Jordan Journal of Chemistry Vol. 11 No.1, 2016, pp. 8-25

8

JJC

Chemosensor Engineering: Effects of Halogen Attached to Carbon-Carbon Triple Bond Substituent on Absorption energy of Pyridine:

DFT-Study

Amer A. G. Al Abdel Hamida, Sofian Kananb, Tareq M. A. Alshboulc, Taghreed M. A. Jazzazi a and Amarat Y. Al-Nemrata

aDepartment of Chemistry, Yarmouk University, Irbid 21163, Jordan

bDepartment of Biology & Chemistry, American University of Sharjah, United Arab Emirates cDepartment of Chemistry and Chemical Technology, Tafila Technical University, Tafila, Jordan

Received on Nov. 8, 2015 Accepted on March 31, 2016

Abstract Pyridine, C5H5N, and pyridine derivatives of the structure C5(S)nH5-nN (S = -C≡C-X; X = F,

Cl, Br, I) have been studied theoretically using DFT computation employing the B3LYP/LanL2DZ

level of theory. Effects of substituent halogenation on electron density enrichment of the pyridine

nitrogen, and thus its effectiveness as an electron donor have been investigated. Computational

results showed that the substituent halogenation does affect the charge density accumulation on

the nitrogen atom of pyridine as well as the C2=N and -C≡C- bond lengths and the C2 N

C6 bond angle. In addition, charge density localization on the nitrogen atom has been found to

depend on the number and position of side substituents.

Hardness of the halogen atom attached to the tail of the side substituent has been proved

to be a determining factor in promoting and qualifying substituted pyridines to act as effective

electron donors. The influence of substituent halogenation on electronic localization or

delocalization is further viewed by showing (1) charge density distribution surfaces and (2)

occupancy of the HOMO molecular orbitals. The conclusions extracted from this investigation

support our previous findings in earlier studies through which we attempt to gain more insights

toward putting hands on key factors that are anticipated to qualify chelates to be good stabilizers

for metal ion complexes that are demanded as chemosensors. Furthermore, this study is

considered an important step of progress in our pursued research work that aims to promote

inorganic complexes to act as accessible and low energy absorbers. This is essential when

inorganic complexes are needed to be employed as colorimertric detectors in the field of

chemosensation.

Keywords: Pyridine; DFT method; Halogenated substituent; Charge density;

Chemosensation.

Introduction Pyridines and substituted pyridines play a crucial role in several domains of

application in chemistry.[1-4] Typically, they are well known for their electron

Corresponding author: e-mail: amerj@yu.edu.jo

9

withdrawing and electron accepting (redox)[5] as well as for their electrochemical

properties.[6-9] Focusing on their role in the field of chemosensation,[10-15] pyridines and

related derivatives have been fruitfully utilized to synthesize organic[16,17] or inorganic[18]

multicomponent functional assemblies designed to undergo photoinduced electron

transfer to form sensitive chemosensors.[13,14,19].

In order to tune both the structural and photochemical properties of pyridines, a

possible approach relies on an extension of their π-systems by introducing a suitably

modified substituent. This strategy was recently applied to metal ion complexes of the

type [Ru(en)2L2]2+, en = ethylenediamine and L= pyridine or pyridine derivatives such

as 2-, 3-, or 4-methylpyridine, 2-, 3-, or 4-acetylpyridine and 2-, 3-, or 4-cyanopyridine,

in order to determine whether their photochemical properties were changed upon

substituent modification (in specific, the energy of absorption as a function of various

substituent parameters). [20] It was experimentally found that not only the quantum yield

and absorptivity were significantly enhanced[21] but also the absorption energy is red-

shifted and extended toward the visible.[22]

In a recently published report, we have theoretically studied pyridine, C5H5N,

and pyridine derivatives of the type C5(X)nH5-nN (X = -C≡C-H, -C≡C-F, -C≡N, -CH(=O))

employing density functional theory (DFT) and time-dependent density functional

theory (TDDFT) calculations at the B3LYP/LANL2DZ level of theory.[23] In the above

mentioned report, we have investigated the effects of substituent modification (number,

type and position) on the electron density enrichment of pyridine nitrogen, and thus its

effectiveness as a donor atom for binding the electron deficient metal ions.

In the referred study and generally speaking, we have found that the

substituents have interesting effects on charge density localization/delocalization,

either on the nitrogen atom of pyridine or on the carbon atoms in proximity. Among all

of the investigated substituents, -C≡C-F was found to be the most effective in

enhancing and localizing the charge density on the nitrogen atom of pyridine. In the

final conclusion of the study, the fluorine atom was held responsible for this

uniqueness in improving the basicity and thus the donating effectiveness of the

pyridine ring holding the -C≡C-F substituent.[23] This finding has raised the question

about the effect of replacing the fluorine atom in -C≡C-F substituent by another

halogen and how this affects the basicity of the pyridine nitrogen.

