Rayleigh scattering properties of small polyglycine molecules Puspitapallab Chaudhuri a, * , Sylvio Canuto b a Departamento de Fı ´sica, Universidade Federal do Amazonas, 3000-Japiim, 69077-000 Manaus, AM, Brazil b Instituto de Fı ´sica, Universidade de Sa ˜o Paulo, CP 66318, 05315-970 Sa ˜o Paulo, SP, Brazil Received 21 July 2005; received in revised form 23 September 2005; accepted 11 October 2005 Available online 7 February 2006 Abstract Density-functional theory calculations of the Rayleigh optical activities of small isolated polyglycine molecules are reported. Fully extended b-sheet-like conformations of polypeptides of glycine, (Gly) n (with nZ1–5) are considered. After geometry optimizations, dipole moments and dipole polarizabilities (both the mean and the anisotropic components) are calculated using the B3LYP and B3P86 functionals in three basis sets. The polarizabilities are used to analyze the Rayleigh scattering activities and depolarization ratios. The convergence of the average dipole polarizability per monomer is analyzed. The differences in activity and depolarization for Rayleigh scattered radiation between the extended b- sheet-like and the folded a-helix-like forms of tetraglycine are analyzed and found to be relevant, suggesting its possible use in experimental characterization. q 2005 Elsevier B.V. All rights reserved. Keywords: Dipole moment; Dipole polarizabilities; Polarizability anisotropy; Rayleigh scattering 1. Introduction Glycine (Gly), being the simplest, yet one of the most important amino acids, has long been a subject of intense theoretical and experimental investigation. Amino acids, as we all know, are the basic building blocks of proteins, which are formed through successive amide linkage (peptide bond) of several amino acids. Since glycine does not posses a side chain, it can easily adopt conformations, which are sterically forbidden for other amino acids, giving high degree of local flexibility on the polypeptide. Glycine occurs abundantly in certain fibrous proteins due to its flexibility and because of its small size it allows adjacent polypeptide chains to pack together closely [1]. Diglycine or glycylglycine (Gly) 2 is the simplest peptide bond with all typical characteristics of the complexing sites of the higher peptides, while triglycine, (Gly) 3 , tetraglycine, (Gly) 4 or pentaglycine, (Gly) 5 represent the higher oligomers. Studies on the simple polypeptides like these ones may reveal important informations regarding the structural and dynamical aspects of the protein formation. The relevance of the polyglycine crystal structures to natural proteins like collagen, silk fibroin and artificial nylon materials is of great scientific interest [2 and the references therein]. No wonder, there exist several studies, both experimental and theoretical, on several different aspect of Glycine polypeptide. The experimental studies on the crystalline structure of polyglycine date back to as far as 1934, when Meyer and Go [3] observed two different X-ray powder pattern of polyglycine and the presence of two different crystalline forms (polyglycine I and polyglycine II) were presumed. This work initiated a flurry of other experimental works to ascertain the exact structure of the two forms. In 1955, Crick and Rich [4] postulated accurately, the three-dimensional structure of the polyglycine II to be a combination of three strands wound around each other to form a triple helix. However, the three- dimensional crystalline structure of polyglycine I, which contains fully extended b-polypeptides, was revised several times [2]. Recently, Kajava [2] re-examined the previously obtained experimental data and structural models of poly- glycine I and concluded that it has “two different three- dimensional structures depending on the molecular weight of the constituent molecules”. Theoretical studies on the glycine and polyglycine have also a long history. The electronic structures and properties of glycine peptides have been studies using both the ab initio self-consistent field (SCF) calculation [5,6] and the semi-empirical calculations [references listed in Refs. 6–9] Scheiner and Kern [10] developed a hybrid procedure combining quantum mechanical and empirical potentials and applied to a longer glycine peptide with 20 peptide units. Improta et al. [11,12] studied four different Journal of Molecular Structure: THEOCHEM 760 (2006) 15–20 www.elsevier.com/locate/theochem 0166-1280/$ - see front matter q 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.theochem.2005.10.039 * Corresponding author. Tel.: C55-92-3647 4131; fax: C55-92-3647 4131. E-mail address: puspito@ufam.edu.br (P. Chaudhuri).