Min Xie, Zhao-li Zhang, Yu Zhang, Xiao-nan Sun, Fu-fei Sun, Yong-jun Hu. Infrared Spectroscopy of Neutral and Cationic Pyrrolidine Monomer in Supersonic Jet[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 43-47. DOI: 10.1063/1674-0068/cjcp1910183
Citation:
Min Xie, Zhao-li Zhang, Yu Zhang, Xiao-nan Sun, Fu-fei Sun, Yong-jun Hu. Infrared Spectroscopy of Neutral and Cationic Pyrrolidine Monomer in Supersonic Jet[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 43-47. DOI: 10.1063/1674-0068/cjcp1910183
Min Xie, Zhao-li Zhang, Yu Zhang, Xiao-nan Sun, Fu-fei Sun, Yong-jun Hu. Infrared Spectroscopy of Neutral and Cationic Pyrrolidine Monomer in Supersonic Jet[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 43-47. DOI: 10.1063/1674-0068/cjcp1910183
Citation:
Min Xie, Zhao-li Zhang, Yu Zhang, Xiao-nan Sun, Fu-fei Sun, Yong-jun Hu. Infrared Spectroscopy of Neutral and Cationic Pyrrolidine Monomer in Supersonic Jet[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 43-47. DOI: 10.1063/1674-0068/cjcp1910183
MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
Pyrrolidine, a five membered heterocyclic molecule, is widely existing in organism. Herein, infrared spectra of pyrrolidine monomer in neutral and cationic states were obtained by vacuum ultraviolet ionization, infrared photodissociation and time of flight mass spectrometry. Both in neutral and cationic states, it is found that their CH stretching vibration bands are red shifted. In the IR spectrum of neutral pyrrolidine, because the electric dipole moment of NH is small, we have not observed the NH stretching vibration bands. However, the NH stretching vibration band of pyrrolidine is greatly enhanced after ionization, and this band red-shifts compared with the previous experiment. The red shifts of CH stretching vibrations in neutral and cationic states are caused by the negative and positive hyperconjugation, respectively. The enhancement and red shift of the NH stretching band are owing to the ejection of the electrons on the N atom after ionization. Through the calculations, it is found that the acidity of the CH bond is a little stronger than that of NH bond. These kinds of studies would be helpful to understand the intrinsic properties of biomolecules in neutral and cationic states, and to provide reference for the further study of living organic macromolecules.
Pyrrolydine (PRL) with a nitrogen-containing saturated five-membered ring is usually involved in the biochemistry, medicinal and pharmaceutical chemistry [1-4]. There are axial- and equatorial- conformations of the PRL, due to the different direction of the N-H bond [5, 6]. In general, these two conformers can interconvert to each other with a very low barrier (∼220 cm−1) for the ring puckering [7]. Thus, it is also one of the important prototypes to study the pseudorotation. What is more, Ho et al. indicated that the side-chain flexibility of the proline residue in the backbone conformation of proteins is closely related to pseudorotation [8]. For a deeper understanding of the relationship between pseudorotation and backbone conformation of proteins, the fundamental studies of the structures and property of the neutral and cationic PRL molecule are necessary.
Theoretical calculations of neutral PRL molecule have been studied and shown that two conformers (PRL-ax and PRL-eq) with very close energy exist. Many experimental methods, such as gas-phase electron diffraction [9-11], infrared and Raman spectroscopy [5, 12, 13], have also been used to detect the structure preferment and pseudorotation of PRL. However, these methods are performed at the room temperature or in liquid phase. In the early study of microwave spectroscopy study, only the PRL-ax conformer has been observed [14]. Due to the improvement of equipment and the better cooling condition of the supersonic jet, the PRL-eq conformer has been found and considered to be the most stable structure [7, 15]. The above studies are all in the neutral state, and no spectroscopic study of gas-phase PRL molecule in its cationic state has been performed.