The aim of the present paper is to answer this question from a theoretical point

of view, and at the same time, to set up a computational protocol capable of predicting

the behavior of pyridines as a result of substituent modification. Herein, we have

carried out this type of calculations on simulates of the type C5(S)nH5-nN (S = -C≡C-X;

X = F, Cl, Br, I). In addition to the parent pyridine molecule, Figure 1a, the four

substituents, -C≡C-F, -C≡C-Cl, -C≡C-Br and -C≡C-I were employed to design a series

of twenty four simulates. The halogenated carbon-carbon triple bond substituents were

introduced onto the pyridine ring as monosubstituents at the 2-, 3- and 4-positions of

10

the pydidne ring, Figure 1b, as well as multisubstituents (di-, tri- and penta-fashions),

Figure 1c.

Responses for substituent modification were monitored by calculating the APT-

charge density on nitrogen and geometrical parameters (bond lengths and bond

angles) of the neighboring carbon atoms to nitrogen.[20,23-27] In addition, the distribution

of charge density within the simulate system was explored by generating the APT-

charge distribution surfaces and the HOMO-molecular orbitals. Effects of substituent

modification on absorption energy were tracked by calculating the HOMO-LUMO gap

and by showing the UV-spectra for each of the twenty four simulates compared to free

pyridine.

This investigation is a pursuing of our research work[13,14,20,21,23] in which we are

interested in introducing substituent modifications[12,21,28-31] in optical active systems to

serve as potential candidates to feasibly engineer low energy/luminescent[11,32,33]

inorganic coordination compounds (like ruthenium complexes of pyridine/substituted

pyridines)[34-43] to be utilized later as low energy colorimetric chemosensors.

Computational details

Nowadays, the combined use of DFT and TDDFT becomes a reliable and

benchmarked tool for analyzing and predicting ground state properties and absorption

spectra of chemical chromophores.[44-48] As such, DFT and TDDFT calculations at

B3LYP level[20,21,49-52] using the basis set LANL2DZ[20,21,49,53,54] were performed to

simulate the molecular structures and to calculate the vibrational frequencies along

with the charge density distribution. The Atomic Polar Tensor (APT) model has been

utilized to assign and evaluate the partial charge localized on nitrogen of the free

pyridine and pyridine simulates.[55,56] The number of excited state-electronic

configurations used in TDDFT was 80, and only singlet excitations were considered.

Structures of pyridine simulates were optimized with no symmetry constraints. The

same functional and basis sets were employed for TDDFT calculations to compute the

UV-spectra and to simulate the charge density surfaces and the frontier HOMO

orbitals-electronic images for all simulates.

All calculations were carried out using the Gaussian 09 program[57] on Toshiba-

Satellite i5 Dual Core, Equipped with Windows 7. Geometry optimization is one of the

most important steps in the theoretical calculations of TDDFT and vibrational spectra.

All geometries converged perfectly, and all vibrational frequencies and intensities were

computed at the same theoretical levels as those used in geometry optimization.

Rather than the free pyridine, Figure 1a, four substituents were employed to design a

series of twenty four pyridine derivatives (simulates) in which the substituents are first

introduced in a monosubstitution fashion at the 2-, 3- and 4-positions, Figure 1b, and in

a multisubstituion (di-, tri- and penta-fashions) on the ring, Figure 1c.

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Results and discussion

Analysis of optimized geometric parameters

The fully optimized geometries of pyridine and pyridine derivatives numbered

from 1 to 25 are shown in Figures 1 and 2, respectively.

Energy minimum structures of all designed simulates are true energy minima,

where in all cases no imaginary vibration was predicted in the frequency calculations.

The calculated optimum energy and the APT-partial charge of the nitrogen atom in

simulates 1-25 are presented in Table 1. The calculated vibrational frequencies of the

C≡C bond and the C2 N C6 moieties as well as the calculated bond lengths of

the C2=N and C≡C bonds for all simulates are included in Tables 2. The calculated

asymmetric stretching vibrational frequencies of -C≡C- and C2 N C6 are

presented in Table 3. On the other hand, the calculated maximum absorption

wavelengths and the HOMO-LUMO separations for all simulates are shown in Table 4.

Similarly as they affect significantly the optimum energy of simulates, Table 1,

the substituent parameters (type, number and position of attachment) do also have a

significant effect on the molecular geometry, particularly for bonds existing in the

vicinity of the nitrogen atom. The variation trends are discussed and explained by

comparing their values with those calculated for free pyridine 1.

N

C5H5N

(a)

NC5H4N(2-S)

NC5H4N(3-S)

(b)

NC5H4N(4-S)

(c)

NC5H3N(2,6-S)

NC5H2N(2,4,6-S)

NC5N(2,3,4,5,6-S)

2

3

4

5

6

2

34

26 2

4

6 2

34

5

6

S

S

S

S

SS S

S

S

S

S

S

S (Substituent) = -C C-X

S

X= F, Cl, Br, I

Figure 1: Oversimplified structures of (a) free (unsubstituted) pyridine (b) mono-substituted pyridine simulations: C5H4N(2-S), C5H4N(3-S), C5H4N(4-S) and (c) di-substituted C5H3N(2,6-S), trisubstituted C5H2N(2,4,6-S) and pentasubstituted pyridine C5N(2,3,4,5,6-S), where S = -C≡C-F, -C≡C-Cl, -C≡C-Br or -C≡C-I.

