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

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

3. A= 5962 B= 910 C= 789 MHz

4. Dimer work in 2012

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

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

7. Experimental All three acids available commercially Melting point 110 C No previous microwave spectroscopy work Estimates of rotational constants –B3LYP/6-311++G** Instrumentation –Flygare-Balle PBFTMW – spectrometer Pressure 10 -7 Sample injection ~ 1Hz

8. Pulsed-Beam Fourier Transform Microwave Spectrometer Microwave Cavity Sample Diffusion Pump 10 -6 Torr ~1% HCl in Neon Fore pump

9. +300V Time Valve Radiation Digitization

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

11. +300V t~1ms HP 8673 Microwave Generator High Speed Microwave Switch Pico Digital Oscilloscope

12. +300V t`=1ms+10  s Mixer FID HP 8673 Microwave Generator Pico Digital Oscilloscope

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

14. Pulse Box

15. What we found with 2-fluorobenzoic acid:

16. 2-Fluorobenzoic Acid A (predicted)*228722642281 B (predicted)*120812111207 C (predicted)*790789 aa 2.12.25.0 bb 0.22.61.4 EE 0235 cm -1 643 cm -1

17. Three species with different intensities

18. 2-Fluorobenzoic Acid A (predicted)*228722642281 B (predicted)*120812111207 C (predicted)*790789 aa 2.12.25.0 bb 0.22.61.4 EE 0235 cm -1 643 cm -1 A (expt)2294.22(1)2284.814( 5)2271.730( 5) B (expt)1210.3561(6)1210.9233( 5)1212.6154( 6) C (expt)793.5764(6)792.0409(3)792.2680(3)  a (detected) √√√  b (detected) √√

19. Distinguishing amongst the conformers of 2-Fluorobenzoic Acid A (predicted)*224722842258 B (predicted)*118211781197 C (predicted)*774777782 aa 2.12.25.0 bb 0.22.61.4 EE 0235 cm -1 643 cm -1 2H2H 2H2H 2H2H Experiment in finished

20. Calc: B3LYP/6-311++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) 2294.2107(79)2287.41082271.7266(69)2264.46892284.8282(63)2281.1913 B expt | B calc (MHz) 1210.35637(64)1208.83801212.61511(90)1211.42711210.92670(78)1207.6947 C expt | C calc (MHz) 793.57867(83)790.8788792.26935(63)789.2178792.04102(66)789.6454 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 -1 235 cm -1 643 cm -1 Calc: B3LYP/6-311++g(d,p)D-2FBzAc – 11 linesD-2FBzAc-R – 11 linesD-2FBzAc-F – 15 lines A expt | A calc (MHz) 2291.5748(93)2284.42832255.40281(105)2247.96022262.8785(32)2258.7090 B expt | B calc (MHz) 1180.37460(60)1178.72941183.56672(159)1182.29981201.27090(96)1197.7560 C expt | C calc (MHz) 780.27584(90)777.5340777.911800(237)774.7993785.25446(77)782.7020 Distinguishing amongst the conformers of 2-Fluorobenzoic Acid

21. Where we were going…

22. Formic Acid -10C 2-Fluorobenzoic 100C 10000 1897.1 / A / 20000 378.0 / B / 30000 319.2 / C / EXP.FREQ. - CALC.FREQ. - DIFF. - EXP.ERR.- 1: 10 0 10 9 0 9 6687.53710 6687.46759 0.06951 0.05500 2: 9 1 9 8 0 8 6666.54000 6666.52793 0.01207 0.05500 3: 10 1 10 9 1 9 6584.39360 6584.47641 -0.08281 0.05500 4: 9 2 8 8 2 7 6146.72950 6147.22619 -0.49669 1.05500 5: 9 1 8 8 1 7 6335.78810 6337.00320 -1.21510 10.00500 6: 7 2 6 6 2 5 4788.21800 4788.24936 -0.03136 0.05500 7: 11 0 11 10 1 10 6807.13130 6807.10798 0.02332 0.05500 1 10000 A / 1722.484(225) -0.000 2 20000 B / 365.5966(119) -0.0000 3 30000 C / 319.7091( 45) 0.0000 MICROWAVE AVG = -0.245867 MHz, IR AVG = 0.00000 MICROWAVE RMS = 0.498072 MHz, IR RMS = 0.00000 10000 1880.3 / A / 20000 376.1 / B / 30000 317.1 / C / 2-Fluoro-benzoic formic acid dimer M06HF/6-311++G** Valve

23. 4-Fluorobenzoic Acid A (predicted)*3866.3 B (predicted)*772.3 C (predicted)*643.7 aa 0.1 bb 1.4 EE 0 A (expt)3856.5879( 53) B (expt)775.28671( 58) C (expt)645.84363( 33)  a (detected)  b (detected) √ ?

24. 3-Fluorobenzoic Acid A (predicted)*26352684 B (predicted)*934923 C (predicted)*689687 aa 0.50.2 bb 0.32.9 EE 09 cm -1

25. 3-Fluorobenzoic Acid A (predicted)*26352684 B (predicted)*934923 C (predicted)*689687 aa 0.50.2 bb 0.32.9 EE 09 cm -1 A (expt) 2636.51( 3)2685.086( 6) B (expt) 937.2300( 7)926.774(2) C (expt)691.7929( 6)689.325(2)  a (detected) √√  b (detected) √

26. Weak doublets

27. If this complex could be observed? Predicted rotational constants (MHZ) using M06HF/6-311++G**: A 1167.5 B 98.6 C 90.9

28. A (predicted)*1167.5 B (predicted)*98.6 C (predicted)*90.9 bb 5 D 0+0+ 0-0- A (expt)1157.01939( 75) 1157.02249( 46) B (expt) 95.45061(199) 95.45110( 74) C (expt)88.21514(124)88.24425( 70) N 18

31. 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!

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