Detailed Photoisomerization Dynamics of a Green Fluorescent Protein Chromophore Based Molecular Switch

Jiang, Chen-Wei; Fang, Ai-Ping; Zhao, Di; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li

doi:https://doi.org/10.1155/2014/597165

International Journal of Photoenergy

On this page

Abstract Introduction Results and Discussion Conclusions Acknowledgments References Copyright Related Articles

Special Issue

Dynamics in Photoexcited DNA Bases and Related Molecules

View this Special Issue

Research Article | Open Access

Volume 2014 | Article ID 597165 | https://doi.org/10.1155/2014/597165

Detailed Photoisomerization Dynamics of a Green Fluorescent Protein Chromophore Based Molecular Switch

Chen-Wei Jiang,¹Ai-Ping Fang,¹Di Zhao,¹Hong-Rong Li,¹Rui-Hua Xie,^1,2and Fu-Li Li¹

Academic Editor: Yusheng Dou

Received25 Apr 2014

Accepted16 Jul 2014

Published03 Sept 2014

Abstract

With density-functional-based nonadiabatic molecular dynamics simulations, trans-to-cis and cis-to-trans photoisomerizations of a green fluorescent protein chromophore based molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH) induced by the excitation to its excited state were performed. We find a quantum yield of 32% for the trans-to-cis photoisomerization of BMH and a quantum yield of 33% for its cis-to-trans photoisomerization. For those simulations that did produce trans-to-cis isomerization, the average excited state lifetime of trans-BMH is about 1460 fs, which is much shorter than that of cis-BMH (3100 fs) in those simulations that did produce cis-to-trans isomerization. For both photoisomerization processes, rotation around the central C2=C3 bond is the dominant reaction mechanism. Deexcitation occurs at an avoided crossing near the / conical intersection, which is near the midpoint of the rotation.

1. Introduction

Molecules with the ability to undergo photoisomerization under radiation would have potential applications in molecular switches and other molecular devices. Photoisomerization mechanisms of stilbene [1–3], fulgide [4–6], diarylethene [7–9], and azobenzene [10–14], together with their derivatives [15–19], have been widely studied during the last two decades. Despite their appealing features as effective molecular switches, azobenzene derivatives and above photochromic compounds are just examples of a whole family of compounds capable of performing controlled isomerization reactions. The discovery of new or alternative photoswitch types could expand the applicability of the switch concept to different and increasingly complex molecular environments.

The chromophore of the green fluorescent protein, as a biomolecule from jellyfish Aequorea victoria, has been widely used as a genetically encoded noninvasive fluorescence marker in bioimaging [20]. Recently, several studies have revealed that the green fluorescent protein chromophore and its different modifications undergo photo-induced Z/E isomerization under radiation [21–26], which offer them the opportunity to be molecular switches. Through investigation of several spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein, Voliani et al. [21] found that cis-to-trans photoisomerization should be a general mechanism of green fluorescent protein chromophores whose efficiency can be modulated by the detailed mutant-specific protein environment. Using femtosecond fluorescence upconversion spectroscopy and quantum chemical calculations, Rafiq et al. [22] investigated two green fluorescent protein chromophore analogs and proposed a multicoordinate relaxation mechanism. Oxazolone analogs, as well-known intermediates in the synthesis of green fluorescent protein derivatives, have attracted relatively little attention in terms of their photoswitching ability. Very recently, several oxazolone analogs of the green fluorescent protein chromophore were synthesized and predicted to be good candidates for molecular switches by Blanco-Lomas et al. [27].

To furnish a deeper and detailed mechanistic understanding of the photoisomerization reaction of those green fluorescent protein chromophore based molecular switches, semiclassical nonadiabatic molecular dynamics simulations were performed for a molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH, named as 2e in [27]) in our group. We found that the average lifetime of the excited state in trans-BMH is about 1450 fs, much shorter than that of cis-BMH (3100 fs), which is in good agreement with the experimental result [27].

This paper is organized as follows. Our semiclassical nonadiabatic molecular dynamics simulation method is briefly reviewed in Section 2. The detailed results and discussions are represented in Section 3, followed by a conclusion in Section 4.

