Documente Academic
Documente Profesional
Documente Cultură
A thesis presented to
the faculty of
In partial fulfillment
Master of Science
Deepika Singh
November 2009
2
by
DEEPIKA SINGH
Gerardine G. Botte
Dennis Irwin
ABSTRACT
water to produce hydrogen and simultaneously denitrificating the waste water. The
proposed reaction mechanisms, preferred pathway and rate determining steps have been
reaction as well as the chemical oxidation reaction mechanisms have been postulated on
the surface of the active catalyst NiOOH. The preferred pathway for electro-oxidation
as the rate limiting step. From the thermodynamic calculations of the chemical oxidation
reactions, it was evident that the presence of OH- catalyzes the reaction. Experimentally,
the effects of varying concentrations of KOH and urea were investigated. The
experimental results supported the argument that a higher concentration of OH- is more
Approved: _____________________________________________________________
Gerardine G. Botte
ACKNOWLEDGMENTS
inspiration for me throughout my career. I would also like to thank my colleagues at the
helping me learn the basic laboratory techniques. In particular, I want to acknowledge the
tremendous contribution of Damilola Daramola who has helped me from the initial stages
of teaching computational techniques right untill the end for editing and formatting of the
submitted publications, apart from mentoring me at all stages in my research. Without his
support none of this would have possible. I would also like to extend my heartiest
gratitude to the Ohio Super Computing Center for providing valuable resources and
I would also like to thank all friends, especially Saurin Shah and Santosh Vijapur
for being there for me all the time. For all the emotional and moral support and for
believing in me, for giving me the strength to persevere, I can never thank both of you
enough. Finally I’d like to thank my immediate family who has always been there with
me mentally, if not physically. For their undying belief, the kind words and unfailing
support. For being with me through thick and thin, at all times of the day. Thank you so
TABLE OF CONTENTS
Page
Abstract ............................................................................................................................... 3
Acknowledgments............................................................................................................... 4
5.3 Urea and NiOOH in the presence of OH- ion: .................................................. 55
LIST OF TABLES
Page
Table 3.1: Bond lengths and bond angles of urea as computed using different basis sets
with the B3LYP correlational functional ...........................................................................20
Table 3.2 : Experimental bond lengths for NiOOH kept constant for the reaction
mechanisms ........................................................................................................................20
Table 4.1: Proposed reaction mechanisms for urea electro oxidation reaction .................25
Table 4.2: Sum of free energies for all the intermediate steps...........................................48
Table 4.3: Kinetics of the reaction pathways and rate constants for intermediate steps ...49
Table 5.1: Binding Energies of different orientations of urea towards NiOOH ................53
Table 5.2: Free Energies differences for Equations 5.1 and 5.2 ........................................55
Table 5.3: Free Energies differences for Equations 5.3 and 5.4 ........................................58
8
LIST OF FIGURES
Page
Figure 4.1: Initial state (a) Transition state (b) and Final structure (c) for
Equation 4.5 ...................................................................................................................... 26
Figure 4.2: Initial state (a), transition state (b) and final structure (c) for
Equation 4.6 ...................................................................................................................... 27
Figure 4.3: Initial state (a), transition state (b) and final structure (c) for
Equation 4.7 ...................................................................................................................... 29
Figure 4.4: Initial state (a), transition state (b) and final structure (c) for
Equation 4.8 ...................................................................................................................... 30
Figure 4.5: Initial state (a), transition state (b) and final structure (c) for
Equation 4.9 ...................................................................................................................... 31
Figure 4.6: Initial state (a), transition state (b) and final structure (c) for re-arrangement
of nitrogen atoms .............................................................................................................. 32
Figure 4.7: Initial state (a), transition state (b) and final structure (c) for Equation 4.10..
.......................................................................................................................................... .34
Figure 4.8: Initial state (a), transition state (b) and final structure (c) for
Equation 4.11 .................................................................................................................... 35
Figure 4.9: Initial state (a), transition state (b) and final structure (c) for
Equation 4.12 .................................................................................................................... 36
Figure 4.10: Initial state (a), transition state (b) and final structure (c) for
Equation 4.13 .................................................................................................................... 37
Figure 4.11: Initial state (a), transition state (b) and final structure (c) for
Equation 4.14 .................................................................................................................... 38
9
Figure 4.12: Initial state (a), transition state (b) and final structure (c) for
Equation 4.15 .................................................................................................................... 39
Figure 4.13: Initial state (a), transition state (b) and final structure (c) for
Equation 4.16 .................................................................................................................... 40
Figure 4.14: Initial state (a), transition state (b) and final structure (c) for rearrangement
of amine groups................................................................................................................. 42
Figure 4.15: Initial state (a), transition state (b) and final structure (c) for Equation
4.17……………………………………………………………………………………….42
Figure 4.16: Initial state (a), transition state (b) and final structure (c) for
Equation 4.18 .................................................................................................................... 44
Figure 4.17: Initial state (a), transition state (b) and final structure (c) for Equation 4.17.
........................................................................................................................................... 45
Figure 5.1: Optimized structures for different orientations of urea towards NiOOH ....... 52
Figure 5.2: Optimized structures for Equations 5.1 and 5.2 ............................................. 54
Figure 5.3: Optimized Transition States for Reactions 2 and 3 ........................................ 55
Figure 5.5: Optimized structures for Equations 5.3 and 5.4. ............................................ 56
Figure 5.6: Transition State Structures for Equations 5.3 and 5.4 .................................... 57
Figure 6.1: Preliminary experiment. Different concentrations of KOH at 20g L-1 urea to
determine lower setpoint. .................................................................................................. 62
Figure 6.2: Urea concentration of 5 g L-1 varying KOH concentrations. Scan rate:
20mV s-1. Speed of rotation: 1000rpm.............................................................................. 63
Figure 6.3: Urea Concentration of 10 g L-1 with varying KOH concentrations. Scan Rate:
20mV s-1. Speed of rotation 1000rpm. .............................................................................. 63
Figure 6.4: Urea concentration of 20 g L-1 with varying KOH concentrations. Scan rate
20mV s-1. Speed of rotation 1000 rpm. ............................................................................. 64
10
Chapter 1 : INTRODUCTION
The use of hydrogen as an alternative fuel has been the focus of attention for many
decades now, especially as the demand for fuels from renewable energy sources is
constantly on the rise. The transition from liquid petroleum to gases over a span of 200
years is as shown in Figure 1.1. According to this trend, there will be a complete shift
from petroleum to hydrogen for meeting world energy requirements by the turn of the
next century1.
The devices that produce hydrogen for the purpose of electricity generation are
called fuel cells. They operate on the principle of recombination of hydrogen with oxygen
to release energy and produce water as a byproduct. Although there are five different
types of fuel cells being developed for commercial applications, proton exchange
membrane fuel cells are considered as viable, low temperature operating devices for both
Proton exchange membrane (PEM) fuel cells working on water electrolysis are
based on the mechanism of splitting up of the water molecule into hydrogen and oxygen
with the liberation of energy in an exothermic reaction. The water electrolysis reaction is
as follows:
University has recently devised a new alternative to the water electrolysis reaction:
follows:
This process produces hydrogen to power PEM fuel cells and is a self sustainable
electrolysis, by means of which urine from animal farms and waste water lagoons can be
directly utilized to produce hydrogen to power fuel cells8. Urea is known to naturally
ammonia emissions9. This process once commercialized will not only help farmers
receive tax cuts for reduced ammonia emissions, but it will also decrease their
waste water from poultry farms as well as residential and commercial areas and using it
as a tool to solve one of the world’s impending energy crises. This following project was
undertaken to understand urea electrolysis for the purpose of generation of hydrogen for
understanding of the electrolysis process. The reaction mechanisms are being studied
techniques involve studying the effect of reaction parameters using a rotating disk
electrode.
13
The purpose of this thesis is to gain a better understanding of the urea electrolysis
viable for fuel cells. The following objectives are proposed to be accomplished with the
techniques along with activation energies and rate constant calculations both in terms
and carbamates. This reaction has been studied in the presence of the catalyst
nickel oxyhydroxide.
The elementary steps involved in the anodic reaction have been studied.
With the help of these reaction mechanisms and by determining the preferred
pathway as well as the rate determining step, measures can be taken to improve
The most important technological impact of this project arises from the utilization
of the most abundant waste on earth, urine, to produce cheap electricity. Apart from
being a significant source of hydrogen production, this technology can also be used to de-
nitrificate waste water, thus saving a huge amount of expenditure on waste water
ammonium nitrate in the atmosphere which pose significant health hazards11. Hence, by
electrolyzing urea to useful products, we are able to bypass the formation of the hazard-
causing products.
Another important aspect is that the electrolytic cell potential required for the
overall reaction to occur is only 0.37 V at standard conditions. When this is compared to
the cell potential required to produce hydrogen (1.23 V), it amounts to generation of 70%
These factors emphasize the need for a better understanding of the ongoing
process, which has been achieved in this project by means of the invaluable tool of
molecular modeling.
