A theoretical investigation into the conformational changes

of dibenzo-p-dioxin, thianthrene, and selenanthrene

Sunghwan Kima, Younghi Kwona, Jong-Phil Leeb, Seung-Youl Choib, Jaebum Choob,*

aDepartment of Chemistry, Hanyang University, Seoul 133-791, South KoreabDepartment of Chemistry, Hanyang University, Ansan 425-791, South Korea

Received 25 November 2002; revised 8 May 2003; accepted 14 May 2003

Abstract

Theoretical ab initio calculations using the HF and B3LYP methods have been carried out to investigate the conformational

differences of three cyclic rings, dibenzo-p-dioxin (DPD), thianthrene (THT), and selenanthrene (SET). The physical origin for

the conformational preference of each molecule has been studied using the natural bond orbital (NBO) analysis. The NBO

results indicate that DPD exists in a planar form due to strong electron delocalization caused by the specific orbital interaction,

np ! ppCC; around the X atom. On the other hand, THT and SET exist as puckered forms with high inversion barriers due to less

effective electron delocalization. The NBO analysis also shows that the conformational stabilization in DPD is caused by a more

effective overlap of the 2pz –ppCC orbitals, compared with the overlap of the 3pz –pp

CC orbitals in THT.

q 2003 Elsevier B.V. All rights reserved.

Keywords: Dibenzo-p-dioxin; Thianthrene; Selenanthrene; Natural population analysis; Natural bond orbital analysis

1. Introduction

Dibenzo-p-dioxin (DPD), thianthrene (THT), and

selenanthrene (SET) are typical examples of tri-cyclic

rings that have a ‘butterfly structure’ folded along one

of the principal molecular axes. It is already known

that the physical properties of a tri-cyclic ring are

closely related to its folding structure [1,2]. For

example, Kobayashi et al. have shown that the toxic

properties and biological activity of polychlorinated

dibenzo-p-dioxins (TCDDs) are closely related to

their folded ring structures [3]. Thus, it is very

important to determine the accurate folding angle

between the two benzene rings to understand the

structure–property relationship. Fig. 1 shows a

definition of the ring folding angle, u; of a tri-cyclic

ring. There have been a large number of experimental

investigations carried out to determine the folding

angle and inversion barrier of each ring molecule

using X-ray crystallography [4–7], photoelectron

spectroscopy [8,9], and solid-state NMR spectroscopy

[10–14]. Table 1 summarizes the folding angles

of DPD, THT and SET studied so far using

these experimental techniques. There have also

been several theoretical studies using MM3 [15,16]

and STO molecular orbital [17–19] calculations.

0022-2860/03/$ - see front matter q 2003 Elsevier B.V. All rights reserved.

doi:10.1016/S0022-2860(03)00326-0

Journal of Molecular Structure 655 (2003) 451–458

www.elsevier.com/locate/molstruc

* Corresponding author. Tel.: þ82-31400-5505; fax: þ82-

31407-3863.

E-mail address: jbchoo@hanyang.ac.kr (J. Choo).

According to previous studies, THT and SET exist as

puckered forms with high inversion barriers, whereas

the most stable form of DPD is planar.

To our knowledge, the physical origin of the

conformational difference between DPD, THT, and

SET, from the quantum mechanical point of view, has

not yet been reported. Therefore, we undertook a

theoretical investigation using ab initio and density

functional theory (DFT) methods. The planar (D2h)

and folded ðC2vÞ structures for each compound were

optimized at the HF level using various basis sets.

Then an electron correlation treatment at the B3LYP

level was performed to predict a reliable inversion

barrier. To better understand the physical origin of the

conformational preference of each molecule, natural

bond orbital (NBO) analysis were performed. Based

on the NBO analysis, some of the factors that

contribute to the conformational differences, such as

atomic charge, bond polarity and adjacent orbital

interactions have been interpreted. It was the aim of

this work to provide a theoretical origin for the

conformational differences that exist between DPD,

THT and SET.

