Molecular Design of Ionization-Induced Proton Switching Element

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Molecular Design of Ionization-induced Proton Switching Element Based on Fluorinated DNA base pair Hiroto Tachikawa, and Hiroshi Kawabata J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.6b00328 • Publication Date (Web): 24 Feb 2016 Downloaded from http://pubs.acs.org on February 27, 2016

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The Journal of Physical Chemistry

Molecular Design of Ionization-induced Proton Switching Element based on Fluorinated DNA base pair

Hiroto TACHIKAWA* and Hiroshi KAWABATA

Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, JAPAN

Abstract: To design theoretically the high-performance proton switching element based on DNA base pair, the effects of fluorine substitution on the rate of proton transfer (PT) in DNA model base pair have been investigated by means of direct ab-initio molecular dynamics (AIMD) method. 2-Amino-pyridine dimer, (AP)2, was used as the model of DNA base pair. One of the hydrogen atoms of AP molecule in the dimer was substituted by a fluorine (F) atom, and the structures of the dimer, expressed by F-(AP)2, were fully optimized at the MP2/6-311++G(d,p) level. The direct AIMD calculations showed that the proton is transferred within the base pair after the vertical ionization. The rates of PT in F-(AP)2+ were calculated and compared with that of (AP)2+ without F-atom. It was found that PT rate is accelerated by the F-substitution. Also, the direction of PT between F-AP and AP molecules can be clearly controlled by the position of F-substitution (AP)2 in the dimer.

Keywords: Ab-initio MD; fluorine substitution; ionization; proton transfer

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1. Introduction Biomimetics are known as the imitation of the superior function and shape of the living body. Recently, the techniques of biomimetics have been applied to the fields of chemistry, engineering and medicine, and the materials chemistry.1-7 The DNA base pair, (A-B), is composed of two or three hydrogen bonds between two bases. The proton or hydrogen atom is easily transferred in the base pairs at the excitedand ion radical-states.8-12 It is known that the transfer of proton or hydrogen atom takes place very fast within 100-200 fs. The transfer is also one of the energy relaxation processes of (A-B)* at the excited state or ion radical state.13-16 The DNA base pair is possibility utilized as a proton ON-OFF switching element. Therefore, artificial modification of DNA base pair is one of the biomimetics approaches. Recently, it has been shown that the halogen substitution changes drastically the structure and electronic states of molecules.17-20 Development of high performance switching device may be possible using the halogen substitution in the DNA base pair. In the present study, we designed a fast proton transfer (PT) molecular element on the basis of ab-initio and direct ab-initio molecular dynamics (AIMD) calculations. The amino-pyridine dimer (AP)2 was employed as a model of DNA base pair. We focus our attention mainly on the effects of halogen substitution on the rate of PT in the ionized state of (AP)2. The amino-pyridine and pyrimidine dimers are known as mimic models of DNA base pair with two hydrogen bonds between AP molecules.12-23 Ionization of (AP)2 causes a proton transfer along the hydrogen bonds, and it forms a defect of hydrogen bond in DNA. Time scale of PT process was estimated to be 100-200 fs, which is a very fast process as a chemical reaction.24 In this work, the halogen substitution effects on the 2


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time scale of PT were investigated theoretically to design the PT switching element base of the DNA base pair. In previous paper,24 we investigated the ionization dynamics of (AP)2 using direct AIMD method and showed that PT takes place without activation barrier after the ionization. In the present work, the similar technique was applied to the F-(AP)2 systems.

2. Computational methods Ab-initio and density functional theory (DFT) calculations were carried out using Gaussian 09.25 All geometry optimizations of F-(AP)2 and (AP)2 dimer were carried out at the MP2/6-311++G(d,p) and long-range corrected B3LYP (CAM)-B3LYP/ 6-311++G(d,p) levels of theory. To confirm the stability of the molecules at all stationary points, the harmonic vibrational frequencies were calculated at the CAM-B3LYP/6-311++G(d,p) level of theory. The structures of (AP)2 and fluorine atom substituted

