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

5

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.

6

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.

7

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



10



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



11



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

12

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.

13

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




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: 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.


Semi-

Empirical

Hartree

Fock

DFT Experimental

value

Assignment[17]

Description



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


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



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[18]

: Infrared spectrum of 2-aminopyridine

20


Semi-

Empirical

Hartree

Fock

DFT Experimental

value

Assignment Description



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







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

References:

[1] The Shodor Education Foundation (2000). Overview of computational chemistry. Retrieved

December 16, 2011, from http://www.shodor.org/chemviz/overview/ccbasics.html

[2] Sherrill, D. (2006). Time-independent Schrödinger equation. Retrieved December 18, 2011, from

http://vergil.chemistry.gatech.edu/notes/quantrev/node8.html

[3] Technical Resources International (2006). Aminopyridines. (Chemical nomination under contract no.

N02-CB-07007), P: 1-38.

[4] Boyd, A. S. F., Frost, M. J. & Howarth, N.M. (2004). Study of the Molecular Structure. Experimental

and ab initio computational studies of self-association: 2-AP and 3-AP. Ref. no: 688, P: 149-158.

[5] Arora, K., Kumar, D., Agnihotri, S., Singh, B. (2010). Quantum chemical study. Vibration modes

studies of 3,4,5-trimethoxy benzaldehyde, 4-hydroxy-3-methoxy benzaldehyde and 4-chloro

benzaldehyde Schiff base of 2-amino pyridine. Vol. 26(4), P: 1361-1368.

[6] Karpagam, J., Sundaraganesan, N., Kalaichelvan, S., Sebastian, S. (2010). Molecular and

Biomolecular Spectroscopy. Anharmonic vibrational analysis of 3, 4-diaminopyridine and 3-

aminopyridine by density functional theory calculation. Ref. no: 76, P: 502-512.

[7]

Thile, W. (2000). Modern Methods and Algorithms of Quantum Chemistry. Semi empirical Methods.

Vol. 3, ISBN 3-00-005834-6, P: 261-283.

[8] Richards, W. G.; Horsley, J. A. (1970). Ab Initio Molecular Calculations for Chemists. Equations of

Hartree-Fock; Oxford University Press: London; P: 1-40.

[9] Sherrill, D. (2002). Introduction to Hartree-Fock. Retrieved December 22, 2011, from

http://vergil.chemistry.gatech.edu/notes/hf-intro/node1.html

[10] Sharma, S. (2005). Introduction to DFT. Retrieved December 28, 2011, from http://www1.mpi-

halle.mpg.de/~sharma/talks/edinburgh.pdf

[11] Certik, O. (2011). Density Functional Theory. Many Body Schrödinger Equation. Retrieved January

12, 2012, from http://theoretical-physics.net/dev/src/quantum/dft.html#id1

[12] Labanowski, J. K. (1998). Density Function Theory. Retrieved January 2, 2012, from

http://www.unc.edu/~shubin/dft.html

[13] NIST (2011). Infrared Spectrum of 3-aminopyridine. Retrieved November 20, 2011, from

http://webbook.nist.gov/cgi/cbook.cgi?ID=C462088&Units=SI&Mask=80#IR-Spec

http://www.shodor.org/chemviz/overview/ccbasics.html

http://vergil.chemistry.gatech.edu/notes/quantrev/node8.html

http://vergil.chemistry.gatech.edu/notes/hf-intro/node1.html

http://www1.mpi-halle.mpg.de/~sharma/talks/edinburgh.pdf

http://www1.mpi-halle.mpg.de/~sharma/talks/edinburgh.pdf

http://www.unc.edu/~shubin/dft.html

http://webbook.nist.gov/cgi/cbook.cgi?ID=C462088&Units=SI&Mask=80#IR-Spec

25

[14] NIST (2011). Pre computed vibrational scaling factors. Correction factor values. Retrieved

December 30, 2011, from http://cccbdb.nist.gov/vibscalejust.asp

[15] Buyunmurat, Y. Akyuz, S. (2001). Study of the Molecular Structure. Theoretical and Experimental

IR spectra and assignments of 3-AP. Ref. no: 563-564, P: 545-550.


http://webbook.nist.gov/cgi/cbook.cgi?Name=4-AMINOPYRIDINE&Units=SI&cIR=on#IR-Spec

[17] Buyunmurat, Y. Akyuz, S. (2003). Study of the Molecular Structure. Theoretical and Experimental

IR spectra and assignments of 4-AP. Ref. no: 651-653, P: 533-539.


http://webbook.nist.gov/cgi/cbook.cgi?ID=C504290&Units=SI&Type=IR-SPEC&Index=2#IR-SPEC

[19]

Von, V., Samoylova, E. (2009). Excited state dynamic of isolated DNA base pairs and related

chromophore clusters. The model system of 2-AP. P: 29-30.

http://webbook.nist.gov/cgi/cbook.cgi?Name=4-AMINOPYRIDINE&Units=SI&cIR=on#IR-Spec

http://webbook.nist.gov/cgi/cbook.cgi?ID=C504290&Units=SI&Type=IR-SPEC&Index=2#IR-SPEC

234-aminopyridine abdallah

Documents

intermolecular

intramolecular

strong bond

accurate bond

nearest frequency

unitssiamp

body schrdinger

partial negative