12

1

2 3 45 6 7

8 910

11 12 13

14 15

20 21

22

16

17

23

1819

24 25

Figure 2: Optimized geometric structures of simulates 1-25: (1) C5H5N, (2) C5H4N(2-C≡C-F), (3) C5H4N(3-C≡C-F), (4) C5H4N(4-C≡C-F), (5) C5H3N(2,6-C≡C-F)2, (6) C5H2N(2,4,6-C≡C-F)3, (7) C5N(2,3,4,5,6-C≡C-F)5, (8) C5H4N(2-C≡C-Cl), (9) C5H4N(3-C≡C-Cl), (10) C5H4N(4-C≡C-Cl), (11) C5H3N(2,6-C≡C-Cl)2, (12) C5H2N(2,4,6-C≡C-Cl)3, (13) C5N(2,3,4,5,6-C≡C-Cl)5,(14) C5H4N(2-C≡C-Br), (15) C5H4N(3-C≡C-Br), (16) C5H4N(4-C≡C-Br), (17) C5H3N(2,6-C≡C-Br)2, (18) C5H2N(2,4,6-C≡C-Br)3, (19) C5N(2,3,4,5,6-C≡C-Br)5, (20) C5H4N(2-C≡C-I), (21) C5H4N(3-C≡C-I), (22) C5H4N(4-C≡C-I), (23) C5H3N(2,6-C≡C-I)2, (24) C5H2N(2,4,6-C≡C-I)3, (25) C5N(2,3,4,5,6-C≡C-I)5.

Effects of substituent modification

a) The effect of substituent modification on charge density of the nitrogen atom

Figures 4 and 5 show the plot of the APT-charges along with the images of

charge density distribution for all simulates. According to the data in the two figures, no

significant increase in the nitrogen charge density is observed in the case of mono-

substituted pyridines relative to free pyridine. This was regardless of the attachment

position of substituent (see simulates 2-4, 8-10, 14-16 and 20-22, Table 1, Figure 3).

In disubstituted pyridines (simulates 5, 11, 17 and 23, Table 1, Figure 3), the

charge density of nitrogen increases with increased number of substituents in

comparison to free pyridine (simulate 1, Table 1, Figure 3) or to monosubstituted

pyridines (simulates 2-4, 8-10, 14-16 and 20-22, Table 1, Figure 3).

The maximum enrichment of charge density around the nitrogen atom was

shown in the case of tri-substituted derivatives (simulates 6, 12, 18, 24, Table 1, Figure

4), while minimum charge density enrichment was found in the case of meta mono-

substituted derivatives (simulates 3, 9, 15, 23, Table 1, Figure 3). In addition, there is a

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Table 1: Calculated optimum energy and Atomic-Polar-Tensor (APT) partial charge of the nitrogen atom in substituted pyridines (simulates 2-25) compared to free pyridine (simulate 1).

No. Compound Eopt (a.u.) APT-partial charge on N-atom (a.u)

(APTsim- APTpy)

1 C5H5N -248.23942110 - 0.337 0.000

2 C5H4N(2-C≡C-F) -423.58462344 - 0.356 -0.019 3 C5H4N(3-C≡C-F) -423.58651781 - 0.340 -0.003 4 C5H4N(4-C≡C-F) -423.58627382 - 0.356 -0.019 5 C5H3N(2,6-C≡C-F)2 -598.92906374 - 0.396 -0.059 6 C5H2N(2,4,6-C≡C-F)3 -774.27459119 - 0.438 -0.101 7 C5N(2,3,4,5,6-C≡C-F)5 -1124.96348093 - 0.427 -0.090 8 C5H4N(2-C≡C-Cl) - 338.69186235 - 0.365 -0.028 9 C5H4N(3-C≡C-Cl) - 338.69413502 - 0.344 -0.007 10 C5H4N(4-C≡C-Cl) - 338.69389271 - 0.368 -0.031 11 C5H3N(2,6-C≡C-Cl)2 - 429.14358392 - 0.419 -0.082 12 C5H2N(2,4,6-C≡C-Cl)3 - 519.59688377 - 0.476 -0.139 13 C5N(2,3,4,5,6-C≡C-Cl)5 - 700.50148248 - 0.469 -0.132 14 C5H4N(2-C≡C-Br) - 336.91657752 - 0.372 -0.035 15 C5H4N(3-C≡C-Br) - 336.91900124 - 0.344 -0.007 16 C5H4N(4-C≡C-Br) - 336.91879150 - 0.376 -0.039 17 C5H3N(2,6-C≡C-Br)2 - 425.59315199 - 0.436 -0.099 18 C5H2N(2,4,6-C≡C-Br)3 - 514.27157291 - 0.502 -0.165 19 C5N(2,3,4,5,6-C≡C-Br)5 - 691.62656007 - 0.493 -0.156 20 C5H4N(2-C≡C-I) - 335.14390950 - 0.380 -0.043 21 C5H4N(3-C≡C-I) - 335.14647287 - 0.345 -0.008 22 C5H4N(4-C≡C-I) - 335.14631562 - 0.385 -0.048 23 C5H3N(2,6-C≡C-I)2 - 422.04798880 - 0.454 -0.117 24 C5H2N(2,4,6-C≡C-I)3 - 508.95411846 - 0.530 -0.193 25 C5N(2,3,4,5,6-C≡C-I)5 - 682.76422247 - 0.519 -0.182