2. Methodology

Our nonadiabatic molecular dynamics simulation method was named semiclassical electron-radiation-ion dynamics (SERID), which has been described in detail elsewhere [28, 29]. We only briefly review it under below.

To obtain the evolution equations of electrons and nuclei, we postulate a mixed classical-quantum action [30–32] , where is the electronic Hamiltonian, is the electronic state, “h.c.” means “Hermitian conjugate,” labels a nucleus with spatial coordinates , and is the repulsive interaction between nuclei and ion cores. As shown in [32], if one makes the usual time-dependent effective-field approximation and employs a nonorthogonal basis, extremalization of this action leads to the time-dependent Schrödinger equation: and to the equation of motion for the nuclei

The Hamiltonian matrix , overlap matrix , and repulsive potential are obtained from the density-functional-based parameterizations of Frauenheim and coworkers [33, 34].

The results of [14, 35–44] calculated with SERID method have provided a clear demonstration of the following features of simulations based on Ehrenfest dynamics: electronic transitions are automatically observed at an avoided crossing near a conical intersection in configuration space predicted by Teller [45, 46], with energy released to molecular vibrations; these transitions occur rapidly, over a time interval of ~2 femtosecond, during which the nuclei do not move appreciably.

In the present work, we have made a little change in the procedure that should lead to better results for the quantum yields. By simply placing an electron in the lowest unoccupied molecular orbital (LUMO) and a hole in the highest occupied molecular orbital (HOMO) in the beginning of nonadiabatic simulations, we focus exclusively on the - excitation, as in other excited state molecular dynamics simulations [47, 48]. However, we still allow deexcitation to occur automatically at an avoided crossing near a conical intersection, since we found that deexcitation was already nearly complete in our present simulations.

3. Results and Discussion

We optimized the cis and trans structures of BMH in the ground state, starting from 300 K through reducing the nuclear velocities by a factor of 0.9997 after each time step of 0.01 fs until the total molecular kinetic energy was less than eV. The optimized geometries of cis and trans BMH are presented in Figure 1, with their geometrical parameters summarized in Table 1. We also optimized both structures with B3LYP/6-311G(d,p) implemented in Gaussian 03 software package [49]. Both results are in good agreement with each other. The electronic energy of cis-BMH is 0.11 eV lower than that of trans-BMH in our SERID calculation, agreeing well with the energy difference (0.13 eV) obtained with B3LYP/6-311G(d,p) method. Both results confirm that cis-BMH is more stable than its trans isomer. Starting from its optimized geometry, each molecule was then heated to 300 K (via random velocities resulting in this temperature) and then allowed to equilibrate and move in the electronic ground state for 10000 fs. The initial conditions for various simulations were then sampled from the configurations during the last half of this 10000 fs interval.

3.1. trans-to-cis Photoisomerization of BMH

Starting from the first excited state of trans-BMH with different initial conditions, 90 simulations have been performed, 29 of which resulted in trans-to-cis isomerization. So the quantum yield of this reaction in our calculation is about 32%. For the 29 simulations which did produce trans-to-cis isomerization, the average lifetime of trans-BMH is about 1460 fs. A detailed discussion of the isomerization mechanism in a representative simulation with a 1740 fs lifetime is presented below.

BMH molecule is excited to the excited state at time fs. To compare the results before and after the excitation, the results before 0 fs are also presented in Figures 2–7 below. Time dependence of the four orbital energies nearest the initial HOMO-LUMO gap are displayed in Figure 2. As we can see, after the excitation at 0 fs, only the HOMO and LUMO energy levels are affected evidently. The energy gap between HOMO and LUMO orbitals, as shown in Figure 2(b), decreases continuously from 2.55 eV to 0.06 eV until 1739 fs. After about 1810 fs, the energy gap between HOMO and LUMO returns to about 2.66 eV and then vibrates around this new value until the end of our simulation. Electron occupations for the four orbitals presented in Figure 2(a) after the excitation are shown in Figure 3. As we can see, BMH deexcites to its ground state at about 1740 fs in 4 fs interval; nearly all electrons return to their ground state. The lifetime of the excited state in trans-BMH is thus about 1740 fs.

