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Juan Ren, Xian-yi Zhang, Xiang-lei Kong. Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations†[J]. Chinese Journal of Chemical Physics , 2020, 33(5): 590-594. doi: 10.1063/1674-0068/cjcp2006089
Citation: Juan Ren, Xian-yi Zhang, Xiang-lei Kong. Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations[J]. Chinese Journal of Chemical Physics , 2020, 33(5): 590-594. doi: 10.1063/1674-0068/cjcp2006089

Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations

doi: 10.1063/1674-0068/cjcp2006089
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  • Corresponding author: Xiang-lei Kong, E-mail: kongxianglei@nankai.edu.cn
  • Part of the special issue on "the Chinese Chemical Society's 16th National Chemical Dynamics Symposium".
  • Received Date: 2020-06-10
  • Accepted Date: 2020-07-03
  • Publish Date: 2020-10-27
  • The infrared multiphoton dissociation (IRMPD) spectrum of the protonated heterodimer of ProPheH$ ^+ $, in the range of 2700-3700 cm$ ^{-1} $, has been obtained with a Fourier-transform ion cyclotron mass spectrometer combined with an IR OPO laser. The experimental spectrum shows one peak at 3565 cm$ ^{-1} $ corresponding to the free carboxyl O-H stretching vibration, and two broad peaks centered at 2935 and 3195 cm$ ^{-1} $. Theoretical calculations were performed on the level of M062X/6-311++G(d, p). Results show that the most stable isomer is characterized by a charge-solvated structure in which the proton is bound to the unit of proline. Its predicted spectrum is in good agreement with the experimental one, although the coexistence of salt-bridged structures cannot be entirely excluded.
  • Part of the special issue on "the Chinese Chemical Society's 16th National Chemical Dynamics Symposium".
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Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations

doi: 10.1063/1674-0068/cjcp2006089

Abstract: The infrared multiphoton dissociation (IRMPD) spectrum of the protonated heterodimer of ProPheH$ ^+ $, in the range of 2700-3700 cm$ ^{-1} $, has been obtained with a Fourier-transform ion cyclotron mass spectrometer combined with an IR OPO laser. The experimental spectrum shows one peak at 3565 cm$ ^{-1} $ corresponding to the free carboxyl O-H stretching vibration, and two broad peaks centered at 2935 and 3195 cm$ ^{-1} $. Theoretical calculations were performed on the level of M062X/6-311++G(d, p). Results show that the most stable isomer is characterized by a charge-solvated structure in which the proton is bound to the unit of proline. Its predicted spectrum is in good agreement with the experimental one, although the coexistence of salt-bridged structures cannot be entirely excluded.

Part of the special issue on "the Chinese Chemical Society's 16th National Chemical Dynamics Symposium".
Juan Ren, Xian-yi Zhang, Xiang-lei Kong. Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations†[J]. Chinese Journal of Chemical Physics , 2020, 33(5): 590-594. doi: 10.1063/1674-0068/cjcp2006089
Citation: Juan Ren, Xian-yi Zhang, Xiang-lei Kong. Structure of Protonated Heterodimer of Proline and Phenylalanine: Revealed by Infrared Multiphoton Dissociation Spectroscopy and Theoretical Calculations[J]. Chinese Journal of Chemical Physics , 2020, 33(5): 590-594. doi: 10.1063/1674-0068/cjcp2006089
  • Interactions between biological molecules such as peptides and proteins are governed by kinds of noncovalent interactions [1, 2]. As the simplest model for studying such interactions, dimers of amino acids in vacuum can provide us some fundamental aspects [3]. In order to perform this, methods based on mass spectrometry, such as, collision induced dissociation (CID), blackbody infrared radiative dissociation (BIRD) and electron capture dissociation (ECD), etc. have been applied for years [3-18]. Among them, the method of infrared multiphoton dissociation (IRMPD) spectroscopy has been thought as one of the most powerful one, especially when it is combined with the density functional theory (DFT) or ab initio theoretical calculations [3, 12-24].

    With the method of IRMPD spectroscopy combined with the electrospray ionization (ESI) technique [25], homodimers of amino acids, such as Gly$ _2 $H$ ^+ $, Thr$ _2 $H$ ^+ $, Pro$ _2 $H$ ^+ $ and Lys$ _2 $H$ ^+ $, have been widely studied in the past twenty years [12-14, 26-36]. Based on the studies, it is now realized that the proton affinity (PA) of the amino acid can be applied as a structural probe [33, 34]. In most cases, a higher PA of the amino acid leads to a more stable salt-bridged (SB) structure for its protonated homodimers. However, it may be not always right, since function groups on side chains also have a great effect on their structures [34, 35]. On the other hand, the research on heterodimers of amino acids is less compared to those of homodimers [3, 12, 27, 35-38]. One possible reason is that the structures and intermolecular interactions in heterodimers are more complicated than those of homodimers. The experimentally observed isomers for heterodimers are difficult to be precisely predicted theoretically. For example, Lorenz and Rizzo have shown that at least five kinds of isomers for protonated heterodimer of phenylalanine (Phe) and serine (Ser) can co-exist even at $ \sim $10 K [3].

