1. Millimeter-Wave Spectrum of Pyrimidine
Zachary N. Heim, Brent K. Amberger, Brian J. Esselman, R. Claude Woods, Robert J. McMahon
University of Wisconsin-Madison
June 22, 2015

2. Background Equilibrium structure yet to be fully determined2
Background
Pyrimidine
0 kcal/mol
(B3LYP/6-31G(d))
mB=2.28 D
Equilibrium structure yet to be fully determined
Not yet unambiguously identified in the interstellar medium
Most stable in family of 6-member dinitrogen heterocycles
Biologically relevant molecule A B C
Caffeine
Uracil
Thymine
Cytosine
Pyridazine ~22.7 kcal/mol
B3LYP/6-31G(d)
Pyrazine ~4.1 kcal/mol
B3LYP/6-31G(d)
B. J. Esselman, B. K. Amberger, J. D. Shutter, M. A. Daane, J. F. Stanton, R. C. Woods, and R. J. McMahon, “Rotational spectroscopy of pyridazine and its isotopologs from GHz: Equilibrium structure and vibrational satellites,” J. Chem. Phys. 139, (2013); doi: /
Z. Kisiel, L. Pszczolkowski, I. R. Medvedev, M. Winnewisser, F. C. De Lucia, E. Herbst, J. Mol. Spectrosc. 233, (2005).
G. L. Blackman, R. D. Brown, F. R. Burden, J. Mol. Spectrosc. 35, (1970).
W. Caminati, D. Damiani, Chem. Phys. Lett. 179, (1991).
Charnley, S., Ehrenfreund, P., & Kuan, Y.-J. 2001, Spectrochim. Acta A, 57, 685

3. The Instrument and Experiment3
The Instrument and Experiment
Produce tone-burst modulated radiation up to 360 GHz (nominally GHz)
10 cm diameter by 3m long absorption cell
Controlled by software made in LabVIEW2010
Commercially available sample
Room Temperature (298 K)

4. Initial Spectrum Collected4
Initial Spectrum Collected
13C and 15N Isotopologues
Main Isotopologue

5. 5
Main Isotopologue 29 28 27 26 26 30 32 34 36 38 40 42
J’=44
ν11 = cm-1 29 28 27 26 26 30 32 34 36 38 40 42
J’=44
ν16 = cm-1
J’=57 55 53 51 49 47 45
Q-branch, ν0
R-branch, ν0
J’=44
J’=44 32 32 30 28 26

6. Experimental and Computational Alphas6
Experimental and Computational Alphas
Mode
Frequency
(cm-1)
aA (MHz)
Comp
aB (MHz)
aC (MHz)
Exp
Nlines
sfit
n16
342.63
-5.977
0.740
3.820
-5.953
0.685
3.897
1754
0.0303
n11
391.28
-2.403
-5.084
3.072
-2.448
-5.151
3.127
1679
0.0302
n24
619.04
3.803
-5.507
-9.389
3.766
-6.136
-9.598
363
0.0249
Calculated with an anharmonic frequency VPT2 calculation at CCSD(T)/ANO1

7. Complications of Turnarounds7
Complications of Turnarounds
J’=57 56 55 54 53 48 49 50 51 52 45 46 47 44 43 42 41 40

8. Main Isotopologue13C and 15N Isotopologues
Sextic S-reduced Hamiltonian Representation IIIr 8
C4H4N2
[2-13C]
[4-13C]
[5-13C]
[1-15N]
A0 (MHz)
(21)
(47)
(20)
(31)
(46)
B0 (MHz)
(23)
(44)
(20)
(27)
(51)
C0 (MHz)
(34)
(60)
(27)
(19)
(71)
DJ (kHz)
(20)
(39)
(12)
(92)
(37)
DJK (kHz)
(34)
(76)
(19)
(26)
(79)
DK (kHz)
(68)
(43)
(14)
(18)
(53)
d1 (kHz)
(42)
(14)
(61)
(16)
(13)
d2 (kHz)
(71)
(41)
(29)
(40)
(58)
HJ (Hz)
(52)
(11)
(23)
[0]
(95)
HJK (Hz)
(82)
(29)
(28)
(99)
HKJ (Hz)
(13)
(35)
(39)
(24)
HK (Hz)
(12)
(15)
(29)
(21)
h1 (Hz)
(14)
h2 (Hz)
(53)
h3 (Hz)
(13)
Nlines
1454
266
604
211
281
σfit
0.0291
0.0383
0.0355
0.0398
0.0393

