234-aminopyridine abdallah
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Transcript of 234-aminopyridine abdallah
1
Abstract:
Computational Chemistry is one of the recent advancement in chemistry field. It involves chemical,
mathematical and computational skills in solving different chemistry problems. In this paper, I discuss
briefly about Hartree Fock (ab initio), Semi-Empirical and Density Functional Theory computational
methods and evaluate the strength and limitation of these methods. We report a theoretical study on
density distribution of 2, 3 and 4-Aminopyridine (Aps) by these methods. We also discuss a combined
experimental and theoretical study on vibrational analysis of these mono APs through these three
methods. By studying electron density distribution, we found that DFT method shows the best result for
all APs. In vibrational frequencies analysis, also DFT method shows very good result for 3 and 4-AP
while Semi-Empirical method shows best result for 2- APs.
2
1- Introduction:
Computational chemistry is one of the most useful tools for solving interesting chemistry problems. It is
basically the application of chemical, mathematical and computing skills to solve the problems.
Computational chemistry used to generate information such as properties of molecules or replicated
experimental results. Nowadays, this sector of chemistry has become very famous because people can
investigate materials that are too difficult to find or expensive to purchase, as well as they can make
prior prediction of chemical properties or reaction before running the actual experiments. By this way
they can make better observation before their experiment. Saving time and environment are the most
important advantages of computational chemistry[1]
.
Quantum Mechanical methods uses Schrödinger equation as the basis of computational chemistry; the
equation models the atoms and molecules with mathematics. Different operators in Schrödinger
equation are used to find out different function such as geometry optimization, electron and charge
distribution, frequency calculation etc. In general form of Schrödinger equation, E is energy, is
wave function and is Hamilton Operator. This equation is also called time-independent Schrödinger
equation because it is not dependent on time:
.
For a single particle movement on an electron field non-relativistic Schrödinger equation is written as:[2]
Here, stands for displacement, is the mass of the particle, is Plank’s Constant h/2.
In this paper, computational studies on 2, 3, and 4-APs were performed. These groups of mono AP came
to the attention of NCI Division of Cancer Biology because of their chronic toxicity and carcinogenic
3
activity[3]
. In this research paper the charge density of these APs, as well as their infrared vibrational
frequencies were calculated by Semi-Empirical, Hartree Fock (ab initio) and Density Function Theory
computational methods.
(a) 2-aminopyridine (b) 3-aminopyridine (c) 4-aminopyridine
Figure 1: (a) 2-aminopyridine, (b) 3-aminopyridine and (c) 4-aminopyridine
There were several experimental paper written about these compounds. The paper of experimental and
ab-initio computational studies of self-association: 2-AP and 3-AP by Boyd, A.S.F, Frost, M. J.,
Howarth, N. M. [4]
explained broadly the difference of self-association between these two compound.,
where, computational treatments of 2AP and 3AP were performed to show the dimer structure and
discussed broadly the thermodynamics of these two compounds. A quantum chemical study of
vibrational model of 3, 4, 5-trimethoxy benzaldehyde, 4-hydroxy-3-methoxy benzaldehyde and 4-chloro
benzaldehyde Schiff base of 2-amino pyridine was done by Arora, K., Kumar, D., Agnihotri, S., Singh,
B. [5]
, AM1 and PM3 modes of Semi-Empirical method used as computational methods and finally PM3
Semi-Empirical method considered as the appropriate chemical method for those compounds. The paper
of anharmonic vibrational analysis of 3, 4-diaminopyridine and 3-aminopyridine by density functional
4
theory calculations was done by Karpagam, J., Sundaraganesan, N., Kalaichelvan, S., Sebastian, S. [6]
In
this paper, MP2 and DFT level of theories utilizing 6-311++G(d,p) basis set were used to determine and
analyzing both the equilibrium geometries and harmonic wavenumbers of 3,4-DAP and 3-AP; as well
as, the anharmonic wavenumbers of 3, 4-DAP and 3-AP were also determined. At last, good agreement
between the calculated and experimental spectra was obtained using DFT method.
