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Juan Wang, Xiao-long Li, Qian Gou, Gang Feng. Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 53-57. doi: 10.1063/1674-0068/cjcp1910186
Citation: Juan Wang, Xiao-long Li, Qian Gou, Gang Feng. Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 53-57. doi: 10.1063/1674-0068/cjcp1910186

Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine

doi: 10.1063/1674-0068/cjcp1910186
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  • Corresponding author: Gang Feng, E-mail: fengg@cqu.edu.cn
  • Part of the special topic on "The 3rd Asian Workshop on Molecular Spectroscopy"
  • Received Date: 2019-10-25
  • Accepted Date: 2019-10-21
  • Publish Date: 2020-02-27
  • The high resolution rotational spectrum of 2-(trifluoromethyl)pyridine in 2$ - $20 GHz was recorded and analyzed. Spectroscopic parameters including rotational constants, nuclear quadrupole coupling constants of $ ^{14} $N as well as the centrifugal distortion constants were determined. The rotational spectra of five mono-substituted $ ^{13} $C and one $ ^{15} $N isotopologues were also measured and assigned in natural abundance. Experimental results complemented by ab initio calculations lead to an accurate determination of the skeleton structure. The values of the planar moment inertia $ P_{cc} $ were determined to be 44.46 uÅ$ ^2 $ for all the measured isotopologues, indicating a C$ _ \rm{s} $ symmetry of this molecule. The molecular electrostatic surface potential was calculated to illustrate the trifluoromethyl substitution effects on the electron distribution.
  • Part of the special topic on "The 3rd Asian Workshop on Molecular Spectroscopy"
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Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine

doi: 10.1063/1674-0068/cjcp1910186

Abstract: The high resolution rotational spectrum of 2-(trifluoromethyl)pyridine in 2$ - $20 GHz was recorded and analyzed. Spectroscopic parameters including rotational constants, nuclear quadrupole coupling constants of $ ^{14} $N as well as the centrifugal distortion constants were determined. The rotational spectra of five mono-substituted $ ^{13} $C and one $ ^{15} $N isotopologues were also measured and assigned in natural abundance. Experimental results complemented by ab initio calculations lead to an accurate determination of the skeleton structure. The values of the planar moment inertia $ P_{cc} $ were determined to be 44.46 uÅ$ ^2 $ for all the measured isotopologues, indicating a C$ _ \rm{s} $ symmetry of this molecule. The molecular electrostatic surface potential was calculated to illustrate the trifluoromethyl substitution effects on the electron distribution.

Part of the special topic on "The 3rd Asian Workshop on Molecular Spectroscopy"
Juan Wang, Xiao-long Li, Qian Gou, Gang Feng. Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 53-57. doi: 10.1063/1674-0068/cjcp1910186
Citation: Juan Wang, Xiao-long Li, Qian Gou, Gang Feng. Microwave Spectrum and Structure of 2-(Trifluoromethyl)pyridine[J]. Chinese Journal of Chemical Physics , 2020, 33(1): 53-57. doi: 10.1063/1674-0068/cjcp1910186
  • Fluorination of a molecule can significantly alter the properties of the substrate. It can influence the conformational preference, p$ K_ \rm{a} $, membrane permeability, lipophicity and metabolism of molecule [1, 2]. Due to its high electronegativity nature, the incorporation of fluorine into a molecule might also provide an additional non-covalent interaction site, e.g., as the hydrogen bonding acceptor [3, 4]. The structural change upon fluorination can be accurately analysed by means of structural determination from microwave spectroscopy. Therefore, studies of model molecules with different kinds of fluorine bearing functional groups will allow to estimate the fluorination effects in different systems to be quantified.

    Similar to fluorine, the incorporation of trifluoromethyl (CF$ _3 $) groups into substrates can also significantly influence their properties [5]. Rotational spectroscopic studies of several phenyl compounds disclosed that trifluoroanisole (PhOCF$ _3 $) prefers an orthogonal conformation [6], different from the anisole (PhOCH$ _3 $) where a planar conformation is favored [7], suggesting a remarkable perturbation to the conformational behavior by introducing a -CF$ _3 $ group into the substances. The -CF$ _3 $ substitution effect also determines the different conformational preferences between thioanisole (PhSCH$ _3 $) and trifluorothioanisole (PhSCF$ _3 $) [8, 9].

