Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies

• Published in: Journal of molecular structure. Theochem 2004-04, Vol.675 (1), p.61-77
• Main Authors: Jalkanen, K.J., Elstner, M., Suhai, S.
• Format: Article
• Language: English
• Subjects: Conformational analysis; Density functional theory; Raman and Raman optical activity; Self-consistent charge density functional tight-binding semi-empirical; Vibrational absorption; Vibrational circular dichroism; Vibrational spectroscopy
• ISSN: 0166-1280; 1872-7999
• DOI: 10.1016/j.theochem.2003.12.045

Here we shall review our studies of peptides, both in zwitterionic and neutral forms, in the gas phase and aqueous solution. Our benchmarking of the ab initio restricted Hartree–Fock and Møller Plesset theory, density functional theory (DFT) (Becke3LYP), semi-empirical and approximate DFT methods for the description of structure, energetics and vibrational properties are also discussed. In addition, in our modeling peptides in both nonpolar solvents and in the isolated state and in aqueous solution, we have also simulated the vibrational absorption, also called IR, vibrational circular dichroism, Raman scattering and Raman optical activity intensities. Our goal in these studies is to understand the structure and function of proteins and other biomolecules and here one is required to be able to interpret the results of experimental studies. As the physical tools used to observe and study biological processes have evolved, so have the theoretical methods and models to interpret, understand and completely utilize the results of these new measurements. The work on developing methods for modeling amino acids, peptides and proteins in both the nonaqueous and aqueous environments has involved, of course, many groups. A review of our contributions to this field will be given and, in addition, we shall try to show how our work fits in the big picture, what are the unique characteristics of our contributions which distinguishes our work. We will discuss our structural, energetical, conformational, and vibrational studies on a variety of systems which have been used to not only to test and validate levels of theory, but also to solve some structural problems.