Dipeptide structure determination by vibrational circular dichroism combined with quantum chemistry calculations.
The solution structure and the local solvation environments of alanine dipeptide (AD, 1 a) and its isotopomer (AD*, 1 b, 13C on the acetyl end C==O) are studied by using infrared (IR) spectroscopy and vibrational circular dichroism (VCD). From the amide I IR spectra of AD* in various protic solvents, it is found that each of the two carbonyl groups is fully H-bonded to two water molecules. However, the number of alcohol molecules H-bonded to each C==O varies from one to two, and the local solvation environments are asymmetric around the two peptides of AD* in alcohol solutions. The amide I VCD spectra of AD and AD* in D2O are also measured, and a series of density functional theory (DFT, B3LYP/6-311++G**) calculations are performed to obtain the amide I normal-mode rotational strengths of AD and the intrinsic rotational strengths of its two peptide fragments. By combining the VCD-measurement and DFT-calculation results and employing a coupled oscillator theory, we show that the aqueous-solution structure of the dipeptide can be determined. We believe that the present method will be of use in building up a library of dipeptide solution structures in water.
Lee
Kyung-Koo
KK
Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
Oh
Kwang-Im
KI
Lee
Hochan
H
Joo
Cheonik
C
Han
Hogyu
H
Cho
Minhaeng
M
D002942:Circular Dichroism / Q000379:methods*; D004151:Dipeptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared; D014732:Vibration
D004151:Dipeptides; C002956:alanylalanine