How van der Waals interactions affect alanine-based polypeptides

van der Waals interactions play a critical role among the intramolecular interactions that stabilize secondary structure folding motifs in polypeptides. In this work, we quantify its influence \textit{ab initio} for the series of helix-forming alanine based polypeptides Ac-Ala$_n$-LysH$^+$ ($n=$ 4-15). We show that: (i) applying a van der Waals (vdW) correction based on the self-consistent electron density [2] to the PBE functional, a clear $\alpha$-helical conformational preference emerges at $n$=8, in agreement with experiment [1], while a mostly 3$_{10}$ helical structure is preferred at plain PBE; (ii) a numeric atom-centered orbital basis enhanced specifically to converge conformational energy differences from explicitly correlated methods (MP2, EX+cRPA and beyond [3]) gives us benchmark capabilities for treatments that include long-range correlations outrightly; (iii) exploring the free energy surface through \textit{ab initio} dynamics for longer helices ($n$=15) we see a dramatic influence of vdW interactions for high temperature stability and surface explored by these molecules. Our results demonstrate that we are now in a position to quantify vdW contributions accurately, and thus unravel their critical qualitative role in comparison to other contributions (strain, H-bonds) in medium-sized biomolecules. [1] Kohtani and Jarrold, JACS 108, 8454 (2004); [2] Tkatchenko and Scheffler, PRL 102, 073055 (2009); [3] http://www.fhi-berlin.mpg.de/aims