2- Computational settings:
2-1- The software:
Semi-Empirical, Semi-empirical (HF) and DFT calculations were performed using “Gaussian-09” and
“Gaussview-05” software program package on a personal computer. The results yielded an atomic
picture of chemical systems and help to characterize and understand the accurate bond order of the
compounds. Geometries of the model 2, 3 and 4-aminoypyridine are consecutively examined by
optimization and frequency using ground energy calculations. The optimized structural parameters were
used in calculating the vibrational frequencies at Semi-Empirical, HF and DFT level were PM3, 6-31G
and (B3PW91) 6-31G level of theory were used respectively.
There were some limitations on the program:
o System size
o Limited time scale
The future perspective of the program:
o Accuracy of electronic structure method
o Improvement of quantum mechanics and molecular mechanics
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2-2- The hardware:
The computer that used in this project was “Dell” brand and “Optiplex-755” model. It has following
specifications: Core 2 Duo, 1.80 GHz; Cache 2MB; RAM: 1GB; HDD: 80GB; VGA: 256 MB;
DVD Writer 700 L.E; Windows XP.
3- Theoretical methods:
3-1- Semi-Empirical:
Semi-Empirical method is a kind of Hartree Fock method including the use of empirical data. This
method has more approximation than any other calculation methods. To give best possible conformity
with experimental data, few parameters or numbers are modified by curve fitting technique. To reduce
the amount of calculation, this method is based on two proposals:
o Removal of core electrons
o Two electron integrals are approximated or completely omitted
Strengths Limitations
Calculations are much faster compared to
other calculation methods. [7]
Mostly good for organic molecules
Calculation can be done for larger
molecules than ab initio or DFT
calculation method.
Calculations are less accurate compared
to ab initio and DFT methods.
This method does not work properly with
the molecule those having H-bonding and
with some transition states. [7]
Also not available for some atoms.
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3-2- Hartree Fock (HF):
Hartree Fock calculation method is one of the most common types of ab initio calculations. In this
method, central field approximation uses as primary approximation. This means, it doesn’t depend
explicitly on the instantaneous motion of the other electron. However, the net effect of electron
repulsion is included in the calculation. For more complicated theoretical methods, HF theory often
provides a good starting point which is better approximation to the electronic Schrödinger equation. For
1-electron operator system the following equation is used in HF method[8]
:
Here, is the generated by the orbital ϕ j for one-electron Fock operator,
is the core Hamiltonian of one-electron, the Coulomb operator is defining the energy which
produced by electron-electron repulsion due to the orbital of the jth electron, the electron exchange
energy is defined by which is the exchange operator.
Strengths[9]
Limitations[9]
Starts calculation from the beginning.
Provides very good result.
Can be improved systematically.
Usually take time than other calculation methods.
Not applicable for some larger molecules.
With chemical reactions simpler technique cannot
be used.
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3-3- Density function theory (DFT):
One of the most successful approaches to compute the electronic structure of matter is Density Function
Theory. It is very recently updated to reach a very accurate result. It is applicable for any kind of atoms,
molecules, solids to nuclei etc[10]. In this method, wave function is replaced by total electron density that
is expressed for total energy.
In DFT calculation method, the Born- Oppenheimer approximation is used to fix the treated atoms of the
nuclei. The electron state (for electrons) of the stationary system is then illustrated by a wave function
that fulfils the many-body Schrödinger equation:
Where is the kinetic term,
is the electron-electron interaction term and
is the interface term between electrons and nuclei. Here, the position of
nuclei is and the number of nucleons in each nucleus is . Hartree atomic units are used for this
calculation method.
8
Strengths[12]
Limitations[12]
Applicable for larger molecule than ab initio
HF method.
Provides very good result for ground state and
equilibrium structures.
Experiment takes place in condensed phase
system.
No systematical way to improve its
results as in the conventional ab
initio theory.
Not applicable for excited states
structures.