(a)

(b)

(a)

(b)

(a)

(b)

(c)

(a)

(b)

(c)

(a)

(b)

(c)

(a)

(b)

(c)

Variations of geometry for BMH are displayed in Figures 4–7. As displayed in Figure 4, dihedral angle C1C2C3C6 vibrates around before the excitation at 0 fs, after the excitation, which increases continuously from to about at 1740 fs when BMH returns to the ground state. After the deexcitation at 1740 fs, the rotation around C2=C3 bond continues. Dihedral angle C1C2C3C6 reaches (the optimized value for dihedral angle C1C2C3C6 in cis-BMH) at about 2040 fs and then vibrates around this new value, which can demonstrate that the molecule arrives at its cis geometry in about 2040 fs. Atomic distance between H20 and N21 displayed in Figure 7(c) can be another confirmation for the final cis geometry. After the excitation at 0 fs, the distance between H20 and N21 decreases continuously from about 4.4 Å to 2.2 Å until 2040 fs and then vibrates around this value until the end of our simulation. Other two dihedral angles C3C2C1C5 and C1C2H12C3 are also displayed in Figure 4. During the whole simulation, C3C2C1C5 vibrates around . That is, there is no evident rotation around C1–C2 bond. C1C2H12C3 also does not vary evidently during the whole simulation and keeps on vibrating around , which demonstrates that H12 atom stays nearly in a plane with atoms C1, C2, and C3 all the time.

Three bond angles in BMH during the trans-to-cis isomerization are presented in Figure 5. As we can see, during the whole simulation, C1C2C3 bond angle keeps on vibrating around , while C2C1C5 bond angle keeps on staying around . C2C3N21 vibrates around (the optimized C2C3N21 value in trans-BMH) before the excitation at 0 fs and then stays around (the optimized C2C3N21 value in cis-BMH) after the deexcitation at 1740 fs.

Time dependence of five bond lengths in BMH is shown in Figures 6 and 7. As shown in Figure 6, after the excitation at 0 fs, C2=C3 bond is weakened, increasing from 1.37 Å to 1.47 Å and then returning to 1.37 Å after the deexcitation at 1740 fs. On the other hand, other two bond lengths presented in Figure 6, C1–C2 and C3–N21, are shortened from 1.47 Å to 1.40 Å and from 1.43 Å to 1.37 Å after the excitation at 0 fs, respectively. After the deexcitation at 1740 fs, both bond angles, C1–C2 and C3–N21, return to their initial values before the excitation. Time dependence of other two carbon-carbon bonds, C3–C6 and C1–C4, which are connected with C2=C3 and C1–C4, respectively, are displayed in Figure 7. As we can see, after the excitation at 0 fs, C3–C6 was also shortened, decreasing from 1.46 Å to 1.43 Å, and returning to 1.46 Å after the deexcitation at 1740 fs. The C1–C4 bond length increases from 1.41 Å to 1.45 Å at 0 fs and comes back to 1.41 Å after 1740 fs.

For the representative trans-to-cis isomerization of BMH discussed above, lifetime of the excited state in trans-BMH is about 1740 fs, while the cis geometry is arrived in about 2040 fs. Rotation around C2=C3 bond is the dominant reaction mechanism. Deexcitation occurs near the midpoint of the rotation, due to an avoided crossing near the / conical intersection.

3.2. cis-to-trans Photoisomerization of BMH

On the basis of 60 simulations, 20 of which did produce cis-to-trans isomerization, we find a quantum yield of 33% for cis-to-trans isomerization of BMH induced by the excitation to its excited state, which is only a little larger than that of trans-to-cis isomerization of BMH. For the 20 simulations which did produce cis-to-trans isomerization, the average lifetime of cis-BMH is about 3100 fs. In order to provide the detailed cis-to-trans reaction mechanism, a single representative simulation with a 3545 fs lifetime is discussed below.