15
2.1 Theoretical
purpose of generating hydrogen for fuel cells. Urea hydrolysis and decomposition
mechanisms have generated interest in the past in varied fields including removal of urea
from the blood using dialyzers and also formulation of urease inhibitors for better soil
fertility. When urea dissociates in the presence of the bio enzyme urea amidohydrolase 13-
15
(urease), it leads to a sudden increase in pH of the soil due to the liberation of ammonia,
leading to its decreased fertility thus rendering it ineffective for agricultural purposes16, 17.
For this reason, biocatalytic decomposition of urea by urease which catalyzes the
reaction has been given considerable attention in the literature18-20. Urease decomposes
urea to ammonia and carbon dioxide under specific reaction conditions according to the
following reactions21:
CO(NH 2 )2 ⎯⎯ ⎯→ NH 3 + HNCO
urease
(2.1)
The enzyme urease comprises of two pseudo-octahedral Ni(II) ions as its active
sites. Suarez et al.13 have proposed the reaction mechanisms for urea hydrolysis.
According to their work, urea binds to the two active nickel sites in urea in a bidentate
manner. The more electrophilic nickel attaches itself to the carbonyl group of urea, while
the other nickel atom attacks one of the amino groups. They have considered a bridging
hydroxide group between the two nickel atoms, which donates a proton to the amino
group that is attached to the second nickel atom as shown in Figure 2.1.
16
The mechanism of urea decomposition in aqueous phase has been further studied
by different authors 15, 22, 23. This study was performed with the presence of urea in water
alone without the urease enzyme. In the aqueous solution, the elimination mechanism
yields isocyanic acid and ammonia, whereas intramolecular proton transfer gives cyanic
acid and ammonia18. It was also concluded that elimination mechanism greatly disrupts
urea in aqueous solution and conclude that urea prefers to eliminate ammonia rather than
undergo hydrolysis.
These mechanisms are relevant in the context of this study because at EERL at
Ohio University, studies are being conducted for the electrolytic dissociation of urea for
the purpose of generating hydrogen for proton exchange membrane fuel cells24. Nickel
has been identified as the active catalyst for the reaction, which is supported by the fact
17
that urea undergoes natural hydrolysis in the presence of the urease enzyme which has
An alkaline medium is used to carry out the electrolysis, and nickel undergoes
oxidation to its active state: nickel oxyhydroxide (NiOOH) in this medium by the
following reaction:
This reaction is hypothesized to occur on the surface of the nickel electrode in the
presence of urea as well. As a result, it is important to study the interaction of the nickel
oxyhydroxide molecule with urea to come up with feasible reaction mechanisms for the
The above mentioned modeling calculations have been performed using Gaussian
comprise of basis sets which are the pre-defined parameters within the confines of which
In the past, quantum chemical calculations have been performed using Linear
߰ ൌ ܿఓ ߶ఓ
ఓୀଵ
18
Where ψi is the ith molecular orbital, cμi are the coefficients of linear combination
andΦμis the μth atomic orbital and n is the number of atomic orbitals.25 These atomic
orbitals (AO) are solutions of the wave functions for a single electron in an atom. A basis
set is a set of these wave functions within the framework of which quantum chemical
calculations are performed. Basis sets play a crucial role in the binding energies obtained
2.2 Experimental
as dialysis and synthesis of carbon nitride thin films. These applications have been
studied in acidic medium with noble metals like platinum, iridium, ruthenium. Simka et
produce non toxic products with this reaction. But it is for the first time that alkaline
electrolysis of urea is being considered for the purpose of hydrogen production. Here we
have considered nickel as the catalyst for this reaction as it is cheap, economically
feasible and shows high activity for urea electrolysis. Currently, high concentrations of
alkali potassium hydroxide (KOH) are being used in the reaction. Typical concentration
investigate if lower concentrations can be used under the given operating conditions.
19
With the primary purpose of elucidating the reaction mechanism, single molecule
interactions of NiOOH with urea have been considered. DFT calculations were carried
out using the Gaussian 03 program27 with the B3LYP correlation functional28. A mixed
basis set was used comprising of Los Alamos National Laboratory of double zeta quality
(LANL2DZ)29-31 and 6-31g*32 for carbon, nitrogen hydrogen and oxygen atoms, also
referred to as the LACVP* basis set. The comparison of the relevant geometrical
features of the urea molecule was reported on the B3LYP level in literature33 (Table 3.1).
These values of bond angles and bond lengths reported using the 6-31g* basis set were
its requirement of less processing time, 6-31g* was chosen as a building block for these
calculations.
20
Table 3.1: Bond lengths and bond angles of urea as computed using different basis sets
For the electro oxidation reaction mechanisms the bond lengths for atoms of
NiOOH were kept constant at their experimental values34, 35 for the electrochemical
Table 3.2 : Experimental bond lengths for NiOOH kept constant for the reaction
mechanisms
Ni-O 1.88
Ni-OH 1.91
O-H 0.956
21
algorithm was used to calculate the vibrational frequency and analytical force constant
calculations on all structures. The transition states for all elementary steps were located
implementing the default Gaussian 03 method. The transition state geometry possessed
NiOOH (the O-H bond) and the other corresponding to the transition state (TS) structure.
Animation of the particular transition state negative frequency verified that the TS
corresponded to the interacting atoms for the particular step under consideration.
The rate constant calculations based on the transition state theory36 were performed using
⎛ ⎞
k BT ⎜ q # ⎟ ⎛ −E i ⎞
k= exp⎜ ⎟ (3.1)
h ⎜⎜ ∏n q ⎟⎟ ⎝ RT ⎠
⎝ j=1 j ⎠
where,
Ei= difference in zero point energies of reactants and transition state structures(J mol-1)
T= 298 K
On solving the above equation for a second order reaction, the rate constant value
The free energies in Gaussian 03 are evaluated from the vibrational frequency analysis,
which is in turn used to determing the partition function based on the harmonic oscillator
model. Therefore, the underlying assumption in this analysis is that the second derivative
matrix is evaluated at a point on the potential energy surface where the gradient is zero.
As such, since the gradient is zero, the coupling between the nuclear degrees of freedom
When using geometry constraints, the non-zero forces are ignored while
evaluating the optimization criteria. As a result, the energy values change and these
intermediate structures were considered with the entering OH- and leaving H2O
molecules with no geometry constraints on the NiOOH molecule. . For the chemical
Within this context the objective in this study is to use Density Functional Theory
(DFT) methods to predict the mechanism and rate determining step of the anodic urea
oxidation reaction on the NiOOH surface. This study is significant in order to understand
and improve overall efficiency of the experimental process of urea electro oxidation. In
order to predict the reaction mechanisms, the electronic energy barriers for the
elementary steps were estimated. Based on these steps, three reaction mechanisms have
summarize the pathways, the first step involved the adsorption of urea onto the NiOOH
catalyst, and was common for all three mechanisms. From here onwards, path 1
demonstrated the initial loss of protons from the amino group H1-N1-H2, while path 2
involved the initial loss of protons from the second amino group H3-N2-H4. In path 3,
the amino groups bonded together by the rotation of the group H1-N1-H2 towards N2-
H3, whereas in paths 1 and 2 this rotation takes place only after the elimination of all
After the withdrawal of all the protons of urea by the approaching hydroxyl ions in steps
2 to 6, the final adsorbed structure at the end of step 6 is identical for all the pathways,
rendering a common mechanism from step 7 onwards. These steps have been discussed
rate constants have been carried out using partition functions obtained from the transition
states and reactants to estimate the rate constants and hence predict the rate limiting step,
as will be discussed in detail later. The initial, transition and final states for all the
reaction pathways are shown in Table 4.1. Each reaction step is illustrated with four
figures: the first structure (a) is the optimized geometry for the initial state. The second
(b) and third figures (c) are the transition and final states respectively.