2. Computational details

The molecular structures of DPD, THT and SET

were fully optimized at the various levels of theory

using the GAUSSIAN 98 software package [20]. The

geometry optimizations were carried out at the HF

level using the 6-31G(d,p), 6-31 þ G(d,p), 6-

311G(d,p) and 6-311 þ G(d,p) basis sets. The effect

of electron correlation on the molecular geometry was

taken into account by using Becke’s three-parameter

hybrid method with the Lee–Yang–Parr correlation

functional (B3LYP) [21] while employing the same

basis sets.

Fig. 1. The numbering scheme and the definition of ring folding angle, u; for dibenzo-p-dioxin and its analogues.

Table 1

Previously reported ring folding angles for the equilibrium

structures of DPD, THT, and SET using various spectroscopic

and computational methods

Molecule Method Folding angle,

u (8)

Reference

X-ray 180 [4]

NMR 180 [10]

STO/3-21G 180 [16]

MM3 180 [11]

X-ray 128 [5]

NMR 144 [12]

STO/4-31G 126 [17]

MM3 125 [11]

X-ray 123 [7]

S. Kim et al. / Journal of Molecular Structure 655 (2003) 451–458452

NBO analysis at the HF/6-311G(d,p) level were

carried out to investigate the atomic charges, bond

polarities and adjacent orbital interactions that

contribute to their conformational preferences [22,

23]. With the NBO deletion procedure, the energy

of the hyper-conjugative interaction of interest was

evaluated by calculating the change in the sum of

the energies of the occupied orbitals upon deletion

of specific off-diagonal elements of the Fock

matrix in the NBO basis set. In this way, the

total energy was decomposed into components

associated with the covalent and non-covalent

contributions, and therefore, the delocalization

effects were estimated from a comparison of the

deletion energies [24,25].

3. Results and discussion

3.1. Molecular structures and inversion barriers

Fig. 2 shows the ring inversion energy profiles

of DPD, THT, and SET calculated at the HF/6-

311G(d,p) level as a function of the folding angle,

u: Table 1 also summarizes the conformational

structures of the three ring molecules studied so

far using different experimental techniques and

computations. According to our calculations, DPD

has a potential energy minimum at u ¼ 1808: On

the other hand, THT and SET have potential

energy minima at u ¼ 126:4 and 125.28, respect-

ively. This means that THT and SET exist as

puckered forms (i.e. C2v), while DPD exists as a

planar form (i.e. D2h). Our calculated folding

angles and ring inversion energy barriers are listed

in Table 2. As can be seen in Tables 1 and 2, our

computational results are in good agreement with

the experimental data.

Table 3 shows the calculated geometrical par-

ameters of the three ring molecules calculated at the

HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels.

These values are also compared to the previously

reported X-ray diffraction data. The C–O bond

length (1.380 A) is considerably shorter than the

C–S and C–Se bond lengths (1. 787 and 1.931 A,

respectively) at the B3LYP/6-311G(d,p) level due to

their different atomic sizes. The bond angles

calculated at both the HF and B3LYP levels were

generally similar. The /C – O – C bond

angle(116.58), the /C–S–C (101.08) bond angle

and the /C–Se–C bond angle (98.98) at the

B3LYP level agree well with the X-ray data. Fig. 3

shows the correlations between the structural

parameters (C–X bond length and /C–X–C bond

angle) and the folding angle, u; for the three ring

molecules. The C–X bond length gradually shortens

when u is increased. This means that the C–X bond

is strengthened in the planar conformation. In

contrast, the larger the /C–X–C bond angle

becomes, the more puckered becomes the central

ring. In fact, the /C–S–C and /C–Se–C bond

angles for the puckered forms are larger by ,78

than the /C–S–C and /C–Se–C bond angles for

the planar forms.

3.2. Natural bond orbital analysis

Natural population analysis was performed to

elucidate the effect of the bond polarity and atomic

charge on the conformational preferences of the three

ring molecules. Table 4 lists the atomic charges

calculated at the HF/6-311G(d,p) level. The data in

Table 4 show that a large negative charge develops on

the oxygen atom (20.5830, D2h) but considerable

positive charge also develop on the sulfur atom

(0.2729, C2v) and the selenium atom (0.4103, C2v).

This is because oxygen is more electronegative

than either sulfur or selenium. Table 4 also listsFig. 2. Ring inversion potential energy profiles of DPD, THT, and

SET at the HF/6-311G(d,p) level.

