Pigment molecules, orientation

A close relationship exists between physicochemical properties of pigment molecules and their ability to be absorbed and thus to exhibit biological functions. Carotenoids are hydrophobic molecules that require a lipophilic environment. In vivo, they are found in precise locations and orientations within biological membranes. For example, the dihydroxycarotenoids such as lutein and zeaxanthin orient themselves perpendicularly to the membrane surface as molecular rivets in order to expose their hydroxyl groups to a more polar environment. 

Substitution patterns, especially that of the diazotized aromatic amine, determine the color of a pigment to some extent but empirical data do not lead to unambiguous conclusions as to the exact influence of a particular substituent on the shade. The problem is intricate, since the substitution pattern also has a bearing on the size and orientation of a pigment molecule and therefore on its crystal structure, including all the interactions associated with it. 

Fig. 1. The structure of the LHCII monomer as derived from electron crystallography [51], A proposed topography of the polypeptide in the photosynthetic membrane. Letters A, B and C indicate the three hydrophobic ix-helices spanning the membrane. Chlorophyll molecules are arranged into two rings roughly parallel to the membrane plane. B Approximate position of the chlorophyll in the upper level (left) and lower level (right) on the membrane plane. Dashed lines outline a-helices A, B and C. Chlorophyll molecules are oriented perpendicular to the membrane plane and are thus represented as black bars. Chlorophylls numbered as 6,7 and 8 are closer to those belonging to the lower layer than the other pigment molecules...

Li et al. [47] fabricated SAMs of ruthenium phthalocyanine (RuPc) on a silver substrate precoated with an SAM of 4-mercaptopyridine (PySH) or l,4-bis[2-(4-pyridyl)ethenyl]-benzene (BPENB). SERS spectroscopy was used to explore the structure and orientation of the self-assembled films, and they successfully observed Raman bands due to vibrational modes of the pigment molecules in the composite films in the SERS spectra. 

Schematic diagram of the surface of a photosystem in the thylakoid membrane. It contains a patch-like mosaic of several hundred chlorophyll and carotenoid antenna molecules oriented in the membrane. An exciton absorbed by an antenna molecule quickly migrates via the pigment molecules to the reaction centre, P700 its path is shown by the coloured arrows. Although all the antenna molecules can absorb light, only the reaction centre molecule can convert the excitation energy into electron flow.

Sauer and Calvin (1962) demonstrated the orientation of some pigment molecules in spinach quantasomes. These particles exhibit electric birefringence and electric dichroism. Thus the orientation of pigment molecules is not solely related to the whole lamellar system, but is a property of the basic macromolecular particle involved in quantum conversion. 

The three-dimensional crystal structure of Pigment Violet 23 (117) elucidates molecular staples whereby the stables of the single molecular planes are arranged in an almost perpendicular orientation to each other. Interactions of the -ir-orbitals as well as van der Waals forces are responsible for the cohesion of the structure. The degree of overlapping is especially high in the dioxazine part of the molecule [3],... 

The nature of the interfacial structure and dynamics between inorganic solids and liquids is of particular interest because of the influence it exerts on the stabilisation properties of industrially important mineral based systems. One of the most common minerals to have been exploited by the paper and ceramics industry is the clay structure of kaolinite. The behaviour of water-kaolinite systems is important since interlayer water acts as a solvent for intercalated species. Henceforth, an understanding of the factors at the atomic level that control the orientation, translation and rotation of water molecules at the mineral surface has implications for processes such as the preparation of pigment dispersions used in paper coatings. 

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