1. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide
International Symposium of Molecular Spectroscopy
WI: Comparing Theory and Experiment
Christopher M. Leavitt †, Caitlyn Shirley†, Paul Raston‡, Grant Moody†, Kevin B. Moore†, Jay Agarwal†, Henry F. Schaefer†, and Gary E. Douberly †
†Department of Chemistry, University of Georgia
‡School of Chemistry and Physics, The University of Adelaide

2. Identifying the underlying interactions that dictate structure in biological molecules
Conformation specific IR spectra obtained using IR-UV double resonance
Ions were cooled to ~10 K using a cryogenic ion trap
Comparison to (scaled) harmonic frequency calculations facilitates structural assignment
What about computed energies?
Stearns, et. al. PCCP 2009, 11,

4. Neutrals work to!
Rotational Spectroscopy
IR-UV requires chromophore

6. (N-acetyl glycine methyl amide)
TARGET – NAGMA
(N-acetyl glycine methyl amide)
GAMEPLAN
Obtain IR spectra of peptides isolated in droplets (no UV chromophore necessary)
Distinguish between various conformers using linear dichroism spectroscopy
Manipulation of the molecular ensemble prior to pick up by the droplets (and is it maintained after pick up)
C5 (ΔE= 360 cm-1)
C7 (ΔE= 0 cm-1)

7. h ~17 K 30 bar Trapping Potential Depth ~ 100 K
Biomolecule pick-up cell h
~17 K
30 bar
T ≈ 0.4 K
Trapping Potential Depth ~ 100 K
Molecular degrees of freedom are brought into thermal
equilibrium with the helium droplet at 0.4 K.

8. h
Infrared cw-OPO
Measure depletion on (CH4N)+ channel 12 16 20 24 28 32 36 40 44 48 52 56 60 64 68 72 76
m/z
Geometric / Electron Impact Ionization Cross Sections are Reduced

9. N-acetyl glycine methyl amide
free NH
stretches
H-bonded
NH stretches
CH stretches
C7 conformer
C5 conformer
2800
2850
2900
2950
3000
3050
3350
3400
3450
3500
Wavenumber (cm-1)
MP2/def2-TZVPD
Scaling factor: 0.961

10. Biomolecule pick-up cell
Orient the molecules with large DC electric field
Measure vibrational transition moment angle (α) for each mode p t   Z

11. Vibrational Transition Moment Determination
calc. μp = D
calc α =36°
calc α =78° 10 20 30 40
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
2.0
ν= cm-1
// Polarization ^
Polarization
I(Field On)/I(Field Off)
a=24°
a=28°
a=32°
a=36°
a=40°
Field Strength (kV/cm)
NH stretches
Field Strength (kV/cm) 10 20 30 40
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
1.1
1.2
1.3
1.4
1.5
a=70°
a=78°
a=80°
a=85°
a=90°
// Polarization
I(Field On)/I(Field Off) ^
Polarization
ν= cm-1
Depletion (arb.)
3325
3350
3375
3400
3425
3450
3475
3500
3525
Wavenumber (cm-1)
MP2/def2-TZVPD

12. Vibrational Transition Moment Determination
calc. μp = D
calc α =45°
calc α =70° 10 20 30 40
0.5
0.6
0.7
0.8
0.9
1.0
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
ν= cm-1 ^
Polarization
a=36°
a=40°
a=45°
a=48°
I(Field On) / I(Field Off)
// Polarization
Field Strength (kV/cm)
Field Strength (kV/cm) 10 20 30 40
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
1.1
1.2
1.3
1.4
a=62°
a=66°
a=70°
a=74°
a=78°
I(Field On)/I(Field Off)
ν= cm-1 ^
Polarization
// Polarization
Depletion (arb.)
3325
3350
3375
3400
3425
3450
3475
3500
3525
Wavenumber (cm-1)
MP2/def2-TZVPD

13. Rapid cooling in He droplets captures gas-phase equilibrium
Establish equilibrium at some temperature
kcool>>kr,f kf
kcool
kcool kr

14. Use IR intensities to determine T-dependent concentration
van‘t Hoff Plot

15. Probability of dopant “pick-up” (Poisson Statistics)
If we raise the temperature of the oven source, the signal from monomers goes away!

16. Two-stage molecular oven
Rough Pump
Tsample ~105°C
T ~115°C
Tss-tube ~125°C
Aperture for Droplet Beam
Tblock °C
Temperature monitored with K-type thermocouples
Tblock and Tsample deviated by no more than 0.3°C for each temperature point

17. C7 conformer has a statistical weight of 2
A little Thermo anyone?
3492
3494
3496
3498
3500
Depletion (arb.)
Wavenumber (cm-1)
C7 conformer has a statistical weight of 2

18. 408 K ln(Ic7/Ic5) 638 K 1/T (K-1) 1.6 1.8 2.0 2.2 2.4 -0.8 -0.7 -0.6
-0.5
-0.4
-0.3
-0.2
-0.1
1/T (K-1)
X10-3
408 K
ln(Ic7/Ic5)
638 K

19. Calculation: Method ΔH (kJ/mol) ΔS (J/mol·K) ΔG (kJ/mol) Exp -4.5±0.1
-18.1±0.2
1.6±0.2
500 K
-3.64
-21.5
4.23
1.6
1.8
2.0
2.2
2.4
-0.8
-0.7
-0.6
-0.5
-0.4
-0.3
-0.2
-0.1
1/T (K-1)
X10-3
408 K
Calculation:
Geometry optimization at MP2/aug-cc-pVTZ
Focal point analysis brings electronic energy to CCSD(T)/CBS level
Harmonic frequencies (MP2/aug-cc-pVTZ) scaled ( ν<1000 cm ν>1000 cm-1)
ln(Ic7/Ic5)
638 K

20. Summary
Collected IR spectrum of a model dipeptide embedded in He nanodroplets
Used linear dichroism experiment to assign particular bands to the C5 and C7 conformers
Determined accurate values of ΔH, ΔS and ΔG, providing a benchmark for theoretical calculations

21. Thank you for your attention!