4- Results and Discussion:
4-1- Charge density of aminopyridines:
4-1-1- Charge density of 2-aminopyridine:
(a) Semi- Empirical (b) Hartree Fock (c) DFT
Figure 2: The charge density of 2-aminopyridine using (a) Semi-Empirical, (b) HF, (c) DFT
9
Table 1: Charge density of 2-aminopyridine using Semi-Empirical, HF and DFT method
Element Semi-Empirical Hartree Fock DFT
N1 -0.128 -0.625 -0.433
N2 0.091 -0.964 -0.765
C2 -0.050 0.591 0.394
C3 -0.194 -0.233 -0.103
C4 -0.031 -0.146 -0.127
C5 -0.197 -0.272 -0.125
C6 -0.024 0.082 0.007
The charge density of N1 and N2 shows high negativity in HF and DFT but in Semi-Empirical it shows
low negative charge on N1 and positive charge on N2 which is very unlikely. The charges on C2 and C6
in HF show positive value while those in DFT and Semi-Empirical show negative charge. In HF and
DFT calculations the amino group became part of the conjugation system with the ring while in Semi-
Empirical it is not a part of the conjugation system. As a result in HF and DFT, N2 shows high negative
charge because nitrogen is more electronegative than carbon and pull the partial negative charge towards
itself. In HF nitrogen atom pulls more partial negative charge than carbon atom, as a result N1 and N2
show highest negative charge while C2 and C6 show positive charge. The ring conjugation in Semi-
Empirical and DFT shows resonance but in HF it has some strong bond order.
4-1-2- Charge density of 3-aminopyridine
(a) Semi- Empirical (b) Hartree Fock (c) DFT
Figure 3: The charge density of 3-aminopyridine using (a) Semi-Empirical, (b) HF, (c) DFT
10
Table 2: Charge density of 3-aminopyridine using Semi-Empirical, HF and DFT method
Element Semi-Empirical Hartree Fock DFT
N1 -0.109 -0.515 -0.368
N2 -0.322 -1.001 -0.818
C2 -0.128 0.012 -0.038
C3 0.009 0.336 0.339
C4 -0.161 -0.187 -0.130
C5 -0.141 -0.222 -0.124
C6 -0.118 0.025 -0.010
The charge density of N1 and N2 shows high negativity in HF and DFT but in S-E it shows low negative
charge on N1 and N2. The charges on C2 and C6 in HF show positive value while those in DFT and S-E
it show negative charge. In HF and DFT calculations the amino group takes part of the conjugation
system with the ring while in S-E did not become part of the conjugation system. As a result in HF and
DFT N2 shows higher negative charge because nitrogen is more electronegative than carbon and pull the
partial negative charge towards itself. In all the calculation methods, C3 shows positive value because
nitrogen is more electronegative and it pulls more partial negative charge than carbon atom hence N2
shows negative charge. The ring conjugation in S-E and DFT shows resonance but in HF it has some
strong bond order.
4-1-3- Charge density of 4-aminopyridine
(a) Semi- Empirical (b) Hartree Fock (c) DFT
Figure 4: The charge density of 4-aminopyridine using (a) Semi-Empirical, (b) HF, (c) DFT
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Table 3: Charge density of 4-aminopyridine using Semi-Empirical, HF and DFT method
Element Semi-Empirical Hartree Fock DFT
N1 -0.113 -0.565 -0.382
N2 0.082 -0.993 -0.805
C2 -0.030 0.070 -0.013
C3 -0.203 -0.274 -0.131
C4 -0.045 0.415 0.327
C5 -0.202 -0.274 -0.131
C6 -0.030 0.070 -0.013
The charge density of N1 and N2 shows high negativity in HF and DFT but in Semi-Empirical it shows
low negative charge on N1 and positive charge on N2 which is very unlikely. The charges on C2, C4
and C6 in HF show positive charge while those in DFT only C4 shows positive charge but in Semi-
Empirical all the carbon atoms show negative charge. In HF and DFT, amino group takes part in the
conjugation system with the ring while in Semi-Empirical it is not a part of the conjugation system. As a
result in HF and DFT, N2 shows higher negative charge because nitrogen is more electronegative than
carbon and pulls the partial negative charge towards it. The ring conjugation in Semi-Empirical and DFT
shows resonance but in HF it has some strong bond order.