    Pyridine (PY) and its derivatives are interesting substrates to model the fluorination effect. Indeed, investigations of mono-fluorinated pyridines [10] demonstrate that fluorination at the ortho position of the PY ring has large influence on the electronic structure. The fluorination effect on PY ring was further proven to be more pronounced deviation in difluoropyridines [11], depending on the fluorinated position and the degree of fluorination. The bonding model with hyperconjugation theory and the experimental results demonstrates that fluorine can donate electron density into the $ \pi $ cloud of PY. It might be interesting to study fluorine substitutions away from the ring, starting with a -CF$ _3 $ substitution on pyridine. In this study, 2-(trifluoromethyl)pyridine (2TFPY) was investigated by using pulsed jet Fourier transform microwave spectroscopy. The experimental results were complemented by ab initio calculations performed at different levels of theory.

  • 2TFPY ($ \sim $98%) was obtained commercially and used directly for collecting its rotational spectrum. 2TFPY was preserved in a reservoir ($ \sim $300 K) coupled in the gas-pipeline. The supersonic expansion was generated by expanding a gas mixture (with Argon as the carrier gas, $ \sim $0.1 MPa) into the Fabry-Pérot cavity using a Series 9 General Valve (0.5 mm). The rotational spectrum was recorded by using a pulsed supersonic-jet Fourier-transform microwave spectrometer with coaxially oriented beam-resonator (COBRA) [12] setup. The frequency range of the spectrometer is 2$ - $20 GHz. The FTMW++ set of programs is used to operate the spectrometer [13, 14]. The spectral signal was recorded in the time-domain with 8$ \times $10$ ^3 $ data points at 100 ns sample intervals. The time-domain signal was then Fourier transformed and converted into the frequency domain. The Doppler effect splits the rotational transition into doublets due to the COBRA setup. The arithmetic means of the two Doppler components is calculated as the rest transition frequency.

  • The Gaussian 16 suite of programs was used for all the calculations [15]. Full geometry optimizations were performed at the B3LYP/aug-cc-pVTZ and the MP2/6-311++G(2d, 2p) level of theory. Harmonic frequency analysis was carried out to obtain the zero-point vibrational energy and to derive the quartic centrifugal distortion constants. The molecular electrostatic surface potentials (ESP) of 2TFPY, 2-fluoropyridine (2FPY), 2-methylpyridine (2MPY) and PY were calculated at the B3LYP/aug-cc-pVTZ level of theory.

  • Table Ⅰ reports the rotational constants ($ A $, $ B $, and $ C $), the nuclear quadrupole coupling constants of $ ^{14} $N ($ \chi_{aa} $ and $ \chi_{bb} $$ - $$ \chi_{cc} $), the electric dipole moment components ($ \mu_a $, $ \mu_b $, and $ \mu_c $), and the centrifugal distortion constants ($ D_J $, $ D_{JK} $, $ D_K $, $ d_1 $ and $ d_2 $) of 2TFPY while the structure, the principal axes of inertia, and the atomic labels are shown in FIG. 1. The B3LYP/aug-cc-pVTZ and MP2/6-311++G(2d, 2p) levels of theory predict close values of spectroscopic parameters for 2TFPY. The values of the dipole moments $ \mu_a $ and $ \mu_b $ are calculated to be 4.0 and 1.8 D respectively, suggesting that 2TFPY should have a strong $ \mu_a $-type transition and a relatively weaker $ \mu_b $-type transition in its pure rotational spectrum. Following the theoretical predictions, the $ \mu_a $-R-type transitions of 2TFPY were initially searched. The rotational transitions of $ J $ = 6$ \leftarrow $5 band with $ K_ \rm{a} $ = 0 and 1 were identified firstly. The spectrum displays hyperfine splittings, as shown in FIG. 2, arising from the quadrupole coupling of the $ ^{14} $N nucleus. The measurements were then extended to $ J_{ \rm{upper}} $ = 3$ - $11 with $ K_ \rm{a} $$ \leq $5. Several $ \mu_b $-type transitions with weaker intensity were also measured.

