University of Groningen
Rationalization of the Mechanism of Bistability in Dithiazolyl-based Molecular Magnets Francese, Tommaso
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Rationalization of the Mechanism of Bistability in Dithiazolyl-based
Molecular Magnets
Tommaso Francese
Rationalization of the Mechanism of Bistability in Dithiazolyl-based Molecular Magnets
Tommaso Francese PhD thesis
University of Groningen The Netherlands
Zernike Institute PhD thesis series 2019-11 ISSN: 1570-1530
ISBN: 978-94-034-1521-5 (Printed version) ISBN: 978-94-034-1520-8 (Electronic version)
The research presented in this thesis was performed in the Grup d’Estructura de Ma- terials Moleculars (GEM2) of the Institute of Theoretical and Computational Chemi- stry of the University of Barcelona (Spain) and in the Theoretical Chemistry Group of the Zernike Institute for Advanced Materials at the University of Groningen (The Netherlands). Part of the work was carried out in the IQTC facility Portal, in the Barcelona Supercomputing Center (Centro National de Supercomputatión), in the Peregrine HPC and Nieuwpoort clusters of the University of Groningen. This PhD project was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement N 642294.
© 2019 Tommaso Francese
Printed by: Gildeprint - The Netherlands
Rationalization of the Mechanism of Bistability in Dithiazolyl-based
Molecular Magnets
Phd thesis
to obtain the degree of PhD of the University of Groningen
on the authority of the Rector Magnificus Prof. E. Sterken
and in accordance with the decision by the College of Deans
and
to obtain the degree of PhD of the University of Barcelona
on the authority of the Rector Prof. J. Elias and in the accordance with the decision by the College of Deans.
Double PhD degree
This thesis will be defended in public on Monday 25 March 2019 at 12.45 hours
by
Tommaso Francese
born on 20 January 1988 in Mirano, Venice, Italy
Supervisors
Prof. H. B. Broer-Braam Prof. J. J. Novoa
Co-supervisors
Dr. J. Ribas
Dr. R. W. A. Havenith
Assessment Committee
Prof. R. C. Chiechi
Prof. C. M. Marian
Prof. V. Robert
Prof. C. Sousa Romero
A Bianca e alla mia Famiglia
“Amor, ch’a nullo amato amar perdona…”
Dante Alighieri, Inferno, V, v. 103
Contents
1 Introduction 3
1.1 From Stones to Molecules . . . . 3
1.1.1 From Bulk to Molecular Magnets: A Glimpse of the Future . . 4
1.2 Short History of Molecular Magnets . . . . 5
1.2.1 The Molar Magnetic Susceptibility . . . . 8
1.2.2 The Dithiazolyl-Based Molecular Magnets . . . . 10
1.3 Thesis Goals and Outlook . . . . 12
2 Methodology 25 2.1 Introduction . . . . 25
2.2 The First-Principles Bottom-Up Method . . . . 26
2.2.1 First Step: Crystal Analysis and Selection of Radical Pairs . . 26
2.2.2 Second Step: Calculation of Magnetic Exchange Interaction (JAB) . . . . 27
2.2.3 Third Step: Construction and Diagonalization of the HDVV Hamiltonian . . . . 30
2.2.4 Fourth Step: Derivation of the Macroscopic Properties: The Susceptibility . . . . 31
2.3 Wave Function-based Methods . . . . 33
2.3.1 The Schrödinger Equation . . . . 33
2.3.2 The Born-Oppenheimer Approximation . . . . 34
2.3.3 The Electronic Wave Function . . . . 36
2.3.4 The Hartree-Fock Method . . . . 37
2.3.5 Different Formalisms of the HF Theory . . . . 39
2.3.6 Variational Methods . . . . 42
2.3.7 Perturbative Methods . . . . 46
