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Conformational stability and flexibility of the ala dipeptide in free space and water: Monte Carlo computer simulation studies
Author(s) -
Ravishanker G.,
Mezei M.,
Beveridge D. L.
Publication year - 1986
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540070311
Subject(s) - intramolecular force , dipeptide , monte carlo method , intermolecular force , chemistry , hydrogen bond , thermodynamics , thermodynamic integration , computational chemistry , crystallography , molecular dynamics , molecule , stereochemistry , physics , peptide , mathematics , organic chemistry , biochemistry , statistics
Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C 7 , C 5 , α R , and P II conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C 7 to C 5 , α R , and P II are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C 7 conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C 7 , α R , and P II are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl‐water hydrogen bond in C 5 , α R , and P II competes successfully with the intramolecular NH…OC interaction in C 7 .