IR absorption (dark gray) and VCD spectra (black) of alanine dipeptide analog in water using the QM/MM MD trajectories highly populated with (a) PII (trajectory X) and (b) -helical conformers (trajectory II). The spectra in (b) are obtained by averaging over five trajectories generated at the RHF/3-21G level QM/MM MD simulation.
Vibrational mode assignment of alanine dipeptide analog by Fourier transforming the bond length or the bend angle autocorrelation function obtained from the trajectories having predominantly (a) PII and (b) -helical conformers. The notation (A-B) is the bond length between the atoms A and B and (A-B-C) is the bend angle between the atoms A, B, and C. The subscripts and denote the acetyl and the amide ends, respectively.
Conformation dependence of the IR absorption (dark gray) and VCD spectra (black) calculated from the trajectories highly populated with (a) (trajectory VIII) and (b) conformers (trajectory VII). The spectra in (a) are produced by averaging over four trajectories generated at the level QM/MM MD simulation.
IR absorption (dark gray) and VCD spectra (black) simulated using trajectories populated with coil conformers and generated with the basis sets (a) 3-21G (trajectory I), (b) 6-31G (trajectory VI), and (c) (trajectory IX), respectively.
Population of secondary structural motifs in percentage (%). The ideal values of and are in parenthesis and the variation of ±30° is allowed to determine the conformation of each snapshot. The arbitrary structure not specified as one of the secondary motifs considered here is defined as coil. The (fully extended) and (-helical) in the right half of the basis set column denote the initial conformation of each trajectory. To reduce the trajectory dependence of the calculation results, five different trajectories were generated, respectively, for the major conformers of interest, but the values averaged over five trajectories, the case predominantly populated with , and the case with the highest PII content only are presented here. The trajectory is numbered in the first column for convenience and the length used to calculate the time-correlation functions and spectra is 1 ns in all cases.
Article metrics loading...
Full text loading...