S. Kim et al. / Journal of Molecular Structure 655 (2003) 451–458 453

the %polarization (%pol) on the X atoms for DPD,

THT and SET. The electro-negativity difference on

the bridging X atom also affects the bond polarization

for the sCX bond. As shown in the table, the sCO bond

of DPD is polarized toward the oxygen atom (%pol of

68.16), whereas the sCS and sCSe bonds of THT and

SET are polarized toward the adjacent carbon atoms

(%pol of 46.13 and 42.31, for THT and SET,

respectively).

According to our calculations, the electron delo-

calization is strongly affected by the electron

population changes caused by the specific orbital

interactions around the X atom. For example, the

occupancy of the p-type lone pair ðnpÞ on the X atom

contributes to the atomic charge redistribution and the

bond polarity, but the population of the s-type lone

pair ðnsÞ does not significantly change the atomic

charge redistribution and the bond polarity. In the case

of a benzene ring, the population of the ppCC orbital

strongly affects the atomic charge redistribution and

the bond polarity. To better understand the changes in

electron population, as the conformation changes, the

adjacent molecular orbital interactions of the bridging

atom, X, using NBO analysis were discussed.

Table 5 summarizes the results of the NBO

analyses at the HF/6-311G(d,p) level for DPD, THT,

and SET. The total SCF energy ðEtotalÞ was decom-

posed into a Lewis energy term (ELewis : non-

delocalized energy) and a delocalization energy

ðEdelocÞ term. The Edeloc term represents the hyper-

conjugative energy caused by delocalization between

occupied and unoccupied orbitals. A negative Edeloc

value means that the system is stabilized by electron

delocalization. As shown in Table 5, the Lewis

energies have lower values in the puckered (i.e. C2v)

forms for all three molecules. This is because the

increased angle strain on the /C–X–C stabilizes the

Lewis structure. Nonetheless, DPD exists as a planar

structure regardless of the destabilization of its Lewis

energy since it has a large electron delocalization

energy compared to THT and SET, and this can

overcome the Lewis energy destabilization.

As mentioned above, the conformational differ-

ence of each ring molecule is mainly caused by the

adjacent molecular orbital interactions around the

central atom, X. To find the main factors contributing

to the conformational energy, the delocalization

energy terms around the C–X bond were decomposed

into two parts: the delocalization energy between the

bridging atom, X and the two benzene rings ðEXÞ; and

the p-delocalization energy on the benzene rings

ðEpÞ: The results of the NBO analysis are listed in

Table 5. In the case of DPD, the large difference of

DEX (10.2) means that delocalization between the X

atom and the benzene rings is increased when the ring

is planar (i.e. D2h). In contrast, this delocalization is

decreased in the planar form for THT and SET

(DEX ¼ 22.0 and 23.4, respectively). On the other

Table 2

Folding angles (8) and ring inversion energy barriers (kcal/mol) of DPD, THT, and SET at variosus levels of theory

u DE

DPD THT SET DPD THT SET

HF/6-31G(d,p) 180.0 127.7 121.3 – 6.6 10.06

HF/6-31 þ G(d,p) 180.0 127.3 121.3 – 6.6 10.97

HF/6-311G(d,p) 180.0 126.4 125.2 – 7.1 7.39

HF/6-311 þ G(d,p) 180.0 127.3 125.2 – 6.4 7.52

B3LYP/6-31G(d,p) 180.0 129.4 121.6 – 5.2 8.41

B3LYP/6-31 þ G(d,p) 180.0 128.8 121.2 – 5.1 9.36

B3LYP/6-311G(d,p) 180.0 127.9 125.9 – 5.6 6.05

B3LYP/6-311 þ G(d,p) 180.0 128.8 125.9 – 5.0 6.07

Experiment 180.0a 128.0b 123.4c – 6.2d –

a Ref. [4].b Ref. [5].c Ref. [7].d Determined from dielectric relaxation measurements [12].

