Structural geometries of halogen∙∙∙halogen synthons

(1)

Structural geometries of halogen

∙∙∙

halogen synthons

G. Gervasio

11

,

_,

E. Bonometti

_{E. Bonometti}

1 1

University of Turin, Department of Chemistry, Via P. Giuria 7 – 10125 TO

References:

[1] K.J. Donald, B.K. Wittmark and C. Crigger,

[1] K.J. Donald, B.K. Wittmark and C. Crigger, J. Phys. Chem. A J. Phys. Chem. A (2010), 114, 7213-7222 (2010), 114, 7213-7222 [2]

[2] Metrangolo, P.; Neukirch, H., Pilati, T.; Terraneo, G.Metrangolo, P.; Neukirch, H., Pilati, T.; Terraneo, G.Acc. Chem. Res. Acc. Chem. Res. 2005, 38, 386-395; Walsh 2005, 38, 386-395; Walsh R.B.,Padgett C.W.,MetrangoloP.,Resnati G., Hanks T

R.B.,Padgett C.W.,MetrangoloP.,Resnati G., Hanks T W. PenningtonW.T., W. PenningtonW.T.,Cryst. Growth DesCryst. Growth Des.2001,1,165- .2001,1,165-175

175

[3]

[3] Auffinger, P.; Hays, F.A.; Westhof, E.; Ho, P.S. Auffinger, P.; Hays, F.A.; Westhof, E.; Ho, P.S. Proc. Natl. Acad. Sci. U.S.A.Proc. Natl. Acad. Sci. U.S.A. 2004, 101 2004, 101,16789-16794,16789-16794 [4]

[4] Forni, A. J. Phys. Chem.A Forni, A. J. Phys. Chem.A2009, 1132009, 113, 3403-3412., 3403-3412. [5] Politzer,

[5] Politzer, P.; P.; MurrayMurray, J. S.;, J. S.; Clark Clark, T. Phys. Chem. Chem. Phys., T. Phys. Chem. Chem. Phys. 2010, 12 2010, 12, 7748, 7748--77577757.. [6]

[6] Lommerse, J.P.M.; Stone, A.J.; Taylor, R.; Allen, F.H. Lommerse, J.P.M.; Stone, A.J.; Taylor, R.; Allen, F.H. J. Am. Chem. Soc.,J. Am. Chem. Soc.,1996, 118, 3108-31161996, 118, 3108-3116 [7]

[7] Wang, W.; Hobza, P.; Wang, W.; Hobza, P.; J. Phys. Chem.AJ. Phys. Chem.A2008, 2008, 112112, 4114-4119., 4114-4119. [8]

[8] Zou, J.W. ; Jiang, Y.J.; Guo, M.; Hu, G. X.; Zhang, B.; Liu, H. C.; Yu, Q. S. Zou, J.W. ; Jiang, Y.J.; Guo, M.; Hu, G. X.; Zhang, B.; Liu, H. C.; Yu, Q. S. Chem. Eur. J. Chem. Eur. J. 2005, 112005, 11, 740-, 740-751.

751.

[9]

[9] Wang, W. Z.; Wong, N. B.; Zheng, W. X.; Tian, A. M. Wang, W. Z.; Wong, N. B.; Zheng, W. X.; Tian, A. M. J. Phys. Chem. J. Phys. Chem. A, 2004, 108A, 2004, 108, 1799-1805., 1799-1805. [10]Desiraju G.R. & Parthasarathy R.

[10]Desiraju G.R. & Parthasarathy R. J. Am. Chem. SocJ. Am. Chem. Soc. (1989), 111, 8725-8726. (1989), 111, 8725-8726

The electron density donation from rich to poor sites is probably the most general way intermolecular interactions can take place. In

our case we focus on halogen atoms Cl, Br and I that give rise to the so called “

our case we focus on halogen atoms Cl, Br and I that give rise to the so called “halogen bondinghalogen bonding” (XB). XB is a strong, specific and ” (XB). XB is a strong, specific and directional interaction R-X

directional interaction R-X

∙∙∙

Y-Z that brings to well-defined supramolecular synthons where the halogens behave as Lewis acids or Y-Z that brings to well-defined supramolecular synthons where the halogens behave as Lewis acids or bases.

bases.

Figure 2: The molecular electrostatic potential (in hartree) mappen on ED

isosurfaces in the four trifluorohalomethanes.

It has been demonstrated

It has been demonstrated[1][1] that that halogenshalogens covalently bonded to an atom (for example C) covalently bonded to an atom (for example C) have a region of positive electrostatic potential have a region of positive electrostatic potential

centered on the C-X axis

centered on the C-X axis (the so called (the so called σσ holehole) ) and is surrounded by a belt of negative electrostatic potentialand is surrounded by a belt of negative electrostatic potential. .

Until now in literature synthons between two or three halogen

atoms are reported (Fig. 3 and 4). Here the hypotized synthons with

4 or 6 XB’s are reported for iodine and bromine atoms (being 5

forbidden for symmetry). Researches in Cambridge Structural

Database (CSD) have lead to the following results:

2) synthons with six XB’s have all CHAIR geometries, and have OPEN and FOLDED structures: in the more open chairs TYPE

2) synthons with six XB’s have all CHAIR geometries, and have OPEN and FOLDED structures: in the more open chairs TYPE I I

and

and IIII XB’s are present XB’s are present

[C]

while the more folded chair presents only TYPE while the more folded chair presents only TYPE IIII bonds bonds [D] _[D](Fig.6).(Fig.6).

