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Johnathan Harvell

Dr. Steve Strauss


CHEM 462-L01
10 March 2016
X-Ray Assignment
1. Copper-Mercury Structure
What elements are present in the structure?
The elements that are present in the Copper-Mercury complex are the following: copper
(Cu), mercury (Hg), oxygen (O), carbon (C), nitrogen (N), and hydrogen (H).
Is the structure composed of molecules or is it an extended ionic structure?
Based on the bond lengths found at the metal centers of Cu and Hg in Table 1 of
Appendix A. It can be said that the copper-mercury structure is an extended ionic structure.
Since the bond lengths are on average of 2.5 angstroms, while most covalent bonds of molecules
have average bond lengths of 1.5 angstroms, this inference can be made with confidence and the
fact that the formal charges and oxidation states of the metal atom centers allow of sufficient
interaction between the corresponding oxygen and nitrogen atoms. It is to be noted that the
ligands of both Hg and Cu do contain covalent bonding within the carbon rings, but do not
necessarily participate in the acting bonding site of the metal center.
If the latter, is it composed of atomic ions or molecular ions, or both?
Since Hg and Cu have valence shells found in the 4s, 6s, 3d, and 5d atomic orbital shells,
Hg and Cu would want to release electrons from the d-orbitals first, which would lead to no
overlap in atomic valence orbitals between oxygen and nitrogen atoms due to each only having
valence shells in the 2s and 2p orbitals; thus, at the metal centers, the interactions and bonding
should be between primarily atomic ions, however, it is necessary to consider the sp mixing
between C-O and C-N bonds in the complex. If sp mixing does occur at this particular bonds, it
can be said that molecular orbitals create by these bonds could also have play in the forming of
the structure at each metal center.
What do you think are the oxidation states of the metal ions in the structures, and how did
you come to those conclusions?
The most common oxidation states of copper are Cu1+ and Cu2+, while the most common
oxidation states of mercury are Hg4+, Hg2+, Hg+, and Hg2-. With the presence of resonance
among the Cu-O and Hg-O bonds in each part of the complex, it was considered of what
oxidation would allow for the most fluctuation in electron density. If Cu2+ is in the complex,
then, based on the reasonable resonance structure that would occur, it would be implied that Hg4+
would be present in the complex as well. With Cu2+ being isoelectronic to Ni, copper would have
an octet 3-d orbital, which makes it less likely to bond to oxygen or nitrogen without the
presence of sp mixing in the molecule, which could allow for some overlap between sp and d-
orbitals to allow for an weak, ionic bond to form. This could be a reason for the average 2.5 bond
lengths in Cu-O and Cu-N in Table 1, as well as the angles of the bonds themselves. The bonds
at the metal centers would want to optimize to allow for the best overlap and best bonding
opportunity, which seems to be mainly around a 90 degree angle in respect to surrounding atoms
of the metal center. Hg4+ would be reasonable in the fact that lanthanide contractions allow to it
keep a reasonable atomic size, but also allows valence electrons to be present in the 5d orbital
shell that may allow reasonable bonding to the molecular sp orbtials that could be found on all
three surrounding oxygens of the Hg metal complex.
I would not say that Cu+ and Hg2+ are the oxidation states of the metals in this complex
due to the face that Hg2+ has an octet d-orbital, which would allow for poor or no bonding to the
surround oxygen atom; just as well, copper would have a lower formal charge at the metal
center, which would lead to even poorer ionic interactions between Cu-O and Cu-N that would
lead to longer bond lengths that may not be considered stable in this complex.
What are the ligands bonded to the metal ions?