4-1-4- Best method in charge density distribution of 2, 3, 4-aminopyridine
(a) 2-aminopyridine (b) 3-aminopyridine (c) 4-aminopyridine
Figure 5: The charge density of (a) 2-aminopyridine, (b) 3-aminopyridine and (c) 4-aminopyridine
using DFT method
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Table 4: Best method in distribution of charge density of 2, 3, 4-AP among Semi-Empirical,
Hartree Fock and DFT method
Element 2-aminopyridine 3-aminopyridine 4-aminopyridine
N1 -0.433 -0.368 -0.382
N2 -0.765 -0.818 -0.805
C2 0.394 -0.038 -0.013
C3 -0.103 0.339 -0.131
C4 -0.127 -0.130 0.327
C5 -0.125 -0.124 -0.131
C6 0.007 -0.010 -0.013
Assuming that based on proper bond order, it is believed that the best results were achieved using DFT.
By comparing the charge density of all APs in DFT method we can see that all the AP’s shows negative
charges on C5, N1 and N2 atoms. But it shows positive charges on C2 and C6 in 2-AP; C3 in 3-AP; C4
in 4-AP respectively. 2-AP has two positive carbon atoms, however 3 and 4-AP have only one positive
carbon atom. In 2-AP C2 and C6 are positively charged, but in the case of 3-AP only C3 and in 4-AP
only C4 is positively charged. In 2-AP C2 and C6 atoms are near to the N1 and N2 atoms; because of
electro negativity of nitrogen they pulls more negative charge towards them, as a result C2 and C6 atoms
shows positive charge. In 3-AP N1 is positioned between C2 and C6 atoms while C3 is connected with
N2 atom. Here only C3 atoms show positive charge but C2 and C6 atoms shows very poor negative
charge. N2 in more negatively charged because it is electro negative hence pulls more charge towards it
as a result C3 shows positive charge. N1 also pulls negative charge but less than N2, as a result C2 and
C6 atoms show poorly negative charge densities. In 4-AP N1 pulls equally C2 and C6 atoms, hence
they shows exactly same charge value. N2 is highly negative charged means pulls more negative charge
towards it hence C4 shows positive charge value. The higher electro negativity of nitrogen than carbon
is the main reason for these dissimilar charge values.
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4-2- Infrared frequencies of aminopyridines
A scaling factor must be applied to the calculated IR-frequency to correct for the anharmonic effects.
The table below shows those used scaling factors:
Table 5: Correction factor used for Semi-Empirical, Hartree Fock and DFT method
Method Semi-Empirical:
PM3
Hartree Fock:
6-31G
DFT: B3PW91,
6-31G
Correction value[14]
0.974 0.9029 0.958
4-2-1: Infrared frequencies of 3-aminopyridine:
Figure 6 is showing the IR spectrum of 3-aminopyridine and Table 6 is showing IR calculations for 3-
aminoypyridine using S-E, HF and DFT compared to experimental data.
Figure 6: Infrared spectrum of 3-aminopyridine[13]
14
S-E method shows nearest frequencies for asymmetric and symmetric stretching of (N-H), which are
respectively 5 1cm less and 73 1cm more than the experimental value. For (C-H) symmetric and
asymmetric stretching of C4 and C5 atoms, DFT shows the best frequencies which are respectively 4
1cm less and 8 1cm more than the experimental value. For (C-H) stretching of C6 and C2 atoms, DFT
and HF shows the best frequencies which are 8 and 19 1cm more than the experimental value. HF
method shows nearest frequency for NH2 scissoring which is 36 1cm more than the experimental value.
For symmetric stretching of (C–C) ring, DFT and HF method shows nearest frequencies which are
respectively 50 and 20 1cm more than the experimental value while for asymmetric stretching DFT and
S-E method shows nearest frequencies which are correspondingly 18, 32 and 23 1cm more than the
experimental value. DFT method shows nearest frequency for (C-N) and ring stretching which is 150+
1cm while other method shows 200+ 1cm more than experimental value. For (C-H) bending of C2,
C3, C4, C6 atoms DFT method shows nearest frequencies which are 7 and 3 1cm more than the
experimental value. S-E and DFT method shows nearest frequencies for (C-H) bending of C4, C5 and
C6 atoms, which are correspondingly 29 and 35 1cm more than the experimental value. DFT method
shows nearest frequency for (C–C) ring breathing, which is only 4 1cm more than the experimental
value.
