Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
The Effect of Halogen Atom Substitution on
Bond Angles in Halogenated Compounds
Word Count
1435 words excluding table, graphs, references and appendix.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Research Question
In this investigation I will look at whether the radius and number of halogen atoms bonded to a
central atom such as carbon will have a significant on the bond angle compared to that predicted by
VSEPR Theory. If the effect is significant I try to see if there is a relationship between halogen atom
identity and the bond angles around tetrahedral centres.
Introduction
We have learned in our IB Chemistry class that Valence Shell Electron Pair Repulsion (VSEPR) theory
can be used to predict molecular geometries and bond angles. According to Brown and Ford1 the key
principles of VSEPR theory are:
•
Electron pairs found in the outer energy level or valence shell of atoms repel each other and
thus position themselves as far apart as possible.
•
The repulsion applies to both bonding and non-bonding pairs of electrons.
•
Double and triple bonded electron pairs are orientated together and so behave in terms of
repulsion as a single unit known as a “negative charge centre”.
•
The total number of charge centres around the central atom determines the geometrical
arrangement of the electrons
•
Non-bonding (lone) pairs of electrons have a higher concentration of charge than a bonding
pair because they are not shared between two atoms and so they cause more repulsion than
bonding pairs. The repulsion decreases in the order:
lone pair-lone pair > lone pair-bond pair > bond pair-bond pair
So according to the VSEPR theory described by Brown and Ford the molecular geometry and bond
angles are only affected by the number of bonding pairs and lone pairs of electrons around the
central atom.
H
Cl
109.5º
109.5º
H
H
H
H
H
Cl
What doesn’t seem to have any effect according to VSEPR Theory is the identity of the atom or
functional group attached to the central atom. So for example methane, CH4 and dichloromethane,
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
CH2Cl2, will have the same tetrahedral geometry and 109.5º bond angles since they both have four
bonding pairs and no non-bonding pairs of electrons around the central carbon.
When looking at some three dimension space filling diagrams like that below for CH2I2 from
ChemSketch I saw that the large iodine atoms overlapped. I would expect that the greater number
of shells of electrons and the large atomic radius would cause the iodine atoms to repel each other
more than the iodines would repel the hydrogen atoms. So I expect the iodine-carbon-iodine bond
angle to be greater than the symmetric tetrahedral bond angle of 109.5º. The other iodine-carbon hydrogen and hydrogen-carbon - hydrogen bond angles would get reduced. This effect will be
greater as the halogen is greater in atomic radius and has more repelling electrons. The smallest
effect will be for fluorine compounds and the biggest would be for iodine compounds.
In this investigation I will look at the effect of halogen-halogen repulsion on the bond angles in
halogenated methane compounds.
Methodology
The bond angles for the tetrahedral centred molecules were determined using the Chemsketch
software downloaded from http://www.acdlabs.com.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
The Help Facility on the ChemSketch Software describes under 3D Optimisation Algorithm how it
calculates the bond angles using a 3D Optimisation algorithm based on modified molecular
mechanics. It does state that the “3D-optimizer is NOT a full-scale molecular mechanics engine. Its
design aims to reliably reproduce reasonable conformations from (possibly very unreasonable) 2D
drawings, rather than to precisely optimize 3D structures.” The full text of the Help feature is
reproduced in Appendix 1.
Once the ACD/3D Viewer ChemSketch software was loaded the following procedure was followed
for each compound.
1. The ChemSketch page opened and the target molecule drawn in.
2. Click on the Tools menu and select 3D-structure Optimisation
3. Click on 3D Viewer icon on top tool bar to enter 3d-Viewer
4. Select 3D-optimization
5. Rotate 3D image into orientation as shown below
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
6. Select Bond Angle icon on Tool bar
7. Click on image in order of substituent atom1 – central atom – substituent atom. Record
bond angle stated in dialogue box
8. Repeat for all six bond angles 1-C-2, 1-C-3, 1-C-4, 2-C-3, 2-C-4, 3-C-4
9. Repeat steps 4- to 8 to reoptimise and record all bond angles.
10. If the first two optimisations do not agree closely repeat steps 4 to 8 again.
11. Some molecules were redrawn to check that calculated angles were standard.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Raw Data
Bond Angles determined through Chemsketch software. The raw data is given by ChemSketch to
three decimal places which I repeat in the tables below.