Time dependence of orbital energies from HOMO − 1 to LUMO + 1 and energy gap between LUMO and HOMO in BMH during the cis-to-trans photoisomerization are shown in Figure 8. For comparison, the results of ortibal energies and LUMO-HOMO energy gap before the excitation are also displayed in this figure. As we can see, after the excitation at 0 fs, only HOMO and LUMO energies are strongly affected by the nuclear motion. The LUMO-HOMO energy gap decreases from 2.7 eV to about 0.5 eV in 2000 fs, increases to about 2.0 eV at about 2500 fs, and decreases again to the minimum value of 0.119 eV in this simulation at 3543 fs. After 3600 fs, the LUMO-HOMO energy gap increases to about 2.7 eV and vibrates around this value until the end of this simulation.

(a)

(b)

Variations of electron occupancies in the orbitals from HOMO − 1 to LUMO + 1 during the cis-to-trans photoisomerization are displayed in Figure 9. Details of the electron occupancies between 3530 and 3560 fs are also shown in this figure. As we can see, after the excitation at 0 fs, BMH stays in the first excited state until the deexcitation occurring at 3543 fs, which is corresponding to an avoided crossing near the / conical intersection, as shown in Figure 8.

(a)

(b)

The geometry of BMH at 3543 fs is displayed in Figure 10. At this point, C1C2C3C6 dihedral angle is equal to , near the midpoint of the rotation. Bond length C2=C3 is equal to 1.47 Å, much longer than the ordinary C=C bond length. Other geometrical values, such as bond lengths and bond angles, are also presented in this figure.

Variations of geometry during the cis-to-trans photoisomerization of BMH are presented in Figures 11–14. Time dependence of three dihedral angles in BMH, C1C2C3C6, C3C2C1C5, and C1C2H12C3, is shown in Figure 11. As shown in this figure, after the excitation at 0 fs, dihedral angle C1C2C3C6 increases from to about in 900 fs, stays around between 900 fs and 2100 fs and then changes the rotation direction, and decreases dramatically from to . When BMH arrives at an avoided crossing near the / conical intersection at 3543 fs, the value of C1C2C3C6 reaches , as shown in Figure 10. C1C2C3C6 arrives at (the optimized C1C2C3C6 value in trans-BMH) at 3623 fs and then vibrates around this new value until the end of our simulation. This new C1C2C3C6 value () can be a demonstration that the molecule arrives at its trans geometry in about 3623 fs. Atomic distance between H20 and N21 presented in Figure 14(c) can be another confirmation for the final trans geometry, which does not vary evidently before 3000 fs but increases continuously from about 2.2 Å to 4.4 Å (the optimized distance between H20 and N21 in trans-BMH) in subsequent 600 fs and then vibrates around this value until the end of our simulation. As can be seen in Figure 11(b), dihedral angle C3C2C1C5 stays around before BMH returns to its ground state at 3545 fs. But due to the energy redistribution among the molecule after deexcitation, BMH starts and keeps on rotating around C1–C2 bond until the end of our simulation. Similar results have been found in photoisomerization of stilbene and azobenzene [14, 40]. C1C2H12C3 also does not vary evidently during the whole simulation and keeps on vibrating around , which can demonstrate that H12 atom stays nearly in a plane with atoms C1,C2, and C3 all the time.

(a)

(b)

(c)

(a)

(b)

(c)

(a)

(b)

(c)

(a)

(b)

(c)

Time variations of three bond angles, C1C2C3, C2C1C5, and C2C3N21, are shown in Figure 12. As we can see, C1C2C3 keeps on vibrating around during the whole simulation, while C2C1C5 stays around . For C2C3N21, it vibrates around before the excitation at 0 fs and decreases slowly to about (the optimized value of C2C3N21 in trans-BMH) when deexcitation occurs at 3543 fs.