25
Table 4.1: Proposed reaction mechanisms for urea electro oxidation reaction
1
CO (NH2)2 + M → [M.CO (NH2)2]ads
[M.CO(NH2)2]ads + OH-
2 [M.CO(NH2)2]ads + OH- → [M.CO(NH2.NH)]ads
→ [M.CO(NH2.NH)]ads
+H2O + 1e-
+H2O + 1e-
[M.CO(NH2.NH)]ads M.CO(NH2NH)ads +
3
+OH- → [M.CONH2N]ads OH-→ [M.CONH2.N]ads Not an Elementary Step
+ H2O + 1e- + H2O
[M.CO.NH2NH]ads +
[M.CO(NH2N)]ads + OH- [M.CO(NH2.N)]ads +
4 OH-→
→ [M.CONHN]ads + H2O OH-→ [M.CONHN]ads
[M.CONH.NH]ads +
+ 1e- + H2O + 1e-
H2O + 1e-
[M.CONHN]ads +OH- [M.CO.NHN]ads + OH- [M.CO.NHNH]ads + OH-
5
→[M.CO.N2]ads +H2O → [M.CO.N2]ads + H2O → M.CO +NH.N + H2O
+1e- + 1e- + 1e-
[M.CO.NHN]ads + OH-
6
Not an Elementary Step → M.CO.N2 + H2O +
1e-
7
[M.CO.N2]ads + OH-→ [M.CO.OH]ads + N2 + 1e-
8
[M.CO.OH]ads + OH-→ [M.CO2]ads + H2O + 1e-
9
[M.CO2]ads→ M + CO2
Step 1
Figure 4.1 shows the first step of the reaction: adsorption of urea onto NiOOH by
M is the catalyst NiOOH. The Gibb’s free energy was calculated as the sum of
energies of the two separate structures of NiOOH and urea. b shows the Transition State
26
(T
TS) whereass c illustrattes urea adsoorbed onto niickel from oxygen
o (O2) as the site of
o
addsorption. The
T interactioon of NiOOH
H with urea changes
c the NH2 (H4-N2-H3) bond
anngle in c, which
w u moleculle is 118.8o and
in the case of the urea a in the finnal structuree
thhe transition state and 1000.58 degreees in the finaal structure. The
T rate connstant calculaated
(a) (b)
(c)
F
Figure 4.1: Initial state (a) Transitioon state (b) and
a Final struucture (c) foor Equation 4.5
4
27
(a) (b)
(c)
nitial state (aa), transition state (b) andd final structture (c) for Equation
Figure 4.2: In E 4.6
Step 2
Figuree 4.2 illustraates the initiaal (a) transitiion state (b) and the finaal structure (cc) for
thhe following
g reaction:
M.CO(NH2)2]ads + OH - →[M.CO(N
[M → NH2.NH)]ads +H2O + 1e- (4.6)
In the initial structure the N1--H1 bond lenngth for the dissociating
d proton is 1.002Å
w
whereas in th
he TS, it increases to 1.122Å. The N2--C distance is
i noted as 1.59Å and the
N
N2-Ni bond length
l is 1.922 Å .The rate constant foor this reactiion was calcuulated as
2.7x1011 L mol
m -1 s-1.
28
Step 3
In step 3 of path 1as shown in Figure 4.3, the NH2 attached is deprotonated by the
Due to the vacant site on N1-H2, it serves as a point of attachment for the free
OH- ion in the initial optimized structure (Figure 4.3a). The N1-(O4H6) bond length in
the initial structure is 1.44 Å, N1-H2 being 1.02 Å. In the TS (Figure 4.3b), H is 1.29 Å
away from N. This OH- then withdraws a proton to leave the system as water.
Subsequently, the N1-C bond becomes shorter in the final structure (1.29 Å) versus the
initial structure (1.43Å). The rate constant for this reaction is 2.8x10-23 L mol-1 s-1.
29
(a) (b)
(c)
Figure 4.3: In
nitial state (aa), transition state (b) andd final structture (c) for Equation
E 4.7
Step 4
In step
p 4, the folloowing reactioon occurs:
W
When H- approachees the secondd NH2 (H3-N
the OH N2-H4) grouup in Figure 4.4a, it pullss
aw
way the entiire NH2 grouup towards it (O4-N2: 1..44 Å, N2-H
H4: 1.02 Å). In the transiition
sttate the proto wards OH-, and the NH (N2-H3) grooup reattachhes back to nickel
on moves tow n
ass shown in th
he final statee (Figure 4.44c). N2-H3 bond
b length in the TS inccreases to 1..13
onstant for this reaction in Equation 4.8 was calcculated to bee 1.1x10-15
Å The rate co
Å.
L mol-1 s-1.
30
(a) (b)
(c)
nitial state (aa), transition state (b) andd final structture (c) for Equation
Figure 4.4: In E 4.8
Step 5
p 5 (Figure 4.5),
In step 4 similar to step 3, duue to a vacannt site on NH O -
H (N2-H3), OH
O4-H6) adso
(O orbs onto thee surface, acccepts a protoon and detacches as waterr according to
t
thhe following
g reaction:
The O4-N2,
O N2-N
Ni and N2-H
H3 bond lengtths in the iniitial state aree 1.43Å, 1.844Å
Inn the final sttate, as obserrved in step 3 before, thee N2-Ni bonnd length deccreases to 1.559Å.
T rate consstant for this reaction froom Equation 4.9 is 2.7x10-24 L mol-1 s-1.
The
31
(a)
(b) (c)
Figure 4.5: In
nitial state (aa), transition state (b) andd final structture (c) for Equation
E 4.99
Step 6
From step 5 (Figuure 4.5c), it is evident thaat the two N (N1 and N22) atoms are at a
sttructure in th
his step, therre is a bond between
b the two Ns (Figgure 4.6c) whhich will enaable
N2 formation as can be seeen later. Aftter having doonated all itss protons to the
t approachhing
(a) (b)
(c)
Figure 4.6: In
nitial state (aa), transition state (b) andd final structture (c) for re-arrangeme
r ent of
nitrogen atom
ms
Step 7
In step
p 7 (Figure 4.7),
4 H- ion is adsorbed on thee surface whhile
the appproaching OH
thhe N2 is deso
orbed simultaneously wiith the follow
wing reactionn:
-
[
[M.CO.N2]ad M.CO.OH]adds + N2 + 1e-
ds + OH → [M (4.110)
nickel. The raate constant for this step is 7.3 x108 L mol-1 s-1.
Step 8
n reaction in step 8 (F
The next Figure 4.8) iss as follows:
- -
[
[M.CO.OH]a + OH → [M.CO2]ads + H2O + 1e
ads (4.111)
33
The last approaching OH- gets adsorbed onto nickel. The Mulliken charge on Ni
reduces from 0.415 in the initial state (Figure 4.8a) to 0.372 in the final state (Figure
4.8c). As a result of this, Ni exhibits a tendency to form a bond with O4, which loses a
proton(H6) to the detaching OH (O5-H7). The rate constant for this step is 1.6 L mol-1 s-1.
Step 9
The final state is CO2 (O1-C-O4) adsorbed onto NiOOH. This gets desorbed in the
The rate constants for the step is 4.3x10-65 L mol-1 s-1 respectively.
34
(a)
( (b)
(c)
Figure 4.7: In
nitial state (aa), transition state (b) andd final structture (c) for Equation 4.10
35
(a) (b)
(c)
nitial state (aa), transition state (b) andd final structture (c) for E
Figure 4.8: In Equation 4.11
36
(a) (b)
(c)
Figure 4.9: In
nitial state (aa), transition state (b) andd final structture (c) for Equation
E 4.12
Step 1
This step
s is comm
mon for all paathways.
Step 2
In an alternative mechanism
m f step 2, wee consideredd the possibility of the NH
for N 2
acccording to the
t followinng reaction:
The kinetics
k of thiis step impliied it was fasster than patth 1as the ratte constant value
v
iss 1.38x1017 L mol-1 s-1 veersus the steep 2 of path 1 with a ratee constant vaalue of 2.7 x11011
L mol-1 s-1. Th
his is most likely
l due to the positionn of the OH- molecule whhere it can
obbtain an H from
fr either N1
N or N2 as shown
s in thee transition state.
s T the two N2-
In the TS,
H bond leng
H3 gths are 1.1Å
Å and N2-H44 is 1.15Å. The
T initial strructure (Figuure 4.10a) iss the
saame as consiidered for paath 1. The traansition state and final structures
s aree as shown in
(a) (bb)
(c)
Step 3
M
M.CO(NH N ads + OH-→ [M.CONH
2NH) H2.N]ads + H2O + 1e- (4.114)
38
(a) (b)
(c)
Step 4
innitial state to
o 1.05Å in thhe final state. (Figure 4.112) The rate constant forr this step waas
(a) (b)
(c)
Step 5
The N-H
N bond lenngth changess from 1.02Å
Å to 1.14Å between
b the initial
i and
sttep 6 of path
h 1 where rottation of nitrrogen needs to be accom
mplished in order
o to faciliitate
40
desorption off the N2 moleecule. The raate constant for this step is 8.8x1015 L mol-1 s-1.
From here on
n the steps foor paths 1,2 and
a 3 are ideentical.
(a) (b)
(c)
Steps 1 and 2
Step 3
p 3 of path 2,
In step 2 NH2 (H1-N
N1-N2) grouup detaches from
f carbon and attaches to
desorption off N2 in the laater steps witthout the neeed to rotate the
t N-atoms towards eacch
otther.
(a) (b)
(c)
42
of amine grou
ups
Step 4
As sho
own in the TS H- withdraw
T (Figure 4.15b), there is a possibillity of the OH wing a
1.43Å to 1.39
9Å.