    The heterodimer of GlyPheH$ ^+ $ studied by IRMPD spectroscopy in the 975-1975 cm$ ^{-1} $ region by Fu et al. also show its structural complexity [38]. The calculated global minimum structure has a charge-solvated (CS) structure in which the cation-$ \pi $ interaction has a great influence on the cluster geometry. By comparing the experimental and predicted spectra of suggested isomers, it is also found that that experimentally formed clusters of GlyPheH$ ^+ $ consist of serval types of isomers, including the global minimum structure characterized by a NH$ \cdots $N intermolecular hydrogen bond (H-bond) between the protonated Phe and the neutral Gly moiety, and a different isomer with higher energy than the first one, which is characterized by a NH$ \cdots $O intermolecular H-bond between the protonated Gly and the neutral Phe moiety.

    In this paper, the IRMPD spectra of the protonated heterodimers of Phe and Proline (Pro) has been studied experimentally, and its structures are also calculated with the DFT method of M062X. The results are valuable in providing us clues for a better understanding of the structural diversity of amino acid heterodimers in the gas phase.

  • IR action spectra were recorded by the method of IRMPD spectroscopy based on a Fourier-transform ion cyclotron (FT ICR) mass spectrometer (MS). The experimental setup has been reported previously in detail [32, 33]. Briefly, a 7T FT ICR MS (IonSpec, Varian Inc., Lake Forest, CA, USA) was combined with a commercial IR OPO laser (Firefly-IR, M Squared, UK) to perform the experiments. The OPO was operated in the normal mode, with an output irradiation tunable from 2700 cm$ ^{-1} $ to 3800 cm$ ^{-1} $ and a line width of 5 cm$ ^{-1} $. The average laser power was 160 mW. The irradiation time of the laser was set to 6 s and controlled by a mechanical shutter (Sigma-Koki, Japan). The spectrum was obtained by scanning the wavelength in a typical step of 5 cm$ ^{-1} $ with a self-developed program. The spectral intensity at each wavelength was calculated as the following equation:

    where $ I_{\rm{p}} $ and $ I_{\rm{f}} $ are the intensities of parent ions and fragment ions, respectively.

    In the experiment, the mixture solution of $ L $-Pro and $ L $-Phe (both 1 mmol/L in 49:49:2 of H$ _2 $O:MeOH:AcOH) was electrosprayed with a probe biased at 3.5 kV. The infusion rate was set as 240 $ \mathtt{ μ} $L/h. The ESI ions were accumulated in a hexapole ion trap for 1.0 ms, then were introduced into the FT ICR cell. Before the laser irradiation, the target ion was selected and isolated in the cell by the method of stored waveform inverse Fourier-transform (SWIFT) [39]. Collision-induced dissociation (CID) experiments were performed by the method of sustained off-resonance irradiation (SORI) excitation of the selected isotopic peak at amplitudes of 0.2-1.8 V ($ V_{\rm{p-p}} $) with a frequency offset of 1000 Hz.

    For theoretical calculations, a variety of initial structures of ProPheH$ ^+ $ have been generated using a self-developed method based on the optimized structures of Pro, ProH$ ^+ $, Phe and PheH$ ^+ $. At the first step, these generated structures were optimized using the semi-empirical AM1 method. Then the 100 isomers with the lowest energies were selected and further optimized by the DFT method at the M062X/6-31+G(d) level [40]. After removing the failed structures and the repetitive ones, 68 isomers were selected to be further optimized at the level of M062X/6-311++G(d, p). Frequencies were then calculated at the same level and scaled with a factor of 0.937. Zero-point energy (ZPE) corrected electronic energies were calculated at 0 K, while their corresponding free energies were calculated at 298 K. All calculations were performed using the Gaussian 09 program [41].

  • FIG. 1(a) shows the total ESI mass spectrum of the mixed solution of Pro and Phe, and both complex ions of ProPheH$ ^+ $ and Pro$ _2 $H$ ^+ $ were observed. The target ion of ProPheH$ ^+ $ can be clearly isolated (FIG. 1(b)) and the IR irradiation can dissociate the complex ion to form the fragment ion of ProH$ ^+ $ readily. No PheH$ ^+ $ ion is observed in all experiments, which is consistent with the CID results (FIG. S1, S2 in supplementary materials). The result can be understood by considering the case as a thermodynamically controlled reaction and the fact of Pro has a higher PA than Phe [42]. And similar results have also been previously reported [37].