What are the idealized coordination geometries of the metal ions in the structures? Are
there distortions from idealized geometries, and if so can you identify reasons why this
might be the case?
For copper, there is a coordination number of four, therefore, based on the angles
between Cu-O and Cu-N bonds at the metal center in Table 1 of Appendix A, it can be inferred
that the copper sub complex has a square planar geometry that is slightly bent due to steric
hindrance of the carbon rings on two of the main ligands.
For mercury, there is a coordination number of three, therefore, based on bond angles
found in Table 1 in Appendix A of the Hg-O bonds, it can be inferred that the mercury sub-
complex is T-shaped in nature due to the resonance between each Hg-O bond on the complex
that allows for minimal bending due to the massive electron density among the -bonds in the
mercury sub-complex.
Are there interesting/unexpected structural features with respect to any of the atoms (metal
atoms or non-metal atoms)?
Due to potential hydrogen bonding between correlating oxygen atoms in Table 2 in
Appendix A, it is possible that the hydrogen bonding provides a driving force against the
potential steric hindrance that can be related to the carbon rings in the copper ligand, which
allows the molecule to hold more closely together; this could lead to the re-stabilization of some
of the ligand-metal bonds found in the complex that may have been affected by the steric
hindrance of the carbon ring, which would lead to the complex becoming more overall stable.
In Figure 4, it is shown that the isolated mercury lattice has parallel atom planes that are
intersected by a semi-perpendicular atom plane. I found this strange in the fact that it seems to go
against a normal lattice structure in the fact that lattices are orderly that reduces hindrance or
bond stress. As seen in Table 3 of Appendix A, it can be seen that these planes are approximately
10 angstroms away from each other, which implies that the copper sub-complex is the main filler
in-between the planes; however, on the mercury lattice planes themselves, it was found that each
mercury atom within their respective planes were approximately 3 angstroms from one another,
which can infer that there is some type of intermolecular interaction between Hg-Hg. Due to the
spread of electron density across Hg-O bonds on each separate metal center, it could be inferred
that some weak ionic interaction between Hg-Hg can occur based on the current resonance
structures of the Hg-O bonds at each metal center. This proximity of Hg-Hg within the lattice
could also lead to the solution of creating a more a stable structure at Hg centers of the complex
due to Hg-Hg interactions causing inhibition of resonance structures to occur on the Hg-O bonds.
Appendix A: Copper-Mercury Complex

Figure 1: Isolated Copper Ligand Sub-Complex


Figure 2: Isolated Mercury Ligand Sub-Complex

Figure 3: Copper-Mercury Complex Unit with Hypothesized O-H Bonding


Table 1: Bonding XRD Data of Copper and Mercury Complex Centers

Bonding Atom Bonding Atom Length of Bond Angle () Atom Respect Type of
#1 #2 Bond () to Bond Angle Bond
Cu O(1) 1.922 91.4 O(2) Ionic
Cu O(2) 1.937 93 O(1) Ionic
Cu N(1) 2.014 92.6 O(2) Ionic
Cu N(2) 1.995 80.4 O(1) Ionic
Hg O(6) 2.101 165.8 O(4) Ionic
Hg O(4) 2.104 93.7 O(3) Ionic
Hg O(3) 2.403 95.4 O(4) Ionic

Table 2: XRD Data of Hypothesized Hydrogen Bonding in Copper-Mercury Complex

Bonding Atom Bonding Atom Length of Bond Angle () Atom Respect


#1 #2 Bond () to Bond Angle
O(4) H(1) 3.020 122.1 C(24)
O(1) H(3) 2.542 131.4 C(13)
O(3) H(5) 2.413 83.3 C(11)
O(1) H(4) 2.407 82.9 C(13)
O(7) H(2) 2.856 156.9 C(26)
O(7) H(1) 3.448 115.6 C(26)
O(1) O(3) 2.403 95.4 O(4)

Figure 4: Isolated Mercury Atom Lattice Unit

*Note: Not all dashed lines in this diagram represent actual, physical bonds between each mercury atom.
Table 3: Data of Isolated Mercury Atom Lattice Planes
Atom #1 Atom #2 Distance () Distance Angle Atom
() Respected to
Angle
Hg(1R) Hg(1E) 13.183 49.4 Hg(1F)
Hg(1U) Hg(1E) 14.137 88.2 Hg(1F)
Hg(1G) Hg(1D) 13.183 67.0 Hg(1F)
Hg(1K) Hg(1D) 10.690 118.8 Hg(1F)
Hg(1J) Hg(1E) 10.690 76.4 Hg(1U)

