title: Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor.
abstract: We have investigated the performance of two classes of fragmentation methods developed in our group (Molecules-in-Molecules (MIM) and Many-Overlapping-Body (MOB) expansion), to reproduce the unfragmented MP2 energies on a test set composed of 10 small to large biomolecules. They have also been assessed to recover the relative energies of different motifs of the acetyl(ala)18NH2 system. Performance of different bond-cutting environments and the use of Hartree-Fock and different density functionals (as a low level of theory) in conjunction with the fragmentation strategies have been analyzed. Our investigation shows that while a low level of theory (for recovering long-range interactions) may not be necessary for small peptides, it provides a very effective strategy to accurately reproduce the total and relative energies of larger peptides such as the different motifs of the acetyl(ala)18NH2 system. Employing M06-2X as the low level of theory, the calculated mean total energy deviation (maximum deviation) in the total MP2 energies for the 10 molecules in the test set at MIM(d=3.5Å), MIM(η=9), and MOB(d=5Å) are 1.16 (2.31), 0.72 (1.87), and 0.43 (2.02) kcal/mol, respectively. The excellent performance suggests that such fragment-based methods should be of general use for the computation of accurate energies of large biomolecular systems.
authors.affiliation: Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Arjun
authors.initials: A
authors.lastname: Saha
authors.affiliation: Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Krishnan
authors.initials: K
authors.lastname: Raghavachari
mesh_terms: D005782:Gels / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D005782:Gels; D010455:Peptides