Between optimisation and redrawing trials the maximum difference was about 0.040º so I have
estimated the uncertainty to approximately ±0.020º
Database values obtained from Computational Chemistry Comparison and Benchmark DataBase at
the National Institute of Standards and Technology website at http://cccbdb.nist.gov/
CH4
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-3
1-C-4
2-C-3
2-C-4
3-C-4
Average Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-2
Bond Angle
(±0.020º )
Substituent 4
Substituent 3
Substituent 2
Substituent 1
Formula
3D Optimisation
Table 1: Bond Angles in Halogenated Methane Compounds of General Formula CH4 and CX4
1st
H
H
H
H
109.454
109.454
109.473
109.478
109.450
109.450
109.460
2nd
H
H
H
H
109.467
109.467
109.473
109.477
109.464
109.481
109.472
Redrawn
1st
H
H
H
H
109.489
109.466
109.461
109.487
109.459
109.465
109.471
CF4
1st
F
F
F
F
109.454
109.480
109.482
109.467
109.470
109.464
109.470
2nd
F
F
F
F
109.459
109.485
109.485
109.468
109.433
109.497
109.471
1st
Cl
Cl
Cl
Cl
109.471
109.472
109.469
109.474
109.469
109.473
109.471
2nd
Cl
Cl
Cl
Cl
109.469
109.469
109.473
109.474
109.465
109.477
109.471
1st
Br
Br
Br
Br
109.488
109.466
109.448
109.469
109.482
109.475
109.471
2nd
Br
Br
Br
Br
109.484
109.452
109.478
109.466
109.474
109.469
109.471
1st
2nd
I
I
I
I
I
I
I
I
109.473
109.476
109.474
109.470
109.463
109.472
109.471
109.462
109.419
109.448
109.465
109.479
109.483
109.459
CCl4
CBr4
CI4
Qualitative observations: All six bond angles are equivalent in each CX4 compound and all bond angls
are very close to the symmetric tetrahedral angle of 109.47º.
Table 2: Bond Angles in Halogenated Methane Compounds of General Formula CH3X
CH3F
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-4
2-C-3
2-C-4
3-C-4
Average Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-3
Bond Angle
(±0.020º )
Substituent 4
Substituent 3
Substituent 2
1-C-2
F
H
H
H
109.991
109.002
109.989
109.437
108.969
109.440
109.471
2nd F
H
H
H
109.986
109.008
109.998
109.444
108.961
109.438
109.473
1st
Cl
H
H
H
110.640
110.624
108.481
108.437
109.319
109.319
109.470
2nd Cl
H
H
H
110.651
110.621
108.477
108.433
109.325
109.334
109.474
Redrawn
1st
Cl
H
H
H
108.476
110.613
110.643
109.350
109.292
108.447
109.470
CH3Br
1st
Br
H
H
H
110.854
110.847
108.300
108.295
109.209
109.252
109.460
2nd Br
H
H
H
110.862
110.799
108.309
108.323
109.256
109.268
109.470
3rd
Br
H
H
H
110.878
110.796
108.301
108.310
109.261
109.271
109.470
Redrawn
1st
Br
H
H
H
110.863
108.311
110.816
109.263
108.333
109.243
109.472
CH3I
1st
I
H
H
H
111.073
111.038
108.139
108.193
109.188
109.179
109.468
2nd I
H
H
H
111.059
111.061
108.121
108.194
109.193
109.193
109.470
1st
H
H
H
111.037
111.076
108.146
108.195
109.161
109.195
109.468
CH3Cl
Redrawn
1st
Substituent 1
3D Optimisation
Formula
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
I
Qualitative observations:
When redrawing structures sometimes the different equivalent Hal-C-H or H-C-H bond angles got
inverted spatially. This makes no difference to the theory. I have left the data in the order that I
recorded it from ChemSketch.