S. Kim et al. / Journal of Molecular Structure 655 (2003) 451–458454

Table 3

Geometrical parameters of DPD, THT, and SET calculated at the HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels (distances, A, angles, degree)

HF/6-311G(d,p) B3LYP/6-311G(d,p) X-raya

XyO XyS XySe XyO XyS XySe XyOb XySc XySed

D2h C2v D2h C2v D2h D2h C2v D2h C2v D2h D2h C2v C2v

C3–X1 1.361 1.779 1.775 1.917 1.914 1.380 1.787 1.783 1.931 1.927 1.383 1.771 1.902

C3–C4 1.380 1.387 1.393 1.388 1.393 1.388 1.397 1.400 1.398 1.401 1.387 1.391 1.394

C3–C8 1.383 1.389 1.383 1.390 1.383 1.397 1.401 1.397 1.399 1.395 1.387 1.394 1.396

C4–C5 1.384 1.383 1.377 1.383 1.378 1.394 1.392 1.389 1.392 1.389 1.400 1.378 1.388

C5–C6 1.384 1.385 1.386 1.384 1.386 1.392 1.394 1.393 1.394 1.394 1.374 1.383 1.365

/C3–X1–C9 116.9 100.3 107.2 98.8 106.1 116.5 101.0 107.2 98.9 106.0 116.3 99.9 98.1

/X1–C3–C4 118.4 119.6 114.3 119.0 113.8 118.2 119.2 114.4 118.8 113.7 – 119.7 –

/X1–C3–C8 121.5 120.6 126.4 121.2 127.0 121.8 121.0 126.4 121.4 127.0 121.9 120.6 121.0

/C3–C4–C5 120.0 120.2 121.2 120.3 121.2 119.9 120.2 121.2 120.2 121.1 119.1 120.2 120.0

/C3–C8–C7 120.1 119.8 119.3 119.7 119.3 120.1 119.7 119.2 119.8 119.3 120.5 119.7 119.6

/C4–C5–C6 120.0 120.0 119.5 120.0 119.5 120.0 120.0 119.6 120.0 119.6 120.5 120.2 120.4

u 180.0 126.4 180.0 125.2 180.0 180.0 128.4 180.0 125.9 180.0 180.0 128.1 123.4

a Some values are averaged over crystallographically distinct values.b Ref. [4].c Ref. [5].d Ref. [7].

S.

Kim

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hand, the variation in the value of Ep is relatively

consistent (16.8, 13.2 and 13.6 for DPD, THT and

SET, respectively). From this point of view, it is

evident that the EX term mainly contributes to the

variation in the value of Edeloc: To more fully

understand the origin of the main orbital interactions

contributing to the EX term, several molecular orbital

interaction components around the C–X bond were

analyzed using the NBO deletion procedure, and the

four important contributions are listed in Table 5.

Here, two types of different lone pair orbitals exist on

the bridging X atom: the p-type orbital, np; which is

perpendicular to the plane of the benzene ring and the

s-type orbital, ns; which is parallel to the ring plane.

As shown in Table 5, the conformations of DPD,

THT, and SET are mainly determined by two

competing molecular orbital interactions: np ! ppCC

and np ! spCC: However, delocalization from the ns

orbital does not have a significant effect on the EX

term. Fig. 4 shows the changes in the two significant

np ! ppCC and np ! sp

CC interactions as a function of

the folding angle. In the case of the puckered forms,

the np ! ppCC interaction is decreased, while the

np ! spCC interaction is increased for these rings. To

gain a better insight into the different interaction

patterns of the lone pair orbitals, their orbital

Fig. 3. Variations of C–X bond lengths and /C–X–C bond angles

of DPD, THT, and SET, calculated at the HF/6-311G(d,p) level.

Table 4

Calculated atomic charges ðqXÞ and %polarizations on the X atoms

for DPD, THT, and SET

XyO ðD2hÞ XyS ðC2vÞ XySe ðC2vÞ

qX 20.5803 0.2729 0.4103

%pola 68.16 46.13 42.31

a %polarization on the X atom is 100lcXl2

in sCX ¼ cC £ hC þ

cX £ hX; where cC and cX are polarization coefficients, and hC and

hX are normalized atomic hybrid orbitals, respectively.

