Quasiplanarity of the peptide bond.
The vibrational motions of the model peptide unit represented by the main-chain carbonyl carbon, oxygen, nitrogen, and amide hydrogen are analyzed quantum-mechanically using formamide, cis-N-methylformamide, trans-N-methylformamide, N,N-dimethylformamide, l-alanyl-l-alanine, and N-benzoylphenylalanine as dynamical models. To make this analysis computationally feasible, the peptide unit vibrational motions were first separated from the remaining molecular vibrational motions by means of the crude adiabatic (Born-Oppenheimer) approximation, and then, using the same approximate separation, the peptide unit dynamical problem was separated into sets of high- and low-frequency subproblems. Importantly, the simplest dynamical (one-dimensional) problem based on the separation of the amide out-of-plane motion from the rest of the peptide unit motions allows for a physically correct description of the effective "ground state" molecular geometry of all studied systems. The separation is thus believed to be also suitable for reliable estimation of the dynamical effects on the geometry of the peptide unit in other molecular systems.
Chalupský
Jakub
J
Center for Biomolecules and Complex Molecular Systems, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám.2, Prague 6, Czech Republic.
Vondrásek
Jirí
J
Spirko
Vladimír
V
D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry; D003198:Computer Simulation; D004126:Dimethylformamide; D005559:Formamides / Q000737:chemistry; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D010649:Phenylalanine / Q000031:analogs & derivatives / Q000737:chemistry; D011789:Quantum Theory; D013237:Stereoisomerism; D014732:Vibration
D005559:Formamides; D010455:Peptides; C031066:formamide; D010649:Phenylalanine; D004126:Dimethylformamide; C053764:benzoylphenylalanine; D000409:Alanine; C002950:methylformamide