An Investigation of Molecular Properties Using Magnetic Shielding Calculations

175 Pages·2014·49.37 MB·English

An Investigation of Molecular
Properties Using Magnetic
Shielding Calculations
Kate Elizabeth Horner MChem(hons)
PhD Thesis
University of York
Chemistry
September, 2014
For my grandparents, Cliff and Irene,
for constant inspiration, support and love,
just to see me in a funny hat.
Abstract
Isotropic shielding calculations were performed across finely spaced two- and
three-dimensionalgridspositionedthroughandaroundawiderangeofmolecules.
These magnetic shielding calculations were used to investigate aromaticity, an-
tiaromaticity and a variety of chemical bonding features.
This technique was found to be incredibly sensitive and able to distinguish be-
tween bonds of different order as well as bonds of the same order but in dif-
ferent environments. The shielding along the whole bonding region, as well as
1 Å above the bond and cross-sections through the bond, can be used to provide
detailedinformationaboutthenatureofthechemicalbondingandtheconjugation
with the rest of the system.
Regions of deshielding have been found around unsaturated nuclei and these
areas can be used to determine relative aromaticities as well as degrees of con-
jugation. The same is true of shielding features found at 1 Å above the molecular
plane. Unsaturated heavy atoms also display these deshielded surroundings, but
they can be harder to observe.
Antiaromatic systems exhibit a dumbbell shaped region of deshielding at the ring
centre as well as significantly bent bonding regions which have been found to be
a result, primarily, of the antiaromaticity rather than ring strain.
H-bonding can also be studied with this technique and it has been found that
the shielding on the atoms involved is most informative. In the case of substituted
malonaldehydes,theoxygenshieldingswereusedtodeterminerelativearomatic-
ities in the pseudo rings and, therefore, H-bond strength.
The sensitivity and information-rich nature of this technique has proven far supe-
riortoexistingmethods, suchasthecommonlyusednucleus-independentchem-
ical shift (NICS) technique, and therefore has great scope for future applications.
3
Contents
Abstract 3
List of Figures 8
List of Tables 11
Preface 13
Acknowledgements 14
Declaration 15
1 Introduction 16
1.1 Investigation of Chemical Bonding . . . . . . . . . . . . . . . . . . 17
1.2 Aromaticity & Antiaromaticity . . . . . . . . . . . . . . . . . . . . . 19
1.2.1 Aromaticity- More Than Just Benzene . . . . . . . . . . . . 19
1.2.2 The Addition of Antiaromaticity . . . . . . . . . . . . . . . . 21
1.2.3 The Importance of Aromaticity & Antiaromaticity . . . . . . 21
1.3 Characterisation of Aromaticity & Antiaromaticity . . . . . . . . . . 23
1.3.1 Magnetic Shielding Calculations . . . . . . . . . . . . . . . 24
1.3.2 NICS Technique . . . . . . . . . . . . . . . . . . . . . . . . 25
1.3.3 Other NICS Indices . . . . . . . . . . . . . . . . . . . . . . 26
1.3.4 Multiple NICS Calculations . . . . . . . . . . . . . . . . . . 27
1.4 Quantum Chemical Methods . . . . . . . . . . . . . . . . . . . . . 28
1.4.1 Many-Body Perturbation Theory . . . . . . . . . . . . . . . 29
1.4.2 Complete Active Space Self-Consistent Field Approach . . 30
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CONTENTS
1.4.3 Density Functional Theory . . . . . . . . . . . . . . . . . . . 30
1.4.4 Basis Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
1.5 Computational Procedure . . . . . . . . . . . . . . . . . . . . . . . 31
2 Chemical Bonding 33
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.2 Small Hydrocarbon Systems . . . . . . . . . . . . . . . . . . . . . 35
2.3 Multiple Double Bonds in a Single System . . . . . . . . . . . . . . 41
2.3.1 Allene and 1,3-Butadiene . . . . . . . . . . . . . . . . . . . 41
2.3.2 Acrolein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
2.4 3-Centre-2-Electron Bonding . . . . . . . . . . . . . . . . . . . . . 47
2.5 Hydrogen Bonding . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
2.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3 Aromaticity & Antiaromaticity 54
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
3.2 Benzene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.3 Cyclobutadiene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
3.4 Cyclobutene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.5 Heavy Element Analogues of Benzene . . . . . . . . . . . . . . . . 66
3.5.1 Hexasilabenzene . . . . . . . . . . . . . . . . . . . . . . . . 66
3.5.2 Hexagermabenzene . . . . . . . . . . . . . . . . . . . . . . 68
3.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
4 Multiple Ring Systems 72
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.2 Naphthalene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
4.2.1 Azulene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.3 Benzocyclobutadiene . . . . . . . . . . . . . . . . . . . . . . . . . 77
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CONTENTS
4.4 Benzodicyclobutadiene . . . . . . . . . . . . . . . . . . . . . . . . 79
4.5 Fulvalenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
5 Charged Cycles 89
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.2 Cyclopropane, Cyclopropene & Cyclopropenyl Cation . . . . . . . 91
5.3 Cyclopentadienyl Anion . . . . . . . . . . . . . . . . . . . . . . . . 96