The three Hal-C-H bond angles split into two similar angles and one smaller angle for each halogen
rather than three equal angles. The same is true for the H-C-H bond angles.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
CH2Cl2
Redrawn
Database
CH2I2
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Average Bond
Angle (±0.020º )
Bond Angle
(±0.020º )
1-C-3
1-C-4
2-C-3
2-C-4
3-C-4
110.510
108.968
109.450
108.958
109.461
109.476
109.471
110.501
108.985
109.479
108.930
109.474
109.477
109.474
Bond Angle
(±0.020º )
Substituent 4
Substituent 3
Substituent 2
1-C-2
1st
2nd
F
F
F
F
H
H
H
H
1st
2nd
Cl
Cl
Cl
Cl
Cl
Cl
H
H
H
H
H
H
1st
2nd
3rd
Ist
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
H
H
H
H
H
H
H
H
H
H
112.424
109.570
107.957
109.574
107.965
109.280
109.462
112.413
109.567
107.949
109.592
107.973
109.281
109.463
112.421
109.578
107.958
109.581
107.963
109.272
109.462
112.437
109.581
107.948
109.549
107.971
109.289
109.463
112.9
108.3
108.3
108.3
108.3
110.9
109.500
I
I
I
I
H
H
H
H
112.964
107.634
109.670
107.618
109.661
109.197
109.457
112.913
107.638
109.660
107.662
109.684
109.189
109.458
Database
CH2Br2
Bond Angle
(±0.020º )
CH2F2
Substituent 1
Formula
3D Optimisation
Table 3: Bond Angles in Halogenated Methane Compounds of General Formula CH2X2
1st
2nd
111.937 108.223 109.523 108.228 109.518 109.364 109.466
111.917 108.243 109.492 108.225 109.548 109.369 109.466
111.783 108.27 108.27 108.27 108.27
112 109.477
Qualitative observations:
The four Hal-C-H bond angles split into two pairs of similar angles rather than four equal angles. The
same is true for the H-C-H bond angles.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
CHF3
CHCl3
CHBr3
Redraw
Database
CHI3
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-3
1-C-4
2-C-3
2-C-4
3-C-4
Average Bond Angle
(±0.020º )
Bond Angle
(±0.020º )
1-C-2
Bond Angle
(±0.020º )
Substituent 4
Substituent 3
Substituent 2
Substituent 1
3D Optimisation
Formula
Table 4: Bond Angles in Halogenated Methane Compounds of General Formula CHX3
1st F
2nd F
F
F
F
F
H
H
110.038
109.428
108.987
109.385
108.983
110.007
109.471
110.028
109.419
108.981
109.396
108.993
110.012
109.472
1st Cl
2nd Cl
Cl
Cl
Cl
Cl
H
H
109.113
110.781
108.511
109.103
110.805
108.527
109.473
109.113
110.781
108.520
109.099
110.815
108.512
109.473
1st Br
2nd Br
1st Br
Br
Br
Br
Br
Br
Br
H
H
H
108.929
108.941
111.107
111.026
108.435
108.411
109.475
108.945
108.948
111.129
111.001
108.425
108.394
109.474
108.944
110.996
108.451
108.937
111.110
108.413
109.475
111.7
1st I
2nd I
I
I
I
I
H
H
107.2
108.715
108.719
111.468
111.240
108.370
108.349
109.477
108.714
108.712
111.471
111.243
108.377
108.342
109.477
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Data Processing
Table 5: Average, Maximum and Minimum Bond H-C-H Angles Determined by ChemSketch and
Comparative data from CCBDB DataBase
Deviation of
Average from
Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
maximum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
minimum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
0.02
-0.02
CCCBDB
Database
Average
Bond
Angle
(±0.01º)
109.47
H-C-H
Average
Bond
Angle
Molecule (±0.02º)
CH4
109.47
Maximum
Angle
(±0.02º)
109.49
Minimum
Angle
(±0.02º)
109.45
0.00
H-C-H
CH3F
109.28
109.44
108.96
-0.19
-0.03
-0.51
H-C-H
CH3Cl
109.03
109.35
108.43
-0.44
-0.12
-1.04
H-C-H
CH3Br
108.94
109.27
108.30
-0.53
-0.20
-1.18
H-C-H
CH3I
108.86
109.20
108.19
-0.61
-0.28
-1.28
H-C-H
CH2F2
109.48
109.48
109.48
0.01
0.01
0.01
H-C-H
CH2Cl2
109.37
109.37
109.36
-0.10
-0.10
-0.11
112.00
H-C-H
CH2Br2
109.28
109.27
109.29
-0.19
-0.20
-0.18
110.90
H-C-H
CH2I2
109.19
109.19
109.20
-0.28
-0.28
-0.27
Bond
111.16
Table 6: Average, Maximum and Minimum Bond Hal-C-H Angles Determined by ChemSketch and
Comparitive data from CCBDB DataBase
Deviation of
Average from
Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
maximum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
minimum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