amino-pyridine

dimer,

F-(AP)2,

were

fully

optimized

at

the

MP2/6-311++G(d,p) level. The hydrogen atom in ortho, meta, para, or 5-position of (AP)2 was substituted by fluorine atom. The fluorine substituted complexes of (AP)2 are expressed by o-F-(AP)2, m-F-(AP)2, p-F-(AP)2, and 5-F-(AP)2. In the direct ab-initio molecular dynamics (AIMD) calculation, first,26-28 the structures of F-(AP)2 and (AP)2 were determined at the MP2/6-311++G(d,p) level. Using the optimized geometries, direct AIMD calculations were performed at the CAM-B3LYP/6-311G(d,p) level. Trajectories for the radical cation systems F-(AP)2 and (AP)2 were then propagated from the vertical ionization point using the optimized structures of the neutral systems. Born-Oppenheimer approximation was used. 3



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The equations of motion were numerically solved by the velocity Verlet algorithm method. No symmetry restriction was applied to the calculation of the energy gradients. The time step size was chosen to be 0.10 fs, and a total of 5,000-10,000 steps were calculated for each dynamics calculation. The trajectory calculations were performed under condition of constant total energy. The drift of the total energy was confirmed to be less than 0.01 kcal/mol. The trajectories for the cation system were run from the geometries of parent neutral systems on the assumption of vertical ionization. The electronic state of the system was carefully monitored during the simulation. We confirmed that the electronic state is kept during the dynamics calculation. More details of the direct AIMD calculations are described elsewhere.30-32 To check the effects of basis set and initial geometry on the reaction rate of proton transfer in F-(AP)2+, the direct AIMD calculations with cc-pVDZ and 6-31G(d) basis sets and optimized geometries of CAM-B3LYP/6-311G(d,p) level. Note that all levels of theory gave the similar results as the PT reaction. In addition to the trajectory from these equilibrium points, the trajectories around the equilibrium points were run. First, the structure of F-(AP)2 was optimized at the B3LYP/6-311++G(d,p) level. From the optimized geometry, we carried out the direct AIMD calculation under constant temperature condition. We choose 10 K as mean temperature. The velocities of atoms at the starting point were adjusted to the selected temperature. In order to keep a constant temperature of the system, bath relaxation time was introduced in the calculation. We applied usual Nose-Hoover thermostat in the trajectory calculations under thermal condition. From the trajectory calculation at 10 K, geometries were selected. The trajectories on the ionic state potential energy surface of F-(AP)2+ were run on the assumption of vertical ionization from neutral state. The 4


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velocity and momentum of each atom took from the thermal distribution at 10 K. The trajectory calculations of F-(AP)2+ were performed under constant total energy condition at the CAM-B3LYP/6-311G(d,p), 6-31G(d), and cc-pVDZ levels. A total of 30 trajectories were run for each system.

2. Results A. Optimized structures The structure of (AP)2 (1) optimized at the MP2/6-311++G(d,p) level is illustrated in Figure 1. The structure of 1 was similar to that obtained at the B3LYP/6-311++G(d,p) level.24 Two hydrogen bonds connect two AP molecules. The intermolecular distances was calculated to be r(N1-N2)=3.038 Å, and the hydrogen bond distance was r(N1H1--N2)=2.015 Å. The N-H bond in the NH2 group was 1.025 Å, and the angle of N1-H1-N2 was 177.0°. The binding energy of AP with AP was calculated to be Ebind=8.6 kcal/mol, where the binding energy is expressed by –Ebind= E(AP dimer) – [2 x E(AP monomer)]. The optimized structures of F-(AP)2 are given in Figure 2. The intermolecular distances were calculated to be r(N1-N2)=R1=3.011 (ortho, 2), 3.020 Å (meta, 3), 3.037 Å (para, 4), and 3.020 Å (5-position, 5), indicating that all F-(AP)2 have the similar intermolecular distances. The distances of hydrogen bond for 2, 3, 4, and 5, were r(N1H1--N2)= 1.986, 1.995, 2.013, and 1.995 Å, respectively. The other geometrical parameters were similar to each other. The binding energies of F-AP and AP were calculated at the MP2/6-311++G(d,p) level (Table 1), where the binding energy of dimer is defined as -Ebind =E(dimer) [E(F-AP) + E(AP)]. The energies of o-, m-, p-, and 5-F-(AP)2 were calculated to be 5