Step 5
Thereafter, the next approaching OH- takes up a proton from the –N1H1 group
(Figure 4.16). The rate constant for this step is 2.5x10-4 L mol-1 s-1 in the following
reaction:
(a) (b)
(cc)
Step 6:
p 6, (Figure 4.17) when the approachhing OH- takkes up the laast proton
In step
acccording to the
t followinng reaction:
The fiinal structuree is the samee as the one obtained froom path 1 steep 6. In this
rootation towaards each othher as in pathh 1. The N2-H3 bond lenngths for the initial (Figuure
4.17a) and traansition statees (Figure 4..17b) are 1.001Å and 1.022 Å. The N1-N2 bond length
45
becomes shorrter in the finnal step (1.43Å) from initial step (1.223Å). The raate constant for
Steps 7, 8 an
nd 9
(a) (b)
(c))
The free energies values as well as the rate constants for the steps for the different
As can be seen from the rate constant values, the desorption of CO2 from NiOOH
is the rate limiting step with a value of the order of magnitude of -65. This conclusion is
supported by the fact that the urea electrolysis reaction rate decreases with time which
can be attributed to a surface blockage of the catalyst when a build up of CO2 takes place
over a period of time8. Thermodynamic calculations also suggest the largest contribution
to the free energy change of the reaction is from the last step. The total free energy
change (ΔG) required is 1227.7 kJ mol-1, whereas the requirement for CO2 desorption
alone is 1242.2 kJ mol-1. Using this value of ΔG, the theoretical value of of the cell
ΔG=-nFEocell (4.20)
where,
atmosphere pressure. The difference between this calculated potential and the theoretical
potential versus SHE8 of -0.46V can be attributed to two main factors. Firstly, in this
system one NiOOH site per molecule of urea has been considered. This system of single
molecule interactions limits the available active catalyst sites per molecule of urea. As a
47
result the overall energy required to desorb the final product CO2 is expected to be higher
in such a system, as compared to systems with larger NiOOH cluster sizes where a
greater number of catalytic sites are available per molecule of reactant. This in turn
explains the higher value of calculated standard potential. Secondly, gas phase
calculations have been performed without using solvent effects in order to simplify the
system. This has also possibly accounted for deviation in calculation of cell potential.
However, since the objective of this study was to gain a relativistic view of the kinetics of
the elementary steps, this has been well accomplished using a considerably simple model
mainly from the preferential adsorption of OH- onto the surface of NiOOH. The binding
energies of CO2 and OH- calculated to be 9.2 kJ mol-1 and 18.0 kJ mol-1 respectively. This
suggested that in excess of OH- ions, the hydroxyl group is more preferentially adsorbed
onto the catalyst’s surface than CO2. This competition between adsorbed OH- and CO2 on
the catalyst’s surface leads to an increased tendency of surface blockage which could
Table 4.2: Sum of free energies for all the intermediate steps
Total 1227.7
49
Table 4.3: Kinetics of the reaction pathways and rate constants for intermediate steps
2 2.3x1011 1.38x1017
Not an Elementary
3 2.8x10-23 2.3x10-21 Step
7 7.3x108
8 1.6
9 4.3x10-65 (rds)
4.5 Conclusion
kinetically, the last step, i.e. desorption of CO2 from the catalyst’s surface is the rate
limiting step. This indicates the occurrence of surface blockage in the presence of a larger
calculations ( Table 4.2)also suggest a large contribution to the free energy change
occurring from the last step. Total free energy change required is 293.1 kcal mol-1,
whereas the requirement for CO2 desorption alone is 296.7 kcal mol-1. Using the free
50
energy, the theoretical value of the cell potential was calculated to be -2.12V. The
difference between this theoretical and experimental value8 of -0.46V obtained can be
attributed to the limitation of using gas phase calculations as well as single molecule
Also, the path of least resistance is path 2, wherein the NH2 migrates to bond with
the NH group initially in step 3, before the remaining proton transfer could take place. As
a result of this migration, it involves no further need to rotate the N molecules towards
each other to bring about N2 desorption, as the atoms are already in the vicinity of each
other. This makes path 2 the preferred pathway. However, even if the reaction progresses
via any given mechanism, the rate limiting step, i.e, desorption of CO2 is common to all
the mechanisms.
51
The objective of this study was to investigate the thermodynamics and kinetics of
the urea decomposition reactions occurring on NiOOH. The first consideration was urea
adsorbed onto the surface of NiOOH, and secondly the inclusion of a hydroxide ion in the
system was considered, to investigate the catalytic effects of OH- in the reaction.
The electrophilic atoms of urea were oriented towards the nucleophilic atoms of NiOOH
and vice versa (Figure 5.1). The configurations obtained are tabulated along with their
binding energies Table 5.1. In Figure 5.1 a, the interaction of Ni with N1 was considered,
wherein no significant interaction between the two species was observed. In Figure 5.1b
NiOOH separated from urea as in Figure 5.1a. In Figure 5.1c, double atomic interactions
of Ni with N2 and OH with C were considered. The resulting output as shown consisted
interacted with N2 while O2 interacted with C. The resulting structure has urea attached
to NiOOH through the point of attachment of carbon. In Figure 5.1 e the interaction of Ni
with N2 and OH- with C was considered, which resulted in breakage of OH from NiOOH
The binding energies of structures in Figure 5.1 b and Figure 5.1 d were the least
in the group, suggesting that these structures were most likely to undergo dissociation.
Since structure in Figure 5.1 d shows a more plausible scenario of multiple atomic
52
innteractions (b
between Ni--N and O-C)), it was conssidered for thhe complete dissociationn
m
mechanism of NiOOH wiith urea.
(a) (b)
(c)
( (d))
(e))
a. 11.7
b. 5.9
c. 11.3
d. 8.3
e. 12.6
NiOOH is as follows:
The optimized reactants, products and transition states are shown in Figure 5.2
and Figure 5.3. Upon attachment to NiOOH, the urea molecule which initially resides in
a single plane has now been changed as the Hs on the amides bend closer to each other
and out of the original plane. The N1-C-N2 bond angle changes from 115.4o in urea
(Figure 5.2a) to 110.4o in intermediate 1(Figure 5.2b). The H1-N1-H2 and H3-N2-H4
bond angles in urea are 118.8o and they reduce in intermediate 1 from 109.2o to 107.9o
respectively. Between the transition state TS I in Figure 5.3a, and intermediate 1(Figure
54
In step
p 2, N2 donaates its protoon to the leavving ammonnia molecule which detacched
reemains boun
nd to NiOOH
H from the pooints of attacchment of Ni
N and O. Thee Ni-N2 bonnd
thhe bound HC
CNO group at
a the Ni-N1 distance off 2.01 Å.
s-1
-
10-6 s-1, indiccating that libberation of ammonia
, k2= 1.54x1 a is the
t rate limiting step in this
t
(a) (b)
(c)
(a) (b)
Table 5.2: Free Energyy differencess for equatioons 5.1 and 5.2
5
O
Overall -2776.3
n OH- was opptimized witth NiOOH, itt resulted in the adsorptiion of the
When
hyydroxide ion
n onto Ni as shown in Fiigure 5.4. Thhe output struucture was then
t further
T proposed
The d reaction meechanism is as follows:
(N
NiO.OHOH))ads + CO(NH
H2)2→ (Ni(O
OH)3.CONH.NH2)ads (
(5.3)
(N
Ni(OH)3CON
NH.NH2)ads →(Ni(OH)3.C
CNO)ads + NH
N 3 (5.4)
56
(a) (b)
(c)
(
Figuree 5.5a illustrrates the optiimized reacttants for Equuation 5.3 annd 5.4. The N1-
N
N distance iss 2.06Å. In thhe intermediiate structuree (Figure 5.55b), the ureaa molecule
Ni
prroximity of N1-H1
N to O2, O2 withdrraws the prooton from N11 while N1 bonds
b to Ni at
a the
saame time. Th
he N1-Ni boond length reeduces to 1.996Å. The N11-C-N2 bondd angle increeases
57
thhe transition state for this step (Figurre 5.6a), the urea molecuule is not rottated, and thee
TS I (aa) TS II (b))
Figure
F 5.6: Transition
T Sttate Structurres for Equattions 5.3 andd 5.4
In equ
uation 5.4, am
mmonia is formed
fo and desorbed,
d leaaving CNO- still adsorbeed
chhange signifficantly at 1.95Å. The Nii-N1-C bondd angle is 1334.4o. The traansition statee for
grroups. H2 iss at a distancce of 1.28 Å from the leaaving NH grooup and 1.322Å from the
H2 group. The rate constaant calculatioons yield thee rate constaant for reactioon
acccepting NH
T reaction profile
The p as a function
f of the
t reaction coordinates is shown in Figure 5.8. The
frree energies for the two steps are givven in Table 5.3.
58
Table 5.3: Free Energy differences for reactions 5.3 and 5.4
Overall -598.7
5.4 Conclusion
The free energy differences between the reactants and products in the both the
mechanisms suggest that the reaction occurs spontaneously. The free energy difference
between the two steps is higher in the presence of OH- rather than without it, suggesting
that the reaction occurs more spontaneously in the presence of OH-. This is validated by
experimental results, as there are traces of ammonia present as a result of the urea
decomposition reaction.
59
Chapter 6 : EXPERIMENTAL
The experimental section is a brief study carried out in order to study the effect of
varying concentrations of KOH and urea on the current density obtained. The urea electro
oxidation reaction has been analyzed by conducting potentiodynamic tests with a rotating
disk electrode. The rotating disk electrode offers several advantages over stationery
electrode experiments. With the disk in constant motion, reaction rates are not diffusion
limited. Hence it throws light on the nature of the reaction taking place37. With
conventional experiments conducted using a rotating disk electrode, a steady state current
profile is obtained with changing potentials. However this is not the case with the urea
electro oxidation reaction, where reactions of a more complex nature seem to be going on
The different operational parameters studied are the concentration of KOH, urea
and temperature effects on the current density of the reaction. Preliminary tests were
obtained. Once the lowest concentration was established, the current density at 5 levels of
concentration of KOH tested for 3 levels of concentration of urea were carried out at
room temperature.
