The Delicate Balance of Hydrogen
Bond Forces in D-Threoninol
Di Zhang, Vanesa Vaquero Vara, Brian C. Dian and
Timothy S. Zwier
Zwier Research Group, Purdue University
19
D-Threoninol: Reduced form of D-Threonine
Threonine
Artificial ¨DNA¨:
Acyclic threoninol nucleic acid (aTNA)*
–
–
(S) (S)
HO – CH2 – CH – CH – OH
NH2 CH3
*H. Kashida et al., Angew. Chem. Int. Ed. 2011, 50, 1285
20
D-Threoninol: Evolution of the structure
HO – CH2 – CH2 – OH (1)
–
HO – CH2 – CH2 – CH2 – OH (2)
HO – CH2 – CH2 – CH – OH (3)
CH3
W. Caminati et al.,
J. Mol. Spectr. 1981, 90(2), 572
W. Caminati et al.,
J. Mol. Spectr. 1995, 171, 394
HO – CH2 – CH– CH2 – OH (2)
W. Caminati et al.,
J. Mol. Struct. 1982, 78, 197
–
OH
–
–
(S)
(S)
HO – CH2 – CH – CH – OH
NH2 CH3
?
V. Ilyushin et al. J. Mol. Spectr. 2008, 251, 129
21
Calculational Methods
1. Force field calculation in Amber* force field
was performed first at low computational cost
with MacroModel commercial program suite.
2. 85 stable conformation structures were
filtered out with a given energy threshold
(50kJ mol-1).
3. Full geometry optimizations were performed
using MP2 with 6-311++G(d,p) basis set.
Predicted lower energy conformers and relative energies
with respect to the global minimum
cw
ccw
instrumentation
1) Pulse Generation
2) Molecular Interaction
3) Detection
Rotational spectrum of D-threoninol from 7.5-18.5 GHz
8000
10000
12000
14000
16000
18000
Predicted lower energy conformers and relative energies
with respect to the global minimum
cw
ccw
Hyperfine structures with their respective 2 2,0 ← 1 1,1 rotational transitions
Hyperfine structures with their respective 3 1,3 ← 2 1,2 rotational transitions
Hyperfine structures with their respective 5 1,4 ← 4 1,3 rotational transitions
Hyperfine structure with its respective 5 1,4 ← 4 1,3 rotational transition
Conclusions
350
①
300
250
200
150
③
②
cycle
chain
100
50
0
3→2→1
1→2→3
1→3→2
0.8
1.2
1.6
2.0
MP2/6-311++G(d,p)
1→2→3
②
300
①
③
2→1→3
200
100
0
① Substituted alkyl chains allow the formation of
networks of intramolecular hydrogen bonds
② Cycles are lowest in energy in both tri-substituted
cases
③ Chains are only slightly higher in energy
• Observe several chain conformers
• Near energies
• Compensation between 3 weak H bonds and 2
strong H bonds
④ Presence of NH2 :
a) Better H-bond acceptor
2.17Å
2.28Å
b) Poorer H-bond donor
• H-bond length
• Distorted structure
2.17Å
cycle
1→3→2
2.57Å
2.34Å
2.35Å
chain
3→2→1
0.8MP2/aug-cc-pVTZ
1.2
1.6
2.0
2.12Å
2.08Å
V.V.Ilyushin et al. J.Mol.Spec. 251 (2008) 129
Acknowledgments
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
Conclusions I
Observed 7 conformers of D-threoninol
• Two hydrogen bonded cycles
• Five hydrogen bonded chains
Rotational constants A,B,C provide information on the
conformation of the molecules
Quadrupole coupling constants χgg (g= a,b,c) provide a
different and independent way to identify different
conformers
Predicted lower energy conformers and relative energies
with respect to the global minimum
+sc -sc
III
402 cm-1
406 cm-1
*Zero point corrected energies at MP2/6-311++G(d,p)
MP2/6311+G(d,p)
3
exp
1
exp
23
exp
10
exp
19
exp
13
exp
5
exp
A (MHz)
3941
3904.0776(11)
3924
3902.91475(69)
3512
3513.6913( 68)
4618
4584.7856 (84)
3461
3482.3760(53)
4194
4171.1102(27)
4550
4525.06(42)
B (MHz)
1936
1931.92598(97)
1945
1938.4299(12)
2064
2037.0863(20)
1579
1568.39713(89)
2070
2026.9310(23)
1732
1722.4785(13)
1583
1570.2817(21)
C (MHz)
1709
1701.1088(13)
1704
1693.2639(11)
1528
1515.8920( 32)
1480
1472.17944(76)
1523
1507.3793(25)
1308
1301.6872(17)
1463
1460.1230(20)
Δ (kHz)
Configuration
0.178(28)
+sc –sc
II3
0.167(30)
+sc –sc
I3
-0.301( 67)
+sc +sc
I2
0.309(49)
-sc –sc
I2
+sc +sc
II2
0.212(25)
-sc +sc
I2
-sc –sc
II2
MP2/6311+G(d,p)
74
39
27
11
9
4
2
12
16
14
A (MHz)
3463
3503
3495
4589
4565
3881
3782
4186
4149
4171
B (MHz)
2050
2054
2007
1567
1571
1988
1987
1733
1714
1716
C (MHz)
1635
1524
1498
1471
1454
1669
1690
1310
1301
1304
+sc +sc
+sc +sc
-sc -sc
-sc -sc
+sc -sc
+sc -sc
-sc +sc
-sc +sc
-sc +sc
Configuration +sc +sc