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Ebind= 8.8, 8.8, 8.4, and 9.2 kcal/mol including the basis set super position error (BSSE), respectively. Since the binding energy in (AP)2 was calculated to be 8.6 kcal/mol, the binding energies of fluorinated AP were similar to that of (AP)2. In case of 5-position dimer, 5-F-(AP)2, the binding energy (9.2 kcal/mol) was slightly larger than the other dimers.

Table 1. Binding energies of (AP)2 dimer and F-(AP)2 dimers calculated at the MP2/6-311++G(d,p) level (in kcal/mol). The binding energies corrected by the basis set super position error (BSSE) are given in parenthesis.

∆E(dimer) (AP)2

(1)

11.5 (8.6)

ortho-(AP)2

(2)

11.8 (8.8)

meta-(AP)2

(3)

11.7 (8.8)

para-(AP)2

(4)

11.3 (8.4)

5p-(AP)2

(5)

12.1 (9.2)

B. Ionization induced proton transfer dynamics Snapshots of o-F-(AP)2+ (2+) after the vertical ionization are illustrated in Figure 3. The optimized structure of F-(AP)2 (2) obtained at the MP2/6-311++G(d,p) level was chosen as the initial structure at time zero. A hole was delocalized over the F-(AP)2+ base pair, although the spin density on F-AP was slightly larger than that of AP. However, the charge distributions in F-AP and AP were slightly different from each other: details of charge distribution will be discussed in the later section. After the ionization, F-AP approached gradually to AP. The intermolecular distances at time=0 and 57 fs were R1=3.011 and 2.794 Å, respectively. However, the N-H bond in the NH2 6


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group was hardly changed within time=0-57 fs: the N-H bond lengths were r2=1.026 Å (time=0) and 1.076 Å (57 fs). At 73 fs, the N-H bond of NH2 group was elongated to be r2=1.281 Å, and the proton approached to the nitrogen atom of AP (r1=1.389 Å). At 79 fs, the position of proton was located at r1=1.644 Å and r2=0.981 Å, indicating that the proton is completely transferred from F-AP to AP during time=73-79 fs. The proton transfer was completed at 78.8 fs in this trajectory.

C. Time evolution of potential energy of the system. Time evolution of potential energy of the system is given in Figure 4. Zero level of potential energy was taken as a vertical energy point after ionization of o-F-(AP)2 (2+). Time profile of potential energy can be classified to three regions: namely, dimer approaching, proton transfer and energy release processes. After the ionization, the potential energy decreased to -5.1 kcal/mol (time = 0-10 fs) due to the internal structural relaxation of F-(AP)2+. The potential energy gradually decreased as a function of time. This energy lowering is caused by approaching of two rings after the ionization (the approaching process between F-AP and AP). At 57 fs, the energy was -6.2 kcal/mol, and the distances were r1=1.729, r2=1.076, and R1=2.794 Å. The potential energy was further stabilized at 73 fs (-10.9 kcal/mol) due to the proton transfer to AP. The arrow indicates the collision of proton to AP, while the proton transfer was completed at 79 fs. After the proton transfer, the energy oscillated strongly due the formation of N-H bond. The excess energy generated by PT was dissipated into the vibrational modes of dimer cation (energy release process). Time evolutions of intermolecular distance (R1) and bond distances of N-H (r1 and r2) are plotted in Figure 4B. At time zero, the interatomic distances were r1=1.986 Å, 7



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r2=1.026 Å, and R1=3.011 Å. The intermolecular distance (R1) decreased with increasing time, and it was minimized at 75 fs. At this point, the proton collided with the AP. Time evolution of r1 and r2 showed a drastic change before and after the PT process. The proton transfer occurred at the shortest N-N bond distance (at 75 fs). Time evolution of intermolecular distance (r1) and the distance of proton from N atom (r2) show that the distances are drastic changed at 75-85 fs: the distance r1 is suddenly shortened, while the distance r2 was elongated. After PT, the N-H bond (r1) was newly formed and vibrated with a large amplitude motion. This indicates that excess energy formed by the proton transfer is efficiently dissipated into the N-H stretching mode.