Catalyst preparation was performed in two stages: one for the preliminary tests
and another for the main set of experiments. The chemicals were obtained from Alfa
Aesar or Fisher Scientific. Electroplating was carried out in a 200 mL beaker at 45° C
60
against a platinum foil counter electrode. The bath composition was as follows:
The Rotor and Motor for the Rotating Disk Electrode Model 616 were obtained
from Pine Industries. A 5mm diameter Titanium removable disk was fitted into a Teflon
block which was then mounted onto the shaft of the rotating disk.
with nickel in the plating bath described above. The electro deposition was carried out at
-0.7 Volts versus Ag/AgCl electrode at 45o C for 15 minutes giving a catalyst loading of
100 mg, effectively 12.5 mg cm-2.. This nickel plated titanium electrode was used to
determine lowest concentration of KOH at which a response was obtained. Urea electro
oxidation to determine the response was carried out at room temperature starting with 2
For the second stage, the titanium removable disk electrode of diameter 5 mm was
electroplated with under the same operating conditions as mentioned above in the same
plating bath. Electroplating was carried out again for 15 minutes giving a deposition of
1.5 mg± 0.2 mg, effectively 5.1 mg cm -2. A platinum ring arrangement was used as the
the human urine) and all experiments were performed at room temperature. The 4 levels
of concentration of KOH tested were 1 M, 0.5 M, 0.25 M and 0.1M. This study was
61
conducted to purely select the lowest concentration at which a response is obtained. The
The second stage of experiments was carried out at five levels of concentration of
The speed of rotation of the rotating disk electrode was set at 1000 rpm, with the Hg-
HgO reference With 0.5 M KOH solution, the three levels of concentration of urea were
concentration of KOH was changed and the three concentrations of urea were again
tested. All experiments were performed at room temperature. The scan rate used was
20mV s-1.
Figure 6.1 represents the set of experiments performed initially to determine the
lower set point of KOH concentrations. 4 concentrations of KOH were tested starting
with 0.1 M. There was no response peak at 0.1 M. The lowest concentration of KOH that
gave a response was 0.25 M. There was not a significant difference between the
maximum current obtained with 0.25 M and 0.5 M. Hence 0.5 M was chosen as the lower
set point.
62
Figure 6.1: Preliminary experiment. Different concentrations of KOH at 20g L-1 urea to
The peaks given in Figure 6.2, Figure 6.3 and Figure 6.4 were obtained for
represents a solution with 1M KOH with no urea present. It is evident from all three
figures that the current density corresponding to the peak is the highest in the case of 5M
KOH. There is not a significant increase in the current density in case of 1 M, 2 M and 3
Figure 6.2: Urea concentration of 5 g L-1 varying KOH concentrations. Scan rate: 20mV
Figure 6.3: Urea Concentration of 10 g L-1 with varying KOH concentrations. Scan Rate:
Figure 6.4: Urea concentration of 20 g L-1 with varying KOH concentrations. Scan rate
6.4 Conclusion
This experimental study was strongly indicative of the fact that the concentration
of KOH plays a significant role in catalyzing the oxidation reaction. The maximum
current density obtained at 5 M KOH supports the argument that a higher concentration
of KOH is more favorable towards the oxidation reaction. However, as can be seen from
the oxidation peak and the rapid decrease of current from potentials of 0.55V to 0.7V,
of adherence of CO2 or the OH- onto the NiOOH surface which causes this rapid rise and
desorption of CO2 as the rate limiting step with the calculated rate constant value of
4.32x10-65 L mol-1s-1 . The desorption step also contributes to the maximum energy
requirement of the path (1242.2 kJ mol-1). Also based on the kinetics of the reaction,
→*CO(OH.OH) →*CO2 has been identified as the preferred pathway among the three
mechanisms. This has been discussed in Chapter 4 as Path 2. In this pathway, the bonding
between the NH2-NH group occurs initially versus the rotation of the nitrogen atoms
towards each other in the later stages as in Path 1. This facilitates easy desorption of the
nitrogen molecule.
blockage, mainly from the preferential adsorption of OH- onto the surface of NiOOH.
The binding energies of CO2 and OH- calculated to be 9.2 kJ mol-1 and 18.0 kJ mol-1
respectively. This suggested that in excess of OH- ions, the hydroxyl group is more
preferentially adsorbed onto the catalyst’s surface than CO2. This competition between
the molecules leading to adsorption onto the NiOOH surface leads to an increased
tendency of surface blockage which explains the decreased rate of reaction as time
progresses.
reaction mechanisms both without and in the presence of OH- has been discussed.
Change in free energy for the oxidation mechanism without OH- is -276.3 kJ mol-1
66
whereas with OH- it is -598.7 kJ mol-1. This indicates a greater spontaneity of the
reaction in the presence of hydroxide ions, which is known to catalyze the reaction. In
both the reaction mechanisms, the desorption of ammonia is the rate limiting step. In
L/mol.s.
current density of the anodic reaction with the highest KOH concentration in the matrix
significant difference in current densities for the lower concentrations of KOH. This is in
agreement with the modeling results which also indicate a greater favorability of the
After the role of OH- and the rate limiting step in the oxidation mechanism has
been established with this study, it is now recommended to look into improvements in the
rate constant approximations with inclusion of solvent effects in the system. Greater basis
sets can also be used to carry out similar calculations. At the same time, an experimental
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19. Estiu, G.; Suarez, D.; Merz, K. M., Quantum mechanical and molecular dynamics
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APPENDIX A
Figure 4.1a.
Cartesian Co-ordinates
C -1.82316000 -0.24239000 0.01975200
O -2.55328600 -1.13695200 -0.35074500
N -1.97383000 1.09072400 -0.14353600
H -1.12406800 1.67220000 -0.09544600
H -2.72889600 1.37104700 -0.75445700
H -0.59547900 -1.56764400 0.95055800
N -0.60348500 -0.56182000 0.78547000
H -0.59210900 -0.06419400 1.67783600
O 0.67900800 1.75585200 0.08121300
Ni 1.16539200 0.02173500 -0.05718900
H 1.30277400 2.39748300 -0.28939300
O 1.88514900 -1.45208300 -0.29295200
Figure 4.1b.
Cartesian Co-ordinates
C 1.41239600 0.01851800 0.08323000
O 1.81069200 -0.21337200 1.34003300
N 0.38580700 1.16294000 0.06431400
H 0.52624400 1.79385800 -0.72441100
H 0.39711300 1.68465100 0.94067000
H 3.34913000 0.14233900 -0.43878800
N 2.44541400 0.26800800 -0.89024100
H 2.36721100 -0.43278900 -1.62530200
O -2.74998500 0.19414100 -0.05149200
Ni -1.03769300 -0.18616900 -0.08272000
H -3.14380200 0.60065900 0.73432400
O 0.59761700 -1.06873400 -0.19956800
Figure 4.1c.
Cartesian Co-ordinates
C 1.41709000 -0.01699400 0.08075200
O 1.83677600 -0.71645200 1.13680100
N 0.39217400 1.04688300 0.49994200
H 0.52026600 1.94794500 0.03881700
H 0.42578200 1.17902500 1.51094400
H 3.22910400 -0.08598300 -0.75036700
N 2.47127100 0.58917500 -0.67591300
H 2.15179700 0.80659800 -1.61984000
O -2.75475400 0.19854100 0.01374500
Ni -1.03883900 -0.13894400 -0.13879000
H -3.16555000 0.21392000 0.89076100
O 0.59040700 -0.92227900 -0.58015900
Figure 4.2a.
Cartesian Co-ordinates
C 1.20477200 -0.76897600 0.05966100
O 1.85529500 -1.68279900 0.64009700
N 0.30534900 0.14547400 1.01417700
H 0.67818100 1.11212400 1.01899500
H 0.26404500 -0.27581900 1.94032500
H 3.02345900 0.25160400 -0.15776700
N 2.11110400 0.28811100 -0.60411100
H 2.19992300 0.07273300 -1.59702100
O -2.99382400 0.53908400 0.05754000
Ni -1.21216700 -0.12352700 -0.12886100
H -3.44559700 -0.01897600 0.69175900
O 0.21439700 -1.07721100 -0.89684500
H 1.03501000 2.35076700 -0.63881400
O 1.67936100 2.41406100 0.08948300
Figure 4.2b.