1-0.337

2-0.356

3-0.340

4-0.356

5-0.396

6-0.438

7-0.427

8-0.365

9-0.344 10

-0.368

11-0.419

12-0.476

13-0.469

14-0.372

15-0.344

16-0.376

17-0.436

18-0.502

19-0.493

20-0.380

21-0.345

22-0.385

23-0.454

24-0.530

25-0.519

-0.6

-0.5

-0.4

-0.3

-0.2

-0.1

01 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

AP

T-C

harg

e (a

.u)

Simulate Figure 3: Variation in APT-charge density of simulates 1-25.

direct proportionality between the charge density on nitrogen and the number of

substituents on simulate. This relationship does hold for all simulates as the number of

substituents increases up in momo-, di- to trisubstituted derivatives, but not in the case

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of pentasubstituted simulates (7, 13, 19, 25, Table 1, Figure 3) where two substituents

are located meta to the nitrogen atom (at positions 3 and 5). It seems that these two

substituents provide no enhancement in the charge density of nitrogen.

The dependence of nitrogen charge density on substituent type is rather

interesting (Table 1 and Figure 3). The values of the APT-charge on nitrogen vary in

the order: -C≡C-F (simulates 2-7) < -C≡C-Cl (simulates 8-13) < -C≡C-Br (simulates 14-

19) < -C≡C-I (simulates 20-25), which is basically the order of decreasing hardness of

halogens.

Table 2: Calculated C2 N C6 bond angle and C2 N and -C≡C- bond lengths of substituted pyridines (simulates 2-25) compared to free pyridine (simulate 1).

No Compound Bond length

(oA) C2 N

Bond angle (deg)

C2 N C6

Bond length (oA) C≡C

1 C5H5N 1.35828 117.7 --- 2 C5H4N(2-C≡C-F) 1.36598 118.0 1.21329 3 C5H4N(3-C≡C-F) 1.35237 118.2 1.21432 4 C5H4N(4-C≡C-F) 1.35846 117.4 1.21399 5 C5H3N(2,6-C≡C-F)2 1.36233 118.3 1.21297, 1.21297

6 C5H2N(2,4,6-C≡C-F)3 1.36276 118.0 1.21269, 1.21268, 1.21339

7 C5N(2,3,4,5,6-C≡C-F)5 1.35648 119.3 1.21255, 1.21255, 1.21342, 1.21342,

1.21296 8 C5H4N(2-C≡C-Cl) 1.36691 118.0 1.21948 9 C5H4N(3-C≡C-Cl) 1.35216 118.2 1.22047 10 C5H4N(4-C≡C-Cl) 1.35840 117.4 1.22028 11 C5H3N(2,6-C≡C-Cl)2 1.36296 118.3 1.21921, 1.21921

12 C5H2N(2,4,6-C≡C-Cl)3 1.36349 118.0 1.21896, 1.21896, 1.21975

13 C5N(2,3,4,5,6-C≡C-Cl)5 1.35714 119.4 1.21881, 1.21881, 1.21971, 1.21972,

1.21927 14 C5H4N(2-C≡C-Br) 1.36732 118.0 1.22229 15 C5H4N(3-C≡C-Br) 1.35229 118.2 1.22336 16 C5H4N(4-C≡C-Br) 1.35859 117.4 1.22308 17 C5H3N(2,6-C≡C-Br)2 1.36315 118.3 1.22204, 1.22203

18 C5H2N(2,4,6-C≡C-Br)3 1.36384 117.9 1.22180, 1.22180, 1.22260

19 C5N(2,3,4,5,6-C≡C-Br)5 1.35751 119.4 1.22166, 1.22165, 1.22254, 1.22254,

1.22211 20 C5H4N(2-C≡C-I) 1.36752 118.0 1.22483 21 C5H4N(3-C≡C-I) 1.35222 118.2 1.22593 22 C5H4N(4-C≡C-I) 1.35872 117.4 1.22567 23 C5H3N(2,6-C≡C-I)2 1.36351 118.3 1.22460, 1.22460

24 C5H2N(2,4,6-C≡C-I)3 1.36411 117.9 1.22521, 1.22438, 1.22438

25 C5N(2,3,4,5,6-C≡C-I)5 1.35778 119.4 1.22426, 1.22426, 1.22516, 1.22516,

1.22471

15

32 4 5 6 7

8 9 10 11 12 13

171614 191815

2220 21 24 2523

1

Figure 4: Images of APT-Charge distribution surfaces of simulates 1-25 showing the accumulation of charge density of simulates as a function of substituent modification.

