Elsevier

Chemical Physics

Volume 294, Issue 3, 1 November 2003, Pages 483-499
Chemical Physics

Molecular orbital study of the primary electron donor P700 of photosystem I based on a recent X-ray single crystal structure analysis

https://doi.org/10.1016/S0301-0104(03)00378-1Get rights and content

Abstract

The X-ray structure analysis of photosystem (PS) I single crystals showed that the primary electron donor P700 is a heterodimer formed by one chlorophyll (Chl) a and one Chl a [Nature 411 (2001) 909]. The electronic structure of the cation radical P700+radical dot of the primary donor, which is created in the charge separation process, has been probed by semiempirical molecular orbital calculations including spin polarization effects (RHF-INDO/SP). The calculations, which were based on the X-ray structure, clearly show that P700 is a supermolecule formed by two chlorophyll species. They furthermore predict an asymmetrical charge and spin density distribution in favor of the monomeric Chl a half of this dimer in accordance with results from earlier EPR and ENDOR studies [J. Phys. Chem. B 105 (2000) 1225]. The stepwise inclusion of various electrostatic interactions of the dimer with its nearest surrounding (one threonine forming a hydrogen bond to the keto group of Chl a and two histidines liganding the Mg atoms of the two chlorophylls) leads to a systematic enhancement of this electronic asymmetry yielding a spin density ratio of almost 5:1 as also found experimentally. A large part of this value is caused by spin polarization effects. This result is only weakly affected by the electrostatic field of more remote amino acid residues and other pigment molecules (‘accessory’ Chl a molecules) present in PS I. A separate group of calculations involving local geometry optimizations by energy minimization techniques yields a further enhancement of the spin density asymmetry. A particularly strong effect is obtained by allowing for variations of the geometry of the vinyl groups on both chlorophylls of the P700 dimer. Theoretical results for individual isotropic proton and nitrogen hyperfine coupling constants, showing a satisfactory agreement with experimental findings, are also presented.

Introduction

Photosystem I (PS I) from the thermophylic cyanobacterium Synechococcus elongatus has recently been crystallized [1] and its three-dimensional structure determined by X-ray structure analysis at 2.5 Å resolution [2]. PS I catalyzes the light induced transmembrane charge separation from plastocyanin (or cytochrome c6), located inside the thylakoids to ferredoxin, located on the stromal side of the membrane. The electrons transferred from PS I to ferredoxin are finally used for the reduction of NADP+ and H+ to NADPH. The latter is subsequently used to reduce carbon dioxide in the following dark reactions of the Calvin cycle [3].

Initially the light reaction generates a powerful reductant, the singlet excited state of the primary donor, P700*. The composition and electronic structure of P700 has been a matter of considerable debate for several decades, for a review see [4]. The X-ray structure shows [2] that P700 is a heterodimer formed by one chlorophyll a (Chl a) molecule and one chlorophyll a (Chl a) molecule, the C132 epimer of Chl a (Fig. 1). The existence of Chl a in PS I had already been proposed earlier [5], [6]. Specifically, in this C132 epimer of Chl a, the two substituents at pos. 34 in ring V are interchanged, causing the carbomethoxy group to be positioned on the same side of the porphyrin macrocycle as the phytyl chain (pos. 17), see Fig. 2. There are no other evident structural differences between Chl a and Chl a from the X-ray structure. The X-ray structural analysis predicts practically equal dihedral angles of ∼−104° for the vinyl groups of Chl a and Chl a, respectively. The macrocycles of both Chl a and Chl a show a dome-like deviation from planarity (cf. Fig. 1). The chlorin planes of the two chlorophylls of P700 are parallel to each other with an interplanar distance of (3.6 ± 0.3) Å and there is partial overlap of corresponding rings I and II. Whereas amino acid residues (AARs) of the surrounding protein form hydrogen bonds to Chl a (see Fig. 1), no hydrogen bonds are found on the Chl a side [2].

