| Literature DB >> 31500265 |
Iwona Kosendiak1, Jussi M E Ahokas2, Justyna Krupa3, Jan Lundell4, Maria Wierzejewska5.
Abstract
Molecular complexes between glycolic acid and nitrogen were studied in a low-temperature argon matrix with FTIR spectroscopy, and supported by MP2 and BLYPD3 calculations. The calculations indicate 11 and 10 stable complex structures at the MP2 and BLYPD3 levels of theories, respectively. However, only one hydrogen-bonded complex structure involving the most stable SSC conformer of glycolic acid was found experimentally, where the nitrogen molecule is bound with the carboxylic OH group of the SSC conformer. The complex shows a rich site structure variation upon deposition of the matrix in different temperatures and upon annealing experiments, which provide interesting prospects for site-selective chemistry.Entities:
Keywords: carboxylic acid; computational chemistry; hydrogen bond; matrix isolation; vibrational spectroscopy
Mesh:
Substances:
Year: 2019 PMID: 31500265 PMCID: PMC6767210 DOI: 10.3390/molecules24183262
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
Figure 1Structures of the three most stable conformers of glycolic acid monomer.
Figure 2The MP2-optimized 1:1 structures of SSC, AAT and GAC complexes with molecular nitrogen.
Interatomic distances (Å), angles (degree) and electron density parameters of the bond (au) of the SSC, GAC and AAT complexes with N2 (1:1) computed at the MP2/6-311++G(2d,2p) level.
| Complex | Intermolecular Parameters | AIM Parameters | ||||
|---|---|---|---|---|---|---|
| Interatomic Distances | Angle | BCP | ρ (r) | ∇2ρ(r) | ||
| H⋯Y | X⋯Y | X–H⋯Y | ||||
| SSC1 | 2.257 | 3.226 | 179.0 | H7⋯N10 | 0.014 | 0.053 |
| SSC2 | 2.475 | 3.363 | 152.8 | H9⋯N10 | 0.009 | 0.037 |
| SSC3 | 3.358 | C1⋯N10 | 0.006 | 0.024 | ||
| 3.280 | C4⋯N10 | 0.006 | 0.024 | |||
| Ring critical point | 0.006 | 0.025 | ||||
| GAC1 | 2.262 | 3.230 | 178.1 | H7⋯N10 | 0.014 | 0.053 |
| GAC2 | 2.363 | 3.304 | 166.4 | H9⋯N10 | 0.012 | 0.045 |
| 3.410 | O6⋯N10 | 0.004 | 0.016 | |||
| Ring critical point | 0.004 | 0.016 | ||||
| GAC3 | 3.249 | O8⋯N10 | 0.006 | 0.022 | ||
| 3.252 | C4⋯N10 | 0.006 | 0.026 | |||
| Ring critical point | 0.005 | 0.025 | ||||
| GAC4 | 3.323 | O5⋯N10 | 0.006 | 0.023 | ||
| 2.971 | 3.684 | 123.1 | H2⋯N10 | 0.005 | 0.017 | |
| Ring critical point | 0.005 | 0.018 | ||||
| GAC5 | 2.832 | 3.521 | 121.5 | H3⋯N10 | 0.004 | 0.016 |
| 3.188 | O8⋯N10 | 0.005 | 0.018 | |||
| Ring critical point | 0.004 | 0.018 | ||||
| AAT1 | 2.459 | 3.212 | 134.2 | H7⋯N10 | 0.010 | 0.040 |
| 1.950 | 2.584 | 120.7 | H7⋯O8 | 0.027 | 0.117 | |
| Ring critical point | 0.025 | 0.143 | ||||
| AAT2 | 2.547 | 3.287 | 133.9 | H9⋯N10 | 0.008 | 0.030 |
| 1.985 | 2.640 | 122.7 | H7⋯O8 | 0.028 | 0.108 | |
| Ring critical point | 0.026 | 0.137 | ||||
| AAT3 | 1.922 | 2.575 | 122.2 | H7⋯O8 | 0.029 | 0.122 |
| 3.184 | C4⋯N10 | 0.006 | 0.027 | |||
| Ring critical point | 0.026 | 0.151 | ||||
Computed interaction energies and relative energies compared to global minimum SSC1 (in kJ mol−1).