Data in Table 1 are further presented schematically in Figure 4 where the

charge density around nitrogen is shown as a red ball located underneath the nitrogen

atom symbol. This visual presentation is identified as the "charge distribution surface"

where intensity and size of the red spot around nitrogen indicate the amount of charge

density around nitrogen. These surfaces are beneficial in mapping the charge density

distribution around the nitrogen atom itself and its neighboring carbon atoms as well.

Hence, these surfaces allow quick estimation of how much charge density is gathered

around each atom.

Studying Figures 4 and 5 together, one may find that for all simulates 1-25, the

charge density (red spot) is localized around the nitrogen atom with no charge density

gathered around the carbon atoms of the pyridine ring. However, in mono-substituted

simulates (simulates 2-4, 8-10, 14-16 and 20-22), the red spots around nitrogen are

barely noticed indicating that mono-substitution has a very weak effect toward

16

enhancing the charge density on nitrogen. In contrast, di-, tri- and pentasubstituted

simulates show more developed red spots around nitrogen, indicating that more

charge density is gained as the number of substituents is increased. Furthermore,

tying up the two parameters (charge density and number of substituents) together

clearly reveals the direct proportional relationship between them. This relationship

holds for mono-, di- and tri-substituted pyridines. However it does not hold for penta-

substituted ones. It is worth noting that the hardness of the halogen atom attached to

the tail of every individual substituent undoubtedly controls the amount of charge

density localized on the nitrogen atom of that simulate. As we see, the amount of

charge density on nitrogen increases as the halogen changes in the order F, Cl, Br and

I, Figure 5. In addition, it is quite interesting to see that the halogen atom (tethered to

the triple bond at the far end of the substituent on pyridine) masters the donation

power of nitrogen and may, thus, promote or prohibit the effectiveness of pyridine as a

stabilizer for electron deficient metal ions. Investing wisely this property in similar

systems would enable synthesizing new pyridine derivatives suitable for engineering

the highly demanded low energy absorbers, the type of inorganic coordination

complexes that are essential in colorimetric chemosensation. Penta-substituted

simulates have less charge density on nitrogen relative to that witnessed in tri-

substituted ones. This may be attributed to the fact that meta-substituents have no

effect on charge density as explained above. It is probable that the crowdness of the

five substituents around the ring in penta-substituted simulates will put some

restrictions on the movement of charge density as it sweeps toward nitrogen.

Altogether, the two effects cause less charge density on nitrogen relative to that in tri-

substituted simulates.

N

-C C-F -C C-Cl

N

-C C-I

N

-C C-Br

N

Figure 5: Simplified graphical representation showing the charge density depression

on nitrogen as the hardness of halogen increases.

This view of charge density transfer from nitrogen toward halogen is illustrated

graphically in Figure 5. In this plot, the amount of charge density driven away from

nitrogen (or that left on behind) is related to the degree of hardness of the halogen

atom. As shown in Figure 5, the harder the halogen atom attached to the substituent,

the weaker would be the donation from nitrogen to electron deficient metal ions.

17

Table 3: Calculated asymmetric stretching vibrational frequencies of C≡C and C2 NC6 bonds of substituted pyridines (simulates 2-25) compared to free pyridine

(simulate 1).

No Compound

Asymmetric stretching vibrational

frequency (cm-1) of C2 N C6

Vibrational frequency (cm-1) of

C ≡ C

1 C5H5N 1307.0 --- 2 C5H4N(2-C≡C-F) 1297.8 2422.6 3 C5H4N(3-C≡C-F) 1298.4 2417.3 4 C5H4N(4-C≡C-F) 1290.1 2419.3 5 C5H3N(2,6-C≡C-F)2 1295.9 2424.0, 2426.3 6 C5H2N(2,4,6-C≡C-F)3 1287.8 2423.0, 2426.0, 2429.0

7 C5N(2,3,4,5,6-C≡C-F)5 1310.7 2417.0, 2418.3, 2421.8, 2423.3, 2427.9

8 C5H4N(2-C≡C-Cl) 1299.11 2332.4 9 C5H4N(3-C≡C-Cl) 1298.24 2326.4

10 C5H4N(4-C≡C-Cl) 1289.69 2327.8 11 C5H3N(2,6-C≡C-Cl)2 1297.99 2335.2, 2333.3 12 C5H2N(2,4,6-C≡C-Cl)3 1286.20 2337.5, 2335.0, 2331.2

