Supplementary material

Conformation-Specific Spectroscopy of Peptide Fragment Ions in a low-Temperature Ion TrapTobias N. Wassermann, Oleg V. Boyarkine, Béla Paizs, Thomas R. Rizzo

UV spectra of b4 and a4 in the region of the phenylalanine chromophore

Figure S1

Photofragment UV spectra of b4 (red trace) and a4 ions (green trace) derived from leucine-

enkephalin YGGFL in the region of phenylalanine (F) electronic excitation with some assignments

based on IR-UV double resonance depletion spectroscopy.

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Variation of the NH3+ stretch wavenumbers with the O–C–N–H

dihedral angle in the b3 ion

Figure S2

Scaled NH stretch wavenumbers (left ordinate axis) of the NH3+ group in N-terminally protonated

oxazolone b3 from YGGFL upon variation of the dihedral angle defined by O–C–N–H (i.e.

rotation of the NH3+ group around the C–N axis, atoms marked in the image; B3LYP/6-31+G(d,p)

harmonic wavenumbers scaled with a factor of 0.954). Blue trace: free NH, red trace: NH

hydrogen-bonded to the π system of the aromatic ring, green trace: NH hydrogen-bonded to the

carbonyl group. In the calculations the dihedral angle was fixed to a given value while all other

coordinates were allowed to relax freely. The resulting relative DFT energies including zero point

corrections are shown with a black dashed line (ordinate axis on the right side). None of the

calculated structures had imaginary frequencies. While the free NH and the NH--π vibrations do

not show strong variations, the value for the NH--OC vibration increases strongly when the

dihedral angle is increased (i.e. the NH--OC is rotated out of the plane of the carbonyl group while

the NH--π can further approach the center of the aromatic ring). This qualitatively illustrates that

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an overestimation of the NH--OC hydrogen bond strength and an underestimation of the NH--π

hydrogen bond strength lead to an overestimation of the NH--OC vibrational red shift.

Fingerprint vibrational spectra of b4 conformations A and B

Figure S3

Selective IR-UV double resonance depletion spectra of the b4 conformers A and B in the

fingerprint region of the vibrational spectrum and comparison to predictions for two candidate

structures for conformer A (B3LYP/6-31+G(d,p), scaling factor 0.98, see also Figure 8 in the

manuscript).

3

Variation of intensity ratios of UV bands of b4 (conformations A and B) from UV spectra

Figure S4

4

Comparison of photofragmentation UV spectra of b4 without (red trace) and with (black trace) pre-

trapping in the octopole.

Fingerprint vibrational spectra of the a4 ion (conformations A and B)

Figure S5

Conformation-selective IR-UV depletion spectra of the two isomers A and B of YGGFL a4 ions in

the fingerprint region in comparison to theoretical predictions (B3LYP/6-31+G(d,p), scaling factor

0.98, see also Figure 11 in the manuscript). Isotopologues derived from 15N YGG*F*L are shown

above the spectra of the normal species. Isotopic red shifts are marked in the spectra.

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Tables of experimentally observed vibrational band positions from IR-UV double-resonance spectra

Table S1

Band positions and assignments of the most characteristic vibrations of the conformations A and B

of the YG b2 ion generated from leucine-enkephalin (YGGFL).

Conformer A Conformer B

Assignment Wavenumber/cm-1 Wavenumber/cm-1

ν (OH) 3641 3641

ν (free NH3+) 3353 3335

ν (bound NH3+) 3136 3135

ν (bound NH3+) 3073 3097

ν (C=Ooxa) 1923 1916

ν (C=N) 1680 1683

δ (NH3+) 1603 1603

δ (NH3+) 1458 1444

Table S2

Band positions and assignments of the most characteristic vibrations of the YGG b3 ion generated

from leucine-enkephalin (YGGFL).

Assignment Wavenumber/cm-1

ν (OH) 3641

ν (Gly amide NH), ν (free NH3+) 3351, 3347

ν (bound NH3+) 3180

ν (bound NH3+) 3113

ν (C=Ooxa) 1908, 1900

Amide I 1721

ν (C=N) 1683

Amide II 1549

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Amide III 1387

Table S3

Band positions and assignments of the most characteristic vibrations of the conformations A, B, C,

and D of the YGGF b4 ion generated from leucine-enkephalin (YGGFL).

Conformer A Conformer B Conformer C Conformer D

Assignment Wavenumber/cm-1 Wavenumber/cm-1 Wavenumber/cm-1 Wavenumber/cm-1

ν (OH) 3643 3643 3643 3643

ν (G1 NH) 3461 3348 3446 3434

ν (G2 NH) 3430 3407 3469 3417

ν (NH3+) 3218 3222 3265 3319

ν (NH3+) 3084 3082 3106 3171

ν (NH3+) 2961 2900 2961 2964

ν (C=Ooxa) 1791 1787

Amide I 1751 1746

Amide I 1703 1703

Amide II 1536 1530

1449 1442

Table S4

Band positions and assignments of the most characteristic vibrations of the conformations A and B

of the YGGF a4 ion generated from leucine-enkephalin (YGGFL).

Conformer A Conformer B

Assignment Wavenumber/cm-1 Wavenumber/cm-1

ν (OH) 3644 3642

ν (NH2 as) 3549 3548

ν (NH2 s) 3439 3438

ν (G2 NH) 3426 3429

3178 3267

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3092 3239

3050 3224

3189

Amide I, ν (C=N) 1766, 1723, 1710, 1703 1758, 1724, 1712, 1705

δ (NH2) 1613 1611

Amide II (G2 NH) 1526 1530

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