2.4 Density Functional Theory . . . . 47
2.4.1 The Kohn-Sham Method . . . . 49
2.4.2 The Kohn-Sham Equations . . . . 50 i
2.4.3 Spin Polarized Calculations . . . . 53
2.4.4 The Broken-Symmetry Approximation . . . . 54
2.4.5 Kohn-Sham in Plane Waves . . . . 57
2.4.6 Pseudopotentials . . . . 57
2.4.7 Semi-empirical Dispersion Functions: Grimme D3 . . . . 61
2.4.8 Energy Decomposition Analysis . . . . 61
2.5 Dynamical Evolution of the System . . . . 62
2.5.1 Ab Initio Molecular Dynamics . . . . 63
2.6 Exploring the Potential Energy Surfaces . . . . 65
2.6.1 The Nudged Elastic Band Method . . . . 66
2.7 CODES . . . . 68
2.7.1 Guassian09 . . . . 68
2.7.2 Quantum Espresso . . . . 68
2.7.3 CP2K . . . . 68
2.7.4 CPMD . . . . 69
2.7.5 Orca . . . . 69
3 The Dithiazolyl-based Materials 81 3.1 Introduction . . . . 81
3.2 TTTA . . . . 85
3.2.1 Crystal Packing Analysis . . . . 85
3.2.2 Magnetic Properties . . . . 86
3.2.3 Beyond the Static Analysis . . . . 87
3.3 4-NCBDTA . . . . 90
3.3.1 Crystal Packing Analysis . . . . 90
3.3.2 Magnetic Properties . . . . 91
3.4 PDTA . . . . 93
3.4.1 Crystal Packing Analysis . . . . 93
3.5 TDPDTA . . . . 96
3.5.1 Crystal Packing Analysis . . . . 96
3.6 Summary . . . . 98
4 Reorganisation of Intermolecular Interactions in the Polymorphic Phase Transition of a Prototypical Dithiazolyl-based Bistable Material 103 4.1 Introduction . . . 104
4.2 Computational Details . . . 108
4.3 Results and Discussion . . . 110
4.3.1 Intermolecular Interactions in Isolated Pairs of TTTA Radicals . . . 110
ii
4.3.2 Intermolecular Interactions Model System Considering
Periodic Boundary Conditions . . . 114
4.3.3 Evaluation of the Nature of the Key Intermolecular Interactions . . . 118
4.4 Conclusions . . . 125
4.5 Acknowledgements . . . 126
5 The Magnetic Fingerprint of DTA-based Molecule Magnets 135 5.1 Introduction . . . 136
5.1.1 Methodological Details . . . 139
5.2 Results and Discussion . . . 140
5.2.1 Magnetic susceptibility curves: calculated vs. experimental . 140 5.2.2 Evaluating the nature of the magnetic interactions in DTA- based materials: magneto-structural correlation maps . . . 143
5.2.3 Electronic vs. structural contributions . . . 150
5.3 Conclusions . . . 153
5.4 Acknowledgements . . . 154
6 Exploiting Spin-Peierls-like Transitions to Induce Two Distinct Mecha- nisms of Bistability in Dithiazolyl-based Materials 161 6.1 Introduction . . . 162
6.2 Susceptibility Curves . . . 167
6.3 Structural Models . . . 170
6.4 Computational Information . . . 173
6.5 Results . . . 174
6.5.1 Optimum Configuration of HT-PDTA and HT-TDPDTA Polymorphs . . . 174
6.6 Dynamics of the HT Polymorphs at Room Temperature . . . 178
6.6.1 Average Structures Configuration . . . 178
6.6.2 Thermal Ellipsoids . . . 181
6.6.3 Distances Distribution Analysis . . . 184
6.6.4 The Pair-Exchange Dynamic Mechanism via Nudged Elastic Band Algorithm . . . 187
6.6.5 Maps Scans: Evidence of the Role of the Longitudinal Slippage 190 6.7 Conclusions . . . 195
7 Outlook and Future Challenges 203
Appendices 209
iii
A Supplementary Information of Chapter 5 211 A.1 Spin Density of TTTA, PDTA, 4-NCBDTA and
TDPDTA . . . 212 A.2 Atomic coordinates of LT and HT magnetically
dominant pairs of radicals for TTTA, PDTA,
TDPDTA, and 4-NCBDTA. . . 213 A.3 Selection of magnetic model of PDTA and