D. Summary of the direct AIMD calculations The similar AIMD calculations were carried out for all dimer systems. The time of PT (i.e., PT rate) are given in Figure 5, where PT rate is defined as a time period from time zero to the PT completed time. The positive PT rate means that PT takes place from F-AP to AP, whereas the negative value means PT from AP to F-AP. In (AP)2, the PT rate of (AP)2 was calculated to be 115.4 fs at the CAM-B3LYP/6-311G(d,p)//MP2/ 6-311++G(d,p) level. In F-(AP)2, the PT rates were 78.7 fs (ortho), -82.1 fs (meta), 82.9 fs (para), and -129.5 fs (5-position). These results indicate that the fluorine substitution in (AP)2 accelerates the PT rate except for [5-(AP)2]+. The meta- and 5-position systems showed negative PT rates. In these cases, PT occured from AP to F-AP. These results suggest that the direction of PT switch can be controlled by the position of F substitution in (AP)2. 8


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The similar calculations were carried out with cc-pVDZ and 6-31G(d) basis sets to check the basis set dependence on the rate and direction of PT. The results are given in Figure 5. Both basis sets gave the same tendency for the rate and direction of PT. In 5-F-(AP)2 calculated with 6-31G(d), the rate of PT was longer than >300 fs.

E. Comparison of time evolutions of potential energy in all dimers Figure 6 shows the time evolutions of potential energy in all F-(AP)2. The direct AIMD calculations were done at the CAM-B3LYP/6-311G(d,p) level using MP2/6-311++G(d,p) optimized geometry. Zero level corresponds to the total energy of o-F-(AP)2+ at the vertical ionization point. The profiles of potential energy were similar to each other except for 5-F-(AP)2+. The rates of PT in F-(AP)2+ (ortho, meta, and para) were concentrated in time= 75-85 fs. In the case of 5-F-(AP)2+, PT occurred at 130 fs, which is significantly longer than the others. This delay is caused by the low excess energy in 5-F-(AP)2+, where 5-F-(AP)2+ has only 10.5 kcal/mol as excess energy (Table S2 in supporting information). In the other dimers, the excess energy was 21.4-23.1 kcal/mol. Therefore, the delay was caused only in 5-(AP)2+.

F. Charge distribution on the dimers at time zero. As discussed in section 3D, the direction of PT is drastically changed by the position of F-substitution in the dimer. It was found that the direction is strongly dependent on the charge distribution on F-(AP)2+ at the vertical ionization point. The charge distributions are given in Figure 7. The calculations were carried using natural population analysis (NPA). The arrow indicates that the direction of PT after the ionization. In o-F-(AP)2+, the proton was transferred from F-AP+ to AP. The PT active 9



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site was composed of H1-N2 hydrogen bond, whereas the PT silent site was H2-N3 hydrogen bond. The charges of proton in F-AP and nitrogen in the PT active site were +0.434 (H1) and -0.551 (N2), respectively. These values were larger than the charges in PT silent site (H2, N4) = (+0.429, -0.537). In case of m-(AP)2+, the proton was transferred from AP+ to F-AP. The charges on proton and nitrogen atoms at the PT active site were (H2, N3) = (+0.441, -0.584), respectively. These values were also larger than the silent site (H1, N2) = (+0.421, -0.523). The similar features were obtained in all F-(AP)2+. Thus, the large dipole is generated in the hydrogen bond by F-substitution. The charge distribution of F-(AP)2+ at time zero dominates strongly the direction of PT in (AP)2+.

