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Frequency CaIculations
Presented by
Nguyen Duy The
Introduction
 Running frequency calculations using Gaussian09, frequency
calculations can serve a number of different purposes:
 To predict the IR and Raman spectra of molecules (frequencies and
intensities). (Content 1)
 To compute force constants for a geometry optimization. (Content 2)
 To identify the nature of stationary points on the potential energy
surface. (Content 3)
 To compute zero-point vibration and thermal energy corrections to
total energies as well as other thermodynamic quantities of interest
such and the enthalpy and entropy of the system (Content 4)
Object: Benzen + Hydro ( C6H6 + H2)
• Files 1(F1) : th1benzen.cml + Benzen1.com + Benzen1.log
▫ F1.1: file structure after optimizating by Avogadro.
▫ F1.2: Input file for gaussian09
▫ F1.3: file log after running
• Files 2(F2): th2benzen.cml + Benzen2.com + Benzen2.log
• Files 3(F3): th3benzen.cml + Benzen3.com + Benzen3.log
Link: https://github.com/nguyenthe123/BTMaterialsScience
Object: File .cml of C6H6 + H2
F1.1 F2.1 F3.1
Chú ý: Các file .com tương ứng F2.1, F3.1 đều không thể
opt trên Gaussian09 do đó chỉ thực hiện được với file
F1.1.
Object: File .com of C6H6 + H2
# RHF/6-31G(d) Freq Pop=full Opt
Benzen Hydro 1
0 1
C 1.2016810000 0.3925400000 -0.0654360000
C 0.3261360000 0.5145560000 -1.7171510000
C -1.5466010000 0.5931780000 -1.7782590000
C -2.5348880000 0.5494680000 -0.1884670000
C -1.6557910000 0.4277120000 1.4555860000
C 0.2085270000 0.3493880000 1.5174730000
H -0.6431300000 1.0452900000 -0.1023190000
H -0.6893590000 -0.1027310000 -0.1626210000
H 2.2809920000 0.3465040000 -0.0164380000
H 0.9048330000 0.5393040000 -2.6319480000
H -2.0625750000 0.6638000000 -2.7271990000
H -3.6145720000 0.5941180000 -0.2107910000
H -2.2241290000 0.4023970000 2.3732440000
H 0.7087820000 0.2791060000 2.4720000000
Content 1: Frequencies and intensities
Spectral line 1 2 3 4 5 6 7 8 9 10 11
Frequencies
(Hz)
198.871
5
332.665
5
518.59
89
558.85
46
609.46
52
745.35
44
836.65
33
865.761
5
908.54
88
997.21
48
1019.
8460
IR Int (cm^-1) 0.2629 0.5802 5.0308 0.0606 0.2734 59.809
1
21.630
3
1.2090 0.4553 5.2517 0.596
3
Spectral line 12 13 14 15 16 17 18 19 20 21 22
Frequencies 1081.74
02
1105.88
42
1110.6
029
1143.
4718
1159.9
245
1277.5
267
1304.
9732
1307.502
0
1387.3
516
1484.8
350
1508.3
326
IR Int 6.2349 0.1908 0.6175 0.140
3
2.5474 0.0026 1.891
4
4.9045 5.2512 0.6725 2.7036
Content 1: Frequencies and intensities
Spectral line 23 24 25 26 27 28 29 30 31 32 33
Frequencies 1541.2
218
1570.77
33
1621.76
40
1636.8
527
1828.36
36
1880.0
548
3164.4
235
3171.75
93
3237.09
54
3238.26
90
3341.5
353
IR Int 1.9241 0.7326 0.9334 0.5977 2.1806 0.6317 17.047
4
70.0087 58.7152 2.8076 0.9271
Spectral line 34 35 36
Frequencies 3349.0890 3366.1518 3376.865
1
IR Int 9.7631 69.4005 26.2481
Content 1: Frequencies and intensities
Content 2: Force constant
Spectral line 1 2 3 4 5 6 7 8 9 10 11
Force
constant
0.0416 0.1462 0.4564 0.3847 1.2006 0.4234 0.6445 0.6917 1.4794 1.3349 1.677
9
Spectral line 12 13 14 15 16 17 18 19 20 21 22
Force
constant
1.8313 0.9113 1.0380 1.400
6
1.4663 0.9950 1.1320 1.1336 1.3443 1.6563 2.1752
Spectral line 23 24 25 26 27 28 29 30 31 32 33
Force
constant
2.1923 2.3991 1.6842 1.7523 14.331
9
11.300
6
6.3553 6.3256 6.7125 6.7778 7.1392
Spectral line 34 35 36
Force
constant
7.1857 7.3377 7.3909
Content 2: Force constant
Content 3: Stationary Points
• There are two pieces of information from the output which are critical
to characterizing a stationary point:
 The number of imaginary frequencies.