Figure 13 displays the time dependence of three bond lengths in BMH. After the excitation at 0 fs, C2=C3 is weakened, increasing from 1.35 Å to 1.46 Å and returning to 1.35 Å after the deexcitation at 3545 fs. Two other bonds shown in Figures 12(a) and 12(b), on the other hand, are shortened after the excitation at 0 fs. C1–C2 decreases from 1.46 Å to 1.40 Å after 0 fs and goes back to 1.46 Å after 3545 fs. C3-N21 decreases from 1.43 Å to 1.38 Å after the excitation and returns to its initial value after the deexcitation. Bond lengths C1-C4 and C3–C6, as shown in Figure 14, are also affected by the excitation and deexcitation. C1–C4 increases from 1.41 Å to 1.45 Å after 0 fs and returns to its initial value after deexcitation. Bond length of C3–C6 decreases from 1.46 Å to 1.43 Å after the excitation and then returns to its initial value 1.46 Å after the deexcitation at 3545 fs.

4. Conclusions

With density-functional-based nonadiabatic molecular dynamics simulations, trans-to-cis and cis-to-trans photoisomerizations of a green fluorescent protein chromophore based molecule 4-benzylidene-2-methyloxazol-5(4H)-one (BMH) induced by the excitation to its excited state were performed. We find a quantum yield of 32% for the trans-to-cis photoisomerization of BMH and a quantum yield of 33% for its cis-to-trans photoisomerization. In those simulations that did produce trans-to-cis isomerization, the range of calculated lifetimes was 700–4000 fs, with a mean value of 1450 fs. For the finished cis-to-trans isomerization, the range of calculated lifetimes was 1200–7000 fs, with a mean value of 3100 fs. The lifetime of cis-BMH is much larger than that of trans-BMH, agreeing well with the experimental result [27].

For the simulation shown in detail, lifetimes of the trans-BMH and cis-BMH are 1740 fs and 3545 fs, respectively. The whole trans-to-cis isomerization is finished in about 2040 fs, while whole time needed for cis-to-trans isomerization is about 3623 fs. For both photoisomerizations, rotation around the central C2=C3 bond is the dominant reaction mechanism; deexcitation occurs at an avoided crossing near the / conical intersection, which is near the midpoint of the rotation.

Conflict of Interests

The authors declare that there is no conflict of interests regarding the publication of this paper.

Acknowledgments

This work was supported by the Natural Science Foundation of China (Grants 21203144, 11074199, and 11174233), Doctoral Fund of Ministry of Education of China (Grant 20120201120056), and the Fundamental Research Funds for the Central Universities.