If the computed electrostatic potential is reported on CF

If the computed electrostatic potential is reported on CF₃₃X molecules it is clear the existence of the X molecules it is clear the existence of the positive (red) and negative (blue) regions around the halogen atoms and the efficiency of the σ hole

positive (red) and negative (blue) regions around the halogen atoms and the efficiency of the σ hole

in the Cl<Br<I sequence.

in the Cl<Br<I sequence. Only few cases of F ad XB acceptor have been reported as a consequence Only few cases of F ad XB acceptor have been reported as a consequence of the size of electropositive area formed on the covalently bonded halogen which increases reducing

of the size of electropositive area formed on the covalently bonded halogen which increases reducing

the electronegativity of X.

The X

∙∙∙

X interaction is better studied with crystallography X interaction is better studied with crystallography and usually XB is monitored in terms of shortness of the

and usually XB is monitored in terms of shortness of the

contacts between halogen atoms and the nucleophile (in the

present case an halogen)

present case an halogen) a_and their angle approach . However, nd their angle approach . However, because the energy of XB spans over a very wide range (5 to

because the energy of XB spans over a very wide range (5 to

180 kJ/mol) from weak Cl∙∙∙Cl interactions in chlorocarbons

to the very strong I

to the very strong I--∙∙∙I_∙∙∙I 2

2 ones in I ones in I3-3- complexes complexes[2][2] there are there are

contradictive data about the nature of these interatomic

interaction. Some works show its primarily electrostatic

character,

character,[3],[3],[4][4],[5],[5] because the second-order contributions, such _{because the second-order contributions, such}

as polarization, dispersion and charge transfer, have been

demonstrated to be small

demonstrated to be small[6][6]._.Other studies_{Other studies}[7],[8],[9][7],[8],[9] highlighted _highlighted

that the electron density transfer from the lone pair of the

Lewis base to the

Lewis base to the σσ*C-Xantibonding orbital or to outer *C-Xantibonding orbital or to outer portions of the halogenated molecule can be in some cases

portions of the halogenated molecule can be in some cases

competitive with the electrostatic contribution.

Desiraju and Parthasarathy

Desiraju and Parthasarathy[10][10] used statistical analysis and classified X…X contacts into_{used statistical analysis and classified X…X contacts into} two major categories:_{two major categories:} TYPE _TYPEI_I (₍θ_θ

1

1 ≅≅ θθ22) and TYPE ) and TYPE II

II ( (θθ₁₁ ≈180°, ≈180°, θθ₂₂≈90°) ≈90°) as shown in fig. 3.as shown in fig. 3. Type I contact is considered to be van der Waals in nature because the nearly symmetrical Type I contact is considered to be van der Waals in nature because the nearly symmetrical approach of halogens is incompatible with the electrophile-nucleophile character of a true halogen bond type

approach of halogens is incompatible with the electrophile-nucleophile character of a true halogen bond type IIII..

A

B

C

D

1) Synthons with 4 units (25 for Br and 11 for I) have planar geometry

[A]

or are deformed towards tetrahedron or are deformed towards tetrahedron

[B]

(Fig.5)

. . Average distances for Br

Average distances for Br••••••BrBr in planar and folded structures are between in planar and folded structures are between 3.476 3.476  3.669 Å 3.669 Å distances. distances. In all planar cases bonds In all planar cases bonds

are of TYPE

are of TYPE IIII. . In folded cases there are both TYPE In folded cases there are both TYPE I I and and II II bonds. bonds.

Conclusions:

The halogen bond continues to draw the attention on crystal engineering because of the scope it offers for design and

application (Fig. 7). Non linear optics, optoelectronic transducers, ferro-, piezo- and pyro-electric materials are required for

applications in chemistry, physics, material sciences and for important technological and industrial applications. Materials

used for these purposes require polar molecules in polar crystals for necessary chemical and physical properties.

The XB bonding are extremely important in crystal engineering to create sites beyond classic ones behaving as nucleophiles or

electrophiles towards acids or basis. For example CHI

electrophiles towards acids or basis. For example CHI₃₃is able to bond three bases creating a non centrosymmetric structureis able to bond three bases creating a non centrosymmetric structure. . In I

In I₄₄ planar there are only TYPE planar there are only TYPE IIII bonds, while in deformed structures B there are TYPE bonds, while in deformed structures B there are TYPE IIII bonds with only one bonds with only one exception. In synthon s with 6 XB’s distances are longer than those with 4 XB’s especially for

exception. In synthon s with 6 XB’s distances are longer than those with 4 XB’s especially for iodine iodine ((3.769 3.769  3.901_3.901 ÅÅ)) while for

while for bromine bromine areare about about 3.510 Å 3.510 Å

Fig.3: Type I and II bonds

Fig. 4 : Geometry of three XB

bonds

Fig. 7: elastic nature of Br

∙∙∙

Br TYPE Br TYPE IIII bond bond

The positive parts can interact with negative parts of other molecules and thus creates the halogen

bonding. The computed data are fully consistent with experimental observation that potency

increases in the order Cl<Br<I with fluorine being inactive (fig.2).

Fig.5: synthons with four units. A is planar , B is

folded

Fig.1: halogen bond

Fig.6: synthons with six units. A is planar , B is

folded