PAPQMD parametrization of molecular systems with cyclopropyl rings: conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid.
The suitability of ab initio, semiempirical and density functional methods as sources of stretching and bending parameters has been explored using the PAPQMD (Program for Approximate Parametrization from Quantum Mechanical Data) strategy. Results show that semiempirical methods provide parameters comparable to those compiled on empirical force fields. In this respect the AMI method seems to be a good method to obtain parameters at a minimum computational cost. On the other hand, harmonic force fields initially developed for proteins and DNA have been extended to include compounds containing highly strained three-membered rings, like 1-aminocyclopropane-1-carboxylic acid. For this purpose the cyclopropyl ring has been explicitly parametrized at the AMI level considering different chemical environments. Finally, the new set of parameters has been used to investigate the conformational preferences of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. Results indicate that such compounds tend to adopt a helical conformation stabilized by intramolecular hydrogen bonds between residues i and i + 3. This conformation allows the arrangement of the cyclic side chains without steric clashes.
Alemán
C
C
Departament d'Enginyeriía Química, E.T.S. d'Enginyers Industrials, Universitat Politècnica de Catalunya, Barcelona, Spain.
Casanovas
J
J
Galembeck
S E
SE
D000596:Amino Acids / Q000737:chemistry*; D000598:Amino Acids, Cyclic; D003521:Cyclopropanes / Q000737:chemistry; D019829:Nevirapine / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
D000596:Amino Acids; D000598:Amino Acids, Cyclic; D003521:Cyclopropanes; D010455:Peptides; C023863:1-aminocyclopropane-1-carboxylic acid; D019829:Nevirapine; C030797:cyclopropane