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J. Phys. Chem. B 2007, 111, 5596-5601
Theoretical Study of r-84 Phycocyanobilin Chromophore from the Thermophilic Cyanobacterium Synechococcus elongatus Costantino Zazza,*,†,‡ Nico Sanna,† and Massimiliano Aschi‡ Consorzio InteruniVersitario per le Applicazioni di Supercalcolo per UniVersita` e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, UniVersita` di L’Aquila, Via Vetoio (Coppito 1), 67010 L’Aquila, Italy ReceiVed: February 5, 2007
Time-dependent density functional theory (TD-DFT) calculations were performed to obtain vertical excitation energies from the ground state to different low-lying singlet excited states of the protonated R-84 phycocyanobilin chromophore (R-84 PCBH+). It clearly emerges that three gradient-corrected approximation functionals (B3LYP, PBE0, and PBEPBE) show a similar description, confirming the proposed valence assignment of the strongest UV-vis absorption band at 618 nm. Moreover, our results show that there are not appreciable differences, in terms of excitation wavelength of the main peak, between the R-84 PCBH+ chromophore and a model system in which the two propionic chains have not been taken into account. Finally, with the precise aim of investigating the effects of R-84 PCBH+ conformational fluctuations on its electronic properties, vertical excitation energies obtained for the potential energy local minimum structure were also refined using a recently proposed TD-DFT/principal component analysis/Car-Parrinello molecular dynamics computational approach. Interestingly, and in line with previous results on another photosensitive complex, this study essentially suggests that interaction with the surrounding environment (protein matrix plus solvent molecules) coupled with the large amplitude fluctuation of the whole C-Phycocyanin (C-PC) pigment protein can affect the electronic properties of the R-84 PCB chromophore and therefore its biological activity.
1. Introduction Light harvesting in cyanobacteria and red algae is a function of phycobilisomes that are located on the surface of photosynthetic membranes1 and has the important role of transferring light energy to a photosynthetic reaction center very efficiently.2-5 The phycobilosomes are essentially formed by assembling biliproteins.6 C-Phycocyanin (C-PC) is one of the most important biliproteins that has covalently bound bilin chromophores known as phycocyanobilins (PCBs)7 (shown in Figure 1a). Crystallographic results have identified three different PCBs termed as R-84 PCB, β-84 PCB, and β-155 PCB according to their position along the primary structure of the protein.8-12 The photophysical properties of these chromophores are of crucial importance for the biological activity of the reaction center. For this reason, in the few last years, we have witnessed a very active interest, in particular, in the electronic properties of R-84 PCB and on the effect of the protein and solvent environment.13-16 According to UV and CD experimental data,15,16 R-84 PCB of C-PC shows quite a large absorption interval in the range between 500 and 650 nm with a maximum at 618 nm, which arises from a valence 1π f π* electronic transition, and a small shoulder at 570 nm. High-level theory quantum chemical calculations13 and semiempirical INDO-CI data14 have suggested that the shoulder peak at 570 nm comes from a chargetransfer (CT) transition from a nearby amino acid residue, Asp87, to the same π* molecular orbital involved in the main absorption of the R-84 PCB molecule. However, despite such * Corresponding author. E-mail:
[email protected]. Tel.: +39 06 44486720. † Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita` e Ricerca. ‡ Universita ` di L’Aquila.
Figure 1. (a) Geometry of R-84 PCBH+ chromophore. Red balls represent O, blue N, bronze C, and white H atoms. (b) Geometry of R-84 s-PCBH+ model system (s-FO-PCBH+).