To obtain the IR spectroscopy of neutral or cationic molecules in supersonic jet, IR dissociation with vacuum-ultraviolet (VUV) photoionization and mass-selected detection has been proven to be a powerful tool [16-20]. In this technique, the VUV (usually 118 nm) light is utilized as an ionization source. With the VUV light, most of biomolecules can be softly ionized, even though there is no any chromophore group in the molecules. With this method, IR spectra of neutral and cationic tetrahydrofuran (THF), another representative compounds with heterocyclic five-membered ring, have been measured. IR spectra of neutral and cationic THF indicated that the acidity of the CH bond next to the oxygen atom of THF is greatly enhanced after ionization, due to the hyperconjugation interaction [21]. The difference between PRL and THF is the heteroatom incorporated to the five-membered ring. Thus, an interesting question that arises is which H atom is more acidic in the cationic PRL, the C-H or the N-H bond?
To answer the question, IR spectra combined with theoretical calculations of neutral and cationic PRL have been carried out. The C-H bond is proved to be more acidic than that of N-H bond in the cationic PRL. Hyperconjugation induced redshift of the CH bands is indicated by the IR spectral features and DFT calculations.
Ⅱ.
METHODS
IR spectra of neutral and cationic PRL were recorded by IR predissociation spectroscopy based on the vacuum-ultraviolet photoionization detection. Details of the experimental setups have been reported previously [22, 23], and only a brief description is given here. Gaseous PRL seeded in the He carrier gas was produced on supersonic expansion through a pulsed valve (Parker General Valve series 9) with total pressure of ∼2 atm. A molecular beam of the mixed gas was formed and introduced into the interaction region of the time-of-flight (TOF) mass spectrometer. The tunable IR light and a VUV light (118 nm) were injected into the interaction region separately with the spatially counter-propagated manner. To obtain the spectroscopy of neutral and cationic PRL, the IR light was introduced 50 ns prior and later to the VUV ionization light, respectively.
The VUV ionization light (118 nm) was generated by tripling the third harmonic output (355 nm) of a Nd:YAG laser through a Xe-Ar mixture (1:10) in the gas cell that was directly attached at the vacuum chamber of TOF-MS. The tunable IR light was generated from the OPO/OPA system (Laser Vision). And its pulse energy were 3-5 mJ/pulse at the region of 2600-3600 cm−1 with a line width of 2-3 cm−1. The wavelength of the IR light was calibrated with the IR spectrum of neutral methanol monomer.
Geometry optimization, IR spectra, and nature bond orbital (NBO) analyses of neutral and cationic PRL molecule were performed with Gaussian 09 packages [24]. All the calculations were performed with B3LYP/6-311++(d, p). Gas-phase acidities (ΔGacid) of the C-H or N-H bond in the cationic molecules are defined by the Gibbs energy changes in the reactions HA+→A⋅+H+, respectively [25]. The energies of HA+ and A⋅ were calculated at the B3LYP/6-311++(d, p) level with the zero-point energy (ZPE) corrections. The calculated gas-phase acidities were evaluated at 298.15 K. The harmonic frequencies of the neutral and cationic PRL are scaled by 0.960.
Ⅲ.
RESULTS AND DISCUSSION
A
Neutral PRL
FIG. 1 shows the observed and calculated IR spectra of neutral PRL in the CH and NH region of 2600-3600 cm−1, and the structures of PRL isomers are inserted. The IR dip spectrum (FIG. 1(a)) was obtained by monitoring the molecular PRL ((C4H9N)+, m/z=71) mass channel. While the IR enhancement spectrum (FIG. 1(b)) was obtained by monitoring the PRL-H ((C4H8N)+, m/z=70) mass channel. Three CH bands appear at around 2810, 2870, and 2950 cm−1, respectively. Due to the small dipole moment of the NH bond in the PRL, the NH band cannot be observed clearly in our experiment. The corresponding peaks of FIG. 1 (a) and (b) indicate the (PRL-H)+ mass channel is the fragmentation of PRL. Two stable structures of PRL-eq and PRL-ax have been proven to coexist in the supersonic condition [7]. FIG. 1 (c) and (d) show the simulated IR spectra of the two optimized structures at B3LYP/6-311++(d, p) level. As can be seen in the calculated spectra, besides two intense CH bands of structure PRL-eq appearing at ∼2810 cm−1, most of the CH bands of structure PRL-eq and structure PRL-ax appear at the region of 2900-3000 cm−1. The peak position of the observed spectra can be well reproduced by the IR spectrum of structure PRL-eq. The intensities of those spectra are totally different, unless considering both structure PRL-eq and structure PRL-ax coexist.
Figure
1.
