title: Conformational Interconversions of Amino Acid Derivatives.
abstract: Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Kaminský
authors.affiliation: Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark.
authors.forename: Frank
authors.initials: F
authors.lastname: Jensen
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives; D000596:Amino Acids / Q000737:chemistry*; D003545:Cysteine / Q000031:analogs & derivatives; D008958:Models, Molecular; D008968:Molecular Conformation; D011789:Quantum Theory; D012694:Serine / Q000031:analogs & derivatives; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D012694:Serine; D003545:Cysteine; D000409:Alanine