Atomic scale characterization of the conformational dynamics of a thermo-sensitive and a non-thermo-sensitive oligomer using vibrational spectra obtained from molecular dynamics

Abstract Molecular dynamics simulations (MD) are used to calculate the vibrational spectra of a thermo-sensitive oligomer, namely, poly(N-isopropylacrylamide) (PNIPAM) and a non-thermo-sensitive oligomer, namely, poly(acrylamide) (PAAM) and characterize the atomic scale conformations. Despite the structural similarity between the two polymers, the response of PNIPAM and PAAM to a thermal stimulus is widely different; a coil-to-globule transition is observed for PNIPAM above a lower critical solution temperature (LCST) of 305 K whereas the same is absent in PAAM. Simulations in both the cases are performed above and below the LCST of PNIPAM, namely at 278 K and 310 K, to evaluate the effect of temperature on the polymer conformations. The vibrational spectra of bonds involving atoms from the polymer backbone and the various side-groups (amide I, amide II, and isopropyl group of PNIPAM and amide I and amide II group of PAAM) of the polymers were analyzed to study the conformational changes in the polymer. The differences in the vibrational spectra are used to understand the dynamics of conformational transitions in the two polymers and identify the changes in the relative interactions between various atoms in the backbone and in the side groups of the polymer with water at two different temperatures, namely at 278 K and 310 K. The systematic trends in the observed peak intensities and frequency shifts at the low, medium, and high frequency end of the spectrum for the various atoms in the two polymers are rationalized on the basis of bond-lengths, local coordination, strength of hydrogen bonding, and neighboring solvation environment. The analysis of the vibrational spectra for amide I and amide II regions of PNIPAM suggests a coil-to-globule transition in going from 278 K to 310 K. The differences are evaluated in terms of the strength, stability, and structure of the hydrogen-bond network between polymer and polymer and between polymer and water. Comparison of the vibrational spectra of isopropyl groups in PNIPAM at 278 K and 310 K suggests dehydration of the isopropyl moieties at 310 K. In the case of PNIPAM, we observe that polymer-water interactions are dominant below the LCST whereas polymer–polymer interactions dominate above the LCST. On the other hand, the vibrational spectra of amide I and amide II group of PAAM, at 278 K and 310 K, do not show any significant difference in terms of the interactions between polymer and polymer and interactions between polymer and water. Analysis of the peak intensities, of the amide II stretching band, observed in the frequency range 3500–3700 cm −1 suggests that the fraction of bonded and non-bonded hydrogen atoms are similar at both 278 K and 310 K. This indicates that the interactions between polymer and polymer and between polymer and water are similar at both the temperatures. The interactions between PAAM and its surrounding environment are found to be unaffected as the temperature is raised from 278 K to 310 K. Comparisons with experimental studies are made where possible. Our study provides useful insights into the nature of various inter-molecular interactions and their role in influencing the atomic scale conformational dynamics in oligomers.