Table 5

NBO analyses of DPD, THT, and SET

XyO XyS XySe

C2v D2h Da C2v D2h D C2v D2h D

Contributions of ELewis and Edeloc to Etotal

Etotal 2382096.2 2382104.3 8.1 2787046.2 2787039.1 27.1 23299919.9 23299912.5 27.4

ELewis 2381058.4 2381035.3 223.1 2786013.0 2785992.6 220.4 23298895.8 23298882.0 213.9

Edeloc 21037.7 21069.0 31.3 21033.2 21046.4 13.3 21024.0 21030.5 6.5

Contributions of EX and Ep to Edeloc

EX 2156.1 2166.3 10.2 2119.5 2117.5 22.0 2101.3 298.0 23.4

Ep 2290.4 2307.2 16.8 2303.4 2316.6 13.2 2302.2 2315.8 13.6

E0delocð¼ EX þ EpÞ 2446.4 2473.4 27.0 2423.0 2434.1 11.1 2403.6 2413.7 10.2

Important contributions to EX

Eðnp! ppCCÞ 239.1 262.5 23.4 227.1 241.9 14.8 222.6 234.1 11.6

Eðnp! spCCÞ 217.1 0.0 217.1 218.4 0.0 218.4 216.0 0.0 216.0

Eðns! ppCCÞ 21.4 0.0 21.4 20.9 0.0 20.9 20.8 0.0 20.8

Eðns! spCCÞ 229.1 233.8 4.7 221.5 226.3 4.8 219.6 223.9 4.3

All energy values in kcal/mol.a D is the difference between the planar ðD2hÞ and puckered ðC2vÞ forms.

S. Kim et al. / Journal of Molecular Structure 655 (2003) 451–458456

orientations were also considered. In the planar form,

the np orbital is perpendicular to the ring plane, but it

is parallel to the ppCC orbital, as shown in Fig. 5. When

the ring is planar (i.e. as in DPD), the np ! ppCC

orbital interaction is maximized, but the np ! spCC

interaction is zero. As the ring puckers (i.e. as in THT

and SET), the np ! ppCC orbital interaction decreases,

and the np ! spCC interaction increases. When we

compare the np ! ppCC orbital interaction of DPD

with that of THT, then the ppCC orbitals of benzene

rings are expected to overlap more effectively with the

lone pairs of the oxygen 2pz orbital than those of the

sulfur 3pz orbital. The DPD np orbital corresponds to

the oxygen atom 2pz atomic orbital, whereas that of

THT corresponds to the sulfur atom 3pz atomic

orbital. Thus, the DPD np orbital can more easily

overlap with the ppCC orbital compared to the THT and

SET np orbitals. Consequently, the conformational

stabilization for the planar conformation of DPD is

mainly caused by the effective overlap of the oxygen

2pz and the DPD ppCC orbitals.

4. Conclusion

We have studied the puckered ring conformations

of three tri-cyclic rings: DPD, THT, and SET, using

ab initio and DFT calculations. According to our

calculations, THT and SET exist as puckered forms

with high inversion barriers, whereas the most stable

conformation of DPD is planar. The calculated barrier

height of each molecule appears to be in reasonable

agreement with previously reported experimental

data. According to our calculations, the C–X bond

length was strengthened in the order: C–Se , C–

S , C–O, and the /C– X– C bond angle was

increased in the order: C–Se–C , C–S–C , C–

O–C. Natural population analysis showed that DHD

exists as a planar form due to a strong electron

delocalization caused by the specific orbital inter-

action, np ! ppCC; around the X atom. On the other

hand, THT and SET exist as puckered forms with high

inversion barriers due to less effective electron

delocalization. NBO analysis also indicated that the

conformational stabilization of the planar confor-

mation of DPD was caused by the effective overlap of

the 2pz –ppCC orbitals, compared to the overlap of the

3pz –ppCC orbitals in THT. In conclusion, NBO

analysis provides a good theoretical basis for the

conformational difference among the three butterfly-

type tri-cyclic rings of DPD, THT, and SET from a

quantum mechanical point of view.

Acknowledgements

This work is supported by the Korea Science and

Engineering Foundation (Grant numbers R14-2002-

004-01000 and R05-2001-00172).

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