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Electron-Vibration Coupling and Its Effects on Optical and Electronic Properties of Single Molecules

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Electron-vibration coupling and its effects on optical and electronic properties of single molecules Guangjun Tian Doctoral Thesis in Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology Stockholm, Sweden 2013 Electron-vibration coupling and its effects on optical and electronic properties of single molecules Thesis for Philosophy Doctor Degree Department of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology Stockholm, Sweden 2013 c Guangjun Tian, 2013 ISBN 978-91-7501-773-0 ISSN 1654-2312 TRITA-BIO Report 2013:10 Printed by Universitetsservice US-AB Stockholm, Sweden 2013 To Li Li and my parents Abstract The thesis is devoted to theoretical investigations of electron-vibration cou- pling and its effects on optical and electronic properties of single molecules, espe- cially for molecules confined between metallic electrodes. A density-matrix approach has been developed to describe the photon emis- sion of single molecules confined in the scanning tunneling microscope (STM). With this new method electronic excitations induced by both the tunneling elec- tron and the localized surface plasmon (LSP) can be treated on an equal foot- ing. Model calculations for porphyrin derivatives have successfully reproduced and explained the experimentally observed unusual variation of the photon emis- sion spectra. The method has also been extended to study the STM induced fluorescence and phosphorescence of C60 molecules in combination with the first principles calculations. In particularly, the non-Condon vibronic couplings have been exclusively included in the calculations. The experimental spectra have been nicely reproduced by our calculations, which also enable us to identify the unique spectral fingerprint and origin of the measured spectra. The observed rich spectral features have been finally correctly assigned. The electron transport properties of molecular junctions with bipyridine iso- mers have been studied in the sequential tunneling (SET) regime by assuming that the molecules are weakly coupled to metallic electrodes. It is shown that the strong electron-vibration coupling in the 2, 2'-bipyridine molecule and the 4, 4'-bipyridine molecule can lead to observable Franck-Condon blockade. Taking advantage of such novel effect, a gate-controlled conductance switch with ideal on-off ratio has been proposed for a molecular junction with the 4, 4'-bipyridine molecule. The effect of the electron-vibration coupling on one-photon and two-photon absorption spectra of green fluorescent protein (GFP) has been systematically examined. The hydroxybenzylidene-2, 3-dimethylimidazolinone molecule in the deprotonated anion state (HBDI−) is used to model the fluorescence chromophore of the GFP. Both Condon and non-Condon vibronic couplings have been consid- ered in the calculations. The calculated spectra are in good agreement with the available experimental spectra. It confirms the notion that the observed blue-shift of the two-photon absorption spectrum with respect to its one-photon absorption counterpart is caused by the non-Condon vibronic coupling. All the calculations are carried out with our own software package, DynaVib. It is capable of modeling a variety of vibrational-resolved spectroscopies, such vi as absorption, emission, and resonant Raman scattering (RRS) spectra. In our package, the Duschinsky rotation and non-Condon effect have been fully taken into account. Both time-independent and time-dependent approaches have been implemented, allowing to simulate the spectra of very large molecules. Preface The work presented in this thesis was conducted during a period of about five years, 2008.09-2013.06, at the Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden. List of papers included in the thesis Paper 1. Density-Matrix Approach for the Electroluminescence of Molecules in a Scanning Tunneling Microscope, Guangjun Tian, Ji-Cai Liu, and Yi Luo, Phys. Rev. Lett. 2011, 106, 177401. Paper 2. Electroluminescence of molecules in a scanning tunneling microscope: Role of tunneling electrons and surface plasmons, Guangjun Tian, and Yi Luo, Phys. Rev. B 2011, 84, 205419. Paper 3. Fluorescence and Phosphorescence of Single C60 Molecules as Stimulated by A Scanning Tunneling Microscope, Guangjun Tian, and Yi Luo, Angew. Chem. Int. Ed. 2013, 52, 4814 - 4817. Paper 4. Isomeric dependent Franck-Condon blockade in weakly coupled bipyridine molecular junctions, Guangjun Tian, and Yi Luo, Submitted. Paper 5. Role of Non-Condon Vibronic Coupling and Conformation Change on Two- Photon Absorption Spectra of Green Fluorescent Protein, Yue-jie Ai, Guangjun Tian, and Yi Luo, Mol. Phys. 2013, in press. List of related papers not included in the thesis viii Paper 1. Two Possible Configurations for Silver-C60-Silver Molecular Devices and Their Conductance Characteristics, Guangjun Tian, and Wenyong Su, Chin. Phys. Lett. 2009, 26, 068501. Paper 2. Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States, Yue-jie Ai, Guangjun Tian, Rong-zhen Liao, Qiong Zhang, Wei-Hai Fang, and Yi Luo, ChemPhysChem 2011, 12, 2899. Paper 3. Thermoelectric Properties of Hybrid Organic-Inorganic Superlattices, Jes´us Carrete, Natalio Mingo, Guangjun Tian, Hans Agren,˚ Alexander Baev, and Paras N. Prasad, J. Phys. Chem. C 2012, 116, 10881. Paper 4. Spectral character of intermediate state in solid-state photoarrangement of α-santonin, Xing Chen, Guangjun Tian, Zilvinas Rinkevicius, Olav Vahtras, Zexing Cao, Hans Agren,˚ and Yi Luo, Chem. Phys. 2012, 405, 40. Paper 5. Blinking, Flickering, and Correlation in Fluorescence of Single Colloidal CdSe Quantum Dots with Different Shells under Different Excitations, Li Li, Guangjun Tian, Yi Luo, Hjalmar Brismar, and Ying Fu, J. Phys. Chem. C 2013, 117, 4844. Comments on my contributions to the papers included I have taken the major responsibility in the papers where I am the first author, that is, Paper 1, 2, 3, and 4. In paper 5, I performed part of the calculations and assisted in the preparation of the manuscript. Acknowledgments I would like to acknowledge a number of people who have made this thesis possible. First I would like to give my sincere gratitude to my supervisor, Professor Yi Luo, for taking me as his student and giving me the opportunity to study at KTH. I also would like to thank him for the continuous encouragement and guidance. I would like to say this thesis definitely would not be possible without his help and support. Many thanks to the head of the Department of Theoretical Chemistry and Biology, Professor Hans Agren,˚ for creating such a wonderful department. And I would like to thank him for coordinating our collaboration with Professor Natalio Mingo and Professor Paras N. Prasad. I would like to thank Dr. Ying Fu for the great collaborations and for his help to me and my family. I would like to thank Dr. Wenyong Su, my supervisor during my study in Beijing Institute of Technology, for guiding me to the filed of scientific research and introducing me to Professor Yi Luo. I would like to thank Professor Jun Jiang for his help at the beginning of my study in Sweden. I have learned a lot from his great knowledge in the field of molecular electronics as well as his skills in writing computer codes. I would like to thank Dr. Yaoquan Tu for his guidance and help. Seniors in the department, Professor Faris Gel'mukhanov, Professor Olav Vahtras, Professor Boris Minaev, Dr. Zilvinas Rinkevicius, Dr. Marten Ahlquist, and Dr. Arul Murugan, are thanked for their help. I would like to thank Dr. Sai Duan, Dr. Weijie Hua, Dr. Yue-Jie Ai, Dr. Xing Chen, Dr. Ji-Cai Liu, Li Li and Yongfei Ji for the great collaborations and all the fruitful discussions. Thanks to Xiao Cheng, Dr. Fuming Ying, Professor Hui Cao, Dr. Bin Gao, Professor Shilv Chen, Dr. Hongmei Zhong, Dr. Qiang Fu, Dr. Yuping Sun, Dr. Lili Lin, Dr. Hao Ren, Dr. Feng Zhang, Dr. Zhijun Ning, Dr. Qiong Zhang, Dr. Xifeng Yang, Dr. Abdelsalam Mohammed, Dr. Ying Zhang, Dr. Xin Li, Dr. Xiaofei Li, Dr. Xiuneng Song, Dr. Bogdan Frecus, Dr. Peng Cui, Dr. Qiu Fang, Dr. Ke Lin, Wei Hu, Ce Song, Yong Ma, Chunze Yuan, Hongbao Li, Xin Li, Xinrui Cao, Keyan Lian, Quan Miao and many other current and former members of the department for their help and for creating a good atmosphere. x Many thanks to Dr. Sai Duan, Dr. Xing Chen, Dr. Lili Lin and Dr. Yue-Jie Ai for reading part of the preprint and providing valuable suggestions. Financial support (2008-2012) from the China Scholarship Council (CSC) is acknowledged. I would like to thank my parents, my two sisters and their family, for their love, support, and understanding. Last but not least, I would like to thank my lovely wife, Li Li, for all the sweet love and encouragement. I am lucky to have you in my life. Guangjun Tian 2013, Stockholm Abbreviations BO Born-Oppenheimier Cam-B3LYP Coulomb-attenuating method-B3LYP CASSCF complete active space self-consistent field CASPT2 complete active space perturbation theory to the second order CI Configuration Interaction CC Coupled Cluster DFT density functional theory EL electroluminescence FC Franck-Condon GFP green fluorescent protein GGA Generalized Gradient Approximation H2TBPP mesotetrakis (3,5-di-terbutylphenyl) porphyrin HOMO highest occupied molecular orbital HBDI hydroxybenzylidene-2, 3-dimethylimidazolinone HF Hartree-Fock HK Hohenberg-Kohn HT Herzberg-Teller HWHM half-width at half-maximum IET inelastic electron tunneling IETS inelastic electron tunneling spectroscopy LDA Local Density Approximation LSDA Local Spin Density Approximation LUMO lowest unoccupied molecular orbital LCM linear coupling model LSP localized surface plasmon MPn Møller-Plesset perturbation theory MCSCF Multi-Configuration Self-Consistent Field xi xii Abbreviations PES potential energy surface RRS resonant Raman scattering SCF self-consistent field SET sequential tunneling STM scanning tunneling microscopy TDDFT time-dependent density functional theory TPLSM two-photon laser scanning microscopy TPP tetraphenyl porphyrin Contents Abbreviations xi 1 Introduction 1 2 Theoretical background 5 2.1 Molecular vibration .........................
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