References

D. H. Waldeck, “Photoisomerization dynamics of stilbenes,” Chemical Reviews, vol. 91, no. 3, pp. 415–438, 1991.
View at: Publisher Site | Google Scholar
T. Baumert, T. Frohnmeyer, B. Kiefer et al., “Femtosecond transition state dynamics of cis-stilbene,” Applied Physics B: Lasers and Optics, vol. 72, no. 1, pp. 105–108, 2001.
View at: Publisher Site | Google Scholar
W. Fuß, C. Kosmidis, W. E. Schmid, and S. A. Trushin, “The photochemical cis-trans isomerization of free stilbene molecules follows a hula-twist pathway,” Angewandte Chemie, vol. 43, no. 32, pp. 4178–4182, 2004.
View at: Publisher Site | Google Scholar
Y. Ishibashi, M. Murakami, H. Miyasaka, S. Kobatake, M. Irie, and Y. Yokoyama, “Laser multiphoton-gated photochromic reaction of a fulgide derivative,” Journal of Physical Chemistry C, vol. 111, no. 6, pp. 2730–2737, 2007.
View at: Publisher Site | Google Scholar
T. Cordes, S. Malkmus, J. A. DiGirolamo et al., “Accelerated and efficient photochemistry from higher excited electronic states in fulgide molecules,” The Journal of Physical Chemistry A, vol. 112, no. 51, pp. 13364–13371, 2008.
View at: Publisher Site | Google Scholar
F. Renth, R. Siewertsen, and F. Temps, “Enhanced photoswitching and ultrafast dynamics in structurally modified photochromic fulgides,” International Reviews in Physical Chemistry, vol. 32, no. 1, pp. 1–38, 2013.
View at: Publisher Site | Google Scholar
M. Takeshita and M. Irie, “Photoresponsive tweezers for alkali metal ions. Photochromic diarylethenes having two crown ether moieties,” Journal of Organic Chemistry, vol. 63, no. 19, pp. 6643–6649, 1998.
View at: Publisher Site | Google Scholar
S. F. Yan, V. N. Belov, M. L. Bossi, and S. W. Hell, “Switchable fluorescent and solvatochromic molecular probes based on 4-amino-N-methylphthalimide and a photochromic diarylethene,” European Journal of Organic Chemistry, vol. 2008, no. 15, pp. 2531–2538, 2008.
View at: Publisher Site | Google Scholar
Y. Li and Q. Li, “Photochemically reversible and thermally stable axially chiral diarylethene switches,” Organic Letters, vol. 14, no. 17, pp. 4362–4365, 2012.
View at: Publisher Site | Google Scholar
I. K. Lednev, T.-Q. Ye, L. C. Abbott, R. E. Hester, and J. N. Moore, “Photoisomerization of a capped azobenzene in solution probed by ultrafast time-resolved electronic absorption spectroscopy,” The Journal of Physical Chemistry A, vol. 102, no. 46, pp. 9161–9166, 1998.
View at: Google Scholar
T. Fujino and T. Tahara, “Picosecond time-resolved Raman study of trans-azobenzene,” Journal of Physical Chemistry A, vol. 104, no. 18, pp. 4203–4210, 2000.
View at: Publisher Site | Google Scholar
H. Satzger, S. Spörlein, C. Root, J. Wachtveitl, W. Zinth, and P. Gilch, “Fluorescence spectra of trans- and cis-azobenzene: emission from the Franck-Condon state,” Chemical Physics Letters, vol. 372, no. 1-2, pp. 216–223, 2003.
View at: Publisher Site | Google Scholar
I. Conti, M. Garavelli, and G. Orlandi, “The different photoisomerization efficiency of azobenzene in the lowest n $π$ ^∗ and $π π$ ^∗ singlets: the role of a phantom state,” Journal of the American Chemical Society, vol. 130, no. 15, pp. 5216–5230, 2008.
View at: Publisher Site | Google Scholar
C.-W. Jiang, R.-H. Xie, F.-L. Li, and R. E. Allen, “Comparative studies of the trans—Cis photoisomerizations of azobenzene and a bridged azobenzene,” Journal of Physical Chemistry A, vol. 115, no. 3, pp. 244–249, 2011.
View at: Publisher Site | Google Scholar
H.-H. Liu, X. Zhang, Z. Gao, and Y. Chen, “Photoconversion of a protonated diarylethene derivative,” Journal of Physical Chemistry A, vol. 116, no. 40, pp. 9900–9903, 2012.
View at: Publisher Site | Google Scholar
G. Haberhauer and C. Kaliweit, “A bridged azobenzene derivative as a reversible, light-induced chirality switch,” Angewandte Chemie, vol. 49, no. 13, pp. 2418–2421, 2010.
View at: Publisher Site | Google Scholar