(a, b) Observed and (c, d) calculated IR spectra of neutral PRL in the CH and NH region of 2600-3600 cm−1. The dip and enhancement spectra ((a) and (b)) were obtained by monitoring the molecular PRL (m/z=71) and PRL-H (m/z=70) mass channel, respectively. The structures of PRL isomers (PRL-eq and PRL-ax) are inserted in the figure. The calculated spectra are obtained at the B3LYP/6-311++G(d, p) level with the scaling factor of 0.960
As we know, the typical CH stretching vibration of alkyl group is at the region of 2850-3000 cm−1. But, some parts of the CH bands in the experimental spectra are clearly beyond this range. The low frequency CH stretching bands only appear at the IR spectra of structure PRL-eq. Thus, to explain the redshift of the CH bands, nature bond orbital (NBO) analyses of the neutral PRL-eq and PRL-ax have been performed. As shown in FIG. 2(a), large overlap between the HOMO (lone pair of Nitrogen) and σ∗ (CαH) orbitals has been found in the structure PRL-eq. While, for the structure PRL-ax, the HOMO largely overlaps with σ∗(CαCβ) orbitals. The value of second-order perturbation energy (E(2)) is a good indictor to reflect the magnitude of delocalization of electrons through (negative) hyperconjugation. The values of E(2) for some selected intramolecule interactions in PRL are list in Table Ⅰ. In the table, only E(2) values larger than 5.0 kJ/mol are listed, and such a strong interaction is limited in the interaction between the lone pair (LP) orbital and CαH or CαCβ bonds. In the structure PRL-eq, the E(2) values between the LP and the σ∗ orbitals of the CαH bonds are 29.76 and 9.50 kJ/mol, respectively, which is much larger than that of other interactions. While, in the structure of PRL-ax, the E(2) values between the LP and the σ∗ orbitals of CαCβ bonds and one of the CαH bonds are 22.05 and 13.18 kJ/mol, respectively. Therefore, the CαH bonds are greatly weakened and the frequency of the CαH bands redshifts, due to the electron of the LP delocalized to the σ∗(CαH), i.e. negative hyperconjugation.
Figure
2.
Nature bond orbitals (NBO) of the (a, b) neutral and (c) cationic PRL. (d) Scheme of PRL with atom labeling. The NBO are obtained by the optimized structures at B3LYP/6-311++G(d, p)
FIG. 3 presents the observed and calculated IR spectra of cationic PRL in the CH and NH region of 2600-3600 cm−1. The only one stable structure of cationic PRL with C2 symmetry is inserted in FIG. 3(c). The same as that of neutral PRL, IR dip and enhancement spectra (FIG. 1 (a) and (b)) were obtained by monitoring the molecular PRL (m/z=71) and PRL-H (m/z=70) mass channel, respectively. Three CH bands and an intense NH band appear at around 2788, 2840, 2890, and 3338 cm−1, respectively. The corresponding peaks of FIG. 3 (a) and (b) indicate the (PRL-H)+ mass channel is the fragmentation of PRL+. FIG. 3(c) shows the simulated spectrum of the cationic PRL. The NH band becomes much more intense than that in the spectrum of neutral PRL. The observed spectra can be well reproduced by the calculated one indicating the PRL+ is C2 symmetric.
Figure
3.
(a) Observed and (b, c) calculated IR spectra of cationic PRL in the CH and NH region of 2600-3600 cm−1. The dip and enhancement spectra ((a) and (b)) were obtained by monitoring the molecular PRL (m/z=71) and PRL-H (m/z=70) mass channel, respectively. The only one stable structure of PRL+ is inserted in the figure (c). The calculated spectra are obtained at the B3LYP/6-311++G(d, p) level with the scaling factor 0.960
As we have mentioned above, the typical CH stretching vibration of alkyl group is at the region of 2850-3000 cm−1. Some of the CH bands in the spectrum of PRL+ are lower than this region. And the NH band is also redshifted from 3356 cm−1 [12] to 3338 cm−1. To investigate the reason of redshift of CH and NH bands, NBO analyses of the cationic PRL have been performed. E(2) values of intramolecule interaction larger than 5.0 kJ/mol of PRL+ are list in Table Ⅰ. The E(2) values between the σ orbitals of the CαH bonds and the LP∗ are 41.60 and 18.08 kJ/mol, respectively. Due to the delocalization of σ(CαH) electron to the LP∗, i.e. positive hyperconjugation, the CαH bonds are greatly weakened and the frequency of the CαH bands redshifts.