| Structure | Interaction Energy | Relative Energy | ||
|---|---|---|---|---|
| MP2 | B3LYPD3 | MP2 | B3LYPD3 | |
| SSC1 | −7.70 | −8.41 | 0.00 | 0.00 |
| SSC2 | −4.48 | −5.15 | 3.23 | 3.27 |
| SSC3 | −5.40 | −5.77 | 2.35 | 2.63 |
| GAC1 | −7.53 | −8.28 | 10.70 | 10.49 |
| GAC2 | −5.61 | −6.23 | 12.80 | 12.68 |
| GAC3 | −5.02 | −5.31 | 13.28 | 13.46 |
| GAC4 | −4.48 | −4.94 | 13.75 | 13.78 |
| GAC5 | −4.02 | - | 14.21 | - |
| AAT1 | −4.85 | −5.56 | 15.71 | 16.23 |
| AAT2 | −9.12 | −9.71 | 12.19 | 12.34 |
| AAT3 | −5.40 | −5.73 | 15.08 | 15.91 |
Computed band positions for the most stable SSC⋯N2 complex (SSC1) compared to the experimental Raman band positions (cm−1) together with computed infrared (km mol−1) and Raman intensities.
| Mode | Band Position | IIR | IRaman | Raman Exp [ |
|---|---|---|---|---|
| ν1 | 3781 | 79 | 477 | |
| ν2 | 3754 | 302 | 1880 | 3562, 3554, 3545 |
| ν3 | 3130 | 7 | 1202 | |
| ν4 | 3087 | 25 | 2536 | |
| ν5 | 2175 | 1 | 674 | |
| ν6 | 1789 | 246 | 739 | 1777, 1775 |
| ν7 | 1518 | 12 | 509 | |
| ν8 | 1492 | 2 | 106 | |
| ν9 | 1372 | 124 | 202 | |
| ν10 | 1315 | 33 | 134 | |
| ν11 | 1271 | 0 | 355 | |
| ν12 | 1190 | 161 | 175 | |
| ν13 | 1112 | 226 | 168 | |
| ν14 | 1053 | 1 | 13 | |
| ν15 | 878 | 28 | 1107 | |
| ν16 | 689 | 108 | 16 | |
| ν17 | 653 | 18 | 518 | |
| ν18 | 540 | 1 | 204 | |
| ν19 | 480 | 18 | 528 | |
| ν20 | 340 | 77 | 7 | |
| ν21 | 287 | 12 | 32 | |
| ν22 | 102 | 0 | 1504 | |
| ν23 | 92 | 8 | 1787 | |
| ν24 | 80 | 5 | 757 | |
| ν25 | 79 | 2 | 224 | |
| ν26 | 23 | 0 | 387 | |
| ν27 | 18 | 1 | 2940 |
MP2/6-311++G(2d,2p) calculated wavenumber shifts Δν (cm−1) and intensities (km mol−1) of the SSC complexes a with nitrogen compared to the corresponding experimental shifts.
| MP2/6-311++G(2d,2p) | Experimental Shifts | Assignment | |||||
|---|---|---|---|---|---|---|---|
| SSC1 | SSC2 | SSC3 * | |||||
| Δν | I | Δν | I | Δν | I | Δν | |
| −5 | 79 | 3 | 119 | 0 | 32 | −4 | (ν1) νOHA |
| −31 | 302 | 1 | 117 | 0 | 140 | −11.5, −14.5, −19.0/−21.0 | (ν2) νOHC |
| −5 | 246 | 1 | 274 | −1 | 249 | 2, −3 | (ν6) νC=O |
| 10 | 124 | −4 | 126 | 1 | 123 | 12, 6 | (ν9) δOHA + δOHC + νC–OC |
| 15 | 161 | −2 | 126 | 0 | 139 | 14, 13, 8, 5, 3 | (ν12) δOHC + νC–OC +ωCH2 |
| 4 | 28 | −1 | 30 | 1 | 28 | 6, 4, 2 | (ν15) νC–C + νC–OC |
a Corresponding positions for the SSC monomer are: 3786, 3785, 1794, 1362, 1175 and 874 cm−1 (MP2/6-311++G(2d,2p)) and 3561, 3561, 1773, 1332, 1143 and 854 cm−1 (Ar matrix [19]). * In SSC3 the νOHC and νOHA vibrations are coupled.
Figure 3The νOH, δOHC and νC=O regions of the infrared spectra of GA co-deposited with N2/Ar = 1/4000 at 15 K, 18 K and 25 K (measurement at 10 K) (traces (b–d), respectively, compared with GA/Ar spectrum (a).
Figure 4Plot showing changes of the νOH value calculated for each point of the relaxed potential energy scan for the bending movement of the N2 molecule in SSC1 complex calculated at the B3LYPD3 and MP2 levels with 6-311++G(2d,2p) basis set versus deviation of the C4O6N10 angle. The zero value of this angle corresponds to the global minimum value.
Figure 5The νOH, δOHC and νC=O regions of the infrared spectra of GA co-deposited with N2/Ar = 1/4000 (a) at 15 K and (b) after annealing at 33 K (measurement at 10 K) and (c) the corresponding difference spectrum (b) minus (a). The bands at 3561.0, 1773.0 and 1143.0 cm−1 belong to the SSC monomer.