investigations, there are still some aspects that need to be better clarified. In particular, R-84 PCB is a relatively flexible molecule whose electronic properties may be heavily affected by conformational transitions.17 All the previous calculations13,14 have been carried out on the R-84 PCB conformation equal or similar to the one present in the complex with biliprotein. The primary goal of the present study is to computationally characterize the
10.1021/jp070994g CCC: $37.00 © 2007 American Chemical Society Published on Web 04/27/2007
Study of R-84 Phycocyanobilin Chromophore intrinsic electronic properties of a flexible R-84 PCB molecule using a recently proposed computational technique,17 which combines TD-DFT calculations18 with principal component analysis (PCA)19 and Car-Parrinello molecular dynamics (CPMD).20 This study also aimed at extending previous theoretical studies, using different levels of theory (different combination of density functionals and basis sets), for estimating the effect of the biological environment (protein and solvent) on R-84 PCB electronic properties. 2. Materials and Methods 2.1. Geometry Optimizations and Vertical Excitation Energies. The structure of R-84 PCB was obtained from the crystal structure of C-PC isolated from the thermophilic cyanobacterium Synechococcus elongatus,10 and the hydrogen atoms were added to the molecule and semiempirically minimized by the AM1 method.21 Although the crystal structure does not give any evidence for the protonation state of the chromophore, the highly conserved Asp87 residue is supposed to transfer a proton to R-84 PCB. Therefore, and in line with previous computational studies,13,14 we have considered the protonated state of R-84 PCB, hereafter indicated as R-84 PCBH+. Geometry optimizations employing the DFT22,23 within generalized gradient-corrected approximation (GGA) were then accomplished for R-84 PCBH+ relaxing first only the hydrogen positions and then all the remaining internal coordinates. For indicating the last situation, we hereafter use the FO (fully optimized) acronym. For this purpose, the B3LYP24,25 and PBE026-28 hybrid functionals were adopted in combination with the 6-31G* and 6-311++G* atomic basis sets.29 TD-DFT calculations were then performed on R-84 PCBH+ to obtain vertical excitation energies from the ground to the lowest singlet electronic excited states. Note that with the development of a linear scaling procedure, the TD-DFT approach is probably, nowadays, the most accurate theoretical approach that can be applied to large and complex systems such as the present one.18 Finally, to roughly evaluate also environmental effects on the spectroscopic response, vertical absorptions were also reevaluated by carrying out the same TD-DFT calculations corresponding to a chemical environment described by the polarizable continuum model (PCM).31 In this respect, to take into account the effects of the C-PC protein, we have considered the protein as an external electric field (with a dielectric constant of 4.0),32 which acts on R-84 PCBH+. To further refine the local structure modeling of the environment around the chromophore, we also computed TD-DFT/PCM absorption energies in the presence of the highly conserved Asp87 amino acid residue and explicit solvent molecules. 2.2. TD-DFT/PCA/CPMD Methodology and Software. For introducing, to a qualitative extent, the thermal effects for studying the relationship between local semiclassical fluctuations and electronic properties of R-84 PCBH+, we carried out damped second-order ab initio molecular dynamics33a within the CP scheme20,33b and PCA procedure19 indicated as the TDDFT/PCA/CPMD methodology. According to this approach, the configurational space accessible to a molecule in its electronic ground state is spanned by means of -CPMD. The trajectory is then analyzed using essential dynamics.19 In this study, we carried out CPMD simulations in the gas phase. Such a choice, although preventing any quantitative interpretation of the results, is the only computationally accessible procedure for qualitatively evaluating the effects of internal fluctuations on the electronic properties of the chromophore and, consequently, also for gaining some information on the mechanical role of the protein