5.4 Tropylium Cation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
5.5 Cyclooctatetraene . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
6 Heterocycles 105
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
6.2 Five-Membered, Single Heteroatom Heterocycles . . . . . . . . . . 107
6.2.1 Furan, Pyrrole & Thiophene . . . . . . . . . . . . . . . . . . 107
6.2.2 Selenophene . . . . . . . . . . . . . . . . . . . . . . . . . . 112
6.2.3 Phosphole & Phospholide Ion . . . . . . . . . . . . . . . . . 115
6.3 Five-Membered Azoles . . . . . . . . . . . . . . . . . . . . . . . . 120
6.4 Six-Membered Heterocycles . . . . . . . . . . . . . . . . . . . . . 124
6.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
7 Substituent Effects 133
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
7.2 Substituted Benzenes . . . . . . . . . . . . . . . . . . . . . . . . . 135
7.3 Substituted Ethenes . . . . . . . . . . . . . . . . . . . . . . . . . . 142
7.4 Malonaldehyde & Derivatives . . . . . . . . . . . . . . . . . . . . . 146
7.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
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CONTENTS
8 Conclusions 155
8.1 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
A Example Fortran Code 160
Abbreviations 166
References 167
7
List of Figures
1.1 Aromatic Natural Products . . . . . . . . . . . . . . . . . . . . . . . 22
2.1 Simple Hydrocarbons- Molecular Plane . . . . . . . . . . . . . . . 36
2.2 Simple Hydrocarbons- Bond Cross-Section . . . . . . . . . . . . . 38
2.3 Simple Hydrocarbons- 1 Å Above . . . . . . . . . . . . . . . . . . . 39
2.4 Ethene- Altered Bond Lengths . . . . . . . . . . . . . . . . . . . . 40
2.5 Allene & trans-1,3-butadiene . . . . . . . . . . . . . . . . . . . . . 42
2.6 Acrolein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.7 Diborane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
2.8 Water Dimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.1 Benzene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.2 Benzene- Theory Comparison . . . . . . . . . . . . . . . . . . . . 59
3.3 Cyclobutadiene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3.4 Benzene & Cyclobutadiene 3D . . . . . . . . . . . . . . . . . . . . 62
3.5 Cyclobutene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.6 Si H . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
6 6
3.7 Ge H . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
6 6
4.1 Naphthalene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.2 Naphthalene Resonance Structures . . . . . . . . . . . . . . . . . 75
4.3 Azulene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.4 Benzocyclobutadiene . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.5 Benzodicyclobutadiene-1 . . . . . . . . . . . . . . . . . . . . . . . 80
4.6 Benzodicyclobutadiene-2 . . . . . . . . . . . . . . . . . . . . . . . 81
4.7 Fulvalene-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
8
LIST OF FIGURES
4.8 Fulvalene-2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.9 Fulvalene-3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.1 Cyclopropane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.2 Cyclopropene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
5.3 Cyclopropenyl Cation . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.4 Cyclopentadienyl Anion . . . . . . . . . . . . . . . . . . . . . . . . 97
5.5 Tropylium Cation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
5.6 COT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
5.7 COT Dianion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.8 COT Dication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
5.9 Na COT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
2
6.1 Furan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
6.2 Pyrrole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
6.3 Thiophene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
6.4 Selenophene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
6.5 Phosphole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
6.6 Phospholide Ion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
6.7 Imidazole, Oxazole & Thiazole . . . . . . . . . . . . . . . . . . . . 122
6.8 Pyridine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
6.9 Pyrimidine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
6.10 Phosphabenzene . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
7.1 Aniline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
7.2 Toluene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
7.3 Phenol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
7.4 2-Nitrophenol & 4-Nitrophenol . . . . . . . . . . . . . . . . . . . . . 138
7.5 Monofluorobenzene . . . . . . . . . . . . . . . . . . . . . . . . . . 140
7.6 Hexafluorobenzene . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
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LIST OF FIGURES
7.7 But-1-en-3-yne . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
7.8 Acrylonitrile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
7.9 Nitroethene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
7.10 Ethenol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
7.11 Malonaldehyde . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
7.12 Malonaldehyde Derivatives . . . . . . . . . . . . . . . . . . . . . . 152
10