Apart from this spatial structure which appears quite asymmetric, a knowledge of the electronic structure of P700 is of importance for an understanding of the functional properties of PS I. In particular, it is important to know whether P700 is also electronically a dimer which must be described by a wave function extending over both dimer halves as found for the bacteriochlorophyll dimers in bacterial reaction centers (RCs). For the paramagnetic oxidized state P700+radical dot created in the ET process, such information can be deduced from electron paramagnetic resonance (EPR) [7], [8], [9], electron-nuclear-double resonance (ENDOR) [9], [10], [11], [12], [13], [14], [15], [16], [17], and electron-spin-echo-envelope-modulation (ESEEM) experiments [18], [19], [20], [21], [22], [23]. However, the spectroscopic data obtained in the past have been interpreted quite differently and various models have been proposed for the primary donor P700 in PS I ranging from a symmetric dimer [7], [11], via asymmetric dimer models [15], [17] to chlorophyll monomers [10], [21]. Based on more recent experimental studies on PS I single crystals [4], [14] and of various PS I mutants [4], [17], [24] it has been concluded that P700+radical dot is also electronically a dimeric species with the spin density predominantly located on the Chl a half of the dimer. Asymmetry factors ranging from 0.7:0.3 to 0.9:0.1 have been discussed [4]. Quantum chemical studies addressing this problem have so far been lacking due to the absence of a reliable spatial model for P700. With the recent X-ray structure analysis at 2.5 Å resolution [2] this problem has now been solved.

It is the aim of the present quantum chemical molecular orbital (MO) study to corroborate the dimer model for the primary donor in PS I and to analyze theoretically in more detail the effects of the various structural features of P700 and its surrounding on: (i) the spin and charge density distribution and (ii) the energetic properties, such as total energies and orbital energies (oxidation potentials) of the oxidized radical species P700+radical dot. Some additional aspects, such as the possible formation of enol structures of Chl a, which have been proposed to play a role for P700 [25], will also be considered.

We have applied the semi-empirical quantum chemical method RHF-INDO/SP [26] which has proved to be quite successful in studies on chlorophyll radical ions in general and in analogous studies on the primary donor cation radicals P865+radical dot [27] and P960+radical dot [28] in bacterial RCs.

Section snippets

RHF-INDO/SP

This method is a variant of the well-known semi-empirical self-consistent-field MO method INDO developed by Pople and Beveridge [29]. INDO uses the full valence orbital basis set which is essential for molecules of low symmetry. Our modified approach avoids the convergence and spin contamination problems of the standard UHF treatment of large open shell systems like P700+radical dot by using the “half-electron-method” introduced by Dewar et al. [30]. This method treats open shell systems similarly to the

Results

The computations were performed on different structural cases described in the following text and compiled in Table 1 for quick reference. These cases are essentially based on the X-ray structural data and characterized by different degrees of sophistication in the consideration of structural details including effects of the medium surrounding P700. They begin with the “bare” dimer halves Chl a and Chl a, abbreviated A and B, respectively, and end with the “dressed” dimer P including all

Spin and charge asymmetry

This section will mainly focus on the possible sources and on the magnitude of the spin and charge asymmetry of the dimer radical cation P700+radical dot. This asymmetry could be of fundamental importance for the detailed understanding of the functional role of the electron donor P700 in the ET process. From experimental studies with ENDOR and TRIPLE resonance methods [14], [17], it has been concluded that the spin density is predominantly located on the Chl a half B of P700 with a ratio RB/A≅5.7 (85% on

Summary and conclusion

We have shown that the observed strong asymmetry of the spin distribution on the P700 dimer radical cation is in qualitative agreement with semiempirical quantum chemical molecular orbital theory if presupposing the spatial structure recently determined by X-ray analysis. The theory predicts an intrinsic electronic asymmetry of RB/A=2.83 (QB/A=1.72) of the “bare” dimer which cannot be traced to a specific structural feature of either half A (Chl a) or B (Chl a). In particular, this intrinsic

Acknowledgments

Arnold Hoff was one of the first researchers to work on the dimer problem in photosynthesis. When working with George Feher at UC San Diego as a postdoc in the early seventies, he showed the existence of the bacteriochlorophyll dimer in bacterial reaction centers using ENDOR spectroscopy. He later also worked on the donors in plant RCs. We enjoyed many fruitful discussions with Arnold that helped in the analysis of our data. We also owe special thanks to Sebastian Sinnecker (Max Planck

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