J. Phys. Chem. B, Vol. 111, No. 20, 2007 5597 matrix with a computational strategy that has been recently successfully applied to similar systems.17 With this purpose, a covariance matrix C of the positional fluctuations of the atoms was constructed and diagonalized. This procedure provides a new set of generalized coordinates associated with the eigenvectors of the matrix. The value of the associated eigenvalues (i.e., the fluctuations along the eigenvectors) allows us to separate the intramolecular large collective essential motions (large eigenvalues) from the remaining small amplitude fluctuations (i.e., in constrained motions). This space defined by the essential motions, finally, allows us to identify the most sampled conformations of the molecule. In the present case, the problem is complicated by the presence of propionic chains whose flexibility would require very long simulation times. For these reasons, we carried out TD-DFT calculations as described in the previous section also on an R-84 PCBH+ system without such groups, hereafter termed as R-84 s-PCBH+ (depicted in Figure 1b). This choice may be justified by the rather low influence17 (see section 3.1 of this paper) of the propionic chains on the backbone conformational fluctuations. For these calculations, we adopted a plane-wave (PW) pseudo-potential (PPs) approach in conjunction with ultrasoft self-consistent PPs;34 the electronic structure calculation is based on density functional theory, using the Perdew-Burke-Ernzerhof (PBE) GGA for exchange and correlation energy.26,27 The PW calculations have been performed in an orthorhombic cell where the charge neutrality has been ensured by a uniform background charge.35a,35b Energy cutoffs of 25 and 200 Ry have been applied to truncate the PW expansion of pseudo-wave functions and of the augmented charge density, respectively.35 A time step of 10 au (0.242 fs) has been applied to integrate the equations of motion. The model system was then heated from 100 to 300 K, and a simulation of 15 ps was carried out in the canonical (NVT) ensemble. Such a simulation time is certainly too short for any quantitative evaluation. However, significantly longer time scales (i.e., on the order of nanoseconds) are computationally rather expensive, and simulations in the range of tens of picoseconds are nowadays commonly used for semiquantitative molecular property evaluations of systems even more complex than the present one.36 However, it is important to stress that, for the goals of the present theoretical investigation, such a relatively short time turned out to be sufficient enough to estimate the semiclassical internal motions characterized by a frequency of about 5 cm-1. The temperature was kept constant by the Nose´ thermostat.37 The CP trajectory was performed with the CP-Vanderbilt code released within the Espresso package.33c We consider this method applicable to gas-phase conditions, liquid-phase organic and organometallic chemistry, and surfaces (in particular, nanostructured systems). PCA decomposition was done using the Gromacs package utilities,19b whereas all the TD-DFT calculations were performed using Gaussian 03.30 Calculations were run on a four-way HP Proliant DL585 server with a Dual-Core AMD Opteron Processor running at 2.4 GHz. Since the PCA decomposition substantially is very fast, the computational cost of this method is that generally required by CPMD simulation and time-dependent calculations carried out taking into account only the selected structures along the largest amplitude fluctuations. 3. Results and Discussion 3.1. Geometry Optimizations and Low-Lying Singlet Excited States. The singlet electronic ground state geometries of free R-84 PCBH+ and R-84 s-PCBH+ were optimized at the B3LYP/6-31G*, PBE0/6-31G*, B3LYP/6-311++G*, and PBE0/
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TABLE 1: Calculated and Experimental Excitation Wavelength (∆E, in nm) of the Lowest Valence 1π f π* Electronic Transition with Corresponding Oscillator Strength (f) at Different Levels of Theorya method
model
∆E
f
TD-B3LYP/6-31+G*13a
FO-PCB FO-PCBH+ FO-PCBH+ + Asp87 PCBH+ FO-PCBH+ FO-PCBH+ s-FO-PCBH+ s-FO-PCBH+ C-PC
539 582 565 588 584 568 592 577 618
1.09 1.32
TD-B3LYP/6-31+G*13a TD-B3LYP/6-31+G*13a INDO-CI14 TD-B3LYP/6-311++G* TD-PBE0/6-311++G* TD-B3LYP/6-311++G* TD-PBE0/6-311++G* exptl value15,16
1.30 1.33 1.35 1.40 1.42
a FO: fully optimized R-84 PCBH+ structure (Figure 1a) and s: simpler PCB structure (without the two propionic groups in Figure 1b).
