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THEORETICAL INFRARED-RAMAN SPECTRA, CONFORMATIONAL STABILITY AND VIBRATIONAL ASSIGNMENT OF GLYCEROL
Ebru KARAKAŞ SARIKAYA, LEVENT ATEŞ, AYHAN ÖZMEN, MÜCAHİT YILMAZ,ÖMER DERELİ
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Presentation Flow
Abstract
Introduction
Methodology
Works
Conclusion and Discussion
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ABSTRACT
The aim of this study is to found stable conformers, optimized geometric parameters ( bond lengths, bond angles and dihedral angles) and to match experimentally observed and theoretically calculated harmonic vibrational frequencies.
As a result of detailed structural and conformational analysis of the GLYCEROL, thirty seven conformers have been obtained. Conformational analysis of Glycerol was performed by Spartan 08 program.
Geometry optimizations of the molecule were performed by Becke3–Lee–Yang–Parr functional with Density Functional Theory by using G(d,p) basis sets and conformations energies were obtained. And most stable conformers determined.
For this conformer, vibrational frequencies were calculated by DFT/B3LYP using G(d,p) basis sets.
The calculated frequencies were compared with experimental values.
The accuracy of the most stable structure has been tested by using vibration frequencies calculations.
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Introduction
Glycerol
Synonyms:
1,2,3-Trihydroxypropane
Glycerin
Glycerine
Glycerol
CAS Number:
Empirical Formula: C3H8O3 or CH2OH-CHOH-CH2OH
Molecular Weight: 92.1 g/mol
Why Glycerol?
Glycerol is a trihydroxy sugar alcohol that is an intermediate in carbohydrate and lipid metabolism. It is used as a solvent, emollient, pharmaceutical agent, and sweetening agent.
Glycerol is a viscous, transparent liquid which has interesting properties as a glass forming material, as a component of biological systems. It is also used for the synthesis of multimetallic alkoxides, precursors of advanced ceramic materials.
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Methodology
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate
Vibrational Frequencies
Vibrational Bands Assignments
Cross Check with Experimental Values
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6. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate
Vibrational Frequencies
Vibrational Bands Assignments
Cross Check with Experimental Values or
Figure 1
Figure 2
If the molecule is in Pubchem, you can download the sdf file from internet site.
If not, you can also draw in Gauss view.
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7. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assignments
Cross Check with Experimental Values
What is conformational analysis?
The different spatial arrangements that a molecule can adopt due to rotation about the internal σ bonds are called conformations.
Structures that only differ based on these rotations are conformational isomers or conformers.
The study of the energy changes that occur during these rotations is called conformational analysis.
Figure 3
Conformer analysis of Glycerol was calculated by using semi empirical method PM3 core type hamiltonian in Spartan 08 [1] Program. As a results of conformational analysis, 37 conformers were obtained.
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8. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assignments
Cross Check with Experimental Values
Figure 4
Conformers of Glycerol in gas phase.
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9. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
As seen in Table 1, the rotation of single bonds causes energy change in the molecule.
Table 1. Conformer energies and dipole moment values of Glycerol molecule
Conformations
Energies (Hartree)
Dipole Moment (D)
conf1
1.5232
conf20
2.515
conf2
2.1807
conf21
3.6891
conf3
2.8408
conf22
3.684
conf4
3.5172
conf23
3.2687
conf5
3.5091
conf24
2.1449
conf6
2.4764
conf25
1.8311
conf7
3.927
conf26
2.0108
conf8
2.8666
conf27
1.7034
conf9
2.1658
conf28
2.1294
conf10
1.6213
conf29
3.8816
conf11
2.0072
conf30
2.1433
conf12
1.747
conf31
3.8443
conf13
2.1362
conf32
4.0577
conf14
2.7509
conf33
3.9315
conf15
1.4877
conf34
3.5608
conf16
1.7907
conf35
2.8506
conf17
1.8961
conf36
3.5317
conf18
2.4578
conf37
2.3184
conf19
2.5878
Figure 5
Conformer 1
From the calculated energies given in Table 1, the conformer 1 is the most stable.
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10. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
Table 2. The calculated geometric parameters of Glycerol, bond lengths in angstrom (Å) and angles in degrees (0).