Table 6: Infrared spectrum value of 3-aminoypyridine by Semi-Empirical, HF and DFT method
Semi-
Empirical
Hartree
Fock
DFT Experimental
value Assignment
[15] Description
3372 3495 3487 3377 as(N-H) NH2 attached to C3
3399 3614 3607 3326 s(N-H) NH2 attached to C3
3121 3081 3092 3096 s(C-H) C4¸ C5 sym. Stretching
3108 3055 3073 3065 as(C-H) C4¸ C5 asym. Stretching
3077 3045 3056 3034 (C-H) C6 stretching
15
3069 3033 3041 3014 (C-H) C2 stretching
1687 1600 1546 1636 NH2 scissoring NH2 attached to C3
1734 1664 1636 1586 s(ring) (C-C) ring sym. Stretching
1696 1616 1578 1560 as(ring) (C-C) ring asym. Stretching
1560 1459 1428 1488 s(ring) (C-C) ring sym. Stretching
1432 1365 1345 1400 as(ring) (C-C) ring asym. Stretching
1324 1300 1305 1347 as(ring) (C-C) ring asym. Stretching
1622 1500 1469 1293 (ring)+ (C-N) Ring + (C-N) stretching
1247 1221 1267 1260 (C-H) C2¸ C3, C6 in plane bending
1211, 1091 1172, 1035 1192, 990 1195 (C-H) C2¸ C4, C6 in plane bending
1161 1046 1032 1132 (C-H) C4¸ C5, C6 in plane bending
1189 1126 1124 1089 (C-H) C4,C5 in plane bending
1121 1037 1019 1015 Ring breathing Ring stretching +
bending NH2
962 1011 960 964 (C-H) C4¸ C5, C6 wagging
919, 899 933, 838 875, 814 897 (C-H) C2¸ C4, C6 wagging
940 963 897 843 (ring)+ (NH2) Ring and (N-H) stretching
821 824 795 800 (C-H) C4¸ C5, C6 wagging
667 727 704 708 ring) In plane ring wagging
615 551 542 660 NH2) NH2 attached to C3
653, 506 636, 436 624, 416 630 (ring) Out of plane bending
565 541 516 544 (ring) Ring bending+
wagging (C-N)
380 362 362 400 Ring o. p Out of plane ring wagging
430 369 374 385 rocking (C-N) NH2 attached to C3
258 290 349 - (NH2) NH2 Wagging
197 228 214 - C-H)+
(C-N)
C2, C4, C5 out of plane bending + wagging (C-N)
Units: 1cm ; Abbreviations: s: symmetric stretching as : asymmetric stretching: bending; : in plane
bending; out of plane bending; wagging
For (C-H) wagging of C2, C4, C5, and C6 atoms, S-E and DFT method shows nearest frequencies
which are respectively 2 1cm more and 22 1cm less than the experimental value. DFT method shows
nearest frequencies for stretching of (C-C) ring, (N-H) and (C-H) wagging of C4 C5 and C6 atoms,
which are respectively 54 1cm more and 5 1cm less than the experimental value. For in plane ring and
16
NH2 wagging, correspondingly DFT and S-E method shows nearest frequencies which are 4 1cm less
and 45 1cm more than the experimental value. For out of plane ring bending, (C-N) wagging and out of
plane ring wagging, HF and S-E method shows nearest frequencies which are respectively 6 1cm more
and 3, 20 1cm less than the experimental value. DFT method shows nearest frequency for rocking of
(C-N), which is 11 1cm less than the experimental value. There are no experimental data found for NH2
Wagging and C2, C4, C5 out of plane bending. Finally, we can say that for 3-AP infrared frequency the
DFT method gives more nearest frequency values than Semi-Empirical or Hartree Fock method.
4-2-2- Infrared frequencies of 4-aminopyridine:
Figure 7 is showing the IR spectrum of 4-aminopyridine and Table 7 is showing IR calculations for 4-
aminoypyridine using S-E, HF and DFT compared to experimental data.