6-311++G* level of theory, respectively. The geometrical parameters did not result in being appreciably sensitive to the level of the computations. TD-DFT calculations were carried out using the same functional basis set combination. In Table 1, we only report, for the sake of brevity, results with the largest 6-311++G* atomic basis set, and the results are presented and compared with experimental data. From the comparison of UV and CD experimental data of C-PC15,16 and considering previous semiempirical (INDOCI)14 and DFT calculations (TD-B3LYP),13 it clearly emerges that, irrespective of the employed atomic basis set, B3LYP and PBE0 provide a similar description of the main excitation both showing π(HOMO) f π*(LUMO) character along the whole aromatic moiety. It is worth noting that the agreement with previous TD-DFT calculations published by Wan et al.13a confirms that the structure of the R-84 PCB antenna complex is similar in two organisms, S. elongatus10 and Fremyella diplosiphon.11 However, both density functionals seem to moderately overestimate the experimental transition energy value even though the B3LYP functional seems to perform slightly better. Moreover, our TD-DFT results provide transition energy differences between s-FO-PCBH+ and FO-PCBH+ within 9 nm; such a result is most likely due to the π f π* character of the main peak, which involves molecular orbitals essentially localized within the aromatic skeleton. Furthermore, corresponding to the R-84 PCBH+ optimized structure, at the B3LYP/ 6-311++G* the level of theory, the electric dipole moments of the lowest excited states were also evaluated. If compared with the ground state, it is quite evident that the lowest valence electronic transition increases the norm of the electric dipole moment of the chromophore (from 5.3 to 8.2 D). Unfortunately, no experimentally determined dipoles are available in the literature for evaluating the quality of the present results.
Nevertheless, this result suggests the importance of the interaction between the light-harvesting center and its biological environment, which allows a more realistic description of the C-PC system in comparison with isolated QM calculations on the R-84 PCBH+ subsystem. As a matter of fact, in a recent paper,13a always using the DFT approach, the authors have shown that the effect of the C-PC protein environment is very important. The model system consisted of the PCBH+ + Asp87 complex embedded in a chemical environment described by the PCM model.31 In this respect, the authors considering the gasphase geometry of the PCBH+ + Asp87 complex and using a dielectric constant of 4.032 to take into account the medium effect of the protein have shown that the excitation wavelength of the main peak, with respect to the ideal gas-phase condition, is redshifted by 29 nm (from 565 to 594 nm, see Tables 1 and 2). The same trend had already been observed by Kikuchi and coworkers.14 In line with previous finding,13a our data reported in Table 2 show that the inclusion of the PCM model shifts the transition energy of the main peak toward the experimental assignment. In fact, with respect to gas-phase results, a redshift (approximately 26 nm for the FO-PCBH+ chromophore and 18 nm for the s-FO-PCBH+ system, respectively) was always obtained after geometry optimization within the PCM model. From the same table, we wish also to remark that at the TD-B3LYP/6-311++G*/PCM level of theory, the s-FOPCBH+ model system and the FO-PCBH+ chromophore provide the same excitation wavelength (i.e., 610 nm, see Table 2). This result suggests that, at least at the levels of theory applied, the complexity (in terms of nuclear and electronic degrees of freedom) of R-84 PCBH+ can be reduced, neglecting the inclusion of two propionic chains to evaluate its electronic properties. Furthermore, the inclusion of diffuse functions in the basis set improves the agreement between theory and experimental assignment; as a matter of fact, it is evident that in comparison with the 6-311++G* basis set, the 6-31G* one systematically underestimates the excitation wavelength of the lowest 1π f π* (data not shown) transition. This finding indicates that for a more realistic quantum mechanics description of the photosensitive active site in the C-PC pigment protein, a basis set including diffuse functions should be used. Since the latter model does not include the microscopic structure of the environment around the solute molecule, similar to previous studies,13a we have also computed the absorption energies in the presence of the Asp87 residue and explicit water molecules. The TD calculations carried out on the FO-PCBH+ + Asp87 model provide shifts in agreement with those previously calculated by Wan et al.13a It is also interesting to remark, from the same table, that at our best level of theory (i.e., TD-B3LYP/6-311++G*/PCM), the lowest CT electronic
TABLE 2: Calculated TD-B3LYP/PCM Vertical Excitation Wavelength (∆E-PCM, in nm) of the Lowest Valence 1π f π* and CT (Asp87 f r-84 FO-PCBH+) Electronic Transitions with Corresponding Oscillator Strength (f-PCM) at Different Levels of Theory, as well as Corresponding Excitation Wavelength (∆E-GP, in nm) in Ideal Gas-Phase Conditions ∆E-GP
f-GP
∆E-PCM
TD-B3LYP/6-31+G*13a TD-B3LYP/6-311++G* TD-B3LYP/6-311++G* TD-B3LYP/6-311++G* TD-B3LYP/6-311++G* TD-B3LYP/6-311++G* TD-B3LYP/6-311++G*
π f π*(Exp 618 nm)15,16 FO-PCBH+ + Asp87 565 FO-PCBH+ 584 FO-PCBH+ + Asp87 569 s-FO-PCBH+ 592 s-FO-PCBH+ + 2H2O(A) 593 + s-FO-PCBH + 2H2O(D) 594 s-FO-PCBH+ + 4H2O(A+D) 596
1.32 1.33 1.34 1.40 1.42 1.43 1.44
594 610 593 610 610 611 614
TD-B3LYP/6-31+G*13a TD-B3LYP/6-311++G*
FO-PCBH+ + Asp87 FO-PCBH+ + Asp87
method
model
f-PCM
1
CT (Exp 570 nm)15,16 583 622
539 567
1.55 1.46 1.47 1.54 1.57 1.56 1,57 0.0005 0.002
Study of R-84 Phycocyanobilin Chromophore
Figure 2. Geometry of (1:4) hydrogen-bonded R-84 PCBH+ complex. Red balls represent O, blue N, bronze C, and white H atoms.
