Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid (SAHA): A Molecule bites its tail Di Zhang, Jacob C. Dean and Timothy S. Zwier Zwier Research Group, Purdue University

Head Tail Tail Head “Head” “Tail” FUNDAMENTAL INTEREST: Prototypical Potential Energy Surface Two hydrogen bonding groups separated by C6 hydrocarbon chain could form head-to-tail or tail-to-head intramolecular H-bonds Single Conformation Spectroscopy of SAHA BIOLOGICAL RELEVANCE Vorinostat (SAHA) Histone deacetylase inhibitor to Class I and class II HDACs at ~50 nM SAHA is currently in advanced clinical trials and showed significant anticancer activity in a broad range of cancers. C6 alkyl chain

Visual summaries of all the conformational minimum and transition states Generated by Amber force field The end of each branch identifies a particular conformational minimum Nodal points represents transition states in the prescribed energy window that connect the minima below them 1277 minima were found connected by 1355 transition states Disconnectivity diagram

Sample 1064 nm Graphite rod Laser desorption Experimental Methods

Experimental energy diagram Resonant ion-dip infrared spectroscopyIR-UV holeburningResonant 2 photon ionization Molecule S 0 Molecule S 1 Molecule + +e - UV Source fixed: Provides selectivity IR Source tuned IR Source fixed: Provides selectivity UV Source tuned Δ t = 200 ns

Four conformations found S 0 -S 1 origin transitions spread over ~450 cm -1 Vibronic structure is similar Based on positions of electronic origins: 3 of one type, 1 of another R2PI and IR-UV Holeburning Spectroscopy X3

Unit: cm -1 Resonant ion-dip Infrared Spectroscopy: Single-conformation IR spectra

Amide I and Amide II region

Calculational Methods 1.Force field calculation in Amber * force field was performed first at low computational cost with MacroModel commercial program suite stable conformation structures were filtered out with a given energy threshold (50kJ mol -1 ). 3.DFT-B3LYP was performed first to refine the 50 geometries with lowest energy imported from Macromodel with 6-31+G* basis set. 4.Low energy outputs from those optimizations were then re-optimized through dispersion correlated density functional methods (M05-2X) with the same basis set.

Energy Level Diagram kJ/mol

Conformer A Tail NH to head C=O C11 C5 Global Minimum 0 kJ/mol M05-2X

Conformer B Head NH to tail C=O C10 C kJ/mol M05-2X

Conformer D C10 C5 Head NH to tail C=O 6.31 kJ/mol M05-2X

Conf C NH-  9.55 kJ/mol Head NH to tail OH 2.53 kJ/mol Head NH to tail OH 6.31 kJ/mol

Conformer C? Conformer A Conformer B Conformer D Energy level diagram

Observed 4 conformers of SAHA – One Tail to Head – Two Head to Tail – One tentative assignment: NH…pi Title: “A molecule bites its tail”: – Head bites the tail – The tail bites the head Remaining work: – Alkyl CH stretch region: Analyzing the C6 alkyl chain – What are the barriers to isomerization? – Can we carry out a population transfer measurement to drive population from H→T to T→H and vice versa? – How does this change in the presence of water molecules? Form bridges? Change the conformational preferences? Nearly the same energy Conclusions and Future Outlook

Prof. Tim Zwier Dr. Vanessa Vaquero Vara Dr. Ryoji Kusaka Evan G. Buchanan Zachary Davis James Redwine Jacob Dean Deepali Mehta Nathan Kidwell Di Zhang Joe Korn Nicole Shimko Patrick Walsh Joseph Gord Acknowledgments