Figure 7: Infrared spectrum of 4-aminopyridine[16]
17
DFT and S-E method shows nearest frequencies for asymmetric and symmetric stretching of (N-H),
which are respectively 49 and 142 1cm more than the experimental values. For (C-H) symmetric and
asymmetric stretching of C3 and C5 atoms, DFT method respectively show values which are 15 1cm
less and on the other case equal to the experimental value. DFT and HF method shows nearest
frequencies for (C-H) stretching of C2 and C6 atoms which are correspondingly 2 1cm less and 7 1cm
more than the experimental value. For NH2 scissoring S-E method shows nearest frequency which is 16
1cm less than the experimental value. For symmetric stretching of (C–C) ring, DFT and HF method
shows nearest frequencies which are respectively 35 and 8 1cm more than the experimental value.
While for asymmetric stretching DFT and HF methods show nearest frequencies, they are respectively
30, 2 1cm more and 23 1cm less than the experimental value.
Table 7: Infrared spectrum value of 4-aminoypyridine by Semi-Empirical, HF and DFT method
Semi-
Empirical
Hartree
Fock
DFT Experimental
value
Assignment[17]
Description
3328 3491 3483 3434 as(N-H) NH2 attached to C4
3442 3610 3605 3300 s(N-H) NH2 attached to C4
2990 3070 3078 3093 s(C-H) C3¸ C5 sym. Stretching
2987 3063 3073 3073 as(C-H) C3¸ C5 asym. Stretching
2956 3042 3056 3058 (C-H) C2, C6 stretching
2953 3041 3055 3034 (C-H) C2, C6 stretching
1632 1590 1541 1648 NH2 scissoring NH2 attached to C4
1724 1668 1637 1602 s(ring) (C – C) ring sym. Stretching
1696 1620 1586 1556 as(ring) (C – C) rings asym. Stretching
1544 1514 1478 1506 s(ring) (C – C) ring sym. Stretching
1454 1442 1417 1440 as(ring) (C – C) rings asym. Stretching
1211 1316 1319 1333 as(ring) (C – C) rings asym. Stretching
1342 1368 1348 1268 (C- NH2) Stretching C- NH2
1144,1118,
1014
1227,1204
, 1030
1267,1213
, 965
1215 (C-H) C2, C3, C5, C6 in plane ring bending
1075 1068 1050 1055 Ring breathing C - C stretching
1044 1043 1011 991 Rocking (C-H) +
NH2
Rocking (C-H) + NH2;
NH2 attached to C3
18
956, 915 1013, 873 957, 829 950 (C-H)+(NH2 C2, C3, C5, C6 out of plane bending +wagging NH2
939, 823 982, 828 947, 812 884 (C-H) C2, C3, C5, C6 out of plane bending
855 859 823 842 C- NH2
(ring)+ C-C)
Stretching C - NH2 ring
bending (C – C) stretching,
796, 645 752, 679 724, 668 822 (C-H) C2, C3, C5, C6 out of plane bending
626 551 529 680 o. p ring deformation
out of plane ring deformation
527 528 519 661 Ring deformation In plane ring deformation
480 435 410 536 o. p (ring) out of plane ring wagging
401 413 397 522 ring)(C-N)
NH2 rocking
wagging ring + wagging
( C-N)NH2 rocking
339 378 384 408 o. p ring) out of plane ring wagging
252 371 370 - NH2 rocking NH2 rocking
195 225 215 - o. pring)
(C-N)
out of plane ring wagging + wagging (C-N)
Unit: 1cm ; Abbreviations: s: symmetric stretching as : asymmetric stretching: bending; in plane
bendingout of plane bending: wagging
S-E method shows nearest frequency for (C-NH2) stretching, which is 74 1cm more than experimental
value. 3 frequency values shows (C-H) bending of C2, C3, C5 and C6 atoms in which HF method shows
nearest frequencies which are respectively 12 1cm more and 11 1cm less than the experimental value.
For breathing of the (C-C) ring and NH2 rocking, DFT method shows nearest frequencies which are
correspondingly 5 1cm less and 20 1cm more than the experimental value. S-E method shows nearest
frequencies for (C-H) out of plane bending of C2, C3, C5 and C6 atoms and wagging of NH2, which are
respectively 6 1cm more and 35 1cm less while for only out of plane bending of C2, C3, C5 and C6
atoms it shows frequencies which are 53 1cm more and 61, 26 1cm less than the experimental value.