CCCBDB
Database
Average
Bond
Angle
(±0.01º)
Hal-C-H
Average
Bond
Angle
Molecule (±0.02º)
109.66
CH3F
Hal-C-H
CH3Cl
109.91
110.65
108.48
0.44
1.18
-0.99
Hal-C-H
CH3Br
110.00
110.88
108.30
0.53
1.41
-1.17
Hal-C-H
CH3I
110.08
111.07
108.12
0.61
1.60
-1.35
Hal-C-H
CH2F2
109.21
109.48
108.93
-0.26
0.01
-0.54
Hal-C-H
CH2Cl2
108.88
109.55
108.22
-0.59
0.08
-1.25
108.27
Hal-C-H
CH2Br2
108.77
109.59
107.95
-0.70
0.12
-1.52
108.30
Hal-C-H
CH2I2
108.65
109.68
107.62
-0.82
0.21
-1.85
Hal-C-H
CHF3
109.33
110.01
109.98
-0.14
0.54
0.51
110.10
Hal-C-H
CHCl3
109.28
110.82
108.51
-0.19
1.35
-0.96
107.98
Hal-C-H
CHBr3
109.32
111.13
108.39
-0.15
1.66
-1.08
107.20
Hal-C-H
CHI3
109.40
111.47
108.34
-0.07
2.00
-1.13
Bond
Maximum
Angle
(±0.02º)
110.00
Minimum
Angle
(±0.02º)
109.00
0.19
0.53
-0.47
107.72
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Table 7: Average, Maximum and Minimum Bond H-C-H Angles Determined by ChemSketch and
Comparative data from CCBDB DataBase
CCCBDB
Database
Average
Bond
Angle
(±0.01º)
Bond
Average
Bond
Maximum Minimum
Angle
Angle
Angle
Molecule (±0.02º) (±0.02º)
(±0.02º)
Deviation of
Average from
Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
maximum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Deviation of
minimum
from Standard
Symmetric
Tetrahedral
Bond Angle
(±0.02º)
Hal-C-Hal
CH2F2
110.51
110.51
110.50
1.04
1.04
1.03
Hal-C-Hal
CH2Cl2
111.93
111.94
111.92
2.46
2.47
2.45
Hal-C-Hal
CH2Br2
112.24
112.44
112.41
2.77
2.97
2.94
Hal-C-Hal
CH2I2
112.94
112.96
112.91
3.47
3.49
3.44
Hal-C-Hal
CHF3
109.62
110.04
109.39
0.15
0.57
-0.08
108.80
Hal-C-Hal
CHCl3
109.67
110.78
109.10
0.20
1.31
-0.37
110.92
Hal-C-Hal
CHBr3
109.63
111.03
108.93
0.16
1.56
-0.54
Hal-C-Hal
CHI3
109.56
111.24
108.71
0.09
1.77
-0.76
Hal-C-Hal
CF4
109.47
109.50
109.43
0.00
0.03
-0.04
109.47
Hal-C-Hal
CCl4
109.47
109.48
109.47
0.00
0.01
0.00
109.47
Hal-C-Hal
CBr4
109.47
109.49
109.45
0.00
0.02
-0.02
109.47
Hal-C-Hal
CI4
109.47
109.48
109.42
0.00
0.01
-0.05
111.78
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Data Analysis and Interpretation
From looking at the data we can draw some clear conclusions although other trends are less easy to
identify.
1. Firstly the bond angles in CH4 CF4 CCl4 CBr4 CI4 were the expected symmetric tetrahedral
angle of 109.47.
2. The single Hal-C-Hal bond angle in the dihalogenated methanes showed the expected
increase in bond angle. Below I have tabulated and plotted the Hal-C-Hal bond angles
against atomic radius for H, F, Cl, Br and I.
Table 8 Hal-C-Hal Bond Angle Deviation
Hal in Hal-C-Hal
H
F
Cl
Br
I
Atomic radius (×10E-12m) *
30
64
99
114
Deviation from Symmetric Bond Angle (±0.02º)
0
1.04
2.46
2.77
*Data from Table 8 of IBO Chemistry Data Booklet for First Examinations 2009
133
3.47
Graph 1 Hal-C-Hal Bond Angle Deviation versus Atomic Radius of the Halogen
Deviation from Symmetric Bond Angle (±0.02º)
4
3.5
3
2.5
2
1.5
1
0.5
0
0
20
40
60
80
100
120
140
Atomic radius (×10E-12m)
3. Other trends are obscured when looking at the average deviation from symmetric angle
because some angles have increased but others have reduced. This is seen in the Hal-C-Hal
bond angles in the CHHal3 molecules in Table 9 below.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Table 9. Graph 1 Hal-C-H Bond Angle Deviation in CHHal3 versus Atomic Radius of the Halogen
Deviation from Symmetric Bond Angle (±0.02º)
Hal in Hal-C-Hal
Atomic radius (×10E-12m)
Maximum Deviation from Symmetric
Bond Angle (±0.02º)
Minimum Deviation from Symmetric Bond
Angle (±0.02º)
Graph 2
H
30
F
64
Cl
99
Br
114
I
133
0
0.57
1.31
1.56
1.77
0
-0.08
-0.37
-0.54
-0.76
2
1.5
1
Maximum Deviation
from Symmetric Bond
Angle (±0.02º)
0.5
0
0
50
100
150
Minimum Deviation
from Symmetric Bond
Angle (±0.02º)
-0.5
-1
Atomic radius (×10E-12m)
Some angles increase significantly and others decrease. But it is clear from Graph 2 as the Atomic
radius of the Halogen increases then the deviation from the symmetric bond angle increases in
magnitude.