9. Main Isotopologue and 13C and 15N Isotopologues9
Main Isotopologue and 13C and 15N Isotopologues
C4H4N2
[2-13C]
[4-13C]
[5-13C]
[1-15N]
A0 (MHz)
(21)
(47)
(20)
(31)
(46)
B0 (MHz)
(23)
(44)
(20)
(27)
(51)
C0 (MHz)
(34)
(60)
(27)
(19)
(71)
Nlines
1454
266
604
211
281
σfit
0.0291
0.0383
0.0355
0.0398
0.0393

10. Synthesis of Deuterium Enriched Samples10
Sample of pyrimidine in LiOtBu/tBuOD buffer
Heated to 125oC for 58 hours
Purified via silica gel column and freeze/pump/thawing

11. Deuterated Isotopologues11
Deuterated Isotopologues
7.1
9.3
1.2
1.0
2.9 ? ?
3.1
8.4

12. Dipole Components Isotopologue mA (D) mB (D) C4H4N2 2.28 [2,4-2H] 1.5012
Dipole Components A
Isotopologue
mA (D)
mB (D)
C4H4N2
2.28
[2,4-2H]
1.50
1.72
[2-13C]
[2,5-2H]
[4-13C]
0.42
2.24
[4,5-2H]
1.55
1.67
[5-13C]
[4,6-2H]
[1-15N]
0.44
[2,4,6-2H]
2.13
0.82
[2-2H]
[4-2H]
0.74
2.16
[4,5,6-2H]
[5-2H]
[2,4,5,6-2H] 4 2 B
C4H4N2 6 A 4 2 B 5
[4,5-2H] 6

13. Quartets in the [4,5-2H] Spectrum13
Quartets in the [4,5-2H] Spectrum
b-type
2819,10⇦ 2718,9
b-type 2818,10⇦ 2719,9
a-type 2819,10⇦ 2719,9
a-type 2818,10⇦ 2718,9

14. Deuterium Substituted Isotopologues
Sextic S-reduced Hamiltonian in Representation IIIr 14
[2-2H]
[4-2H]
[5-2H]
[2,4-2H]
[4,5-2H]
[4,6-2H]
[4,5,6-2H]
A0 (MHz)
(37)
(21)
(42)
(11)
(97)
(33)
(38)
B0 (MHz)
(39)
(18)
(45)
(11)
(16)
(35)
(40)
C0 (MHz)
(84)
(20)
(30)
(41)
(64)
(14)
(47)
DJ (kHz)
1.3454(74)
(96)
(17)
1.2065(39)
(57)
(16)
(23)
DJK (kHz)
(84)
(14)
(28)
(47)
(14)
(37)
(60)
DK (kHz)
1.0007(16)
(97)
(17)
(89)
(78)
(22)
(38)
d1 (kHz)
-0.13(10)
(79)
(53)
-0.001(29)
(73)
(11)
(13)
d2 (kHz)
-0.24(21)
(73)
(18)
0.023(38)
(23)
(39)
(61)
HJ (Hz)
[0]
(17)
(64)
HJK (Hz)
(24)
(13)
HKJ (Hz)
(37)
(13)
HK (Hz)
(24)
(61)
h1 (Hz)
(35)
h2 (Hz)
(63)
h3 (Hz)
Nlines
108
913
586
202
177
422
195
σfit
0.0425
0.0373
0.0365
0.0390
0.0278
0.0346
0.0299

15. Deuterium Substituted Isotopologues15
Deuterium Substituted Isotopologues
[2-2H]
[4-2H]
[5-2H]
[2,4-2H]
[4,5-2H]
[4,6-2H]
[4,5,6-2H]
A0 (MHz)
(37)
(21)
(42)
(11)
(97)
(33)
(38)
B0 (MHz)
(39)
(18)
(45)
(11)
(16)
(35)
(40)
C0 (MHz)
(84)
(20)
(30)
(41)
(64)
(14)
(47)
Nlines
108
913
586
202
177
422
195
σfit
0.0425
0.0373
0.0365
0.0390
0.0278
0.0346
0.0299

16. Equilibrium Structure Calculation16
Equilibrium Structure Calculation
A0, B0, C0 taken from fits and converted to determinable form A0”, B0”, C0”
Vibration-rotation and electron mass corrections added
Distance and angle parameters least squares fit
Vibration-rotation corrections calculated with an anharmonic frequency VPT2 calculation at the CCSD(T)/ANO1 level.
Electronic corrections calculated at the CCSD(T)/ANO1 level

