Theoretical approach towards accurate molecular interactions with low-dimensional substrates

149 Pages·2016·14.76 MB·English

Theoretical approach towards
accurate molecular interactions with
low-dimensional substrates
Yasmine Shauket Al-Hamdani
A dissertation submitted for the degree of
Engineering Doctorate
Department of Chemistry
University College London
December 2016
Declaration
I, Yasmine Shauket Al-Hamdani, confirm that the work presented in this thesis is my own.
Whereinformationhasbeenderivedfromothersources,Iconfirmthatthishasbeenindicated
in the thesis. The work contains nothing which is the outcome of work done in collaboration
except where specifically indicated in the text.
Yasmine Shauket Al-Hamdani
December 2016
2
Acknowledgements
Alas, my time at UCL has come to an end after some wonderful years. I have had the plea-
sure of working with my supervisor, Angelos Michaelides. I could not be more grateful for the
guidance and care that he has provided during my PhD. I also extend my gratitude to my
co-supervisorsDarioAlfèandAnatolevonLilienfeld, whohaveadvisedmeandgivenmetheir
invaluable insights throughout my PhD. I would also like to thank Mariana Rossi, Alexander
Tkatchenko, Georg Kresse, Andreas Grüneis, Ming Ma, and Laurent Joly for helpful discus-
sions and collaborations. In addition, the work in this thesis would not have been possible
without the generous computational resources provided by Argonne National Lab on MIRA,
Oak Ridge National Lab on TITAN, and the LCN services at UCL.
I truly value my time in the ICE group and thank all members, past and present, for the
great environment in which we work. In particular, I would like to thank my friends and
peers: Stephen Cox, Gabriella Graziano, Gabriele Tocci, and Erlend Davidson, for offering
their support when I first joined the group. In addition, I have made life-long friends here,
perhaps too many to name, but I cherish them and thank them dearly for making the last
few years of my life the happiest.
Finally, I dedicate this work to my mother, Dr. Alia Al-Hamdani, and my father, Dr. Ali
Shauket. They have made countless sacrifices in order for me to have opportunities, and have
raised me to value academia as one. I am eternally grateful for their never-ending love and
encouragement.
3
Contents
1 Introduction 11
2 Theoretical background 17
2.1 Quantum mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.1.1 Born-Oppenheimer approximation . . . . . . . . . . . . . . . . . . . . 19
2.2 Quantum chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2.1 Post Hartree-Fock methods . . . . . . . . . . . . . . . . . . . . . . . . 21
2.3 Density functional theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.3.1 Exchange-correlation functionals . . . . . . . . . . . . . . . . . . . . . 27
2.3.2 Random phase approximation . . . . . . . . . . . . . . . . . . . . . . . 31
2.4 Quantum Monte Carlo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.4.1 The Monte Carlo technique . . . . . . . . . . . . . . . . . . . . . . . . 33
2.4.2 Variational Monte Carlo . . . . . . . . . . . . . . . . . . . . . . . . . . 35
2.4.3 Diffusion Monte Carlo . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.5 Calculations in practice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.5.1 Localised basis sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
2.5.2 Plane-waves and Bloch’s theorem . . . . . . . . . . . . . . . . . . . . . 40
3 Water and 1,2-azaborine: role of exact exchange 43
3.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.3.1 Computational Methods . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.3.2 Water and 1,2-azaborine Setup . . . . . . . . . . . . . . . . . . . . . . 47
4
3.4 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.4.1 Stability Trends for water on 1,2-azaborine . . . . . . . . . . . . . . . 48
3.4.2 From benzene to borazine . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.5 Discussion and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4 Establishing the adsorption energy of water on h-BN from DMC 58
4.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
4.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
4.5 Conclusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
5 Further insights from water adsorption on BN substrates 65
5.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
5.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
5.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
5.4.1 Water adsorption on borazine and boronene . . . . . . . . . . . . . . . 69
5.4.2 Water on h-BN surface and the impact from long-range correlation . . 73
5.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
5.6 Conclusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
6 Physisorption inside/outside a carbon nanotube 79
6.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
6.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
6.4.1 Performance of xc functionals: Challenge of internal interaction . . . . 86
6.4.2 Reliable water-carbon potentials for water/CNT? . . . . . . . . . . . . 90
6.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
6.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5
7 Tuning dissociation at 2D surfaces 97
7.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
7.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.3.1 System setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
7.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
7.4.1 Dissociative adsorption of water on graphene, h-BN, BNDG and 2CBN 102
7.4.2 Dissociative adsorption of hydrogen, methane, and methanol. . . . . . 107
7.5 Discussion and general framework . . . . . . . . . . . . . . . . . . . . . . . . . 110