Cartesian Co-ordinates
C -1.00853200 0.38715800 0.09992600
O -1.79221700 0.91899500 0.93547700
N -0.00754200 -0.67147100 0.75841700
H -0.18298600 -1.64336300 0.50613300
H -0.02112300 -0.54339800 1.76945600
H -1.93274400 0.22917700 -1.71882000
N -1.64546300 -0.46021200 -1.02067400
H -2.59039100 -0.92884500 -0.63632000
O 3.23163000 -0.62758900 -0.00731400
Ni 1.46783800 0.09830500 -0.10838500
H 3.60446200 -0.30301000 0.81330000
O -0.02117600 1.16827400 -0.52359800
H -3.37570400 -0.00699700 0.54014400
O -3.79058100 -0.70433700 -0.02992300
Figure 4.2c.
Cartesian Coordinates
C -0.98825400 -0.61353200 -0.08341100
O -1.89510300 -0.78725900 -0.99862700
N -0.28348700 0.80947600 -0.17768400
H -0.65390500 1.46341900 0.51023900
H -0.47033000 1.17283700 -1.11154800
H -1.84394100 -1.62838700 1.34744900
N -1.62676500 -0.63177300 1.21994800
H -3.11019500 0.94708400 0.86349900
O 3.17859200 0.75770900 0.16281800
Ni 1.44396400 -0.02770900 0.01353500
H 3.46707600 1.02064700 -0.71205600
O 0.17247500 -1.40458300 -0.13455200
H -3.05429100 0.68477300 -0.58135600
O -3.38897900 1.37822600 0.03403700
Figure 4.3a
Cartesian Coordinates
C 1.45975300 0.00492500 -0.04374900
O 1.52767800 1.10600600 0.53073600
N -1.41977700 1.46060300 -0.65833300
H -2.23479800 1.85756100 -0.17860800
H -0.59904700 1.87629000 -0.20172900
H 2.66707100 -1.60381100 -0.22294400
N 2.69410500 -0.60726300 -0.42678900
O -3.17691400 -0.50928800 0.50907400
Ni -1.36679900 -0.26902300 -0.05115700
H -3.16970400 -0.16791400 1.40415900
O 0.43525600 -0.68025000 -0.39450700
H 3.32800200 0.72784200 0.70572700
O 3.78898500 -0.06150100 0.32771400
Figure 4.3b
C -1.46935900 0.06621100 -0.10310400
O -1.97486000 1.07859000 -0.55952800
N 1.18200300 1.44064700 0.62516000
H 2.09753600 1.89108600 0.53065700
H 0.57108700 1.91237200 -0.05207400
H -3.96278600 -0.92103600 0.31696000
N -1.52080100 -0.91249800 0.73525900
O 3.35823800 -0.33933700 0.00554800
Ni 1.45144900 -0.24042900 -0.04419700
H 3.62261800 0.04461000 -0.83138200
O -0.32334900 -0.66667900 -0.49453300
H -3.89480800 0.50498900 -0.15340800
O -4.54584000 -0.17186100 0.11382100
Figure 4.3c.
C -1.46935900 0.06621100 -0.10310400
O -1.97486000 1.07859000 -0.55952800
N 1.18200300 1.44064700 0.62516000
H 2.09753600 1.89108600 0.53065700
H 0.57108700 1.91237200 -0.05207400
H -3.96278600 -0.92103600 0.31696000
N -1.52080100 -0.91249800 0.73525900
O 3.35823800 -0.33933700 0.00554800
Ni 1.45144900 -0.24042900 -0.04419700
H 3.62261800 0.04461000 -0.83138200
O -0.32334900 -0.66667900 -0.49453300
H -3.89480800 0.50498900 -0.15340800
O -4.54584000 -0.17186100 0.11382100
Figure 4.4a.
C 2.02492500 -0.38489000 -0.00241700
O 1.99230200 0.91605100 0.08180300
N -0.61064000 1.43887000 0.56088100
H -1.36543800 2.04508800 0.88167600
H 0.16339300 1.45952600 1.23586300
N 3.10461800 -1.09422100 0.09749400
O -2.81349600 -0.74968000 -0.07955800
Ni -0.91949600 -0.52005600 0.01063900
H -3.23848300 0.10260600 0.02417000
O 0.86501000 -1.07525700 -0.19354400
H 0.87111100 1.60390300 -0.56236200
O -0.08032800 2.06478900 -0.61762000
Figure 4.4b.
C 2.01170900 -0.35367700 0.00509000
O 2.18295300 0.86382800 0.29183800
N -0.97253500 1.00690500 1.05888200
H -0.90336700 1.85766900 0.31385400
H -0.07156000 1.03695000 1.55617200
N 3.21320000 -0.94561200 -0.18820800
O -2.76489000 -0.75587600 -0.29843000
Ni -0.89091900 -0.51640500 -0.01738600
H -3.16585000 -0.08689400 0.25785900
O 0.92016600 -1.01324400 -0.10412700
H 0.66233400 2.05342800 -0.57228000
O -0.25457200 2.31669100 -0.78853600
Figure 4.4c.
C 1.96280600 -0.43774300 0.00690100
O 2.15911500 0.75955800 0.29045100
N -1.01634500 0.81115600 1.12483600
H -0.52846700 2.35796200 -0.09843000
H -0.07393700 0.78283100 1.55640600
N 3.10837800 -1.22417600 -0.20758200
O -2.82974900 -0.56562900 -0.38717700
Ni -0.95133400 -0.54084800 -0.04215000
H -3.13908700 0.18970600 0.11436400
O 0.85033100 -1.07380200 -0.10819300
H 0.94280400 2.18654700 -0.37593500
O 0.19717400 2.77291100 -0.60488200
Sum of electronic and zero-point Energies= -620.073313
Figure 4.5b.
C -1.80307200 -0.43587900 -0.03111000
O -2.06590800 0.82757900 -0.32615400
N 1.40802000 1.26871100 -0.77548000
H 1.18727100 2.05879800 0.03327100
N -3.05916200 -0.53880500 0.22860600
O 1.84845500 -1.49960600 0.69189800
Ni 0.88835200 -0.20613000 -0.33436800
H 1.15059400 -1.81839300 1.26559500
O -0.73322100 -1.10888000 -0.03446300
H -0.49570300 1.86977900 0.71847700
O 0.40822500 1.92683000 1.08868700
Figure 4.6b.
C -1.63484600 -0.09523300 -0.00410300
O -2.83955600 -0.37128000 0.01681500
N 1.11450600 1.52061700 0.62042600
N -1.06448400 0.94766600 -0.61927200
O 2.02456000 -1.19952400 -0.27830400
Ni 0.70852500 0.17304800 -0.09887300
H 1.65641400 -1.86311300 0.30640300
O -0.68952800 -0.89029800 0.57131000
Figure 4.6c.
C -1.77365400 -0.14105900 0.00890900
O -2.97989100 -0.30110800 0.03424500
N -0.00409200 1.34012200 -0.02902100
N -1.22717800 1.28134900 -0.01027800
O 2.76664500 0.03632900 -0.05209600
Ni 0.88179200 -0.27035900 -0.01508000
H 2.96961400 0.44625400 0.78964600
O -0.83662600 -1.03273900 -0.00037100
Figure 4.7a.
C 1.20477200 -0.76897600 0.05966100
O 1.85529500 -1.68279900 0.64009700
N 0.30534900 0.14547400 1.01417700
H 0.67818100 1.11212400 1.01899500
H 0.26404500 -0.27581900 1.94032500
H 3.02345900 0.25160400 -0.15776700
N 2.11110400 0.28811100 -0.60411100
H 2.19992300 0.07273300 -1.59702100
O -2.99382400 0.53908400 0.05754000
Ni -1.21216700 -0.12352700 -0.12886100
H -3.44559700 -0.01897600 0.69175900
O 0.21439700 -1.07721100 -0.89684500
80
Figure 4.7b.
C 1.11893100 -0.73269800 0.05283800
O 1.92178300 -1.43583100 0.82940900
N 0.31997700 0.37140100 0.75932000
H 0.79280000 1.35376400 0.57014000
H 0.29309100 0.14710300 1.75441800
H 2.20324600 1.06996200 -0.52331000
N 2.03676700 -0.02633800 -0.82170100
H 2.72240500 -0.64937200 -1.23704700
O -2.91919800 0.74401700 0.00072800
Ni -1.24860500 -0.17519500 -0.11003000
H -3.32197200 0.46847600 0.82511500
O 0.08690300 -1.41727000 -0.56617600
H 1.38512900 2.75363600 -0.67991600
O 1.86994300 2.32691200 0.04742200
Figure 4.7c.
C 0.99746100 -0.78442200 0.08853800
O 1.81397600 -1.49510900 0.90042200
N 0.38280100 0.42593500 0.66379300
H 1.45038100 1.81702300 0.39054500
H 0.30536100 0.23990700 1.66850400
H 2.56283500 0.41764900 -0.60344900
N 1.98359200 -0.35347000 -0.94270900
H 2.53471600 -1.14934600 -1.25722700
O -2.92928800 0.86073800 -0.05867100
Ni -1.28226400 -0.10614900 -0.08192800
H -3.35673400 0.65211500 0.77291200
O -0.05528100 -1.48195200 -0.45081800
H 1.82922200 2.65544200 -0.82412500
O 2.17410300 2.43365500 0.05506900
Figure 4.8a.