17. Calculated and Experimental Equilibrium Structures17
Calculated and Experimental Equilibrium Structures
Bond Lengths
And Angles
Experimental
Re (Å)
CCSD(T)/ANO1
Re (Å)
RC(2)-N(3)
1.3346(9)
1.340
RN(3)-C(4)
1.3366(8)
1.341
RC(4)-C(5)
1.3834(6)
1.392
RC(2)-H
1.0813(9)
1.084
RC(4)-H
1.0830(7)
1.085
RC(5)-H
1.0812(8)
1.081
θC(2)-N(3)-C(4)
115.52(6)
θN(3)-C(4)-C(5)
122.35(5)
θC(4)-C(5)-C(6)
116.85(5)
θN(1)-C(2)-H
116.29(6)
θC(4)-C(5)-H
121.58(5)
θC(5)-C(4)-H
121.46(9)
RC(4)-H
RC(2)-N(3)
RN(3)-C(4)
RC(5)-H
RC(4)-C(5)
RC(2)-H
θC(5)-C(4)-H
θC(4)-C(5)-H
θN(1)-C(2)-H
θC(2)-N(3)-C(4)
θN(3)-C(4)-C(5)
θC(4)-C(5)-C(6)

18. Importance of Corrections18
Importance of Corrections
Isotopologue
Di (mÅ2)
a corrected
a and e- corrected
C4H4N2
0.0350
[2-13C]-C4H4N2
0.0352
[4-13C]-C4H4N2
0.0355
[5-13C]-C4H4N2
0.0360
[1-15N]-C4H4N2
0.0356
[2-2H]-C4H4N2
0.0308
[4-2H]-C4H4N2
0.0318
[5-2H]-C4H4N2
0.0329
[2,4-2H]-C4H4N2
0.0285
[4,5-2H]-C4H4N2
0.0299
[4,6-2H]-C4H4N2
0.0275
[4,5,6-2H]-C4H4N2
0.0269
Vibration-rotation corrections calculated with an anharmonic frequency VPT2 calculation at the CCSD(T)/ANO1 level.
Electronic corrections calculated at the CCSD(T)/ANO1 level

19. Comparison to Other Structures19
Comparison to Other Structures
Experimental
Computational
Parameters
Re (Å)
CCSD(T)/ANO1
Substitution
Rs (Å)
Kisiel et al.
Piccardo et al.
Rese (Å)
RC(2)-N(3)
1.3346(9)
1.340
1.338
1.337(2)
1.3334(1)
RN(3)-C(4)
1.3366(8)
1.341
1.344
1.332(3)
1.3355(1)
RC(4)-C(5)
1.3834(6)
1.392
1.393
1.393(2)
1.3867(3)
RC(2)-H
1.0813(9)
1.084
1.087 -
[1.0822]
RC(4)-H
1.0830(7)
1.085
1.086
[1.0826]
RC(5)-H
1.0812(8)
1.081
1.082
[1.0795]
θC(2)-N(3)-C(4)
115.52(6)
115.80
115.8(3)
115.69(1)
θN(3)-C(4)-C(5)
122.35(5)
122.38
122.4(3)
122.27(2)
θC(4)-C(5)-C(6)
116.85(5)
116.42
116.4(2)
116.72(1)
θN(1)-C(2)-H
116.29(6)
116.39
116.31(1)
θC(4)-C(5)-H
121.58(5)
121.79
121.64(1)
θC(5)-C(4)-H
121.46(9)
120.96
[121.36]
Z. Kisiel, L. Pszczolkowski, I. R. Medvedev, M. Winnewisser, F. C. De Lucia, E. Herbst, J. Mol. Spectrosc. 233, (2005).
M. Piccardo, E. Penocchino, C. Puzzarini, M. Biczysko, V. Barone, J. Phys. Chem. 119, (2015).

20. Thanks! The McMahon-Woods Research Group 20 Robert J. McMahon
R. Claude Woods :30 Friday in 217 Noyes Lab (FE01)
Brian J. Esselman
Brent K. Amberger :47 Friday in 217 Noyes Lab (FE02)
Ben C. Haenni
Stephanie N. Knezz 5:00 Thursday in 217 Noyes Lab (RJ13)
Nick A. Walters :12 Friday in 217 Noyes Lab (FE06)
Vanessa L. Orr
Cara E. Schwarz Next!
Maria A. Zdanovskaia
P. Matisha Kirkconnell