-fly surface-hopping program system N ewton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems

The great importance of ultrafast phenomena in photochemistry and photobiology has made dynamics simulations an essential methodology in these areas. In this work, we present the N ewton-X program package containing a new implementation of a direct dynamics approach to perform adiabatic (Born–Oppenheimer) and nonadiabatic simulations. The nonadiabatic dynamics is based on Tully's surface hopping approach. The program has been developed with the aim of (1) to create a flexible tool to be used in connection with a multitude of third-party electronic-structure program packages and (2) to provide the most common options for excited-state dynamics simulations. Benchmark calculations on the nonadiabatic dynamics are presented for the methaniminium, butatriene and pentadieniminium cations. The simulation of UV absorption spectra is presented for the methaniminium cation and pyrazine.

Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine

A simple approach for numerically exact simulations of nonadiabatic quantum dynamics in multidimensional systems is introduced and applied to the description of the photoabsorption spectroscopy of pyrazine. The propagation scheme generalizes the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] to simulations of nonadiabatic quantum dynamics. The time-evolution operator is applied, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state expansions. These representations are obtained by combining the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting computational approach are demonstrated in calculations of time-dependent survival amplitudes and photoabsorption cross sections, using a model Hamiltonian that allows for direct comparisons with benchmark calculations. Simulations in full-dimensional potential energy surfaces involve the propagation of a 24-dimensional wave packet to describe the S(1)S(2) interconversion of pyrazine after S(0)-->S(2) photoexcitation. The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems.

Photoexcited breathers in conjugated polyenes: an excited-state molecular dynamics study.

pi-conjugated polymers have become an important class of materials for electronic devices. Design of these devices requires understanding such processes as photochemical reactions, spatial dynamics of photoexcitations, and energy and charge transport, which in turn involve complex coupled electron-vibrational dynamics. Here we study nonlinear photoexcitation dynamics in the polyene oligomers by using a quantum-chemical method suitable for the simulation of excited-state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. The method is based on the adiabatic propagation of the ground-state and transition single-electron density matrices along the trajectory. The simulations reveal formation of a self-localized vibronic excitation ("breather" or multiquanta bound state) with a typical period of 34 fs and allows us to identify specific slow and fast nuclear motions strongly coupled to the electronic degrees of freedom. The effect of chain imperfections and chemical defects on the dynamics is also investigated. A complementary two-dimensional analysis of corresponding transition density matrices provides an efficient way to monitor time-dependent real-space localization of the photoexcitation by identifying the underlying changes in charge densities and bond orders. Possible correlated electronic and vibrational spectroscopic signatures of photoexcited breathers are predicted, and generalizations to energy localization in complex macromolecules are discussed.

Direct semiclassical simulation of photochemical processes with semiempirical wave functions

We describe a new method for the simulation of excited state dynamics, based on classical trajectories and surface hopping, with direct semiempirical calculation of the electronic wave functions and potential energy surfaces (DTSH method). Semiempirical self-consistent-field molecular orbitals (SCF MO’s) are computed with geometry-dependent occupation numbers, in order to ensure correct homolytic dissociation, fragment orbital degeneracy, and partial optimization of the lowest virtuals. Electronic wave functions are of the MO active space configuration interaction (CI) type, for which analytic energy gradients have been implemented. The time-dependent electronic wave function is propagated by means of a local diabatization algorithm which is inherently stable also in the case of surface crossings. The method is tested for the problem of excited ethylene nonadiabatic dynamics, and the results are compared with recent quantum mechanical calculations.

1E1600 バクテリオロドプシンの光異性化プロセスの励起状態ダイナミクスシミュレーション

1E1600 バクテリオロドプシンの光異性化プロセスの励起状態ダイナミクスシミュレーション

Excited state dynamics in chlorophyll-based antennae: the role of transfer equilibrium

We present computer simulations of excited state dynamics in models of PS I and PS II which are based upon known structural and spectral properties of the antennae. In particular, these models constrain the pigment binding sites to three-dimensional volumes determined from molecular properties of the antenna complexes. The simulations demonstrate that within a 10-30 ps after light absorption, rapid energy transfer among coupled antenna chlorophylls leads to a quasiequilibrium state in which the fraction of the excited state on any antenna chlorophyll, normalized to the total excited state remaining on the model, remains constant with time. We describe this quasiequilibrium state as a "transfer equilibrium" (TE) state because of its dependence on the rates of processes that couple excited state motion and quenching in the antenna as well as on the individual antenna site energies and temperature. The TE state is not a true equilibrium in that loss of the excited state primarily due to photochemistry (but also due to fluorescence, thermal emission, and intersystem crossing) continues once TE is established. Depending on the dynamics of the system, the normalized distribution of excited state at TE may differ substantially from the Boltzmann distribution (the state of the model at infinite time in the absence of any avenues for decay of excited state). The models predict lifetimes, equilibration times, and photochemical yields that are in agreement with experimental data and affirm trap-limited dynamics in both photosystems. The rapid occurrence of TE states implies that any excited state dynamics that depends on antenna structure and excitation wavelength must occur before the TE state is established. We demonstrate that the excited state distribution of the TE state is central to determining the excited state lifetime and quantum efficiency of photochemistry.