transition (Asp87 f R-84 FO-PCBH+) drops at 567 nm, in agreement with the experimental assignments at 570 nm.15,16 Finally, hydrogen-bonded complexes, including from two (1:2) to four (1:4) solvent molecules, were also considered for geometry optimizations and TD calculations in the PCM model. In these complexes, the water molecules would roughly simulate the inner solvent shell, interacting with each carbonyl group of the light-harvesting complex. Interestingly, for the 1:2 microsolvated structures, we note essentially the same behavior characterized by a solvatochromic shift in the range previously predicted considering only the mean field approach. On the other hand, the calculations carried out on the highest coordination model (1:4, see Figure 2) provide a stronger solvatochromic shift corresponding to an excitation energy value (614 nm at the TD-B3LYP/6-311++G*/PCM level) in excellent agreement if compared to the experimental data of 618 nm.15,16 In this respect, our calculations provide, up to now, the most accurate (in terms of atomic basis set and level of theory) evaluation of the relative low-lying valence state excitation energy present in the literature. In line with previous computational data,13a,14 our results show that the effects on the low-lying valence PCB excited states can be summarized as being due to (i) protonation of the PCB chromophore, (ii) interaction with the highly conserved Asp87 residue, and (iii) long-range interaction with the protein environment, and (iv) hydrogen-bonding network with explicit solvent molecules. 3.2. Effect of Conformational Transitions. The previous section indicates that the employed computational methods provide a rather suitable tool for investigating electronic transitions in PCB. This allows us to safely address the central question of the present study as to whether and to what extent local conformational motions of the photosensitive center affect its own spectroscopic features. The TD-DFT/PCA/CPMD methodology was then applied to the simplified R-84 s-PCBH+ system whose low-lying valence excitation energies were rather close to R-84 PCBH+ (see Table 1). CP simulation of 15 ps followed by essential dynamics show that the conformational transitions of gaseous R-84 s-PCBH+ are characterized by a fluctuation along a single eigenvector. From a mechanical point of view, this motion may be described as a torque-like motion in which the terminal rings provide the largest contribution (see Figure 3). In Figure 4a, we reported the 1π f π* (TD-B3LYP/6311++G*) vertical excitation wavelength calculated for different structures sampled along the first essential eigenvector; the related oscillator strengths are reported in Figure 4b. From these figures, one can observe that, although the oscillator
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Figure 3. Extreme configurations (-1, 1) selected along the first essential eigenvector as obtained by Car-Parrinello molecular dynamics simulation. Zero is the averaged structure of the R-84 PCBH+ model system. Red balls represent O, blue N, and bronze C atoms.