For (C-NH2) stretching, ring bending and out of plane ring deformation S-E method shows nearest
frequencies which are correspondingly 13 1cm more and 54 1cm less than the experimental value. HF
19
method shows nearest frequency for in plane ring deformation, which is 133 1cm less than the
experimental value. For out of plane ring wagging, S-E and DFT method shows nearest frequencies
which are respectively 56 and 24 1cm less than the experimental value. HF method shows nearest
frequency for ring wagging, (C-N) wagging and NH2 rocking, which is 109 1cm less than the
experimental value. There are no experimental data for NH2 rocking, out of plane ring and (C-N)
wagging. Finally we can say that, for 4-AP infrared frequency the DFT method gives more precise
frequency values than Semi-Empirical or Hartree Fock method.
4-2-3- Infrared frequencies of 2-aminopyridine:
Figure 8 is showing the IR spectrum of 2-aminopyridine and Table 8 is showing IR calculations for 2-
aminoypyridine using S-E, HF and DFT compared to experimental data.
Figure 8[18]
: Infrared spectrum of 2-aminopyridine
20
Table 8: Infrared spectrum value of 2-aminoypyridine by Semi-Empirical, HF and DFT method
Semi-
Empirical
Hartree
Fock
DFT Experimental
value
Assignment Description
3330 3494 3485 3415 as(N-H) NH2 attached to C2
3440 3622 3619 3270 s(N-H) NH2 attached to C2
3006 3078 3100 3150 s(C-H) C3¸ C4, C5 sym. Stretching
2994 3057 3078 2960 as(C-H) C3¸ C4, C5, C6 asym. stretching
2980 3052 3063 2850 as(C-H) C3¸ C5, C6 asym. stretching
2957 3036 3059 2738 as(C-H) C3¸ C4, C5, C6 asym. stretching
1626 1647 1549 1900 NH2 scissoring NH2 attached to C2
1725 1623 1612 1820 s(ring) (C-C) ring sym. Stretching
1700 1598 1583 1708 as(ring) (C-C) ring asym. Stretching
1514 1506 1472 1635 s(ring) (C-C) ring sym. Stretching
1484 1464 1437 1610 as(ring) (C-C) ring asym. Stretching
1332 1347 1333 1570 as(ring) (C-C) ring asym. Stretching
1220 1328 1313 1495 (ring)+ (NH2) Ring stretching+ NH2 rocking
1140 1227 1277 1450 (C-H) C3¸C4, C5 in plane bending
1120 1155 1162 1380 (C-H) C3, C4, C5, C6 in plane bending
1092 1132 1116 1340 (C-H) C3, C4, C5 in plane bending
1081 1052 1031 1328 (C-H) C3,C5, C6 in plane bending
1041 1041 1004 1290 Ring breath Ring stretching + bending(N-H)
1003, 976 1025, 983 974, 954 1160 C-H) C3, C4, C5, C6 out of plane bending
926, 753 903, 762 947, 728 1145 C-H) C3, C4, C5, out of plane bending
902 844 850 1038 C-H)+ NH2 C4, C6 out of plane bending + Wagging NH2
834 813 774 987 C-H)+C-N) C3, C4, C5, C6 bending +
stretching (C-N)
666 640 629 960 C-H) + NH2 C3, C5, C6 out of plane bending + Wagging NH2
852 844 835 855 NH2 rocking NH2 rocking
624 561 553 844 ring) ring wagging
525 477 547 770 ring) o. p out of plane ring wagging
457 430 468 738 C-H)+
(C-N)
C4, C5, C6 out of plane bending + C-N wagging
371 387 411 662 ring) +
(C-N)
Ring wagging+ Wagging (C-N)
21
360 368 380 - C-H) +
(C-N)
C3, C4 out of plane bending + wagging (C-N)
273 217 358 - NH2) NH2 Wagging
Unit: 1cm ; Abbreviations: s: symmetric stretching as : asymmetric stretching: bending; in plane
bending out of plane bending ; : wagging
From the figure-2 of 2-AP we can see that, two nitrogen atoms are near to each other. So there is
possibility to form intramolecular hydrogen bond between these two nitrogen atoms and already there is
intermolecular hydrogen bond[19]
, while for 3, 4-AP only the formation of intermolecular hydrogen bond
is possible. The experimental frequency values were collected from condensed phase spectrum and the
theoretical frequency values were done in gas phase. So we assuming that the possibility of
intramolecular hydrogen bond is the reason of huge difference between the experimental and theoretical