    Figure 1.  (a) ESI mass spectrum of the mixture solution of Pho and Phe, (b) the isolation of the complex ions of ProPheH$ ^+ $ and (c) IRMPD mass spectrum of ProPheH$ ^+ $ after a 6 s IR irradiation at 3560 cm$ ^{-1} $.

  • FIG. 2(a) shows the IRMPD spectrum of ProPheH$ ^+ $ in the range of 2700-3700 cm$ ^{-1} $. A sharp peak at 3565 cm$ ^{-1} $ is observed, accompanied with broad peaks at 2935 and 3195 cm$ ^{-1} $. The spectrum is very different from the previously reported IRMPD spectrum of Pro$ _2 $H$ ^+ $ [25], which contains a strong absorption at $ \sim $3600 cm$ ^{-1} $ corresponding to the OH stretching vibration, a weak peak at $ \sim $3400 cm$ ^{-1} $ corresponding to the free NH stretch of the zwitterionic Pro, and a peak at $ \sim $3260 cm$ ^{-1} $ from a red-shift NH vibration. If it is compared with the previously reported isomer-specific IR spectra of PheSerH$ ^+ $ by Rizzo et al. [3], some common futures can be found. For example, all IR spectra also show sharp peaks at $ \sim $3565 cm$ ^{-1} $, corresponding to the free carboxylic acid OH stretches; in Rizzo's work, some isomer also shows NH stretches in the range of 3100-3250 cm$ ^{-1} $, close to the 3195 cm$ ^{-1} $ vibration observed here. They also observed very weak absorptions in the range of 2900-3100 cm$ ^{-1} $, which is from the CH stretches.

    Figure 2.  (a) Experimental IRMPD spectrum of ProPheH$ ^+ $ in the region of 2700-3700 cm$ ^{-1} $, and the calculated IR spectra of (b) PF-ProH-CS-1, (c) PF-PheH-CS-1, (d) PF-PheH-SB-1, and (e) PF-ProH-SB-1.

  • To understand the experimental results, DFT calculations were performed and the lowest-energy structures were identified. Total 68 isomers have been studied here. These isomers can be classified as four types: (i) the proton is bound to the unit of Pro, and the unit of Phe has a non-zwitterionic structure (PF-ProH-CS); (ii) the proton is bound to Pro, and Phe has a zwitterionic structure (PF-ProH-SB); (iii) the proton is bound to Phe, and Pro has a non-zwitterionic structure (PF-PheH-CS); and (iv) the proton is bound to Phe, and Pro has a zwitterionic structure (PF-PheH-SB). By comparing their energies relative to their structure types, some general idea can be reflected. As shown in FIG. 3, the most stable isomer is characterized by a structure of type 1 (PF-ProH-CS). And the proportion of this configuration is as high as 50% in these total 68 isomers. It is also reflected that the ratio of the CS-typed dimers (60%) is much higher than that of the SB-typed dimers (40%).

    Figure 3.  A view on the 68 optimized structures, corresponding to their energy orders and structural types.

    The structures of the most stable isomers of the four types are shown in FIG. 4. The energies of these isomers are listed in Table Ⅰ. Base on the method of M062X/6-311++G(d, p), the energy of PF-PheH-CS-1 is 0.08 kJ/mol higher than that of PF-ProH-CS-1, while the SB isomers are $ \sim $4-22 kJ/mol higher in energy. Further single point energy calculation based on CCSD/6-311+G(d, p) shows the same energy order. But these isomers are $ \sim $8-32kJ/mol higher than that of PF-ProH-CS-1 in energy (Table Ⅰ).

    Figure 4.  Optimized structures of the most stable isomers of ProPheH$ ^+ $ in four kinds of configurations on the level of M062X/6-311++G(d, p). The H-bonds are identified as dash lines and the lengths are shown in Å.

    Table Ⅰ.  Relative energies and free energies (both in kJ/mol) of the four isomers of ProPheH$ ^+ $$ ^{\rm{a}} $.

    Not only the position of the proton and the structure type, but also the H-bonds among the complexes should be noticed. Both intermolecular and intramolecular H-bonds have been found in these isomers, and they are summarized in Table Ⅱ. For the most stable isomer PF-ProH-CS-1, an intermolecular (N-H$ \cdots $N) H-bond (1.71 Å, 176$ ^\circ $) exists with a weak intramolecular (N-H$ \cdots $O) H-bond (2.07 Å, 114$ ^\circ $). The NBO analysis reflects that the intermolecular H-bond (N-H$ \cdots $N) can be mainly contributed to the LP(1)N18$ \rightarrow $BD$ ^* $(1)N4-H31 (the label of the atoms in the structure can be found in the supplementary materials), which has a second-order interaction energy ($ E $(2)) of 194.6 kJ/mol. For PF-PheH-CS-1, only one strong intermolecular (N-H$ \cdots $N) H-bond (1.60 Å, 176$ ^\circ $) is found. For salt-bridged structures, the intermolecular N-H$ \cdots $O H-bonds are both greatly enhanced by the charge interaction (1.45 Å, 164$ ^\circ $ and 1.51 Å, 173$ ^\circ $). For example, the NBO analysis shows that the intermolecular (N-H$ \cdots $O) H-bond in PF-PheH-SB-1 has a $ E $(2) as high as 343.3 kJ/mol (from LP(2)O8$ \rightarrow $BD$ ^* $(1) N18-H32). Besides, these two SB structures also show some intramolecular N-H$ \cdots $O H-bonds.