13 C5N(2,3,4,5,6-C≡C-Cl)5 1281.03 2337.0, 2331.1, 2329.0, 2323.4, 2322.5

14 C5H4N(2-C≡C-Br) 1297.55 2305.2 15 C5H4N(3-C≡C-Br) 1297.88 2298.7 16 C5H4N(4-C≡C-Br) 1289.56 2300.5 17 C5H3N(2,6-C≡C-Br)2 1297.09 2307.8, 2305.9 18 C5H2N(2,4,6-C≡C-Br)3 1285.96 2309.8, 2307.5, 2303.5

19 C5N(2,3,4,5,6-C≡C-Br)5 1279.97 2294.0, 2295.6, 2301.5, 2303.4, 2309.9

20 C5H4N(2-C≡C-I) 1296.68 2283.6 21 C5H4N(3-C≡C-I) 1297.75 2276.9 22 C5H4N(4-C≡C-I) 1289.51 2278.4 23 C5H3N(2,6-C≡C-I)2 1296.21 2285.8, 2284.0 24 C5H2N(2,4,6-C≡C-I)3 1285.80 2281.5, 2285.5, 2287.8

25 C5N(2,3,4,5,6-C≡C-I)5 1278.71 2270.6, 2273.0, 2279.2, 2281.3, 2288.4

2) The effect of substituent modification on bond geometry of nitrogen atom and neighboring carbons

Correlating vibrational bond energies and bond parameters (Tables 2 and 3)

with the APT-charges (Table 1) supports the findings concluded previously. In the

preceding section, the halogen atom attached to the tail of substituent was found to

control the charge density on the nitrogen atom, Figure 5. As this perturbation of

charge density is taking place around the nitrogen atom, it is anticipated that the bond

distances and the bond angles near the nitrogen atom would, in consequence, be

somehow affected. Tracking such changes in bond geometries is therefore thought to

provide additional insights toward understanding the key factors that would promote

the donation effectiveness of pyridine. This would be attained through careful

interpreting and analyzing the data included in Tables 1, 2 and 3.

18

Analyzing the results displayed in Table 2 leads to the following conclusions:

1) Compared to free pyridine 1, only meta-monosubstituted simulates (simulates 3, 9,

15 and 21) and pentasubstituted simulates (simulates 7, 13, 19 and 25) have exhibited

C2=N bond shortening accompanied with C2 N C6 bond angle widening,

regardless of substituent type. These two classes of simulates have meta-substituents

in common. When the position of the substituent(s) is related to the charge density on

nitrogen on one side and with the C2=N bond distance and C2 N C6 bond angle

on the other side, it could be concluded that the existence of at least one substituent

meta to nitrogen, contributes negatively toward the charge density enrichment on

nitrogen. It seems that the placement of the substituent in meta position to the nitrogen

atom tends to drive the charge density away from nitrogen along the C=N bond. This,

in effect, induces C2=N bond shortening and C2 N C6 bond angle widening due

to electron density passage through the C=N path.

2) Second, tri-substituted simulates have exhibited C2=N bond lengthening

accompanied with a slight bond angle widening compared to free pyridine 1. Since tri-

substituted simulates have recorded the highest values of charge density enrichment

on nitrogen (in Table 1), it may be concluded that placing the substituent(s) at the 2, 4

and 6-positions increases effectively the charge density on the nitrogen atom.

However, it seems that substitution at the 4-position (para position) affects neither the

C2=N bond length nor the C2 N C6 bond angle. Going back to Table 1, it can be

seen that these para-substituted simulates have recorded charge density values very

close to those recorded by ortho-substituted simulates. This, in other words, indicates

that substituents at the 4-position do not affect sterically bond geometries, though they

electronically affect the charge density on the nitrogen atom.

3) Ortho mono- or di-substituted simulates have shown distinguished C2=N bond

lengthening accompanied with normal bond angle widening compared to free pyridine

1. The data in Table 1 reveal that both classes of simulates have recorded high values

of charge densities. This means that placing substituent(s) at the ortho position(s)

(either position 2 only or positions 2 and 6 together) is effective in enhancing the

charge density on the nitrogen atom. In fact, introducing two groups at the 2- and 6-

positions enriches the charge density to an extent greater than introducing only one

group at either position.

Accordingly, the change in the C2=N bond length reflects the charge density

localization or delocalization on the nitrogen atom. This conclusion is based on the fact

that as more charge is localized on the nitrogen atom, less charge is swept away from

nitrogen through the C2=N bond and the force constant of the bond would be smaller.

On the other hand, the C2 N C6 bond angle widening or narrowing tends

to be less reliable in responding to the electronic effects exerted by the attached

substituent(s). The steric effect which builds up within simulates as a result of

19

substituents crowdness is believed to stand behind this weakness in response.

Nevertheless, the charge density delocalization over the C2 N C6 moiety would

increase the bond angle as a result of the electronic repulsion between C2 N and N

C6 bonding pairs. Accordingly, penta-substituted simulates (simulates 7, 13, 19

and 25) have shown greater C2 N C6 bond angle widening than trisubstituted

ones despite having less charge density on the nitrogen atom.

