ORIGINAL PAPER A PM6 study of Rhodopseudomonas Acidophila light harvesting center II B800 bacteriochlorophylls in representative protein environment Sina Türeli & Tereza Varnalı Received: 4 May 2010 / Accepted: 18 August 2010 / Published online: 4 September 2010 # Springer-Verlag 2010 Abstract Bacterial light-harvesting II (LH-II) centers con- tain two types of Bacteriochlorophylls (Bchl). One is named B800 and found as a single molecule within one monomer of the complex while the other named B850 is found as a dimer. Their names indicate their peak of UV absorbance around red spectrum. Both types of molecules are attached to the protein chain via ligation of their central Magnesium atom to an either Histidine or Deoxymethio- nine amino acid. They are also coordinated by peripheral hydrogen bonds that they accept with their carboxyl side group. Both the ligation and the hydrogen bonding are thought to have an effect on electronic structure of the Bchl hence its UV absorbance and energy transfer rate. Experi- ments and theoretic studies performed on this subject support the above idea. This theoretical molecular modeling study case aims to mimic the experimental mutations performed on certain amino acids in silico and study its effects on the electronic structure of Bchl. By comparison with experimental results it was observed that the likely place for the nearby Arginine is not below the plane of the Bchl as in the X-ray crystallographic structure but above the plane defined by the four nitrogen atoms and their rings. It was also seen that the coordination of the acetyl group is very sensitive to changes in ligation of the Bchl molecule. Keywords Acidophila . Bacteriochlorophyll . B800 . LHC . Light harvesting center . Molecular dynamics . PM6 Introduction The first implications that photosynthetic units might have been composed of different units originated from experi- ments performed by Emerson and Arnold in 1932 [1]. They observed that it required more than two thousand chloro- phyll molecules to reduce one molecule of CO 2 under saturating light. Further more they demonstrated that samples with low chlorophyll amounts were not easily saturable with even their most intense light sources. These results influenced them and the other scientists working in this area into speculating that only a few chlorophylls in their samples of thousand of chlorophyll molecules were capable of reducing CO 2 when activated with light. They were right and today the distinction is made by naming the light absorbing sections as light harvesting centers and the reducing sections as reaction centers. Since 1932 researchers have learned a lot about these photosynthetic units. Especially with the advance of X-ray crystallography, the availability of observing these centers in atomic resolution and molecular aspects revealed new perspectives into the field such as possibility of applying ideas and techniques from other fields like computational chemistry and molecular biophysics. From the information gathered over the years on the subject, a general organizational structure of photosynthetic unit can be deduced, which applies to many cases of plants and purple bacteria. In this model each reaction center (RC) is located inside a larger complex called light harvesting complex I (LH-I). More over this light complex is itself surrounded by about 12 smaller light harvesting complexes S. Türeli (*) Department of Physics, Faculty of Arts&Sciences, Boğaziçi University, 34342 Bebek, İstanbul, Turkey e-mail: sina.tureli@boun.edu.tr T. Varnalı Department of Chemistry, Faculty of Arts&Sciences, Boğaziçi University, 34342 Bebek, İstanbul, Turkey J Mol Model (2011) 17:1273–1281 DOI 10.1007/s00894-010-0828-z