frequency value. DFT and S-E method shows nearest frequencies for asymmetric and symmetric
stretching of (N-H) which are correspondingly 70 and 170 1cm more than the experimental value. For
(C-H) symmetric and asymmetric stretching of C3, C4, C5 and C6 atoms, DFT and S-E method shows
nearest frequencies which are respectively 50 1cm less and 34, 130 and 219 1cm more than the
experimental value. HF method shows nearest frequency for NH2 scissoring which is 253 1cm less than
the experimental value. For symmetric stretching of (C–C) ring, Semi-Empirical method shows nearest
frequencies which are correspondingly 95, 121 1cm less than the experimental value while for
asymmetric stretching Semi-Empirical and HF method shows respectively 8, 126 and 223 1cm less than
the experimental value. HF method shows nearest frequency for ring stretching and NH2 rocking, which
is 167 1cm less than the experimental value. For (C-H) bending of C3, C4, C5 and C6 atoms DFT
method respectively shows 173, 218 1cm and for (C-H) bending of C3, C5 and C6 atoms HF and S-E
method correspondingly shows 208, 247 1cm less frequencies than the experimental value. Both HF
and Semi-Empirical method shows nearest frequency for (C–C) ring breathing, which is 249 1cm less
22
than the experimental value. For (C-H) out of plane bending of C3, C4, C5 and C6 atoms, (C-N)
stretching and NH2 wagging, HF, DFT, S-E method shows nearest frequencies which are respectively
135, 177, 198, 153, 294 1cm less than the experimental value while for C4 and C6 atoms (C-H) out of
bending and NH2 wagging, S-E method shows nearest frequency which is 225 1cm less than the
experimental value. S-E method shows nearest frequencies for NH2 rocking and ring wagging which are
correspondingly 3 and 220 1cm less than the experimental value. For out of plane ring wagging, (C-H)
out of plane bending of C4, C5 and C6 atoms and wagging of (C-N), DFT method respectively show
nearest frequencies which are 223, 270, 251 1cm less than the experimental value. There are no
experimental data for the frequencies of C3, C4 out of plane bending, wagging (C-N) and NH2 Wagging.
Finally we can say that, for 2-AP infrared frequency the Semi-Empirical method gives more nearest
frequency values than DFT or Hartree Fock method.
6- Conclusion:
Electron density distribution and vibrations analysis has been made in the present work for proper
wavenumber assignment for 2, 3, and 4-AP. The ground state geometries of 2, 3, and 4-AP were
determined and analyzed with S-E, HF and DFT level of theories utilizing MP3, 6-31G and (B3PW91)
6-31G basis sets. DFT calculation method showed very accurate bond order for all APs and hence has
very good charge distribution result. Experimentally DFT calculation method showed nearest vibrational
wave-numbers to the theoretical value for 3 and 4-AP. In assumption, the presence of intramolecular
hydrogen bond between two nitrogen atoms is the cause of massive difference between theoretical and
experimental vibrational wavenumber of 2-AP. On that case, S-E showed closer to the theoretical
frequency values. Finally it can be state that, DFT calculation method is perfect in computational study
23
instead other calculation methods are very good for comparison; hence we can’t depart any of them.
Thus, in computational chemistry DFT calculation method can be successfully used for the prediction of
charge distribution and vibration modes of making more active ligand and other molecules.
Acknowledgement:
I am very thankful to Dr. Nessreen A. Al-Hashimi and Dr. Yasser H. A. Hussein for their dedication on
proper guiding in this research project. I also thank my colleague Mohammad Al-Qahtani for working
and discussing together in the whole course.
24
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