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Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study.

Al-Otaibi JS - Springerplus (2015)

Bottom Line: The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets.The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra.Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, 11951 Saudi Arabia.

ABSTRACT

Background: 2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP).

Results: Møller-Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000-400 cm(-1)). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra.

Conclusion: Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.

No MeSH data available.


Related in: MedlinePlus

Optimized geometry at MP2/6-31++G(d,p) showing all bond lengths
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Fig1: Optimized geometry at MP2/6-31++G(d,p) showing all bond lengths

Mentions: The optimized molecular structures of 2A3MP and 2A4MP are obtained at different computational methods. The optimized structural parameters were shown in Additional file 1: Tables S1 and S2 for 2A3MP and 2A4MP in the Additional files respectively. By allowing the relaxation of all parameters, the calculations converge to optimized geometries, which correspond to true energy minima, as revealed by the lack of imaginary frequencies in the vibrational mode calculation. These molecules have three CN, two NH, five CC and six CH bonds. It was reported that the HF approximation is, in general, insufficient to study the geometry of amino group-containing compounds (Sponer and Hobza 1994a, b, c; Sponer et al. 1996). Thus MP2 with high basis sets was used to examine the molecular structure and amino group pyramidalization of 2A3MP and 2A4MP. The geometrical parameters at the MP2 methods are shown in Fig. 1 and in Additional file 1: Tables S3 and S4 for 2A3MP and 2A4MP respectively. As shown in Fig. 1, the C-Npy bond lengths are slightly different. The one closer to the amino group is shorter by a value of 0.004 and 0.005 Å for 2A3MP and 2A4MP respectively as predicted by MP2/6-31++G(d,p). This could be due to the interaction of the amino nitrogen lone pair with the C-Npy bond. This interaction leads to the increase of double bond character of the C-Npy bond and hence the shortening of the bond closer to the amino group. All methods used throughout this work prove the pyramidalization of the amino group as displayed in Additional file 1: Tables S1–S4. However, the inclusion of d-polarization functions in the amino group hydrogen is quite essential. The non-planarity of the amino group was mostly found to be much larger at the MP2 level, compared with the uncorrelated methods. Computations reveals the asymmetry of the amino group hydrogen dihedral angles, which is due to the repulsive electrostatic interactions with the neighboring hydrogens. The calculations revealed a significant difference between the correlated and uncorrelated results. It is easily noticed from Additional file 1: Tables S1–S4 that the B3LYP/6 311++G(d,p) method overestimates bond lengths, particularly the CH bonds. The CC bond distances are differing in value. The reasons for that may be the replacement of hydrogen atoms in the pyridine ring by methyl groups and the distortion of the aromatic ring hexagonal symmetry in the pyridine ring. Geometry based on MP2 and B3LYP calculation shows that the average bond lengths of CC and CH in the pyridine ring are 1.394 and 0.990 Å, for 2A3MP and 2A4MP. Comparing MP2 and B3LYP methods, the predicted N–H (amino group) bond lengths are found at 1.011 and 1.009 Å for 2A3MP and 2A4MP, respectively. The experimental value (1.001 Å), is more closer to that predicted by B3LYP method (Fukuyo et al. 1982). The optimized CN bond length is 1.347 and 1.340 Å for 2A3MP and 1.348 and 1.342 Å for 2A4MP by MP2 and B3LYP methods, respectively. Both methods predict the C–N bond length very close to each other but shorter than the measured value (1.402 Å measured for a similar aromatic ring, aniline) (Fukuyo et al. 1982). Some calculated ring angles, C2–C1–C6 and C5–C6–C1 are deviating from the perfect hexagon value (120°) at C1 and C6 atom positions for 2A3MP and the same deviation is also shown at the corresponding atom positions, C2 and C6 for 2A4MP. This could be due to the substitutions of –NH2 and –CH3 groups. This effect results from the interaction of the N lone pair of electrons with the aromatic ring.Fig. 1


Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study.