G. Time dependence of spin density in F-(AP)2+ Snapshots of spin densities on o- and m-F-(AP)2+ are illustrated in Figure 8. In the o-F-(AP)2+ at time zero, the spin densities on F-AP and AP were calculated to be 0.51 and 0.49, respectively. The hole was almost equivalently distributed in both F-AP and AP, although the value of spin density on F-AP was slightly larger than that of AP. The spin density at 51 fs was fully localized on F-AP+ of o-F-(AP)2+. The values of spin densities on F-AP+ and AP were calculated to be 0.99 and 0.01, respectively, indicating that the localization of hole rapidly takes place before PT. In the m-F-(AP)2+, the spin densities on F-AP and AP were 0.30 and 0.70, respectively, at time zero. The density was fully localized on AP+ in m-F-(AP)2+ at 51 fs. The values of spin densities were 0.02 (F-AP) and 0.98 (AP). The position of hole localization in meta form was opposite to that of o-form. At final state, the proton was transferred as F-AP+→ AP in otho-form and AP+ → 10


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F-AP in the meta-form. Thus, the position of F atom in (AP)2 drastically changes the direction of PT.

H. HOMO shapes of neutral F-(AP)2 dimers Figure 9 shows the highest occupied molecular orbitals (HOMOs) of neutral states of F-(AP)2. The HOMO was widely distributed around ortho-F-(AP)2, although the distribution in F-AP moiety was slightly larger than AP moiety. In case of meta-form, the distribution was purely localized on the right part of F-(AP)2 (i.e., AP). The similar feature was obtained in 5-position-form. In m- and 5-position-forms, PT takes place from AP to F-AP after the ionization. This is due to the fact that the hole is localized on AP in two forms. On the other hand, HOMO in para-form was localized on the left part of F-(AP)2 (i.e., F-AP). PT occurs from F-AP+ to AP. Thus, it is possible to predict the direction of PT from the shape of HOMO, i.e., PT takes place from the AP part with the large distribution of HOMO to AP with the low distribution.

I. Effects of thermal activation on the PT rate In previous sections, the reaction dynamics from the equilibrium point (optimized geometry) was only examined because the probability of geometry is largest at the equilibrium point. However, actual structure is fluctuated around the equilibrium point even at low temperature. Including the effect of temperature on the PT rate in F-(AP)2+, thermal sampling method was employed in the direct AIMD calculation. First, all structures of F-(AP)2 were fully optimized at the B3LYP/6-311++G(d,p) level. Second, the AIMD calculations were carried out at 10K (See, supporting

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information). The direct AIMD calculations at 10 K were carried out at the B3LYP/6-311++G(d,p) level. Next, the ionization dynamics of F-(AP)2 systems were calculated at several levels of theory. Thirty trajectories were run from the selected geometry generated at 10 K, and the PT rates were averaged. The time of PT thus obtained is given in Figure 10. In (AP)2, the PT rate of (AP)2 was calculated to be 119.7 fs at the CAM-B3LYP/6-311G(d,p) level. In F-(AP)2, the PT rates were 83.2 fs (ortho), -85.2 fs (meta), 84.0 fs (para), and -121.7 fs (5-position). These results were agreed well with those of AIMD from the optimized structures. The similar calculations were carried out with cc-pVDZ and 6-31G(d) basis sets to check the basis set dependence on the rate and direction of PT. Both basis sets gave the same tendency for the rate and direction of PT.

4. Discussion 4.1. Conclusion The direct AIMD calculations showed that (1) the rate of proton transfer (PT) in F-(AP)2+ is significantly faster than that of (AP)2+ without F atom, although the PT rate in the 5-position is close to that of (AP)2+, and (2) the direction of PT is controlled by the position of F atom in F-(AP)2+. The fast PT in F-(AP)2+ is originated from the generation of large dipole moment in the hydrogen bond.