7.6 Conclusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
8 Using alchemical derivatives for efficient screening 114
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
8.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
8.2.1 System Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
8.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
8.5 Conclusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
9 Conclusions and Outlook 127
6
List of Figures
3.1 Water/1,2-azaborine molecule configurations. . . . . . . . . . . . . . . . . . . 48
3.2 The percentage difference between ∆CCSD(T) interaction energy and that
from DMC, MP2 and the various DFT xc functionals. . . . . . . . . . . . . . 51
3.3 Water/1,2-azaborine interaction energies with different amounts of exact ex-
change. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
4.1 Water monomer on different sites above h-BN surface. . . . . . . . . . . . . . 61
4.2 Interaction energy curves for water situated above the N site in h-BN. . . . . 63
5.1 Water adsorption configurations on BN substrates. . . . . . . . . . . . . . . . 69
5.2 Interaction energy curves for water situated above the N site in a borazine
molecule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
5.3 Interaction energy curves for water situated above the N site in boronene
molecule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
5.4 Interaction energy curves for water situated above the N site in h-BN. . . . . 74
5.5 Long range correlation energy from MP2, RPA and DFT+MBD. . . . . . . . 76
6.1 Unit cell of water outside and inside a CNT(10,0). . . . . . . . . . . . . . . . 83
6.2 Unit cell of H outside and inside a CNT(10,0). . . . . . . . . . . . . . . . . . 84
2
6.3 Interaction energies of water inside/outside a CNT with DMC and a range of
xc functionals.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
6.4 Interaction energies of H inside/outside a CNT with DMC and a range of xc
2
functionals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
6.5 Non-local correlation contribution to the interaction energy of water outside
and inside the CNT(10,0). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
7
6.6 Ratio of vdW-DF to PBE+D3 interaction energies for water inside/outside of
CNTs with different diameters. . . . . . . . . . . . . . . . . . . . . . . . . . . 95
6.7 Radial distribution function of oxygen and carbon within the unit cells of
CNT(10,0), CNT(14,0) and CNT(20,0). . . . . . . . . . . . . . . . . . . . . . 96
7.1 Unit cells of isoelectronic doping in h-BN and graphene. . . . . . . . . . . . . 100
7.2 The dissociative adsorption energy of water on graphene, BNDG, 2CBN and
h-BN is shown for different adsorption structures. . . . . . . . . . . . . . . . . 103
7.3 Themoststabledissociativeadsorptionstructuresofwaterongraphene, h-BN,
BNDG and 2CBN. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
7.4 Dissociative adsorption energies including ZPE contributions of H , methane,
2
water, and methanol on graphene, BNDG, 2CBN and h-BN. . . . . . . . . . . 108
8.1 (7 × 7) unit cell of graphene doped with two pairs of BN and two hydrogen
atoms adsorbed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
8.2 Schematics of the alchemical mutations. . . . . . . . . . . . . . . . . . . . . . 120
8.3 Charge density plot of the Kohn-Sham highest occupied molecular orbital for
the initial states in screening. . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
8.4 The relative absolute errors and combined HOMO charges are shown for each
path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
8.5 Calculated PBE dissociative adsorption energies of water for paths in the BN
pair 1 scheme against the alchemically predicted energies. . . . . . . . . . . . 123
8.6 Configurations of dissociative adsorption from alchemical screening. . . . . . . 125
8
List of Tables
3.1 Water/1,2-azaborine molecule geometry. . . . . . . . . . . . . . . . . . . . . . 48
3.2 Absolute interaction energies in (meV) of water on 1,2-azaborine. . . . . . . . 50
3.3 Absolute interaction energies of water with benzene, 1,2-azaborine, and borazine 54
5.1 Reference interaction energies of water on borazine and boronene . . . . . . . 70
5.2 Finite size effects in the water adsorption on h-BN. . . . . . . . . . . . . . . . 75
6.1 Interaction energies of water on graphene, outside the CNT, and inside the CNT. 87
6.2 Interaction energies of H on graphene, outside of CNT, and inside of CNT in
2
meV. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
7.1 Bond strengths for H and OH on graphene, h-BN and BNDG sheets with
respect to a gas phase hydrogen atom or OH molecule. . . . . . . . . . . . . . 106
8.1 Statistical analysis of data from four schemes and resolved for mesomerically
active and passive classification using a threshold HOMO charge. . . . . . . . 124
9
Publications
Parts of this dissertation have been published, or submitted for publication, as follows.
Chapter 3: Yasmine S. Al-Hamdani, Dario Alfè, O. Anatole von Lilienfeld, and Angelos
Michaelides, “Water on BN doped benzene: A hard test for exchange-correlation functionals
and the impact of exact exchange on weak binding.”, J. Chem. Phys. 141, 18C530 (2014)
Chapter 4: Yasmine S. Al-Hamdani, Ming Ma, Dario Alfè, O. Anatole von Lilienfeld,
and Angelos Michaelides, “Water on hexagonal boron nitride from diffusion Monte Carlo”, J.
Chem. Phys. 142, 181101 (2015)
Chapter 7: Yasmine S. Al-Hamdani, Dario Alfè, O. Anatole von Lilienfeld, and Angelos
Michaelides, “Tuning dissociation using isoelectronically doped graphene and hexagonal boron
nitride: water and other small molecules.”, J. Chem. Phys. 144, 154706 (2016)
10