C 2.07533200 0.15923400 0.05206000
O 1.91428500 1.35279200 0.33248100
N -0.98069100 1.13176900 -0.60469600
H -0.19066600 1.64968800 -0.19527700
H 4.03864900 0.18640400 0.54568700
N 3.39767200 -0.35319800 -0.02314400
H 3.44676700 -1.34977100 0.15291500
O -2.52425600 -1.00716700 0.24593200
Ni -0.68445500 -0.59698500 -0.06226100
H -2.59765000 -0.95643800 1.19976900
O 1.18239400 -0.73350200 -0.23729300
O -2.09995500 1.63084400 0.16401700
H -2.68296300 0.83655000 0.08163100
Figure 4.8b.
Figure 4.8c.
Figure 4.9a.
C -1.10122000 0.39373100 -0.18453500
O -0.55989300 1.65287000 0.10855100
N 0.80418900 1.66410000 0.23462000
H -2.83943900 1.29120000 -0.18867400
N -2.40089700 0.38732100 -0.36498100
H -3.02709300 -0.40148200 -0.20352100
O 2.73944200 -1.48309000 -0.03380100
Ni 1.47603800 -0.05218100 0.03261500
H 3.62369500 -1.14916200 0.12225100
O -0.30589800 -0.58011800 -0.25090900
O -4.08180100 -1.23072900 0.24513900
H -3.63676600 -1.87328000 0.82461900
Figure 4.9b.
C 1.03551900 0.06890400 0.27798200
O 0.72848200 1.41223800 0.05818700
N -0.60113600 1.66506400 -0.15052500
H 3.09045600 0.40864900 0.15097200
N 2.29896700 -0.15961800 0.55800600
H 2.79023400 -1.05148900 0.28024500
O -2.99256100 -1.18496100 -0.07399000
83
Figure 4.9c.
C 1.22622900 0.73729100 -0.00670100
O 0.32081600 1.80642100 0.01919000
N -1.02153600 1.44997900 0.00145100
H 2.63257000 1.99918400 0.03851600
N 2.49045500 0.98969800 0.00967500
H 3.42709400 -0.79707400 0.03125800
O -3.03500200 -0.86549300 -0.03561600
Ni -1.19376300 -0.35769400 -0.02680700
H -3.36695000 -0.65886100 0.83895700
O 0.68449700 -0.43699000 -0.04275500
O 3.36652200 -1.77574000 0.03426500
H 2.39816700 -1.85489400 0.00353100
Figure 4.10a.
C 1.28372000 0.36211600 -0.05855400
O 0.77513400 1.51590400 0.06553200
N -0.83279900 1.44016300 0.03944000
H 3.14490000 0.93437400 0.41503000
N 2.68242300 0.26792300 -0.19951600
O -3.12296400 -0.43741700 0.02286800
Ni -1.22047900 -0.28288700 -0.04619700
H -3.30299800 -0.25129400 0.94520700
O 0.60760900 -0.71283000 -0.13363700
O 3.15887000 -1.03249500 0.20545400
H 2.33261900 -1.55683400 0.12340100
Figure 4.10b.
C 1.07048800 1.22872700 0.01385300
O 1.87619200 2.11851100 -0.23583100
N -2.82397300 -0.22638400 -0.41218900
H 2.15024300 -0.70207600 -0.07420300
N 1.50094800 0.00940000 0.53803600
O 0.37911500 -0.93155500 0.61282500
Ni -1.28692600 -0.17631400 0.06326300
H 0.81515100 -1.65751900 0.16492600
O -0.24553100 1.37622300 -0.13554800
O 2.14338100 -2.06472300 -0.60101200
H 2.68153000 -2.54474400 0.05039800
Figure 4.10c.
C -1.03104100 -0.61339600 0.02962100
O -2.01134700 -1.38501600 0.06616600
N 3.16613400 -0.32873800 0.14334800
H -3.62230600 -0.35434900 0.00499100
N -1.20226600 0.73400000 0.12515900
O 0.14225200 1.31385500 -0.06078000
Ni 1.63771900 0.12580200 -0.04638300
H 0.07969200 2.19215700 0.31662700
O 0.21561600 -1.10288000 -0.09498200
O -4.15372800 0.47130500 -0.03992200
H -3.41670700 1.10516200 -0.04402100
Figure 4.11a.
C -1.43331000 -0.57440100 0.05632800
O -2.46176500 -1.22281500 -0.17251000
N -1.54662400 0.82412800 0.27775200
H -0.73200100 1.34066500 -0.04021800
H -3.22462500 0.72246100 -0.71904600
N -2.76397700 1.44029300 -0.14895600
H -3.35303500 1.49551600 0.68451700
O 3.06344400 0.79265900 -0.13256200
Ni 1.40847700 -0.15263700 -0.00766600
H 3.69522900 0.19496600 0.26915300
85
Figure 4.11b.
C 1.67138600 -0.23508800 -0.01004800
O 2.85490100 -0.05748600 0.25548100
N 0.81855100 -1.23915400 0.45123400
H 0.95356300 -1.46292600 1.43577200
H -0.82075600 2.18524000 1.23917600
N -0.74859600 2.70981400 0.35181500
H 0.06312900 2.25077100 -0.09945700
O -2.45950900 -0.75164800 0.25640100
Ni -0.66286500 -0.28575000 -0.19427500
H -2.64313900 -1.55311300 -0.23522800
O 0.91578500 0.52125300 -0.81958300
Figure 4.11c.
Figure 4.13a.
C -1.05145600 0.82665700 -0.15465900
O -2.03201400 1.53156600 0.10256500
N -1.25927300 -0.51796800 -0.62364400
H -0.59857500 -1.14814600 -0.16008800
H -2.59701900 -1.90944500 -0.82555400
N -2.60321200 -0.92134600 -0.57442200
O 3.38847000 -0.84863400 0.09637700
Ni 1.73762200 0.11055000 0.04379800
H 3.13720800 -1.74107200 0.33759300
O 0.18726700 1.16947800 -0.05353100
O -3.05519400 -0.99596900 0.82535900
H -3.15712200 -0.03301700 0.96996400
Figure 4.13b.
C 0.90139800 1.23664100 -0.02634000
O 1.75293600 2.09188700 -0.15191200
N 1.31962600 -0.11823100 0.43495000
H 0.56100200 -0.81719800 0.41730300
H 2.67775400 -1.46271800 0.74953700
N 2.52076000 -0.41539300 0.71600300
O -3.19803000 -1.19682900 0.09359400
Ni -1.71774300 -0.00042700 -0.06600200
H -2.80602100 -2.06904500 0.15131600
O -0.36915000 1.30236700 -0.20174300
O 3.22145900 -1.92062400 -0.58611700
H 4.11525200 -1.53795900 -0.59929400
Figure 4.13c.
C 0.45338500 1.62193200 0.00034500
O 1.06372000 2.66592200 0.00334700
N 1.30628900 0.29921100 -0.00983600
H 0.64645600 -0.53745400 -0.01105300
H 3.43696500 -1.44664900 -0.01457500
N 2.51444900 0.23624500 -0.01471100
O -2.84091100 -1.81938300 -0.00510000
Ni -1.72880600 -0.26656300 0.00337600
H -2.23087000 -2.55803800 -0.00675700
O -0.79682800 1.36617000 0.00380000
O 4.09381200 -2.18429600 0.00245500
H 4.93020100 -1.70119900 0.07159100
Figure 4.14a.
C 1.87237300 -0.12034900 -0.06347700
O 3.10232700 -0.11537100 -0.06692000
N 1.15502300 1.10443100 -0.07318500
H 1.68057300 1.86216600 0.35722700
N -0.15046500 0.98959200 0.50297200
O -2.59182200 -0.31285700 0.01764400
Ni -0.71911900 -0.68791800 0.03788800
H -2.81104200 -0.31614500 -0.91493100
O 1.09370600 -1.17198500 -0.07935100
O -0.99680800 1.89219600 -0.25532200
H -1.85957300 1.44374200 -0.05923000
Figure 4.14b.
C 1.47486200 -0.66919400 0.06258000
O 2.58927600 -1.11176000 0.23345300
N 1.07900000 0.61611900 0.72037600
H 1.82346400 1.17489400 1.13909100
N -0.13958400 0.87589900 0.94022500
O -2.98581800 0.26133800 -0.00660300
Ni -1.14870600 -0.25355200 -0.09609000
H -3.04988400 1.07419400 -0.50951900
O 0.43474400 -1.18296600 -0.50016200
89
Figure 4.14c.
C -0.97219500 -1.46887400 0.01016600
O -1.86348000 -2.29451100 0.04041400
N -1.34638900 0.00638600 -0.01146900
H -2.89407200 1.46493500 0.01137300
N -0.38306600 0.76807900 -0.03326900
O 2.62666500 1.30733700 -0.04417700
Ni 1.26491900 -0.03170300 -0.01733200
H 2.57281700 1.74824200 0.80462600
O 0.30860600 -1.65025500 -0.00497000
O -2.96390500 2.43822500 0.00474700
H -2.02021400 2.66010900 -0.04664700
Figure 4.15c.