2. BiS2 Structure
What elements are present in each structure?
Elements that are included in the structure are bismuth, and sulfur.
Is the structure composed of molecules or is it an extended ionic structure?
According to the bond lengths between bismuth and sulfur in both Tables 4-5 in
Appendix B, it appears that the bonds are main ionic based on the assumption that strong
covalent bonds occur at lengths of 1.5 angstroms or lower; however, the ionic interaction
between each BiS2 layer may be weaker than every BiS2 unit due to increased atomic
distance in comparison of the Bi-S bonds within each unit as seen in Table 4. The layers
appear to be offset to one another and of different shapes per layer as seen in Figure 6,
which implies that, when packed, the structure forms different geometries and offsets
itself to allow for the most efficient ionic bond to occur between the layers even it if it is
weak in magnitude.
If the former, are there relevant intermolecular interactions?
In between the layers, there appears to be an alternation pattern between potential
weak ionic Bi-S bonds as the structure extends due to increase atomic distance between
the bismuth and sulfur atoms in each layer as seen in Figure 6 in Appendix B Although
the distance between these alternating distance are not sufficient to create a potential
weak, ionic bond, there may still be some van der Waals forces occurring between them
allow for better stabilization of the solid structure. This can be further implied by the
isolated sulfur structure in Figure 8 in Appendix B, in which the sulfur lattice pattern is
seen to be quite different than the bismuth lattice patter found in Figure 7 in Appendix B.
Due to this difference in pattern, the alternate geometries of each layer of the lattice can
be formed, which allows for different distances between the bismuth and sulfur atoms
throughout the lattice and allowing inference of van der Waals forces being present.
If the latter, is it composed of atomic ions or molecular ions, or both?
With the bond lengths and angles found in Tables 4-5 in Appendix B, as stated
earlier, there appears to be weak ionic bond present within each unit, which implies that
the structure is made only of atomic ions, and not molecular ions due to no evidence of
covalent bonding throughout the structure.
What do you think are the oxidation states of the metal ions in the structures, and how did
you come to those conclusions?
Since the most common, stable oxidation states of bismuth are +5 and +3, the
sulfurs were the main determinant of what the oxidation states are of each atom. In Figure
6, it can be seen that bismuth atoms are bonding to either 2-3 sulfur atoms at a time
throughout the lattice, which implies that each bismuths oxidation state cannot be +5 due
to each sulfur atom having maximum oxidation of -2; therefore, each bismuth atom must
have an oxidation state of +3, while each sulfur atom alternates between -1 and -2
oxidation states. This alternation in oxidation state can also be attributed to the unit bond
lengths found in Table 4, which also implies different formal charges on the sulfur atoms
due to different bond lengths calculated; however, it is to be noted that the bond angle
between each sulfur atom in the BiS2 unit in Figure 5 is less than 90 degrees, which can
imply a weak attractive force between the two sulfur atoms in the units. Since one sulfur
atom has a -1 charge and the other sulfur atom has a -2 charge, it can be inferred that
there some type of ionic interaction between the two sulfur atoms since the -1 charged
sulfur may have partial positive charge in respect to the -2 charged sulfur atom. There
may be van der Waal forces between these atoms that allow for further stability in the
unit and structure as well.
What are the ligands bonded to the metal ions?
The only ligands bonded to bismuth are S- and S-2, alternating.
What are the idealized coordination geometries of the metal ions in the structures?
The idealized coordination geometries of the bismuth ions in this structure would
alternate between coordination numbers of 2 and 3 depending on the location within each
layer. If the bismuth ion has a coordination number of 2, then it can be predicted that the
unit will have a bent structure. If the bismuth ion has a coordination number of 3, it is to
be predicted that the unit will have a trigonal planar structure to it as seen in Figure 6.
Are there distortions from idealized geometries, and if so can you identify reasons why this
might be the case?
The only possible distortions that can be seen in regards to idealized geometries is
the fact that most of the Bi-S bonds throughout the structure have bond angles 90,
which can lead to some stress points throughout the structure that may allow some
destabilization. Since the structure appears to be offset between each layer, this possible
distortion may be the source of the offset to allow for better stabilization throughout the
structure by promoting better bond angles for potential ionic Bi-S bonds.
Are there interesting/unexpected structural features with respect to any of the atoms
(metal atoms or non-metal atoms)?
The alternating ring structures throughout each layer is the most unexpected due
to the observation that the developments of Bi-S rings do not seem to have a determined
pattern although the lattices of both bismuth and S seem to have distinct patterns of their
own in Figures 7 and 8; however, since the isolated sulfur lattice has a very obscure
pattern comparted to the bismuth isolated lattice, it can be inferred that the non-pattern
like nature could be attributed to what oxidation states the sulfur atoms are at along the
structure as well at what angles they are in correlation to bismuth atoms to form bonds.
The presence of Bi-S rings in the structure could be interpreted as correction point to
allow for the best ionic bonding to occur and to keep the structure stable throughout the
lattice.
Appendix B: BiS2 Complex