4) The trend in the corresponding change in bond length of C≡C triple bond supports

also the conclusions drawn about the effect of X hardness on the charge density on

the nitrogen atom. As X changes through F, Cl, Br and I, an elongation in the C≡C

bond is observed which can be attributed to the decrease in the withdrawal effect of X

as its hardness decreases. In effect, the C≡C bond would vibrate at lower frequency as

X goes in the order F, Cl, Br and I, Table 2 and 3. Correlating the bond energies of the

C2=N and C≡C bonds with the hardness of X leads to the conclusion that higher

vibrational frequencies are expected for the two bonds as X gets harder, Figure 5.

c) The effect of substituent modification on the occupation of HOMO orbitals

Tuning the shapes of HOMOs (highest occupied molecular orbitals) shown in

Figure 6 with the images of charge density distribution surfaces shown in Figure 4

enables mapping the charge density distribution on nitrogen in specific and

neighboring carbons in general.

Figure 6 shows that: (1) The HOMOs in simulates 8-10, 14-16 and 20-22

delocalize over the C2 N C6 atoms, similar to the HOMO in free pyridine 1. Keeping

in mind that these simulates have shown APT-charges equal to that in free pyridine 1,

it may be concluded that ortho-, meta-, and para-monosubstitution with -C≡C-X, where

X= Cl, Br, I, do not extend the HOMO-loops beyond that shown for free pyridine 1. In

effect, the obtained patterns for the HOMOs do not support charge density enrichment

on the nitrogen atom. (2) In the -C≡C-F monosubstituted simulates (simulates 2-4), the

HOMOs are extended over the C2-C3, C5-C6, -C≡C bonds and over the nitrogen atom.

The three simulates have APT-charges lower than that calculated for any of their

corresponding analogues (mono-substituted simulates of X=Cl, Br, I) or even for free

pyridine 1. (3) Di-, tri- and pentasubstituted simulates (simulates 5-7, 11-13, 17-19, 23-

25) show similar distribution patterns for the HOMOs, where they spread over both

sides of nitrogen (C2-C3 and -C≡C- from the right side and C5-C6 and -C≡C- from the

left side) without including the nitrogen atom itself in the overlap network.

Nevertheless, these simulates have shown an increase in the APT-charge density as

they go from di-, tri- to pentasubstituted ones. Noticeably, two interesting observations

are made: The first one is that the p-orbitals of the nitrogen atom do not overlap with

any of the neighboring carbon atoms. The second one is that no overlap is observed in

para-substituted simulates between the atomic orbitals of the substituent and any of

the atomic orbitals of the surrounding atoms. This indicates that the para-position is not

the right place for enhancing the charge density localization on the nitrogen atom. This

20

is specifically seen for all classes of simulates holding para-substituent, whether tri-

substituted or penta-substituted simulates.

2

3

4

8

10

9

14

16

15

20

21

22

5

6

7

11

12

13

17

18

19 25

23

24

1

Figure 6: Frontier HOMO molecular orbitals of simulates 1-25.

Apparently, this pattern of overlapping between p-orbitals of carbon atoms

surrounding nitrogen without including p-orbitals of nitrogen itself, reflects the high

charge density enrichment of nitrogen. This is clearly seen, when APT-charge density

values in Table 1 are tuned with the plots shown in Figures 5 and 6 (simulates 5-7, 11-

13, 17-19, 23-25). (4) Moreover, simulates holding same number of halogenated

substituents show very similar and comparable HOMO shapes, this is regardless of the

substituent type (simulates 5-7, 11-13, 17-19, 23-25). In other words, crowdness of

substituents in these simulates does not offer enough freedom for HOMOs to extend

over all of the participated atoms. Thus, HOMOs become less sensitive to changes in

halogen hardness and therefore the effect on charge density localization over nitrogen.

21

d) The effect of substituent modification on absorption energy of simulates

It was found in Table 1 that APT-charge density increases with increasing

number of substituents on simulates regardless of the substituent type. Taking the

substituent type in consideration, the APT-charge density on nitrogen increases as the

attached halogen goes in the order F, Cl, Br, I. Applying the same argument for the

relationship between APT-charge density and absorption energy of simulates leads to

conclude that as more charge is localized on nitrogen, larger red shift in the absorption

energy would be observed, corresponding to smaller energy gap between the HOMO

and LUMO orbitals. Simulates 20-25 and 2-7, Tables 1 and 4, provide good examples

for this finding. As seen in the two tables, simulates of high APT-charge density on

nitrogen are showing absorption bands of longer wavelength. This finding is

considered the most interesting and advantageous finding in this study because it

suggests the ability to control the absorption energy (red- or blue-shifting) of a

particular simulate by playing with the hardness of the halogen atom attached to the

tail of substituents in that simulate, Table 4.

Table 4: Calculated maximum absorption wavelengths and HOMO-LUMO separation of substituted pyridines (simulates 2-25) compared to free pyridine (simulate 1).