Parameters
Calculated
Bond lengths
Bond angles
O1,C4
1.43
C4,C6,H10
109.8
O1,H12
0.97
C4,C6,H11
110.0
O2,C5
H10,C6,H11
108.1
O2,H13
0.96
O3,C6
Dihedral angles
O3,H14
H12,O1,C4,C5
102.8
C4,C5
1.53
H12,O1,C4,C6
22.4
C4,C6
H12,O1,C4,H7
140.4
C4,H7
1.10
H13,O2,C5,C4
74.4
C5,H8
1.09
H13,O2,C5,H8
165.1
C5,H9
H13,O2,C5,H9
47.9
C6,H10
H14,O3,C6,C4
59.8
C6,H11
H14,O3,C6,H10
179.2
H14,O3,C6,H11
63.5
C4,O1,H12
106.8
O1,C4,C5,O2
64.0
C5,O2,H13
107.5
O1,C4,C5,H8
177.9
C6,O3,H14
106.9
O1,C4,C5,H9
58.9
O1,C4,C5
109.7
C6,C4,C5,O2
59.5
O1,C4,C6
110.2
C6,C4,C5,H8
58.6
O1,C4,H7
C6,C4,C5,H9
177.6
C5,C4,C6
113.1
H7,C4,C5,O2
179.3
C5,C4,H7
107.6
H7,C4,C5,H8
61.1
C6,C4,H7
108.5
H7,C4,C5,H9
57.8
O2,C5,C4
112.3
O1,C4,C6,O3
49.6
O2,C5,H8
106.2
O1,C4,C6,H10
67.4
O2,C5,H9
110.4
O1,C4,C6,H11
173.7
C4,C5,H8
C5,C4,C6,O3
73.6
C4,C5,H9
109.4
C5,C4,C6,H10
169.4
H8,C5,H9
108.3
C5,C4,C6,H11
50.5
O3,C6,C4
111.5
H7,C4,C6,O3
167.1
O3,C6,H10
105.8
H7,C4,C6,H10
50.1
O3,C6,H11
111.4
H7,C4,C6,H11
68.8
The optimized geometry parameters of Glycerol were given in Table 2. Geometry optimizations of the molecule were performed by B3LYP functional with DFT by using G(d,p) basis sets. This conformers were used in vibrational frequencies calculations. Because the most stable conformation will be tested by comparing the experimental data with the calculated vibration frequency.
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11. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
Vibrational frequency calculations was performed by B3LYP functional with DFT by using G(d,p) basis sets. All the calculations were made by Gaussian 03 program [2]. Glycerol molecule has 14 atoms, which possess 36 normal modes of vibrations.
Experimentally observed and theoretically calculated harmonic vibrational frequencies are seen in Table 3.
The computed harmonic vibrational frequencies are good agreement with experimental values which is taken form referances [3,4].
The experimental IR spectrum [3] and Raman spectrum [4] is shown in Figure 6 and 7, respectively.
Theoretically calculated IR spectrum and Raman spectrum is shown in Figure 8 and 9, respectively.
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12. Necmettin Erbakan University
Works
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
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Conclusion and Discussion
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
Figure 6. The experimental IR spectrum [3]
Figure 7. The experimental Raman spectrum [4]
Figure 8. The theoretical IR spectrum
Figure 9. The theoretical Raman spectrum
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Conclusion and Discussion
Determine Molecular Structure
To construct conformational space
Optimized Conformers (OPT-FREQ)
Describe Most Stable Conformer
Calculate Vibrational Frequencies
Vibrational Bands Assigments
Cross Check with Experimental Values
Theoretically calculated vibrational frequency (and proposed in the article) were compared with the experimental counterparts.
As a result, conformer 1 is the most stable conformer because experimental and theoretical results are good agreement each other.
Furthermore, this study showed that theoretical investigation is very important for vibrational assignment.
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THANK YOU!
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16. References
[1] Spartan 08, Wavefunction Inc., Irvine, CA 92612, USA, 2008.
[2] Frisch, M.J.T., G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A, Gaussian , Gaussian, Inc.: Wallingford CT.
[3]
[4] Mendelovici, Efraim, Ray L. Frost, and Theo Kloprogge. "Cryogenic Raman spectroscopy of glycerol." Journal of Raman Spectroscopy (2000):