    Table Ⅰ.  The theoretical spectroscopic parameters of 2TFPY from the B3LYP/aug-cc-pVTZ and MP2/6-311++G(2d, 2p) levels of calculations and comparison with the experimental values (Watson's $ S $ reduction, $ I^ \rm{r} $ representation)

    Figure 1.  B3LYP/aug-cc-pVTZ calculated structure, the principal axes of inertia and the atomic labels of 2TFPY. The $ r_ \rm{s} $ coordinates of the isotopically substituted atoms are qualitatively shown as blue spheres

    Figure 2.  The hyperfine structure of the recorded 6$ _{06} $$ \leftarrow $5$ _{05} $ transition of 2TFPY. The hyperfine components ($ F $-$ F' $) display as the Doppler doubling ($ \sqcap $)

    The measured transitions were analyzed with the SPFIT program [16] using the Watson's Hamiltonian of $ S $-reduction in $ I^ \rm{r} $ representation [17]:

    where $ H_ \rm{R} $ stands for the rigid rotational term, $ H_{ \rm{CD}} $ stands for the centrifugal distortion contributions, and the $ H_ \rm{Q} $ represents the term of $ ^{14} $N quadrupole coupling to the overall rotation. The determined spectroscopic parameters are reported in Table Ⅰ.

    In addition, the rotational spectra of the singly substituted isotopologues of $ ^{13} $C and $ ^{15} $N were measured in natural abundance. Since the number of lines in the isotopologue fits is not enough to determine the centrifugal distortion constants and the quadrupole coupling constants, all values of these parameters were fixed at those values reported in Table Ⅰ for the parent species. The rotational spectrum of the $ ^{15} $N isotopologue is free from the quadrupole coupling splitting because the $ ^{15} $N nuclear spin quantum number is 1/2. To analyse the spectrum of $ ^{15} $N species, the $ H_ \rm{Q} $ term of Eq.(1) is removed from the Hamiltonian. As indicated in FIG. 1, the C2 atom is near its center of mass, hence its rotational spectrum is mostly overlapped with the parent species and therefore unmeasurable. Table Ⅱ reports the determined spectroscopic constants for all the substituted isotopologues. The transition frequencies of all the measured isotopologues are present in the supplementary materials.

    Table Ⅱ.  Comparison of the substituted coordinates ($ r_ {\rm{s}} $) with the $ r_ {\rm{e} }$ coordinates of 2TFPY

  • The planar moment of inertia ($ P_{cc} $), presenting the mass distributions out of the $ ab $ plane, has identical values for the parent and all the singly substituted isotopologues (Tables Ⅰ and ), suggesting that all those atoms are in the $ ab $ plane. The rotational constants of the parent and all the singly substituted isotopologues were used to calculate the $ r_ \rm{s} $ coordinates of the atoms using the Kraitchman's equations [18] with the corresponding Costain's errors [19]. The obtained $ r_ \rm{s} $ coordinates are summarized in Table Ⅲ which are also included in FIG. 1 represented by blue spheres for the directly visual comparison. The $ r_ \rm{e} $ coordinates (B3LYP/aug-cc-PVTZ) match the $ r_ \rm{s} $ values quite well. In order to deduce the bond lengths and the valence angles of the whole skeleton (Table Ⅳ), the $ r_ \rm{e} $ coordinates of C2 were used in the structural calculations. The $ r_0 $ structure was reproduced by a least-squares fit taking all sets of rotational constants into account using the STRFIT program [20] to obtain the effective structure of 2TFPY. The determined effective structure is apparently the same as the equilibrium structure calculated at the B3LYP/aug-cc-pVTZ level of theory (Table S8 in supplementary materials).

    Table Ⅲ.  Comparison of NPA charge distributions of PY, 2FPY, 2MPY, and 2TFPY

    Table Ⅳ.  Comparison of $ r_ {\rm{s}} $-structure and $ r_ {\rm{e}} $-structure (B3LYP/aug-cc-pVTZ) of PY, 2FPY, and 2TFPY.