I. K. Lednev, T.-Q. Ye, P. Matousek et al., “Femtosecond time-resolved UV-visible absorption spectroscopy of trans-azobenzene: dependence on excitation wavelength,” Chemical Physics Letters, vol. 290, no. 1–3, pp. 68–74, 1998.
View at: Publisher Site | Google Scholar
T. Pancur, F. Renth, F. Temps et al., “Femtosecond fluorescence up-conversion spectroscopy of a rotation-restricted azobenzene after excitation to the S1 state,” Physical Chemistry Chemical Physics, vol. 7, no. 9, pp. 1985–1989, 2005.
View at: Publisher Site | Google Scholar
R. Siewertsen, H. Neumann, B. Buchheim-Stehn et al., “Highly efficient reversible Z-E photoisomerization of a bridged azobenzene with visible light through resolved S1(npi*) absorption bands,” Journal of the American Chemical Society, vol. 131, no. 43, pp. 15594–15595, 2009.
View at: Publisher Site | Google Scholar
M. Chalfie, Y. Tu, G. Euskirchen, W. W. Ward, and D. C. Prasher, “Green fluorescent protein as a marker for gene expression,” Science, vol. 263, no. 5148, pp. 802–805, 1994.
View at: Publisher Site | Google Scholar
V. Voliani, R. Bizzarri, R. Nifosì et al., “Cis-trans photoisomerization of fluorescent-protein chromophores,” The Journal of Physical Chemistry B, vol. 112, no. 34, pp. 10714–10722, 2008.
View at: Publisher Site | Google Scholar
S. Rafiq, B. K. Rajbongshi, N. N. Nair, P. Sen, and G. Ramanathan, “Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: Evidence for cis-trans isomerism,” Journal of Physical Chemistry A, vol. 115, no. 47, pp. 13733–13742, 2011.
View at: Publisher Site | Google Scholar
J.-S. Yang, G.-J. Huang, Y.-H. Liu, and S.-M. Peng, “Photoisomerization of the green fluorescence protein chromophore and the meta- and para-amino analogues,” Chemical Communications, vol. 2008, no. 11, pp. 1344–1346, 2008.
View at: Publisher Site | Google Scholar
P. Naumov, J. Kowalik, K. M. Solntsev et al., “Topochemistry and photomechanical effects in crystals of green fluorescent protein-like chromophores: Effects of hydrogen bonding and crystal packing,” Journal of the American Chemical Society, vol. 132, no. 16, pp. 5845–5857, 2010.
View at: Publisher Site | Google Scholar
X. He, A. F. Bell, and P. J. Tonge, “Synthesis and spectroscopic studies of model red fluorescent protein chromophores,” Organic Letters, vol. 4, no. 9, pp. 1523–1526, 2002.
View at: Publisher Site | Google Scholar
A. Kikuchi, E. Fukumura, S. Karasawa, H. Mizuno, A. Miyawaki, and Y. Shiro, “Structural characterization of a thiazoline-containing chromophore in an orange fluorescent protein, monomeric kusabira orange,” Biochemistry, vol. 47, no. 44, pp. 11573–11580, 2008.
View at: Publisher Site | Google Scholar
M. Blanco-Lomas, P. J. Campos, and D. Sampedro, “Benzylidene-oxazolones as molecular photoswitches,” Organic Letters, vol. 14, no. 17, pp. 4334–4337, 2012.
View at: Publisher Site | Google Scholar
Y. Dou, B. R. Torralva, and R. E. Allen, “Semiclassical electron-radiation-ion dynamics (SERID) and cis-trans photoisomerization of butadiene,” Journal of Modern Optics, vol. 50, no. 15–17, pp. 2615–2643, 2003.
View at: Publisher Site | Google Scholar
R. E. Allen, T. Dumitrica, and B. Torralva, “Electronic and structural response of materials to fast intense laser pulses,” in Ultrafast Physical Processes in Semiconductors, K. T. Tsen, Ed., chapter 7, Academic Press, New York, NY, USA, 2001.
View at: Google Scholar
R. E. Allen, “Electron-ion dynamics: a technique for simulating both electronic transitions and ionic motion in molecules and materials,” Physical Review B, vol. 50, no. 24, pp. 18629–18632, 1994.
View at: Publisher Site | Google Scholar
R. E. Allen, “Coupling of electrons to the electromagnetic field in a localized basis,” Physical Review B, vol. 78, no. 6, Article ID 064305, 2008.
View at: Publisher Site | Google Scholar
R. E. Allen, T. Dumitrică, and B. Torralva, Ultrafast Physical Processes in Semiconductors, chapter 7, Academic Press, New York, NY, USA, 2001, edited by K. T. Tsen.
