Structural geometries of halogen
Structural geometries of halogen
∙∙∙
∙∙∙
halogen synthons
halogen synthons
G. Gervasio
G. Gervasio
11,
,
E. Bonometti
E. Bonometti
1 1University of Turin, Department of Chemistry, Via P. Giuria 7 – 10125 TO
University of Turin, Department of Chemistry, Via P. Giuria 7 – 10125 TO
References:
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.
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[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
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
Until now in literature synthons between two or three halogen
atoms are reported (Fig. 3 and 4). Here the hypotized synthons with
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
4 or 6 XB’s are reported for iodine and bromine atoms (being 5
forbidden for symmetry). Researches in Cambridge Structural
forbidden for symmetry). Researches in Cambridge Structural
Database (CSD) have lead to the following results:
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]
[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 electronegativity of X.
The 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 theand usually XB is monitored in terms of shortness of the
contacts between halogen atoms and the nucleophile (in the
contacts between halogen atoms and the nucleophile (in the
present case an halogen)
present case an halogen) aand 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
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
contradictive data about the nature of these interatomic
interaction. Some works show its primarily electrostatic
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
as polarization, dispersion and charge transfer, have been
demonstrated to be small
demonstrated to be small[6][6]..Other studiesOther studies[7],[8],[9][7],[8],[9] highlighted highlighted
that the electron density transfer from the lone pair of the
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.
competitive with the electrostatic contribution.
Desiraju and Parthasarathy
Desiraju and Parthasarathy[10][10] used statistical analysis and classified X…X contacts intoused statistical analysis and classified X…X contacts into two major categories:two major categories: TYPE TYPE II ( (θθ
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
A
B
B
C
C
D
D
1) Synthons with 4 units (25 for Br and 11 for I) have planar geometry
1) Synthons with 4 units (25 for Br and 11 for I) have planar geometry
[A]
[A]
or are deformed towards tetrahedron or are deformed towards tetrahedron[B]
[B]
(Fig.5)
(Fig.5)
. . Average distances for BrAverage 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:
Conclusions:
The halogen bond continues to draw the attention on crystal engineering because of the scope it offers for design and
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
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
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.
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
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 CHI3 3 is 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.3: Type I and II bonds
Fig. 4 : Geometry of three XB
Fig. 4 : Geometry of three XB
bonds
bonds
Fig. 7: elastic nature of Br
Fig. 7: elastic nature of Br
∙∙∙
∙∙∙
Br TYPE Br TYPE IIII bond bondThe positive parts can interact with negative parts of other molecules and thus creates the halogen
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
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).
increases in the order Cl<Br<I with fluorine being inactive (fig.2).
Fig.5: synthons with four units. A is planar , B is
Fig.5: synthons with four units. A is planar , B is
folded
folded
Fig.1: halogen bond
Fig.1: halogen bond
Fig.6: synthons with six units. A is planar , B is
Fig.6: synthons with six units. A is planar , B is
folded