Rep:Mod:chocolatefudge9

Contained within these wiki pages is the report by Martin Champion (mjc07) for the Third Year Inorganic Computational Project, Department of Chemistry, Imperial College London (March 2010).

Computational modelling of Inorganic systems

The first part of this project looks how using molecular mechanics approaches (bond lengths and angles) can be used to reasonably approximate real systems and thus how reactivity properties of a molecule(reaction) can be predicted by comparing different geometries of molecules and there isomers.

Modelling and Properties of BH₃ and BCl₃

BH₃

Fig 1: Optimised BH₃structure (trigonal planar)

Table 1: Calculation Parameters and Properties of BH₃

Calculation Type	opt
Method	DFT/B3LYP
Basis set	3-21G
Calculation time	19.0 s
Energy (Hartree)	-26.46
RMS Gradient Norm (Hartree)	0.0002067
B-H Bond length (A)	1.19
H-B-H Bond angle	120.0

Initial investigations began around optimising the structure of BH₃. In Gauss View 5 a trigonal planar Boron unit was drawn and the Hydrogens added automatically. The B-H bond lengths were set at 1.5 A as instructed to. Next a Gausian optimisation calculation was set up using Density functional theory (DFT) with the B3LYP method and

NBO analysis: Charge computed for B: 0.332 and H: -0.111

Table 2: Computed Vibrations for BH₃

No	Vibration	Frequency	Intensity (IR)	Symmetry in D3h
1	umbrella motion: all H atoms move up and down in z axis together, B atom moves in opposite direction	1144	92.9	A2"
2	scissoring of two H atoms in plane, remaining B-H moves opposite direction	1204	12.3	E'
3	in plane rocking: one H atom rocks closer to one H away from the other, remaining to H rock opposite directions to each other (one towards the original rocking H) but the H-B-H bond angle does not change. B moves into the space created by rocking H	1204	12.3	E'
4	completely symmetric in plane B-H bond stretching	2598	0.00	A1'
5	in plane, one H remains stationary whilst the other two move in and out on their B-H bond axis alternately, B atom moves towards the H atom which is coming in	2737	103.7	E'
6	in plane, two H atoms move out in concert (on B-H axis) whilst remaining H moves towards B, B atom also move towards this atom	2737	103.7	E'

Fig 2: Computed IR spectrum of BH₃

It can be seen from that computed IR spectrum that only three vibrations are shown yet 6 different vibrations have been calculated and displayed in table above. One reason is because there are two sets of Vibrations with E' symmetry thus there two sets of degenerate vibrations. Because of this they will have the same wavelength and thus coincide on the spectrum, so only two peaks are seen instead of four.

The final vibration that is not seen is completely symmetric A₁' at 2598 cm^-1. It is completely symmetric stretch of all three B-H bonds simultaneously which means there is no change in dipole moment. Stretches or vibrations which exhibit no change in dipole moment are not IR active so won't be displayed in an IR spectrum (IR selection rules). This is also why it is computed to have 0 intensity.

MO

MO calculations of BH₃ checkpoint file for mjc07: https://www.ch.imperial.ac.uk/wiki/images/3/3b/Mjc07_bh3_pop.chk

BCl₃

Fig 3: Optimised BCl₃ structure (trigonal planar)

Table 3: Calculation Parameters and Properties of BH₃

Calculation Type	opt
Method	DFT/B3LYP
Basis set	LANL2MB
Calculation time	8.0s
Energy (Hartree)	-69.44
RMS Gradient Norm (Hartree)	0.00005905
B-Cl Bond length (A)	1.87
Cl-B-Cl Bond angle	120.0

Modelling structure and properties of Five-Membered Arsenic-Sulfur-Nitrogen Heterocycles

The asymmetry of the ring means in effect there are two chiral isomers of each cycle 1-6 depending whether the R group points up or down (the inversion that is observed for Nitrogen doesn't occur at room temperature for heavier pnictogens elements). There is no immediately obvious reason as to which one might be preferred, or if one is produced exclusively (as is suggested for 5 and 6). The structures of 5 and 6 were given in by the authors in form of x-ray single crystal structures which defines which face the R group is in, but no such information (largely because they did crystallise) thus a guess was made for structures 1-4 as to which face the R group is in.