C
Ionization and dehydrogenation process
As shown in the FIG. 1 and FIG. 3, the PRL-H (m/z=70) mass channel is the main fragment mass channel of PRL (m/z=71). What is the formation mechanism of cationic PRL-H (m/z=70)? To answer this question, the energy diagram of the VUV single-photon ionization of PRL from its neutral ground state and the dehydrogenation process is present in FIG. 4. The ionization energy of PRL is calculated to be 8.67 eV, which is lower than the energy of 118 nm (10.48 eV) ionization light. After the VUV light ionization, the two vertical ionization conformers (PRL-eq and PRL-ax) isomerize to the C2 type PRL+ without an energy barrier. The dehydrogenation process of NH and CαH bonds has been performed and shown in FIG. 4. The energy barrier of NH dehydrogenation process is as large as 13.03 eV, which is much higher than the ionization energy (10.48 eV). However, the energy barrier of CαH dehydrogenation process is 9.41 eV, which is much lower than that of NH bond and the ionization energy. That is the reason that both of dehydrogenation (m/z=70) and molecular PRL (m/z=71) mass channel appear in the mass spectrum, when only the 118 nm light is radiated. The Mulliken charge distributions of the products of the dissociations are added in FIG. S1 of the supplementary materials. The values of the charge of the dissociated H atoms (0.004 and 0.035) indicate the atoms are H⋅ radical rather than H+. And the resonance IR light absorbed by neutral or cationic PRL would increase the efficiency of the dehydrogenation, so that the depletion of m/z=71 channel and the enhancement m/z=70 channel occur.
Figure
4.
Energy diagram of the VUV single-photon ionization of PRL from the neutral ground state. The stable structures and transition state structures with relative energies (in eV) were obtained by optimization at the B3LYP/6-311++G(d, p) level
The redshifts of the CαH and NH bonds indicate that those bonds are weakened (become acidic) after ionization. But, which bond is more acidic (more easy to be deprotonated), the CαH or NH bond? With the calculations, it is found that the gas phase acidity of the CαH and NH bonds are 955.6 and 957.4 kJ/mol, respectively, which also demonstrates the CαH bond is a little bit more acidic than NH in PRL+. Note that the gas phase acidity of HCl and CH4 are 1391.1 and 1737.0 kJ/mol, respectively [26]. It implies that both CαH and NH bonds in the cationic PRL are strongly acidic.
Ⅳ.
CONCLUSION
Hyperconjugation induced redshift of the CH bond in the neutral and cationic PRL was investigated by IR-VUV spectroscopy combined with theoretical calculations. With the negative hyperconjugation, the electron in the HOMO mainly delocalizes to σ∗(CαH) and σ∗(CαCβ) orbitals of neutral PRL-eq and PRL-ax, respectively. After ionization, however, the σ(CαH) orbitals are positive hyperconjugation with the SOMO orbital. The hyperconjugation causes the weakening of the CαH bonds strength in both the neutral and cationic PRL, so that the CαH stretching bands are red shifted. Acidity enhancements of cationic CH and NH bonds have been investigated for some protic molecules [21, 27, 28]. Through the calculation of the gas phase acidity and deprotonation process of PRL, it is found that the acidity of the CH bond is much stronger than that of NH bond in its cationic state. The hyperconjugation mechanism demonstrated in neutral and cationic PRL would play an important role in understanding the intrinsic properties of biomolecules, and provide reference for the further study of living organic macromolecules.
Supplementary materials: Mulliken charge distributions of the products after dehydrogenation processes of cationic PRL predicted with B3LYP/6-311++G(d, p) are available in FIG. S1.
Scheme
S1.
Mulliken charge distributions of the reaction products of (a) N-H and (b) C-H dehydrogenation processes
This work was supported by the National Natural Science Foundation of China (No.U1732146, No.21273083) and the Project under Scientific and Technological Planning Grant (No.201805010002) by Guangzhou City.
†Part of the special topic on "The 3rd Asian Workshop on Molecular Spectroscopy"
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