4.2. Comparison with previous work The PT processes in DNA base pairs have been extensively investigated from experimental and theoretical points of view.29-33 Kumar and Sevilla investigated theoretically the hydration effects on the energy barrier of PT in Guanine-Cytosine

12


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radical cation (G-C)+ base pair. Their calculations showed that the hydration diminishes the activation barrier of PT in (G-C)+. In the present calculation, the solvent effects on the PT time were neglected because we simplified extremely the reaction model of PT process. To check the solvent effects on the PT process, a simple polarizable continuum model (PCM) was applied to the potential energy curves in o-F-(AP)2+ (Fig.S3 in supporting information). The activation barrier for the forward reaction slightly increased by the water, but the reverse reaction was changed to the endothermic reaction. The PT reaction of F-(AP)2+ was thus affected by the solvent water. To elucidate the effect of solvent on the PT reaction in details, more accurate treatment would be required in the calculation. In previous paper,24 we investigated the ionization dynamics of (AP)2 using direct AIMD method at the HF/6-311G(d,p) level and showed that PT takes place without activation barrier after the ionization. The time of PT was calculated to be 86 fs at the HF/6-311G(d,p) level. This time is slightly shorter than those of the present calculations. The long-range interaction would need to treat the PT process in DNA base pair.

4.3. Remarks In the present study, several approximations were employed in the calculations. First, zero point energies (ZPEs) was completely neglected in the dynamics calculations because the effects of F-substitution on the reaction dynamics are purely interested in this work. In actual system, however, the DNA base pair possesses ZPEs. To simulate the actual system, the inclusion of ZPEs would be needed as a future work. To check the dependence of initial geometry on the reaction dynamics, the direct AIMD calculation from the B3LYP/6-311G(d,p) and CAM-B3LYP/6-311++G(d,p) 13



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geometries were run. However, the similar results were obtained. Next, the CAM-B3LYP functional was used in the direct AIMD calculation because this level is limited in our computer facility. To elucidate more detail of the reaction dynamics, more accurate wave functions, e.g. CASSCF and MP2, are required. Despite several approximations employed here, it has been shown that a theoretical characterization of PT dynamics enable us to obtained valuable information on the effects of F-substitution on the reaction mechanism.

Acknowledgment. The author (HT) acknowledges partial support from JSPS KAKENHI Grant Number 15K05371 and MEXT KAKENHI Grant Number 25108004.

Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI. >Vertical ionization and reaction energies. Potential energy curves for the proton transfer (PT). PT rates calculated at several levels of theory.

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Figure captions

Figure 1. (Color online). (A) Chemical structure of amino-pyridine dimer (AP)2 and (B) optimized structure of (AP)2 calculated at the MP2/6-311++G(d,p) level. Notations of o-, m-, p-, and 5-positions mean the F substitution position in (AP)2. Bond lengths are in Å. Figure 2. (Color online). Optimized structures of fluorinated amino-pyridine dimers F-(AP)2. The calculations were carried out at the MP2/6-311++G(d,p) level. Bond lengths are in Å. Figure 3. (Color online). Snapshots of o-F-(AP)2+ following the ionization of o-F-(AP)2 calculated by direct AIMD calculation. Distances are in Å.

Figure 4. (Color online). Time evolution of potential energy and bond distances of o-F-(AP)2+ obtained by direct AIMD calculation. Figure 5. (Color online). Rates of proton transfer in (AP)2+ and F-(AP)2+ after the ionization. Figure 6. (Color online). Time evolution of potential energies of all F-(AP)2+ obtained by direct AIMD calculation. Figure 7. (Color online). NPA atomic charges on hydrogen bond sites in F-(AP)2+ at the vertical ionization point. The values were calculated at the CAM-B3LYP/6-311G(d,p) //MP2/6-311++G(d,p) level. Figure 8. (Color online). Snapshots of spin densities on o-F-(AP)2+ after the ionization of the neutral state: (Left) o-F-(AP)2+, (Right) m-F-(AP)2+. Calculations were carried out at the CAM-B3LYP/6-311G(d,p) level.

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Figure 9. (Color online). Spatial distributions of HOMO of o-, m-, p-, and 5-(AP)2. Arrow indicates the direction of proton transfer (PT) after the ionization. Figure 10. (Color online). Average rates of proton transfer in (AP)2+ and F-(AP)2+ after the ionization. The geometries were generated by 10 K simulations.

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Figure 1.

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Figure 2

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Figure 3.

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Figure 4.

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Figure 5.

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Figure 6.

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Figure 7.

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Figure 8.

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Figure 9.

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Figure 10.

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Graphical Abstract

31


Molecular Design of Ionization-Induced Proton Switching Element

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