Probing Molecular Dynamics with Microwave Spectroscopy Adam Daly, Stephen G. Kukolich

Hydrogen Bonding Formic Acid-Formamide, Formic Acid Propriolic Acid PROTEINS  SECONDARY AND TERTIARY STRUCTURE DNA  BASE PAIRS: 

A= 5962 B= 910 C= 789 MHz

Dimer work in 2012

If this complex could be observed? What about these dimers with strong b-dipole?

If this complex could be observed? What about these dimers with strong b-dipole?

Experimental All three acids available commercially Melting point 110 C No previous microwave spectroscopy work Estimates of rotational constants –B3LYP/ G** Instrumentation –Flygare-Balle PBFTMW – spectrometer Pressure Sample injection ~ 1Hz

Pulsed-Beam Fourier Transform Microwave Spectrometer Microwave Cavity Sample Diffusion Pump Torr ~1% HCl in Neon Fore pump

+300V Time Valve Radiation Digitization

t=0 General Valve SCR Molecules in Ne +300V Pico Digital Oscilloscope HP 8673 Microwave Generator

+300V t~1ms HP 8673 Microwave Generator High Speed Microwave Switch Pico Digital Oscilloscope

+300V t`=1ms+10  s Mixer FID HP 8673 Microwave Generator Pico Digital Oscilloscope

Transmit Delay Valve Signal Transmit Signal Receive Signal Receive Delay Generating delays with 74LS123

Pulse Box

What we found with 2-fluorobenzoic acid:

2-Fluorobenzoic Acid A (predicted)* B (predicted)* C (predicted)* aa bb EE 0235 cm cm -1

Three species with different intensities

2-Fluorobenzoic Acid A (predicted)* B (predicted)* C (predicted)* aa bb EE 0235 cm cm -1 A (expt) (1) ( 5) ( 5) B (expt) (6) ( 5) ( 6) C (expt) (6) (3) (3)  a (detected) √√√  b (detected) √√

Distinguishing amongst the conformers of 2-Fluorobenzoic Acid A (predicted)* B (predicted)* C (predicted)* aa bb EE 0235 cm cm -1 2H2H 2H2H 2H2H Experiment in finished

Calc: B3LYP/ g(d,p)2FBzAc – 15 lines Conformer 1 2FBzAc-R – 17 lines Conformer 2 2FBzAc-F – 16 lines Conformer 3 A expt | A calc (MHz) (79) (69) (63) B expt | B calc (MHz) (64) (90) (78) C expt | C calc (MHz) (83) (63) (66) Dipole moments µ a = 2.1 Debyeµ a = 2.2 Debyeµ a = 5.0 Debye µ b = 2.1 Debyeµ b = 2.6 Debyeµ b = 1.4 Debye µ c = 0.0 Debye ΔE 0 cm cm cm -1 Calc: B3LYP/ g(d,p)D-2FBzAc – 11 linesD-2FBzAc-R – 11 linesD-2FBzAc-F – 15 lines A expt | A calc (MHz) (93) (105) (32) B expt | B calc (MHz) (60) (159) (96) C expt | C calc (MHz) (90) (237) (77) Distinguishing amongst the conformers of 2-Fluorobenzoic Acid

Where we were going…

Formic Acid -10C 2-Fluorobenzoic 100C / A / / B / / C / EXP.FREQ. - CALC.FREQ. - DIFF. - EXP.ERR.- 1: : : : : : : A / (225) B / (119) C / ( 45) MICROWAVE AVG = MHz, IR AVG = MICROWAVE RMS = MHz, IR RMS = / A / / B / / C / 2-Fluoro-benzoic formic acid dimer M06HF/ G** Valve

4-Fluorobenzoic Acid A (predicted)* B (predicted)*772.3 C (predicted)*643.7 aa 0.1 bb 1.4 EE 0 A (expt) ( 53) B (expt) ( 58) C (expt) ( 33)  a (detected)  b (detected) √ ?

3-Fluorobenzoic Acid A (predicted)* B (predicted)* C (predicted)* aa bb EE 09 cm -1

3-Fluorobenzoic Acid A (predicted)* B (predicted)* C (predicted)* aa bb EE 09 cm -1 A (expt) ( 3) ( 6) B (expt) ( 7) (2) C (expt) ( 6) (2)  a (detected) √√  b (detected) √

Weak doublets

If this complex could be observed? Predicted rotational constants (MHZ) using M06HF/ G**: A B 98.6 C 90.9

A (predicted)* B (predicted)*98.6 C (predicted)*90.9 bb 5 D A (expt) ( 75) ( 46) B (expt) (199) ( 74) C (expt) (124) ( 70) N 18

Summary Climbing the staircase of complexity towards simplest system that reveals the dynamics of the base pairs All three monomers have been detected: –2F-Bza with three conformers –3F-Bza with two conformers –4F-Bza with one conformer A dimer with (B+C)/2 has been detected showing dynamics!

Acknowledgements Steve Kukolich Lazlo Sarkozy Spencer Carey Jo O’Malley Dominic Sacchetti