Figure 5: BiS2 Unit Isolated

Table 4: Bond Angle and Length XRD Data of BiS2 Isolated Unit
Bonding Bonding Bond Type of Angle of Atom
Atom #1 Atom #2 Length () Bond Bond () Respected
to Angle
Bi(1) S(1) 2.603 Ionic 77.6 Bi(1)
Bi(1) S(2) 2.912 Ionic
Figure 6: BiS2 Grown Lattice Sub Unit

Table 5: Bond Length and Angle Data of BiS2 Grown Lattice Sub Unit

Bonding Bonding Bond Length Type of Bond Angle of Atom


Atom #1 Atom #2 () Bond () Respected to
Angle
Bi(2) S(1A) 3.596 Weak ionic 90.2 Bi(1C)
Bi(1C) S(3EA) 3.345 Weak ionic 70.1 Bi(2)
Bi(2F) S(1E) 3.596 Weak ionic 90.4 Bi(1C)

Figure 7: Isolated Bi Atom Lattice


Table 6: Bond Length Data of Isolated Bismuth Atom Lattice
Bonding Atom #1 Bonding Atom #2 Bond Length ()
Bi(1C) Bi(1U) 5.286
Bi(1E) Bi(1W) 5.286
Bi(1G) Bi(1Y) 5.286
Bi(1A) Bi(1S) 5.286

Figure 8: Isolated Sulfur Lattice

Table 7: Bond Length and Angle Data of Isolated Sulfur Lattice


Bonding Atom Bonding Atom Bond Length Bond Angle () Atom
#1 #2 () Respected to
Angle
S(3E) S(1W) 3.252 118.4 S(3O)
S(2S) S(1W) 3.465 74.4 S(3O)
S(2S) S(3A) 3.751 102.6 S(3O)
S(3A) S(3T) 3.533 125.9 S(2S)
S(3T) S(2B) 5.238 78.3 S(3A)
S(3O) S(2B) 3.751 77.4 S(2S)
S(3A) S(2B) 5.694 64.3 S(3T)
S(3O) S(2S) 5.694 109.4 S(3T)
S(3O) S(3E) 3.533 64.3 S(2S)
3. Uranium-Aluminum Structure
What elements are present in each structure?
Elements that are present in the structure are uranium, carbon, aluminum, and hydrogen.
Is the structure composed of molecules or is it an extended ionic structure?
According to the values found in both Tables 8 and 9, it seems that the structure seems to
be more ionic in nature; however, due to the hybridization of the carbon atoms throughout the
structure, it can be inferred that the uranium and aluminum atoms form ionic-covalent bonds due
to the distribution of electron density upon the pentane rings on uranium and the methyl groups
on aluminum. With the assumption that electron density will be mainly unified at the corners of
the rings and methyl groups, a more ionic interaction occurs between carbon and each
uranium/aluminum atom, which may explain why aluminum can form five bonds and uranium
can form twelve.
If the former, are there relevant intermolecular interactions?
The intermolecular interactions that are most likely to occur are between the methyl
groups of each layer of the uranium-aluminum lattice due to both steric hindrance and possible
ionic attraction between carbons depending on the placement of the electron density/dipole
moment along each carbon at the time of the interaction. Due to aluminum atoms forming bonds
within themselves within the four membered Al-C ring in the aluminum sub-complex. The
aluminum atoms allow themselves to become arranged in an alternate arrow pattern as seen in
Figure 12, which in turn allows the uranium atoms to be separated at a distance that
intermolecular forces should not occur within each layer of the uranium-aluminum lattice.
If the latter, is it composed of atomic ions or molecular ions, or both?
The molecular ions of this complex are the carbon rings and methyl groups throughout
the structure, while the atomic ions are the uranium and aluminum atoms.
What do you think are the oxidation states of the metal ions in the structures, and how did
you come to those conclusions?
Since it has been inferred that the bonds formed on aluminum and uranium ions appear to
be ionic covalent, which has allowed them to form more bonds than usual, there has been an
assumption made that the oxidation state of each uranium/aluminum atom is equivalent to the
following:
#
= (1)
2