Figure 4. TD-B3LYP/6-311++G* vertical excitation wavelength (dashed line) (a) and oscillator strengths (b) for the lowest valence 1π f π* electronic transition (strongest UV-vis absorption band in the range between 300 and 700 nm) of the R-84 s-PCBH+ model system in ideal gas-phase conditions along the first essential eigenvector as compared to the excitation wavelength (solid line) at the local minimum structure. Zero is the averaged structure of the R-84 s-PCBH+ model system.
strength undergoes rather small fluctuations, the semiclassical conformational transitions sharply alter the excitation wavelength that spans a region as large as 30 nm. In Figure 4a,b, we also indicate the corresponding value previously calculated for the gas-phase FO-R-84 s-PCBH+ (592 nm at the same level of theory, i.e., TD-B3LYP/6-311++G*). This finding clearly demonstrates the dramatic influence of the semiclassical molecular fluctuations onto the first lowest valence electronic transition of such a chromophore.
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Figure 5. 300 K Helmholtz free energy (dashed line) as a function of TD-B3LYP/6-311++G* vertical excitation wavelength of the lowest valence 1π f π* electronic transition (strongest UV-vis absorption band in the range between 300 and 700 nm) of the R-84 s-PCBH+ model system in ideal gas-phase conditions as obtained by cluster analysis.
In conclusion, our results on the present TD-DFT/PCA calculations show that the largest backbone internal fluctuation (reported in Figure 3) tunes the electronic properties of the PCB molecule, lowering the vertical excitation energy of the strongest absorption band in the range between 300 and 700 nm. As a final step in the investigation, we also evaluated the actual gas-phase spectrum (i.e., the excitation energy distribution and spectral transition weighted for the statistically relevant conformations of R-84 s-PCBH+ at 300 K according to our CPMD simulation). To this end, we carried out cluster analysis on the same CP trajectory. The TD-B3LYP/6-311++G* calculations were performed for eight structures with a RMSD value (mass weighted, neglecting the hydrogen atoms) between 0.14 and 0.58 nm. The weight of each structure was then found by using the relative Helmholtz free energy calculated with respect to a reference structure as -RT ln(Pi/Pref), where Pi is the occurrence frequency of the ith structure and Pref is the occurrence frequency of the reference. The results of this analysis, reported in Figure 5, indicate that the most stable conformation absorbs at a higher energy, whereas the conformation resembling the crystal structure (i.e., the local free energy minimum at +4.4 kJ/mol) absorbs at about 592 nm as was previously indicated. According to our results, we can assess that the protein matrix, in this case, should act not only as a perturbation on the electronic properties but also as a mechanical constraint, allowing R-84 s-PCBH+ to adopt a structure found in the crystal that actually represents a high-energy conformation. It is worth noting that, if the selected structures along the first essential eigenvector as well as those extracted from the cluster analysis were locally fully relaxed, the main absorption band was systematically found to be equal to its previously obtained value taking into account only the local minimum conformation; the agreement between the fully and the locally relaxed conformations suggests that the conformational sampling is essentially confined within the region characterized by the local minimum energy structure. The same trend was observed starting from the protein constrained (PC) conformation, even thought the X-ray structure of the R-84 PCB antenna complex was basically never sampled during the CP simulation. This last finding, at least within the range explored, indicates that the C-PC protein probably modulates the PCB chromophore in its configurational space and, consequently, in its electronic responses.
Zazza et al.
Figure 6. TD-B3LYP/6-311++G* UV-vis spectrum for gas-phase R-84 s-PCBH+ at 300 K (see text).