D. Porezag, T. Frauenheim, T. Köhler, G. Seifert, and R. Kaschner, “Construction of tight-binding-like potentials on the basis of density-functional theory: application to carbon,” Physical Review B, vol. 51, no. 19, pp. 12947–12957, 1995.
View at: Publisher Site | Google Scholar
G. Seifert, D. Porezag, and T. Frauenheim, “Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme,” International Journal of Quantum Chemistry, vol. 58, no. 2, pp. 185–192, 1996.
View at: Publisher Site | Google Scholar
Y. Dou and R. E. Allen, “Detailed dynamics of a complex photochemical reaction: Cis-trans photoisomerization of stilbene,” The Journal of Chemical Physics, vol. 119, no. 20, pp. 10658–10666, 2003.
View at: Publisher Site | Google Scholar
Y. Dou, B. R. Torralva, and R. E. Allen, “Interplay of electronic and nuclear degrees of freedom in a femtosecond-scale photochemical reaction,” Chemical Physics Letters, vol. 392, no. 4–6, pp. 352–357, 2004.
View at: Publisher Site | Google Scholar
P. Sauer and R. E. Allen, “Dynamics of the photoinduced ring-opening of stilbene, a prototypical diarylethene,” Chemical Physics Letters, vol. 434, no. 4-6, pp. 260–264, 2007.
View at: Publisher Site | Google Scholar
P. Sauer and R. E. Allen, “Influence of laser pulse parameters on dynamical processes during azobenzene photoisomerization,” Journal of Physical Chemistry A, vol. 112, no. 44, pp. 11142–11152, 2008.
View at: Publisher Site | Google Scholar
C.-W. Jiang, R.-H. Xie, F.-L. Li, and R. E. Allen, “Photocyclization of trans-stilbene induced by an ultrafast laser pulse,” Chemical Physics Letters, vol. 487, no. 4–6, pp. 177–182, 2010.
View at: Publisher Site | Google Scholar
C. Jiang, R. Xie, F. Li, and R. E. Allen, “Trans-to-cis isomerization of stilbene following an ultrafast laser pulse,” Chemical Physics Letters, vol. 474, no. 4–6, pp. 263–267, 2009.
View at: Publisher Site | Google Scholar
C.-W. Jiang, R.-H. Xie, F.-L. Li, and R. E. Allen, “Ultrafast cis-to-trans photoisomerization of a bridged azobenzene through nπ excitation: rotational pathway is not restricted,” Chemical Physics Letters, vol. 521, pp. 107–112, 2012.
View at: Publisher Site | Google Scholar
Y. Dou, Y. Lei, A. Li et al., “Detailed dynamics of the photodissociation of cyclobutane,” The Journal of Physical Chemistry A, vol. 111, no. 6, pp. 1133–1137, 2007.
View at: Publisher Site | Google Scholar
W. Zhang, S. Yuan, A. Li, Y. Dou, J. Zhao, and W. Fang, “Photoinduced thymine dimerization studied by semiclassical dynamics simulation,” Journal of Physical Chemistry C, vol. 114, no. 12, pp. 5594–5601, 2010.
View at: Publisher Site | Google Scholar
S. Yuan, W. Zhang, L. Liu, Y. Dou, W. Fang, and G. V. Lo, “Detailed mechanism for photoinduced cytosine dimerization: a semiclassical dynamics simulation,” Journal of Physical Chemistry A, vol. 115, no. 46, pp. 13291–13297, 2011.
View at: Publisher Site | Google Scholar
E. Teller, “The crossing of potential surfaces,” The Journal of Physical Chemistry, vol. 41, no. 1, pp. 109–116, 1937.
View at: Publisher Site | Google Scholar
M. Baer, Beyond Born-Oppenheimer: Electronic Nonadiabatic Coupling Terms and Conical Intersections, Wiley-Interscience, Hoboken, NJ, USA, 2006.
View at: Publisher Site | MathSciNet
C. Nonnenberg, H. Gaub, and I. Frank, “First-principles simulation of the photoreaction of a capped azobenzene: the rotational pathway is feasible,” ChemPhysChem, vol. 7, no. 7, pp. 1455–1461, 2006.
View at: Publisher Site | Google Scholar
Y. Norikane and N. Tamaoki, “Photochemical and thermal cis/trans isomerization of cyclic and noncyclic azobenzene dimers: effect of a cyclic structure on isomerization,” European Journal of Organic Chemistry, no. 5, pp. 1296–1302, 2006.
View at: Publisher Site | Google Scholar
M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN, Inc., Wallingford, CT, 2004.

Copyright

Copyright © 2014 Chen-Wei Jiang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PDF Download Citation

Download other formats

Order printed copies

Views

1267

Downloads

880

Citations