Investigation of the cis–trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute–solvent interactions and effects of terminal positively charged amino acid residues

Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74–76 cm−1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm−1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm−1, whereas the PPI has bands at 365, 660, and 960 cm−1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm−1 mode comprising the motion of a C 
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 O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.


Figure S1
Experimental (top) and calculated (below) Raman spectra of polyproline PPII crystals. The calculated curve is obtained by using Crystal 17 B3LYP-D3/6-31G(d). The assignments of vibrational modes are displayed.

Figure S2
Optimized geometry, dipoles, and electrostatic potential surfaces of P12, KP11, RP11, P11K, and P11R type PPI in propanol and PPII in H2O using GAUSSIAN package. Figure S3 Raman curves of poly-L-proline II and I and the calculated spectra using CRYSTAL 17 at the B3LYP-D3/6-31G(d,p) level.

Figure S4
Raman curves of P12 series (a) PPI in prOH and (b) PPII in aqueous solution. The intensity is normalized to the 365 and 310 cm -1 band, respectively. Figure S5 Raman spectra of powder P12 series PPII form.

Figure S6
Raman spectra of the PPII form of P12 series in aqueous solution.

Figure S7
Raman spectra of the PPI form of P12 series powder.

Figure S8
Plots of circular dichroism (CD) signals at 214 nm (PPI) versus the percentages of prOH in phosphate buffer for P12 series peptides.

Figure S9
Mode analysis results of PPII conformation of poly-L-proline. Panels A and B show mode analyses on the amide-type motions and the collective type motions where all atoms participate in the motions, respectively. In the amide-type motions, the number of each type (O, N, C, and H) atom is counted if the displacement is larger than 0.01 Å for each direction (a, b, and c-axis). In the collective type motions, we use the total displacement larger than 0.059 Å which is determined on the basis of the three acoustic S3 phonon modes (ω=0). In Panel A, * represents the motions due to the ring deformations. Figure S10 Mode analysis results of PPI conformation of poly-L-proline. Panels A and B show mode analysis results on the amide-type motions and the collective type motions in which all atoms participate in the motions, respectively. In the amide-type motions, the number of each type (O, N, C, and H) atom is counted if the displacement is larger than 0.01 Å for each direction (a, b, and c-axis). In the collective type motions, we use the total displacement larger than 0.032 Å which is determined on the basis of the three acoustic phonon modes (ω=0). In Panel A, * represents the motions due to the ring deformations. Figure S11 (a) 1D and 3D crystal structure of poly proline peptide, (b) H-bond in polyproline II, and (c) H-bond in polyproline I. Table S1. Experimental and simulated crystal lattice of PPI and PPII conformations of poly-Lproline by using Crystal 17 at the B3LYP-D3/6-31G(d,p) level with the coupledperturbed Kohn-Sham scheme.

Table S2
Vibrational modes of poly-L-proline II and assignments based on CRYSTAL 17 calculations.

Table S3
Vibrational modes of poly-L-proline I and assignments based on CRYSTAL 17 calculations.   counted if the displacement is larger than 0.01 Å for each direction (a, b, and c-axis). In the collective type motions, we use the total displacement larger than 0.059 Å which is determined on the basis of the three acoustic phonon modes (ω=0). In Panel A, * represents the motions due to the ring deformations. In the collective type motions, we use the total displacement larger than 0.032 Å which is determined on the basis of the three acoustic phonon modes (ω=0). In Panel A, * represents the motions due to the ring deformations. S16 3D crystal structure is quite different from 1D polymer structure as shown in Fig. S11. Both panels are views along the a-axis (1D) and c-axis (3D). Orange allow in each panel shows the distance between two carbon atoms: 1D polymer (3.067 Å) and 3D crystal (3.120 Å). This difference can be due to the existence of inter-peptide hydrogen bonding in 3D crystal case. To see this, we should note that there are two types of hydrogen bonding in 3D crystal of the polyproline II ( Figure S11    103(E), ** 104(E), * 105 (A) 1702.8(E), 1716.8(A) a mixing of wagging and Amid II * and ** represent the largest and the second largest Raman intensities in the band, respectively.
A and E represent symmetry: E is a doubly degenerated state Note collective motions in the lower frequency region (< 500cm -1 ) may need more detailed analysis (see  * and ** represent the largest and the second largest Raman intensities in the band, respectively. Note collective motions in the lower frequency region (< 500cm -1 ) may need more detailed analysis (see Fig. S10).