  • In order to illustrate the fluorination effects, the molecular electrostatic surface potentials (ESP) of PY, 2FPY, 2MPY and 2TFPY were calculated (FIG. 3). For all the four molecules, the lone pair of the N atom represents the most negative potential site (red). The substitution of H with fluorine at the ortho-position of the pyridine ring induces a decrease of the N atom electron density, where F atom provides an additional negative electron density site. The methyl substation at the ortho-position affects the N atom electron density insignificantly but it induces an increase of the pyridine ring electron density. Substitution of -CF$ _3 $ at the ortho-position noticeably reduces the electron density of the pyridine ring and also the electron density of hydrogen atoms. The N atom and the -CF$ _3 $ group represent the negative electron density. The change of electron distribution due to the incorporation of F or -CF$ _3 $ group into the pyridine ring can also be reflected by the atomic charge of the N and the C of ortho-position. Table Ⅴ reports the atomic charge of the N and the ortho-C atoms from a natural population analysis. The incorporation of the -CF$ _3 $ group at the ortho-position of the pyridine weakens the nucleophilicity of the N atom distinctly. F substitution at the ortho-position enhances the electropositivity of the ortho-C atom.

    Figure 3.  The MESPs of PY, 2FPY, 2MPY, and 2TFPY. The isosurface was chosen at the 0.0004 electrons/bohr$ ^{3} $

    Table Ⅴ.  Comparison of NPA charge distributions of PY, 2FPY, 2MPY, and 2TFPY

  • The rotational spectra of 2-(trifluoromethyl)pyridine in 2$ - $20 GHz and its six mono-substituted isotopologues were measured and assigned. The structure of the heavy atoms skeleton was experimentally determined. The analysis of the experimental rotational constants suggests that $ P_{cc} $ values of the parent and all the measured mono-substituted isotopologues are 44.46 uÅ$ ^2 $, indicating a C$ _ \rm{s} $ symmetry of the molecule. The incorporation of -CF$ _3 $ group into the pyridine ring at the ortho-position reduces the electron distribution of the $ \pi $ electron of the pyridine ring and the N atom.

    Supplementary materials: The measured transition frequencies for 2TFMPY (Tables S1-S7) and the effective structure ($ r_0 $) of 2TFMPY (Tables S7) are given.

  • This work was supported by the National Natural Science Foundation of China (No.21703021 and No.U1931104), Chongqing University under the program of the Foundation of 100 Young, Fundamental and Frontier Research Fund of Chongqing (No.cstc2017jcyjAX0068 and No.cstc2018jcyjAX0050), and Venture & Innovation Support Program for Chongqing Overseas Returns (No.cx2018064).

  • Content:

    1) Tables S1: Transition frequencies of the 2TFMPY parent isotopologue in MHz.

    2) Tables S2: Transition frequencies of the 2TFMPY 15N1 isotopologue in MHz.

    3) Tables S3: Transition frequencies of the 2TFMPY 13C3 isotopologue in MHz.

    4) Tables S4: Transition frequencies of the 2TFMPY 13C4 isotopologue in MHz.

    5) Tables S5: Transition frequencies of the 2TFMPY 13C5 isotopologue in MHz.

    6) Tables S6: Transition frequencies of the 2TFMPY 13C6 isotopologue in MHz.

    7) Tables S7: Transition frequencies of the 2TFMPY 13C7 isotopologue in MHz.

    8) Tables S8: The effective structure (r0) of 2TFMPY.

    Table S1.  Transition frequencies of the 2TFP parent isotopologue in MHz.

    Table S2.  Transition frequencies of the 2TFMPY 15N1 isotopologue in MHz.

    Table S3.  Transition frequencies of the 2TFP 13C3 isotopologue in MHz.

    Table S4.  Transition frequencies of the 2TFP 13C4 isotopologue in MHz.

    Table S5.  Transition frequencies of the 2TFP 13C5 isotopologue in MHz.

    Table S6.  Transition frequencies of the 2TFP 13C6 isotopologue in MHz.

    Table S7.  Transitions frequencies of the 2TFP 13C7 isotopologue in MHz.

    Table S8.  The effective structure (r0) of 2TFMPY

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