 The normal mode corresponding to the imaginary frequency.
lmanginary Frequencies are listed in the output of a frequency calculation
as negative numbers. By definition, a structure which has n imaginary
frequencies is an nth order saddle point
Content 3: Stationary Points
From: Exploring Chemistry with Electronic Structure Methods - James B. Foresman
Aleen Frisch
Content 3: Stationary Points
F1.3 F2.3 F3.3
The number of imaginary
frequencies
0
Content 4: The Zero-point and Thermal Energy-corrected
The zero-point energy is a correction to the electronic energy of the molecule or hamal mayy cdon. to account for
the effects of molecular vibrations which persist even at 0 K.
From: Exploring Chemistry with Electronic Structure Methods - James B. Foresman
Aleen Frisch
F1.3 F2.3 F3.3
Zero-point vibrational energy 345650.2 (Joules/Mol)
82.61238 (Kcal/Mol)
238397.0 (Joules/Mol)
56.97825 (Kcal/Mol)
237582.3 (Joules/Mol)
56.78352 (Kcal/Mol)
Zero-point correction 0.131651 (Hartree/Particle) 0.090801 (Hartree/Particle) 0.090490 (Hartree/Particle)
Thermal correction to Energy 0.136509 0.097207 0.096498
Thermal correction to Enthalpy 0.137454 0.098151 0.097443
Thermal correction to Gibbs Free
Energy
0.103571 0.061294 0.061095
(E0) Sum of electronic and zero-point
Energies
-231.700246 -193.443437 -230.767603
(E) Sum of electronic and thermal
Energies
-231.695388 -193.437031 -230.761595
(H) Sum of electronic and thermal
Enthalpies
-231.694444 -193.436087 -230.760651
(G) Sum of electronic and thermal
Free Energies
-231.728327 -193.472944 -230.796998
Content 4: The Zero-point and Thermal Energy-corrected
Nhận xét: Mặc dù không thể opt 2 file F2 và F3 xong có
thể tạm nhận xét năng lượng E0 của F1 là bé hơn so với
trường hợp E0 khi chưa opt. Và số điểm ảo của tần số
cũng không có => Minimum => Có xu hướng về cấu trúc
này trong tự nhiên.
Frequency CaIculations
Presented by
Nguyen Duy The

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Frequency ca iculations finnal

  • 2. Introduction  Running frequency calculations using Gaussian09, frequency calculations can serve a number of different purposes:  To predict the IR and Raman spectra of molecules (frequencies and intensities). (Content 1)  To compute force constants for a geometry optimization. (Content 2)  To identify the nature of stationary points on the potential energy surface. (Content 3)  To compute zero-point vibration and thermal energy corrections to total energies as well as other thermodynamic quantities of interest such and the enthalpy and entropy of the system (Content 4)
  • 3. Object: Benzen + Hydro ( C6H6 + H2) • Files 1(F1) : th1benzen.cml + Benzen1.com + Benzen1.log ▫ F1.1: file structure after optimizating by Avogadro. ▫ F1.2: Input file for gaussian09 ▫ F1.3: file log after running • Files 2(F2): th2benzen.cml + Benzen2.com + Benzen2.log • Files 3(F3): th3benzen.cml + Benzen3.com + Benzen3.log Link: https://github.com/nguyenthe123/BTMaterialsScience
  • 4. Object: File .cml of C6H6 + H2 F1.1 F2.1 F3.1
  • 5. Chú ý: Các file .com tương ứng F2.1, F3.1 đều không thể opt trên Gaussian09 do đó chỉ thực hiện được với file F1.1.
