B. Author manuscript; offered in PMC 2014 April 11.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; available in PMC 2014 April 11.Figure 4.Simulation of the (A) isotropic Raman, (B) anisotropic Raman, (C) IR, and (B) VCD amide I’ band profile of anionic AAA in D2O with a model which explicitly considers uncorrelated inhomogeneous broadening on the two interaction oscillators. The strong lines outcome from a simulation for which the organic band profile with the two oscillators (half-half width of five.5 cm-1) was convoluted with two Gaussian distributions of eigenenergies with a common half-halfwidth of 12 cm-1. For the other two simulations we assumed that aspect on the inhomogeneous broadening is correlated. The uncorrelated broadening was set to c,1=c,2 =9cm-1 (dashed) and c,1=c,2=6.3-Butynoic acid Price six cm-1 (red), the respective correlated broadening for the excitonic transitions was 1=2=8cm-1 (dashed) and 1=2=10 cm-1 (red).Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; available in PMC 2014 April 11.Figure 5.(A) Isotropic Raman, (B) anisotropic Raman, (C) IR, and (D) VCD band profiles of your amide I’ mode of AdP in D2O.Formula of 2,3-Dibromo-4-methylpyridine The solid lines result from the simulation described in the text.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptFigure 6.UVCD spectra of (A) cationic AAA, (B) zwitterionic AAA,, and (C) the AdP as a function of temperature.PMID:33711093 Cationic AAA spectra range from 0-90 with T=10 . Zwitterionic AAA as well as the alanine dipeptide range from 5-85 with T=5 .J Phys Chem B. Author manuscript; obtainable in PMC 2014 April 11.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptFigure 7.3J(HN,H)[Hz] in the central (left panel) and C-terminal residue amide (right panel) plotted as a function of temperature for cationic AAA (circles), zwitterionic AAA (squares) along with the AdP (triangles). The strong lines outcome in the two-state thermodynamic model fitting procedure described inside the text.J Phys Chem B. Author manuscript; available in PMC 2014 April 11.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; offered in PMC 2014 April 11.Figure 8.Ramachandran plots for (A) the cationic and (B) zwitterionic AAA and (C) AdP obtained by MD simulations making use of the OPLS force field and SPC/E water model.Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; readily available in PMC 2014 April 11.Figure 9.Distribution of durations, N(t), with the (A) pPII, (B) -strand, and (C) helical conformations for cationic AAA (black circles) and AdP (red circles) derived by MD. The solid line represents exponential fits (see Table 7).Toal et al.PageNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptJ Phys Chem B. Author manuscript; offered in PMC 2014 April 11.Figure 10.Radial distribution functions, g(r), of water molecules (making use of H- and O-atoms of water) about the amide proton in the central residue of cationic AAA and AdP (see Figure 1, atoms depicted in blue), derived by MD. Distributions from the (B) cationic AAA and (C) AdP conformations with respect towards the dihedral angle plus the distance amongst the nitrogen atom with the third residue and also the side-chain atom C from the central residue in AAA as well as the correspon.