No. Compound ʎmax, (Ɛ) (nm)

HOMO-LUMO gap (eV)

1 C5H5N 166.7 (35338 sh, s) 5.578 2 C5H4N(2-C≡C-F) 220.2 (8351 b, m) 4.327 3 C5H4N(3-C≡C-F) 220.0 (8348 b, m) 4.245 4 C5H4N(4-C≡C-F) 217.5 (8350 b, m) 4.435 5 C5H3N(2,6-C≡C-F)2 220.0 (18000 b, s) 4.082 6 C5H2N(2,4,6-C≡C-F)3 223.7 (36500 sh, vs) 4.027 7 C5N(2,3,4,5,6-C≡C-F)5 249.2 (38200 sh, vs) 4.871 8 C5H4N(2-C≡C-Cl) 228.4 (13000 b, m) 5.578 9 C5H4N(3-C≡C-Cl) 225.0 (19523 b, m) 5.442

10 C5H4N(4-C≡C-Cl) 223.3 (11250 b, m) 5.279 11 C5H3N(2,6-C≡C-Cl)2 228.1 (23800 b, s) 5.524 12 C5H2N(2,4,6-C≡C-Cl)3 232.7 (45000 sh, vs) 5.252 13 C5N(2,3,4,5,6-C≡C-Cl)5 263.3 (48500 sh, vs) 4.680 14 C5H4N(2-C≡C-Br) 232.1 (16000 b, m) 5.578 15 C5H4N(3-C≡C-Br) 235.8 (15000 b, m) 5.415 16 C5H4N(4-C≡C-Br) 230.2 (13500 b, m) 5.279 17 C5H3N(2,6-C≡C-Br)2 235.7 (27500 b, s) 5.442 18 C5H2N(2,4,6-C≡C-Br)3 238.2 (47500 sh, vs) 5.143 19 C5N(2,3,4,5,6-C≡C-Br)5 271.4 (54300 sh, vs) 4.599 20 C5H4N(2-C≡C-I) 240.1 (15000 b, m) 5.143 21 C5H4N(3-C≡C-I) 242.8 (16000 b, m) 4.816 22 C5H4N(4-C≡C-I) 237.9 (25853 b, m) 4.735 23 C5H3N(2,6-C≡C-I)2 244.9 (30000 b, s) 5.007 24 C5H2N(2,4,6-C≡C-I)3 249.6 (48000 sh, vs) 4.789 25 C5N(2,3,4,5,6-C≡C-I)5 281.1 (61000 sh, vs) 4.490

ʎmax = maximum absorption wavelength in nm, Ɛ = Molar absorbtivity, sh = shoulder, vs = very strong, s = strong, b = broad, m = medium.

22

Conclusions

In this study, pyridine and pyridine derivatives of the structure C5(S)nH5-nN (S = -

C≡C-X; X = F, Cl, Br, I) were studied using density functional theory (DFT) and time-

dependent density functional theory (TDDFT) at the B3LYP/LANL2DZ level of theory.

Variations in charge density on the nitrogen atom as a result of substituent

halogenation in various simulates were monitored by calculating the APT-charge on

nitrogen along with related geometrical parameters, namely, bond lengths and bond

angles in the neighborhood of the nitrogen atom. To figure out how the charge density

is distributed over the simulate structure, images of the HOMOs and APT-charge

distribution surfaces are also worked out. The conclusions are summarized as follows:

(1) halogenated substituents have pronounced effects on charge density enrichment

on the nitrogen atom of the examined simulates. In addition, the C2=N and C≡C bond

lengths and the C2 N C6 bond angle have been affected as well. (2) Besides its

dependence on the number and position of the halogenated substituents, the charge

density distribution has also been found to depend highly on the hardness of the

halogen atom tethered to the far end of the attached substituent (3) Among the four

substituents (-C≡C-F,-C≡C-Cl,-C≡C-Br,-C≡C-I), -C≡C-I was found to be the most

effective in enriching the charge density on the nitrogen atom, increasing thus its ability

to donate electrons to incoming metal ions. This was attributed to the weak electronic

withdrawal effect of the iodine atom compared to the other halogen members.

Fluorinated substituents, on the other hand, are capable, due to the high

electronegativity of fluorine, of driving the majority of the charge density toward

themselves and away from the nitrogen atom leading to increased electron deficiency

on the nitrogen atom and making it less effective for electron donation. (4) One of the

most interesting findings of this investigation is that substituted pyridines were proven

to be more qualified and effective for electron donation than unsubstituted pyridine. (5)

Substituent modification (halogenation in our case) can be employed as a tool for

controlling the donation effectiveness of the nitrogen atom of pyridine. (6) Outcomes of

this investigation have deepened our understanding toward applying substituent

modifications in the field of chemosensation and to feasibly produce low-energy

optically active luminescent inorganic compounds.

Acknowledgments This work was supported by Yarmouk University, Faculty of Graduate Studies

and Scientific Research, Grant number 13/2011. We acknowledge the support by the

Emirates Foundation Group for supporting this work at the American University of

Sharjah.

23

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