TDPDTA. . . 215 A.4 Benchmarking the JABmagnetic coupling interactions computed at
DFT/UB3LYP level with Difference Dedicated Configuration Interac- tion (DDCI-3) method. . . 220 A.5 TDPDTA shifted configurations. . . 227 A.6 Interaction Energy Maps of TTTA, PDTA,
4-NCBDTA, and TDPDTA. . . 229
Summary 233
Samenvatting 239
Resum 245
Curriculum Vitae 247
Acknowledgements 253
iv
Glossary
ADP Anisotropic Displacement Parameters
AFM Antiferromagnetic
AIMD Ab-Initio Molecular Dynamics
BCP Bond Critical Point
BE Binding Energy
BO Born-Oppenheimer
BO-MD Born-Oppenheimer Molecular Dynamics
BS Broken-Symmetry
CAS(n,m) Complete Active Space with n electrons and m orbitals CASSCF Complete Active Space Self-Consistent Field CERN Conseil Européen pour la Recherche Nucléaire CCDC Cambridge Crystallographic Data Center
CGS Centimeter-Gram-Second
CI Configuration Interaction CP-MD Car-Parrinello Molecular Dynamics CSF Configuration State Functions
CSVR Canonical Sampling through Velocity Rescaling DDCI Difference Dedicated Configuration Interaction DFT Density Functional Theory
DFT-D2 Dispersion-corrected DFT (Grimme D2 method) DFT-D3 Dispersion-corrected DFT (Grimme D3 method) dIP Interplanar Distance
dLG Longitudinal Slippage
dSL Lateral Slippage
EDA Energy Decomposition Analysis EPR Electron Paramagnetic Resonance
FES Free Energy Surface
FM Ferromagnetic
FPBU First-Principles Bottom-Up
GEO Geometry Optimisation
GGA Generalised Gradient Approximation
GS Ground State
v
HDVV Heisenberg-Dirac van Vleck
HF Hartree-Fock
HK Hohenberg-Kohn
HOMO Highest Occupied Molecular Orbital
HP Hartree Product
HS High Spin
HT High Temperature
IEM Interaction Energy Map
JAB Magnetic Coupling between Two Magnetic Centres A and B
KS Kohn-Sham
LCAO Linear Combination of Atomic Orbitals LDA Local Density Approximation
LHC Large Hadron Collider
LS Low Spin
LT Low Temperature
LUMO Lowest Unoccupied Molecular Orbital MCSCF Multiconfiguration Self-Consistent Field
MD Molecular Dynamics
MEP Minimal Energy Path
MMM Minimal Magnetic Model
MR-CI Multi Reference Configuration Interaction MR-PT Multi Reference Perturbation Theory NCPP Norm-Conserving Pseudo Potentials
NEB Nudged Elastic Band
NEVPT2 N-Electron Valence State Second-Order Perturbation Theory
NVT Canonical Ensemble (Particles = N, Volume =V, Temperature = T)
OO Orbital Overlap
PBC Periodic Boundary Conditions PDF Probability Distribution Functions
PED Pair-Exchange Dynamics
PES Potential Energy Surface
PP Pseudo Potentials
vi
Atom Colors Legend
PW Plane Waves
RASSCF Restricted Active Space Self-Consistent Field RHF Restricted Hartree-Fock
ROHF Restricted Open-Shell Hartree-Fock SCF Self-Consistent Field
SOMO Singly Occupied Molecular Orbital TDSE Time-Dependent Schrödinger Equation
TF Thomas-Fermi
TISE Time-Independent Schrödinger Equation UHF Unrestricted Hartree-Fock
UPP Ultrasoft Pseudo Potentials VC Variable-Cell Optimisation
WF Wave Function
Molecules
DTA Dithiazolyl
PDTA 1,3,2-pyrazinodithiazol-2-yl
TDA Thiadiazole
TDPDTA 1,2,5-thidiazole[3,4-b]pyrazine TTTA 1,3,5-trithia-2,4,6-triazapentalenyl 4-NCBDTA 4-cyanobenzo-1,3,2-dithiazolyl
vii
Units
Energy:
1 hartree = 627.509 kcal mol-1 1 hartree = 2 rydberg 1 rydberg = 313.755 kcal mol-1 Distance:
1 bohr = 0.529 angstrom Time:
1 ns = 1000 ps 1 ps = 1000 fs
viii
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