    Table Ⅱ.  H-bonds of the four most stable isomers of ProPheH$ ^+ $ shown in FIG. 4. Both PF-PheH-SB-1 and PF-ProH-SB-1 have double intramolecular H-bonds.

    The calculated spectra of the four isomers are also shown in FIG. 2. All structures show the absorptions at $ \sim $3565 cm$ ^{-1} $, which comes from the free carboxyl O-H stretching vibrations. Both CS structures have two free carboxyl O-H groups, while the SB structures only have one. By comparing the relative intensity of the peak with other peaks in experimental spectrum at 3565 cm$ ^{-1} $, it can be found that the calculated spectra of CS structures fit better than those of SB structures. Besides, the calculated peak at 3190 cm$ ^{-1} $ (coming from the H-bonding N-H stretching vibration) of the most stable isomer of PF-ProH-CS-1 matches the absorption at 3195 cm$ ^{-1} $ in FIG. 2(a) well, indicating it gives the main contribution to the existing isomers. For PF-PheH-CS-1, absorptions in the region of 3200- 3310 cm$ ^{-1} $ are predicted, which are from N-H stretching (from Pro), symmetric and antisymmetric stretching vibrations of NH$ _2 $ (from Phe). For PF-PheH-SB-1 and PF-ProH-SB-1, the H-bonds make the N-H stretching vibrations red-shift to 2900 cm$ ^{-1} $ and 2990 cm$ ^{-1} $, respectively. Considering the intensity of the broad peak at $ \sim $2935 cm$ ^{-1} $ and the widely observed coexistence of multi isomers in similar experiments [3, 43-45], the contributions from the SB type structures might not be totally neglected, even the calculated Boltzmann ratios of them are less than 3% at 298 K [34, 35, 43].

  • The structures of protonated heterodimers, ProPheH$ ^+ $, have been investigated by the method of IRMPD spectroscopy and theoretical calculations. The experimental spectrum was obtained on a FT ICR mass spectrometer combined with an IR OPO laser in the range of 2700-3700 cm$ ^{-1} $. Besides the sharp peak at 3565 cm$ ^{-1} $ that corresponds to the free carboxyl O-H stretching vibration, weak and broad peaks centered at 2935 and 3195 cm$ ^{-1} $ are also observed. Calculation results show that the structures of ProPheH$ ^+ $ can be classified into four types, according to the position of proton and the interaction type between the two units (SB or CS). The most stable isomer PF-ProH-CS-1 is characterized by a CS structure in which the proton is bound to the unit of Pro. The CS type isomer of PF-PheH-CS-1, in which the proton is bound to Phe, has an energy 0.08 kJ/mol higher than that of PF-ProH-CS-1 on the level of M062X/6-311++G(d, p). And the two most stable SB structures, PF-PheH-SB-1 and PF-ProH-SB-1, have energies 4.3 and 22 kJ/mol higher, respectively. The calculated spectrum of the lowest energy isomer PF-ProH-CS-1 is found to be in good agreement with the experimental spectrum, although the simultaneous existence of other isomers is also possible.

    Supplementary materials: Structures of the four isomers optimized at the level of M062X/6-311++G(d, p) are available.

  • This work was supported by the National Natural Science Foundation of China (No.21627810) and the Fundamental Research Funds for the Central Universities, Nankai University (No.63191523).

  • Table S1.  The relative energies, free energies at 298K (both in kj/mol) and their calculated ratios at 298K of all 68 isomers calculated on the level of M062X/6-311++G (d, p).

    Figure S1.  The CID mass spectra of ProPheH+ under two different CID experimental condtions: a) Vp-p= 1.0 V and b) Vp-p= 1.5 V.

    Figure S2.  Relative intensities of fragment and precursor ions of ProPheH+ under different CID conditions.

    Figure S3.  The top 20 isomers calculated on the level of M062X/6-311++G (d, p).

    Structures of the four isomers optimized at the level of M062X/6-311++G(d, p) are available.

    Table 1.  PF-ProH-CS-1

    Table 2.  PF-PheH-CS-1

    Table 3.  PF-PheH-SB-1

    Table 4.  PF-ProH-SB-1

Reference (45)

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