Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields.
An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.
Hermida-Ramón
Jose Manuel
JM
Theoretical Chemistry, Center for Chemistry and Chemical Engineering, University of Lund, POB 124, S-221 00 Lund, Sweden.
Brdarski
Steve
S
Karlström
Gunnar
G
Berg
Ulf
U
D000465:Algorithms; D005998:Glycine / Q000031:analogs & derivatives* / Q000737:chemistry*; D006860:Hydrogen Bonding; D008962:Models, Theoretical; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
C407066:N-formylglycinamide; D011506:Proteins; D014867:Water; D005998:Glycine