  • 6. Object: File .com of C6H6 + H2 # RHF/6-31G(d) Freq Pop=full Opt Benzen Hydro 1 0 1 C 1.2016810000 0.3925400000 -0.0654360000 C 0.3261360000 0.5145560000 -1.7171510000 C -1.5466010000 0.5931780000 -1.7782590000 C -2.5348880000 0.5494680000 -0.1884670000 C -1.6557910000 0.4277120000 1.4555860000 C 0.2085270000 0.3493880000 1.5174730000 H -0.6431300000 1.0452900000 -0.1023190000 H -0.6893590000 -0.1027310000 -0.1626210000 H 2.2809920000 0.3465040000 -0.0164380000 H 0.9048330000 0.5393040000 -2.6319480000 H -2.0625750000 0.6638000000 -2.7271990000 H -3.6145720000 0.5941180000 -0.2107910000 H -2.2241290000 0.4023970000 2.3732440000 H 0.7087820000 0.2791060000 2.4720000000
  • 7. Content 1: Frequencies and intensities Spectral line 1 2 3 4 5 6 7 8 9 10 11 Frequencies (Hz) 198.871 5 332.665 5 518.59 89 558.85 46 609.46 52 745.35 44 836.65 33 865.761 5 908.54 88 997.21 48 1019. 8460 IR Int (cm^-1) 0.2629 0.5802 5.0308 0.0606 0.2734 59.809 1 21.630 3 1.2090 0.4553 5.2517 0.596 3 Spectral line 12 13 14 15 16 17 18 19 20 21 22 Frequencies 1081.74 02 1105.88 42 1110.6 029 1143. 4718 1159.9 245 1277.5 267 1304. 9732 1307.502 0 1387.3 516 1484.8 350 1508.3 326 IR Int 6.2349 0.1908 0.6175 0.140 3 2.5474 0.0026 1.891 4 4.9045 5.2512 0.6725 2.7036
  • 8. Content 1: Frequencies and intensities Spectral line 23 24 25 26 27 28 29 30 31 32 33 Frequencies 1541.2 218 1570.77 33 1621.76 40 1636.8 527 1828.36 36 1880.0 548 3164.4 235 3171.75 93 3237.09 54 3238.26 90 3341.5 353 IR Int 1.9241 0.7326 0.9334 0.5977 2.1806 0.6317 17.047 4 70.0087 58.7152 2.8076 0.9271 Spectral line 34 35 36 Frequencies 3349.0890 3366.1518 3376.865 1 IR Int 9.7631 69.4005 26.2481
  • 9. Content 1: Frequencies and intensities
  • 10. Content 2: Force constant Spectral line 1 2 3 4 5 6 7 8 9 10 11 Force constant 0.0416 0.1462 0.4564 0.3847 1.2006 0.4234 0.6445 0.6917 1.4794 1.3349 1.677 9 Spectral line 12 13 14 15 16 17 18 19 20 21 22 Force constant 1.8313 0.9113 1.0380 1.400 6 1.4663 0.9950 1.1320 1.1336 1.3443 1.6563 2.1752 Spectral line 23 24 25 26 27 28 29 30 31 32 33 Force constant 2.1923 2.3991 1.6842 1.7523 14.331 9 11.300 6 6.3553 6.3256 6.7125 6.7778 7.1392 Spectral line 34 35 36 Force constant 7.1857 7.3377 7.3909
  • 11. Content 2: Force constant
  • 12. Content 3: Stationary Points • There are two pieces of information from the output which are critical to characterizing a stationary point:  The number of imaginary frequencies.  The normal mode corresponding to the imaginary frequency. lmanginary Frequencies are listed in the output of a frequency calculation as negative numbers. By definition, a structure which has n imaginary frequencies is an nth order saddle point
  • 13. Content 3: Stationary Points From: Exploring Chemistry with Electronic Structure Methods - James B. Foresman Aleen Frisch
  • 14. Content 3: Stationary Points F1.3 F2.3 F3.3 The number of imaginary frequencies 0
  • 15. Content 4: The Zero-point and Thermal Energy-corrected The zero-point energy is a correction to the electronic energy of the molecule or hamal mayy cdon. to account for the effects of molecular vibrations which persist even at 0 K. From: Exploring Chemistry with Electronic Structure Methods - James B. Foresman Aleen Frisch
  • 16. F1.3 F2.3 F3.3 Zero-point vibrational energy 345650.2 (Joules/Mol) 82.61238 (Kcal/Mol) 238397.0 (Joules/Mol) 56.97825 (Kcal/Mol) 237582.3 (Joules/Mol) 56.78352 (Kcal/Mol) Zero-point correction 0.131651 (Hartree/Particle) 0.090801 (Hartree/Particle) 0.090490 (Hartree/Particle) Thermal correction to Energy 0.136509 0.097207 0.096498 Thermal correction to Enthalpy 0.137454 0.098151 0.097443 Thermal correction to Gibbs Free Energy 0.103571 0.061294 0.061095 (E0) Sum of electronic and zero-point Energies -231.700246 -193.443437 -230.767603 (E) Sum of electronic and thermal Energies -231.695388 -193.437031 -230.761595 (H) Sum of electronic and thermal Enthalpies -231.694444 -193.436087 -230.760651 (G) Sum of electronic and thermal Free Energies -231.728327 -193.472944 -230.796998 Content 4: The Zero-point and Thermal Energy-corrected
  • 17. Nhận xét: Mặc dù không thể opt 2 file F2 và F3 xong có thể tạm nhận xét năng lượng E0 của F1 là bé hơn so với trường hợp E0 khi chưa opt. Và số điểm ảo của tần số cũng không có => Minimum => Có xu hướng về cấu trúc này trong tự nhiên.

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