Conclusion
By looking at the data tables and through graphical analysis it is clear that the increasing atomic
radius of the Halogen can lead to increasing distortion of the bond angles and a deviation away from
the symmetric tetrahedral bond angle of 109.47º. The maximum distortion was 3.47º in the case of
the I-C-I bond angle in CH2I2. This is a similar amount of bond angle distortion to that caused by a
lone pair of electrons according to VSEPR theory but is not mentioned in the textbook.
Evaluation
The precision in the data generated by Chemsketch was very good and the uncertainty between
trials was no higher than ±0.02º. However the ChemSketch Help feature does stress that it is not its
purpose to precisely optimize 3D structures so it is possible that the bond angle values obtained
were not accurate at all.
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
Comparison with available literature values (see tables 5,6,7) obtained from the CCCBDB database at
http://cccbdb.nist.gov/ leads to a mixed view as to the accuracy of the Chemsketch data. In cases
where there was just one bond angle to consider of a given type then the agreement was good.
However where the ChemSketch had come up with two very different bond angles for a given type
then the agreement with the averaged value in CCCBDB database was poor.
Overall the conclusions that
(i)
atomic radius does affect bond angles around a tetrahedral centre
and
(ii)
increasing atomic radius of the halogen increases the amount of distortion of the bond
angle away from the symmetric 109.47º
seem well justified but some of my other findings relating to smaller changes in the other bond
angles and the splitting of equivalent bond angles into two values are not very certain.
Suggestions for further work:
Further comparison between Chemsketch and database bond angles in other compounds could be
studied. If Chemsketch appears to be accurate it could be used to predict shape and size effects of
other atoms or functional groups around a central atom. Also it could be used to look at these
substituent effects on other geometries around the central atom such as Phosphorus trigonal
bipyramid or Sulphur octahedral centres.
Sources
1. C. Brown and M. Ford, Higher Level Chemistry, pp 120-121, Pearson Baccalaureate, 2009
2. ChemSketch Software, http://www.acdlabs.com Last accessed 29-2-2012
3. Experimental Descriptions Of Bond Angles With Experimental Data. http://cccbdb.nist.gov/
Last accessed 29-2-2012
4. IBO Chemistry Data Booklet for First Examinations 2009
Appendix 1
3D Optimisation Algorithm Help Facility on the ChemSketch Software
“The 3D optimization algorithm rapidly transforms the planar (2D) structure from
ChemSketch into a realistic 3-dimensional structure. It is based on modified molecular
mechanics which take into account bond stretching, angle bending, internal rotation and
Van der Waals non-bonded interactions. Modifications include minor simplification of
potential functions and enforcement of the minimization scheme by additional heuristic
algorithms for dealing with "bad" starting conformations.
The 3D optimization algorithm is a proprietary version of molecular mechanics with the
force field initially based on CHARMM parametrization (refer to B.R. Brooks, R.E. Bruccoleri,
Chemistry: A Focus on Internal Assessment - Investigation Report B (ii)
B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus. CHARMM: A program for
macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187217 (1983)). The modifications involve some simplification and were intended to increase
the stability and speed of computation. Note that 3D-optimizer is NOT a full-scale molecular
mechanics engine. Its design aims to reliably reproduce reasonable conformations from
(possibly very unreasonable) 2D drawings, rather than to precisely optimize 3D structures.
Occasionally the 3D optimization produces a molecular conformation different from what
you have expected. It is the very essence of the conformational analysis that structures
typically have many possible conformations. The optimizer finds only one, and it is not
necessarily the one you have expected. For example, you probably expect a cyclohexane
fragment to be a chair, but the optimizer may generate a twist-boat, which is also one of its
suitable conformations (indeed, in many structures this fragment exists in a twisted form).
To obtain another conformation, move some atoms in the resultant 3D structure to make
the initial structure closer to the final conformation, and then optimize the structure once
again.”