Al-Otaibi JS - Springerplus (2015)

Optimized geometry at MP2/6-31++G(d,p) showing all bond lengths
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4628003&req=5

Fig1: Optimized geometry at MP2/6-31++G(d,p) showing all bond lengths
Mentions: The optimized molecular structures of 2A3MP and 2A4MP are obtained at different computational methods. The optimized structural parameters were shown in Additional file 1: Tables S1 and S2 for 2A3MP and 2A4MP in the Additional files respectively. By allowing the relaxation of all parameters, the calculations converge to optimized geometries, which correspond to true energy minima, as revealed by the lack of imaginary frequencies in the vibrational mode calculation. These molecules have three CN, two NH, five CC and six CH bonds. It was reported that the HF approximation is, in general, insufficient to study the geometry of amino group-containing compounds (Sponer and Hobza 1994a, b, c; Sponer et al. 1996). Thus MP2 with high basis sets was used to examine the molecular structure and amino group pyramidalization of 2A3MP and 2A4MP. The geometrical parameters at the MP2 methods are shown in Fig. 1 and in Additional file 1: Tables S3 and S4 for 2A3MP and 2A4MP respectively. As shown in Fig. 1, the C-Npy bond lengths are slightly different. The one closer to the amino group is shorter by a value of 0.004 and 0.005 Å for 2A3MP and 2A4MP respectively as predicted by MP2/6-31++G(d,p). This could be due to the interaction of the amino nitrogen lone pair with the C-Npy bond. This interaction leads to the increase of double bond character of the C-Npy bond and hence the shortening of the bond closer to the amino group. All methods used throughout this work prove the pyramidalization of the amino group as displayed in Additional file 1: Tables S1–S4. However, the inclusion of d-polarization functions in the amino group hydrogen is quite essential. The non-planarity of the amino group was mostly found to be much larger at the MP2 level, compared with the uncorrelated methods. Computations reveals the asymmetry of the amino group hydrogen dihedral angles, which is due to the repulsive electrostatic interactions with the neighboring hydrogens. The calculations revealed a significant difference between the correlated and uncorrelated results. It is easily noticed from Additional file 1: Tables S1–S4 that the B3LYP/6 311++G(d,p) method overestimates bond lengths, particularly the CH bonds. The CC bond distances are differing in value. The reasons for that may be the replacement of hydrogen atoms in the pyridine ring by methyl groups and the distortion of the aromatic ring hexagonal symmetry in the pyridine ring. Geometry based on MP2 and B3LYP calculation shows that the average bond lengths of CC and CH in the pyridine ring are 1.394 and 0.990 Å, for 2A3MP and 2A4MP. Comparing MP2 and B3LYP methods, the predicted N–H (amino group) bond lengths are found at 1.011 and 1.009 Å for 2A3MP and 2A4MP, respectively. The experimental value (1.001 Å), is more closer to that predicted by B3LYP method (Fukuyo et al. 1982). The optimized CN bond length is 1.347 and 1.340 Å for 2A3MP and 1.348 and 1.342 Å for 2A4MP by MP2 and B3LYP methods, respectively. Both methods predict the C–N bond length very close to each other but shorter than the measured value (1.402 Å measured for a similar aromatic ring, aniline) (Fukuyo et al. 1982). Some calculated ring angles, C2–C1–C6 and C5–C6–C1 are deviating from the perfect hexagon value (120°) at C1 and C6 atom positions for 2A3MP and the same deviation is also shown at the corresponding atom positions, C2 and C6 for 2A4MP. This could be due to the substitutions of –NH2 and –CH3 groups. This effect results from the interaction of the N lone pair of electrons with the aromatic ring.Fig. 1

Bottom Line: The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets.The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra.Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, 11951 Saudi Arabia.

ABSTRACT

Background: 2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP).

Results: Møller-Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000-400 cm(-1)). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra.

Conclusion: Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.

No MeSH data available.


Related in: MedlinePlus