Semiquantitative model for response of biological molecules containing C, N, O and H to laser pulses, with initial application to dipicolinic acid

Sauer, Petra; Allen, Roland E.

doi:10.1080/09500340600898247

Cited by 5 publications

(3 citation statements)

References 23 publications

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“…The detailed description of the method has been published elsewhere [34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50] and only a brief explanation is presented here. The one-electron wave function ⌿ j is expressed by a set of localized basis functions l␣ ͑x͒ 34,42…”

Section: Theoretical Methodsmentioning

confidence: 99%

Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Zhao

Han

Lei

et al. 2007

The Journal of Chemical Physics

101

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Detailed simulation study is reported for the excited-state dynamics of photoisomerization of cis-tetraphenylethylene (TPE) following excitation by a femtosecond laser pulse. The technique for this investigation is semiclassical dynamics simulation, which is described briefly in the paper. Upon photoexcitation by a femtosecond laser pulse, the stretching motion of the ethylenic bond of TPE is initially excited, leading to a significant lengthening of ethylenic bond in 300 fs. Twisting motion about the ethylenic bond is activated by the energy released from the relaxation of the stretching mode. The 90 degrees twisting about the ethylenic bond from an approximately planar geometry to nearly a perpendicular conformation in the electronically excited state is completed in 600 fs. The torsional dynamics of phenyl rings which is temporally lagging behind occurs at about 5 ps. Finally, the twisted TPE reverts to the initial conformation along the twisting coordinate through nonadiabatic transitions. The simulation results provide a basis for understanding several spectroscopic observations at molecular levels, including ultrafast dynamic Stokes shift, multicomponent fluorescence, viscosity dependence of the fluorescence lifetime, and radiationless decay from electronically excited state to the ground state along the isomerization coordinate.

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Section: Theoretical Methodsmentioning

confidence: 99%

Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Zhao

Han

Lei

et al. 2007

The Journal of Chemical Physics

101

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“…Sauer and Allen developed a scheme to include the pairwise interactions between nitrogen and oxygen. 37 The electronic states were calculated with a density-functional-based method 36,38 , which has similar strengths and limitations as TDDFT. Reliability of our simulation method for light-driven molecular dynamics has been calibrated and verified systematically for a series of light-responding molecules [33][34][35]39,40 .…”

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confidence: 99%

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Shao

Lei²,

Wen³

et al. 2008

The Journal of Chemical Physics

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Non-adiabatic dynamical simulations were carried out to study cis-to-trans isomerization of azobenzene under laser irradiation and/or external mechanical loads. We used a semiclassical electron-radiation-ion dynamics method that is able to describe the co-evolution of the structural dynamics and the underlying electronic dynamics in a real-time manner. It is found that azobenzene photoisomerization occurs predominantly by an out-of-plane rotation mechanism even under a non trivial resisting force of several tens pN. We have repeated the simulations systematically for a broad range of parameters for laser pulses, but could not find any photoisomerization event by a previously suggested in-plane inversion mechanism. The simulations found that the photoisomerization process can be held back by an external resisting force of 90-200 picoNewtons depending on the frequency and intensity of the lasers. This study also found that a pure mechanical isomerization is possible from the cis to trans state if the azobenzene molecule is stretched by an external force of ~ 1250 -1650 pN. Remarkably, the mechanical isomerization first proceeds through a mechanically activated inversion, and then is diverted to an ultrafast, downhill rotation that accomplishes the isomerization. Implications of these findings to azobenzene-based nanomechanical devices are discussed.

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“…We call our approach semiclassical electron-radiation-ion dynamics (SERID) in order to emphasize its limiting approximations . The time-dependent electronic Schrödinger equation is solved at each time step in a nonorthogonal basis set, with the Hamiltonian matrix, overlap matrix, and effective ion−ion repulsion parametrized from density functional calculations. , As in all density-functional-based calculations, exchange and correlation effects are included only through an effective one-electron potential.…”

Section: Methodsmentioning

confidence: 99%

Influence of Laser Pulse Parameters on Dynamical Processes during Azobenzene Photoisomerization

Sauer

Allen

2008

J. Phys. Chem. A

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When a molecule is subjected to a short intense laser pulse, the ensuing dynamical processes depend qualitatively on the pulse parameters, including duration, frequency, and fluence. Here we report studies of cis to trans photoisomerization of azobenzene following femtosecond-scale laser pulses which are relatively short (10 fs) or long (100 fs) and which have a central frequency matched to either the first excited state (S1, or HOMO to LUMO in a molecular orbital picture) or the second (S2, or HOMO-1 to LUMO). The results presented here demonstrate that photoisomerization involves a rather intricate sequence of connected steps, with the nuclear and electronic degrees of freedom inextricably coupled. One important feature is the de-excitation required for the molecule to achieve its new ground-state after isomerization. If the primary excitation is to S1, then we find that only a single HOMO/LUMO avoided crossing is required and that this crossing occurs halfway along a rotational pathway involving the central CNNC dihedral angle. If the primary excitation is to S2, then the same HOMO/LUMO avoided crossing is observed, but it must be preceded by another avoided crossing that permits transfer of holes from the HOMO-1 to the HOMO, so that the HOMO is then able to accept electrons from the LUMO. We find that this earlier crossing can occur in either of two geometries, one near the cis configuration and the other near the trans. The fact that S2 (pi pi*) isomerization requires two steps may be related to the fact that isomerization yields are smaller for this (UV) excitation than for the S1 (n pi*, visible-light) excitation.

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Semiquantitative model for response of biological molecules containing C, N, O and H to laser pulses, with initial application to dipicolinic acid

Cited by 5 publications

References 23 publications

Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Influence of Laser Pulse Parameters on Dynamical Processes during Azobenzene Photoisomerization

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