This equation is based on the inference that, in the presence of an ionic-covalent


relationship between uranium/aluminum and carbon atoms in the complex, there is only a
maximum molecular orbital overlap equivalent to half the probability of an electron be present in
each molecular orbital at a time. This retains the idea that hybridization of each carbon exists and
that the majority of electron density is centered on the carbons for both the methyl groups and
pentagonal rings throughout the structure. With the use of equation (1) then, it can be inferred
that uranium has an oxidation state of +6 and aluminum of +2.5; since oxidation states are
typically reported as whole integers, each aluminum atom can be inferred to have a +3 oxidation
state with the capability of forming a maximum of 6 ionic-covalent bonds in this complex.
What are the ligands bonded to the metal ions?

What are the idealized coordination geometries of the metal ions in the structures?
The idealized coordination geometries of each metal ion, based on oxidation states, can
be seen as a coordination number of 6; however, due to the hybridization of carbon throughout
the complex, the coordination of each atom is halved to a coordination number of 3. With a
coordination number of 3, uranium and aluminum are allowed to form trigonal planar geometries
with each of their ligands, with carbon atoms acting as the connecting ends of each geometry.
This is further seen in Figure 12 where the aluminum atoms are seen to be planar with one
another throughout each layer without much angle differentiation between each atom and layer.
Are there distortions from idealized geometries, and if so can you identify reasons why this
might be the case?
The only potential distortion that can be imposed on this structure would be through the
pentagonal carbon rings attached to the uranium atoms and the methyl groups present throughout
the structure. Each carbon structure imposed steric hindrance throughout the structure, which
may allow for stress on U-C and Al-C bonds; however, this destabilization of bonds is mostly
likely overcame by the introduction of ionic-covalent bonds on the uranium and aluminum atoms
to allow them to form more bonds than usual to allow for better stability.
Are there interesting/unexpected structural features with respect to any of the atoms
(metal atoms or non-metal atoms)?
The most unexpected feature of the complex would be the observation of aluminum and
uranium atoms forming more bonds that previously predicted based on most common
oxidation states for each atom and how the additional bonds provide better stabilization
of the structure due to the hindrance of the carbon groups.
Appendix C:
Figure 9: Uranium-Aluminum Unit Cell Complex

Table 8: Bond Length and Angle Data of Uranium-Aluminum Unit Cell Complex
Bonding Bonding Bond Length Type of Bonding Atom
Atom #1 Atom #2 () Bond Angle () Respect to
Angle
U(1) C(1) 2.754 49.5 C(2)
U(1) C(2) 2.692 29.8 C(1)
Al(1) C(23) 1.983 104.5 C(25)
Al(1) C(24) 1.986 113.2 C(23)
Al(1) C(25) 2.075 106.1 C(23)
Al(2) C(27) 1.968 112.5 C(25)
Al(2) C(28) 1.969 Ionic- 109.4 C(25)
Al(2) C(26) 2.095 Covalent 103.5 C(25)
Al(2) C(25) 2.104 166.3 Al(1)
Al(3) C(25) 2.016 98.5 Al(1)
Al(3) C(26) 2.219 102.2 C(25)
Al(3) C(29) 1.972 102.2 C(25)
Al(3) C(30) 1.969 114.8 C(25)
Al(2) Al(3) 2.627 169.2 C(25)
Figure 10: Uranium Sub-Complex

Figure 11: Aluminum Sub-Complex


Figure 12: Aluminum Sub-Lattice

Table 9: Mean Plane and Average Aluminum Atom Distance of Aluminum Sub Lattice
Mean Atom Plane Distance () Average Aluminum Atom Distance ()
9.1783 2.627