Finally, in Figure 6, we show the corresponding spectrum from which we may infer a blue-shift of 40 nm with respect to the experimental detection in the protein matrix in solution. Therefore, when the PCB molecule is confined within the local minimum conformation, our calculations nicely reproduce the experimental observation if the inclusion of the environment perturbation is considered (see Table 2). If, on the other hand, the chromophore is left to fluctuate, its intrinsic spectroscopic features are rather altered (see Figure 6); as a matter of fact, during CPMD simulation at 300 K, the PCB chromophore is rather flexible, and its electronic properties cannot be addressed by only considering the potential energy absolute minimum (then neglecting the inclusion of thermal effects). We wish also to remark that the use of a different functional (PBE) does not alter the picture. Although further investigations are obviously needed, the combined use of the TD formalism and essential dynamics clearly shows that the spectroscopic features of the R-84 PCB (not occurring in crystal but in physiological conditions where internal fluctuations are conceivable) cannot be completely addressed by only using a static approach. In fact, an interesting correlation between electronic properties and conformational fluctuations in R-84 PCBH+ has emerged, suggesting a possible conformational regulation mechanism of the photochemical activity. The surrounding protein, from this study, is supposed to act both as a perturbation of the electronic properties of the chromophore as well as a conformational constraint. 4. Conclusion In this article, we used the density functional theory within its time-dependent formalism to investigate the influence of the surrounding environment on vertical excitation energies from the ground state to different low-lying singlet excited states of the R-84 phycocyanobilin chromophore. Moreover, for the first time, a direct computational evaluation of the R-84 PCB chromophore internal motion on the spectroscopic features of this system has been carried out and may be of some relevance also to experimentalists. Our TD-DFT results being in agreement with the experimental value and in analogy with previous results obtained by means of semiempirical and ab initio calculations show that (i) even for the evaluation of low-lying excitation transitions, in combination with TD-DFT formalism, a rather large basis set is mandatory. (ii) Both environmental effects due to C-PC protein and semiclassical fluctuations of the R-84 PCB chromophore are found to have a decisive influence on the valence excited state electronic properties. (iii) The environment
Study of R-84 Phycocyanobilin Chromophore (protein matrix and solvent) is suggested to act not only as an electrostatic perturbation on chromophore electronic properties but also as a mechanical guide, allowing the chromophore itself to adopt a relatively high-energy conformation. It is also obvious that our data intrinsically suffer for the limitation of our CP-MD simulation. However, in this respect, our next work will be essentially based on a recently developed QM/MM methodology, where the effect of the environment is modeled as an external electric field acting on the unperturbed eigenstates of the chromophore.38 Acknowledgment. The authors gratefully acknowledge Prof. V. Barone for stimulating discussions about density functional theory and the polarizable continuum model. Thanks are also due to the Supercomputing Center for University and Research (CASPUR) for the support given for this computational study. References and Notes (1) Glazer, A. N.; Lundell, D. J.; Yamanaka, G.; Williams, R. C. Ann. Microbiol. (Paris) 1983, 134, 159. (2) Danks, S. M.; Evans, E. H.; Whittaker, P. A. Photosynthetic Systems; Wiley: New York, 1984. (3) Feher, G.; Allen, J. P.; Okamura, M. J.; Rees, D. C. Nature 1989, 339, 111. (4) Poter, G.; Tredwell, C. J.; Searle, C. J.; Barber, G. F. W. J. Biochim. Biophys. Acta 1978, 501, 232. (5) Mimuro, M.; Yamazaki, I.; Murao, T.; Yamazaki, T.; Yoshihara, J.; Fujita, Y. AdVances in Photosynthetic Research; Sibesma, C., Ed.; Mijhoff, M. and Junk W. Publishers: Hague, The Netherlands, 1984; Vol. I, p 21-28. (6) Glazer, A. N. Biochim. Biophys. Acta 1984, 768, 29. (7) Lundell, D. J.; Williams, R. C.; Glazer, A. N. J. Biol. Chem. 1981, 256, 3580. (8) Deisenhofer, J.; Michel, H.; Huber, R. Trends Biochem. Sci. 1985, 10, 243. (9) Dale, R. E.; Teale, F. W. J. Photochem. Photobiol., A 1970, 12, 99. (10) Nield, J.; Rizkallah, P. J.; Barber, J.; Chayen, N. E. J. Struct. Biol. 2003, 141, 149. (11) Guerring, M.; Schmidt, G. B.; Huber, R. J. Mol. Biol. 1991, 217, 577. (12) Stec, B.; Troxler, R. F.; Teeter, M. M. Biophys. J. 1999, 76, 2912. (13) (a) Wan, J.; Xu, X.; Ren, Y.; Yang, G. J. Phys. Chem. B 2005, 109, 11088. (b) Ren, Y.; Wan, J.; Xu, X.; Zhang, Q.; Yang, G. J. Phys. Chem. B. 2006, 110, 18665. (14) Kikuchi, K.; Sugimoto, T.; Mimuro, M. Chem. Phys. Lett. 1997, 274, 460.
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