Methylpyrochlorophyllide A monohydrate monoetherate

Kratky, Christoph; Isenring, Hans Peter; Dunitz, J.D.

doi:10.1107/s0567740877004038

Cited by 33 publications

(14 citation statements)

References 1 publication

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“…In the HF/6‐31G* and B3LYP/6‐31G* optimized 1:1 acetone complexes the Mg atom is shifted 0.45 and 0.36 Å, respectively. This result agrees with the several experimental X‐ray structures were the Mg atom of the porphyrin ring is five coordinated 6–8, 29, 33–36. In the X‐ray structure of ethyl chlorophyllide a dihydrate molecule with five coordinated Mg atom, the Mg atom is 0.385 Å out of plane on the same side as the linking water molecule (see Table 2).…”

Section: Resultssupporting

confidence: 90%

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

Linnanto

Korppi-Tommola

2003

J Comput Chem

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The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.

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Section: Resultssupporting

confidence: 90%

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

Linnanto

Korppi-Tommola

2003

J Comput Chem

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“…In ethyl and methyl chlorophyllide a 2H2O, the crosslinking is between the carbomethoxy groups in one primary chain and the ester C=O of the phytyl groups in an adjoining chain. It has been suggested that two-dimensional sheets could also be formed with only the Mg-coordinated water molecule present, because a small change in the conformation of the propionic acid side-chain allows direct hydrogen-bonding between the propionic ester C=O and the water coordinated to Mg in an adjoining chain (18). A model for the P740 Chla/water micelle based on the small-angle neutron scattering data and crystal structure considerations is shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Small-angle neutron scattering studies of chlorophyll micelles: Models for bacterial antenna chlorophyll

Worcester

Michalski

Katz

1986

Proc. Natl. Acad. Sci. U.S.A.

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Micelles of hydrated chlorophyll a (P740), bacteriochlorophyll a (P865), bacteriochlorophyll c (P750), and pheophytin a prepared in organic media have been studied by small-angle neutron scattering to determine their shape, size, and mass per unit length. All of the micelles are hollow cylinders of well-defined size. The P740 and P750 cylinders are essentially monolayers of macrocycles crosslinked by water, probably in an arrangement similar to that of crystals of chlorophyll derivatives. The P865 micelle is more nearly a bilayer of macrocycles. We show that the curvature necessary to form cylinders probably results from intrinsic curvature of the five-coordinated chlorophyll macrocycle. Studies of P740 micelle formation and the disaggregating effects of another nucleophile (pyridine) are described. As the P750 micelles are nearly identical in size and optical spectra to the rod-shaped structures observed in chlorosomes, and the P865 micelles have optical properties very similar to the in vivo properties of the long-wavelength antenna of purple photosynthetic bacteria, we propose that features of the hydrated cylindrical micelles of these chlorophylls provide good models for antenna chlorophyll in photosynthetic bacteria.Many artificial chlorophyll systems (colloidal dispersions, films, monolayers, adsorbates) are of interest because their visible absorption maxima are red-shifted relative to the corresponding monomeric chlorophyll, a feature that is also characteristic of chlorophylls in vivo (1). Of particular importance are the chlorophyll/water micelles formed in nonpolar organic solvents. Chlorophyll a/water micelles so formed are red-shifted from 660 nm (monomer) to 740 nm and are photoactive in red light (2). Bacteriochlorophyll a/water micelles (P865) have red-shifted optical spectra that strongly resemble those of intact purple photosynthetic bacteria (3). As no direct structural information on these systems exists, we have undertaken a small-angle neutron-scattering study of chlorophyll/water micelles in organic media, using the In- MATERIALS AND METHODS Materials. Chlorophyll a (Chla), bacteriochlorophyll a (Bchla), Chlorobium chlorophyll (Bchlc), and pheophytin a (Pheoa) were prepared by literature methods (4). Purity was established by HPLC and by californium-252 plasma desorption mass spectroscopy (5). Deuterated solvents (Aldrich) contained <1% 1H.Chlorophyll/water micelles were prepared by addition of microliter amounts of 'H20 or 2H20 to previously dried chlorophyll dissolved (=10 mg/ml) in a nonpolar solvent.Mild sonication (30 sec) was used to disperse the water. Rigorous drying of the chlorophylls and the solvents (6) before hydration was necessary as the structures formed from undried or partially dried starting materials can vary. Samples for small-angle neutron scattering were sealed in 2-to 5-mm-thick quartz cells. Neutron Scattering. Chlorophylls of natural isotopic composition were studied in deuterated solvents to enhance the scattering intensity in much the same way neutrons h...

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“…The first structural determination of a chlorophyll-related molecule was done by Hoppe, Will, Gassmann and Weichselgartner on phyllochlorin ester in 1969. Since then a number of chlorophyllides (1, 3) (Strouse, 1973;Chow, Serlin and Strouse, 1975;Serlin, Chow and Strouse, 1975;Dunitz, 1975, 1977;Kratky, Isenring and Dunitz, 1977) and one pheophorbide (2) (Fischer, Templeton, To whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

Structure and conformation of photosynthetic pigments and related Compounds

Senge¹

1992

Zeitschrift Für Kristallographie - Crystalline Materials

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The crystal stnicture of the title Compound (5) (C34H38N4O3, M^ = 550.7) has been determined by X-ray diffraction methods in order to determine the influence of the carbomethoxy group on ring V upon the aggregation behaviour of Chlorophylls. The crystals are green parallelpipeds and crystallize in the orthorhombic Space group P2i2i2iwitha = 8.120 (6), 6 = 14.431(10), c = 24.405(8) Ä, K=2860(3)Ä^ Z = 4, ß = 1.279Mg/m^ >l(Mo/:,) = 0.71069 Ä, // = 0.077 mm"F(000) 1176,130 K. The fmal R value is 0.055 for 1338 observed reflections. The molecules are closely packed by interactions of the propionic ester side chains with each other and by dose contacts of the ClO-meso-proton with the carbonyl group on ring V.

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Methylpyrochlorophyllide A monohydrate monoetherate

Cited by 33 publications

References 1 publication

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

Small-angle neutron scattering studies of chlorophyll micelles: Models for bacterial antenna chlorophyll

Structure and conformation of photosynthetic pigments and related Compounds

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