C -1.51305700 -0.99905100 0.02089600
O -2.61158000 -1.40528200 -0.32088400
N -1.01175700 2.42502400 0.37036200
N -1.48718000 2.67041300 -0.59690900
O 3.02054600 0.28074300 0.22431900
Ni 1.25514200 -0.32156200 -0.18638400
H 2.99958700 0.47718500 1.16172800
O -0.44890900 -0.90362500 -0.72657900
O -1.35425600 -0.57776200 1.33634100
H -0.41907400 -0.29979600 1.41190700
Figure 4.16a.
C 1.95169500 -0.14060800 0.04005900
O 3.05976200 -0.64582300 0.15361100
O -2.76653900 -0.39470300 0.34836600
Ni -0.90896200 -0.30726900 -0.08737100
H -2.77721800 -0.26993600 1.29814700
O 0.88502900 -0.78408700 -0.38509100
O 1.77194400 1.17261900 0.35679900
H 0.83480500 1.43149500 0.15065600
O -0.78521400 1.46528700 -0.37543900
H -1.63667100 1.77926800 -0.02875300
Figure 4.16b.
C 1.79641700 -0.00963800 0.13052900
O 3.01358100 -0.19572800 0.16389200
O -2.54966500 -0.23536600 0.55097800
Ni -0.76634400 -0.42748000 -0.10549700
91
Figure 4.16c.
C 1.74801200 0.34345300 0.03470600
O 2.80315800 0.94982800 0.08126800
O -2.19391200 -0.81692000 0.14615900
Ni -0.29431100 -0.72541800 -0.03060100
H -2.38395800 -0.87326100 1.08342800
O 1.54657900 -0.90880200 -0.36510600
O 0.54518500 0.83864600 0.39620700
H -1.26952200 1.99212100 -0.10830200
O -2.22596700 1.95512400 -0.27659400
H -2.39422600 0.98911600 -0.18200300
Figure 4.17a.
C -1.57006600 -0.05627200 0.00681100
O -2.78384100 -0.18973200 0.02369600
O 2.60967800 -0.20197200 -0.07037200
Ni 0.72906000 0.12738300 -0.01651300
H 2.87080600 -0.37518500 0.83493100
O -0.88717500 1.08717500 0.01487600
O -0.67167200 -1.05221100 -0.01987800
Figure 4.17b.
C -1.83991200 0.00009500 0.02852300
O -2.40824700 -1.06644000 -0.32254400
O 2.84993300 0.00044600 -0.50413500
Ni 1.03944500 -0.00029500 0.10433300
H 3.50864600 0.00181000 0.19146500
O -0.73053400 -0.00034400 0.73803200
O -2.40785800 1.06707400 -0.32184500
APPENDIX B:
Figure 5.1a.
Cartesian Co-ordinates
Figure 5.1b.
C -1.79914400 -0.20186200 -0.00811300
O -0.69068500 -0.79472300 0.08449100
N -2.94461500 -0.93478100 0.13396200
H -3.80994000 -0.58804200 -0.25565400
H -2.81538600 -1.93683600 0.10789800
H -1.01264300 1.64306800 -0.16896100
N -1.90334600 1.12072100 -0.23359600
H -2.77604700 1.60150300 -0.07094700
O 2.59110700 -0.93860000 -0.17292700
Ni 1.11318100 0.02580200 -0.02517600
H 3.02872500 -1.16549900 0.66263400
O 0.71793200 1.68744200 0.23544500
Figure 5.1c.
C 1.87733800 0.03577100 -0.01829500
O 3.05747600 -0.11991500 0.17401700
N -2.18224100 -1.08778200 0.05514600
H -2.27774300 -1.68407000 0.87698900
H -2.33964100 -1.65468600 -0.77825000
H 1.30893300 1.98016200 -0.02933900
N 1.00353700 1.02227400 -0.13759700
H -2.87274100 -0.33059300 0.09564000
O 0.98987200 -1.15452300 -0.17801600
Ni -0.60526100 0.09471300 -0.01894200
H 1.33476600 -1.86541000 0.38892400
O -1.69976800 1.41775900 0.08691800
Figure 5.1d.
C 1.41709000 -0.01699400 0.08075200
O 1.83677600 -0.71645200 1.13680100
N 0.39217400 1.04688300 0.49994200
H 0.52026600 1.94794500 0.03881700
H 0.42578200 1.17902500 1.51094400
H 3.22910400 -0.08598300 -0.75036700
N 2.47127100 0.58917500 -0.67591300
H 2.15179700 0.80659800 -1.61984000
O -2.75475400 0.19854100 0.01374500
Ni -1.03883900 -0.13894400 -0.13879000
H -3.16555000 0.21392000 0.89076100
O 0.59040700 -0.92227900 -0.58015900
Figure 5.1e.
Figure 5.2a.
C -1.82316000 -0.24239000 0.01975200
O -2.55328600 -1.13695200 -0.35074500
N -1.97383000 1.09072400 -0.14353600
H -1.12406800 1.67220000 -0.09544600
H -2.72889600 1.37104700 -0.75445700
H -0.59547900 -1.56764400 0.95055800
N -0.60348500 -0.56182000 0.78547000
H -0.59210900 -0.06419400 1.67783600
O 0.67900800 1.75585200 0.08121300
Ni 1.16539200 0.02173500 -0.05718900
H 1.30277400 2.39748300 -0.28939300
O 1.88514900 -1.45208300 -0.29295200
Figure 5.2b
Figure 5.2c
C 1.80583200 -0.10139700 -0.02411800
O 2.99247700 -0.25106700 0.13320400
N 1.06771100 1.07737400 -0.19009400
H -1.99019300 -1.86640800 -0.80621600
H 1.29348200 1.78728400 0.50805800
H -1.88257900 -1.93002200 0.83565300
N -1.98112700 -1.29915900 0.04096500
H -2.86411400 -0.79402500 0.11557100
O -1.75674700 1.34830200 0.06994200
Ni -0.51757500 0.09400300 -0.01451300
H -1.35873700 2.22838400 -0.03206100
O 0.87091400 -1.08428800 -0.08139800
Figure 5.3a
C 1.42994700 -0.20637300 0.15512900
O 2.22621200 -0.80468300 0.86427400
N 0.26590400 0.76317100 0.77391800
H 0.93513500 1.55074100 0.02319100
H 0.13619100 0.70011700 1.78818100
H 2.90432300 1.27488800 -0.40529800
N 1.94848300 1.05870700 -0.68477700
H 1.88734900 0.93076800 -1.69438200
O -2.61170700 0.30015600 0.21530900
Ni -1.00679800 -0.21065100 -0.17878900
H -2.75577800 1.02453200 0.84312400
O 0.51083600 -0.88269000 -0.71752000
Figure 5.3b
Figure 5.5
Figure 5.6a.
Figure 5.6b.
Ni 0.92295100 -0.03617000 0.00837800
O 1.39352400 -1.76795800 -0.02652200
H 2.36208900 -1.67892600 -0.04308500
O 0.53345700 1.69433000 0.00480500
O 2.70598700 0.38481100 0.00399100
H 2.64403800 1.35359800 -0.01291100
H -0.45139900 1.74977300 -0.00781700
N -0.91081200 -0.63003800 0.03209900
C -2.06835900 0.02977300 -0.01341700
H -0.95967000 -1.63836300 -0.06357300
O -2.21020700 1.27173100 -0.01610800
N -3.25590600 -0.76759000 -0.09154100
H -3.19725600 -1.62560900 0.44898100
H -4.04533000 -0.20627500 0.21107900
Figure 5.6c.
Ni 0.92295100 -0.03617000 0.00837800
O 1.39352400 -1.76795800 -0.02652200
H 2.36208900 -1.67892600 -0.04308500
O 0.53345700 1.69433000 0.00480500
O 2.70598700 0.38481100 0.00399100
H 2.64403800 1.35359800 -0.01291100
H -0.45139900 1.74977300 -0.00781700
N -0.91081200 -0.63003800 0.03209900
C -2.06835900 0.02977300 -0.01341700
H -0.95967000 -1.63836300 -0.06357300
O -2.21020700 1.27173100 -0.01610800
N -3.25590600 -0.76759000 -0.09154100
H -3.19725600 -1.62560900 0.44898100
H -4.04533000 -0.20627500 0.21107900
Figure 5.7a
Ni 0.83634700 -0.07634100 0.11034500
O 0.60221200 1.68834200 0.44563300
H 1.45141100 2.02002800 0.10458000
O 1.08594600 -1.80350200 -0.25112100
O 2.53840800 0.34014500 -0.48601700
H 2.85374500 -0.52784100 -0.78337000
H 0.22323800 -2.14191100 0.05900000
N -0.95152800 -0.56450300 0.74511300
C -2.05826300 -0.07983900 -0.01519700
H -0.99293300 -0.11575600 1.66394400
O -3.07267200 -0.74841000 -0.21582500
N -1.92630000 1.18710800 -0.52384700
H -1.05107600 1.69437000 -0.37504200
H -2.63888500 1.51686500 -1.15781800
Figure 5.7b.