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| 2. |
- Ai, Yuejie, 1982-
(författare)
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Theoretical studies on photophysics and photochemistry of DNA
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels. Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments. We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.
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| 3. |
- Cao, Hui, 1969-
(författare)
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Dynamic Effects on Electron Transport in Molecular Electronic Devices
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions. In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices. An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network.
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| 4. |
- Cao, Xinrui
(författare)
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First-Principles Modeling of Selected Heterogeneous Reactions Catalyzed by Noble-Metal Nanoparticles
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Heterogeneous catalysis is an important branch in catalysis, in which the catalyst and reactants are in different physical phases. In this thesis, we have carried out extensive first-principles calculations to explore the selected heterogeneous reactions catalyzed by the noble-metal nanoparticles. The major results of the thesis fall into two categories: (1) the discovery of the scaling relations for predicting the catalytic activity of nanoparticles; (2) the computational characterization of the catalytic activity and mechanism for specific catalytic reactions. For the first category, we have made efforts to develop the scaling relations for binary noble-metal nanoparticles. The obtained results show that the scaling relation not only holds at the nanoscale, but can also be unified with those obtained for the extended surfaces. Our findings shed new light for the efficient screening of nanoparticles with superior catalytic properties. The second part of the thesis summarizes our studies on different catalytic systems. One of the focuses is to study the catalytic properties of the single Pd-doped Cu55 nanoparticle toward H2 dissociation and propane dehydrogenation. The possible reaction mechanisms and effects of the single and multiple Pd doping on the catalytic activity have been extensively examined. Our calculations reveal that single-Pd-doped Cu55 cluster bears good balance between the maximum use of the noble metal and the high activity, and it may serve as a promising single-atom catalyst. We have also systematically studied the reduction process of graphene fluoride catalyzed by the Pt-coated metallic tip under different atmospheres, aiming to provide a feasible strategy for scanning probe lithography to fabricate electronic circuits at the nanoscale on graphene fluoride. It is found that the tip-induced reduction of graphene fluoride with assistance of pure hydrogen atmosphere is facile despite the release of hazard hydride fluoride. The ethylene molecule is predicted to be an excellent acceptor for fluoride abstraction from graphene fluoride, but the corresponding defluorination cycle can not be recycled. Our calculations have finally revealed that under the mixture hydrogen and ethylene atmosphere, the Pt-coated tip can effectively and sequentially reduce graphene fluoride with the release of relatively harmless reduction product, fluoroethane. The proposed cyclic reduction strategy is energetically highly favorable and is ready to be employed in experiments. Our theoretical studies provide yet another convincing example to demonstrate the power of the density functional theory for studying the nano-catalysis. It should also been mentioned that the present calculations are restricted to relatively small-sized clusters due to the limited computational resources. It is highly desirable to further study complicated interfacial systems and to provide a full picture of heterogeneous catalysis with the aid of ab initio molecular dynamics simulations in the future.
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| 5. |
- Duan, Sai
(författare)
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Geometrical and Electronic Structures at Molecule-Metal Interfaces from Theoretical Modeling
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, we focus on theoretical investigations on metal interfaces where many heterogeneous chemical reactions take place. Surface-enhanced Raman scattering (SERS) spectroscopy and the modern electrochemical methods are important in-situ techniques that have been widely employed for a variety of applications. Theoretical simulations have become an indispensable tool to infer the molecular details of interfacial structures that are not directly accessible from experimental measurements. In this context, we have proposed several new theoretical models for both SERS and interfacial electrochemistry, which allow us to provide molecular-level understanding of the interfacial structures under the realistic experimental conditions. The first part of the thesis has addressed the basic theory of SERS that offers the vibrational structure of the interfacial molecules. It is well known that the huge enhancement of Raman intensity in this technique can be attributed to two independent factors, namely the physical and chemical enhancements. The former is resulted from the enhanced electromagnetic field induced by the plasmonic excitations, while the latter comes from the changing of interaction between the molecule and the surface. The interplay between these two enhancement factors, which has long been an issue of debate, is revealed in this thesis. They are coupled through molecular polarizability. A practical computational approach is proposed and used to demonstrate the importance of the coupling on different molecular systems. It is found that for certain systems the coupling factor can be as large as 106. This finding is of great importance towards a comprehensive understanding of the SERS mechanisms and a quantitative prediction of the enhancement factor. The other part of the thesis is devoted to the theory of interfacial electrochemistry, in particular the effects of water solution. A novel protocol that combines classical molecular dynamics (MD) and the first principles density functional theory (DFT) calculations is proposed to address the statistical behavior of interfacial properties. Special attention has been paid to the work function of Pt(111) surface and CO adsorption energy on Pt(111) surface in aqueous solution. It has been found that in this case the work function of Pt surface illustrates a surprisingly broad distribution under the room temperature, sheds new light on the understanding of reaction activity of the surface. The proposed protocol is able to provide results in very good agreement with experiments and should be applied routinely in future studies.
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| 6. |
- Fu, Qiang, 1983-
(författare)
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Understanding the Structure and Reaction of Single Molecules on Metal surfaces from First Principles
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The study of surface adsorption and reaction is not only interesting from a scientific point of view, but also important in many application fields such as energy, environment, catalysis, corrosion, electronic device, and sensor. Theoretical calculations are essential in these studies. In this thesis, first principles studies for the structure and reaction of some important single molecules on the surface are presented. Dehydrogenation of single trans-2-butene molecule on a Pd(110) surface is the first example. The adsorption configurations of both reactant and produce are assigned and the whole dehydrogenation pathway is revealed. Our calculations show that the reactant, i.e. trans-2-butene molecule, undergoes a rotation before dehydrogenation occurs, which is an important detail that cannot be observed directly in scanning tunneling microscopy (STM) experiments. The dissociation and rotation processes of single oxygen molecule on a Pt(111) surface have been a subject of extensive studies in the past. A new intermediate state with a peculiar configuration is identified. The puzzled adsorption site is well explained. The calculated energy barriers agree well with experimental results for both dissociation and rotation processes. Another aspect addressed in this thesis is the mechanism of molecular electronic switches induced by molecular structural changes. By carefully examining the tautomerization process of a naphthalocyanine molecule, an intermediate state is located on the potential surface of the tautomerization. Our calculations indicate that the experimentally observed switching involves four-states, rather than the two-state as proposed by the experimentalists. In a joint experimental and theoretical study the dehydrogenation, tautomerization, and mechanical switching processes of a single melamine molecule on a Cu(100) surface have been comprehensively examined. A new dual-functional molecular device with integrated rectifying and switching functions is made for the first time. In collaborating with another experimental group, we have simulated the switching process of a single 1,1,2,3,4,5-hexaphenylsilole molecule on a Cu(111) surface. The role of the orientation of the molecule is carefully examined and a new switching mechanism is proposed. Switching processes are strongly associated with the inelastic electron tunneling. We have proposed a statistical model that allows explaining the non-integer exponent in the power-law relationship between the switching rate and tunneling current. In this model, the importance of the randomness in inelastic electron excitations and the lifetime of the immediate state are emphasized. It has shown that the inelastic electron tunneling is a collection of various n-electron processes with different statistical weight.
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| 7. |
- Hua, Weijie
(författare)
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Structure and spectroscopy of bio- and nano-materials from first-principles simulations
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules.
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| 8. |
- Ji, Yongfei, 1984-
(författare)
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Theoretical Studies on the Molecular Mechanisms of Photo-Catalytic Reactions on TiO2 Surfaces
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Photocatalysis is a promising technology that can effectively convert the solar energyinto sustainable green energy. However, theoretical studies on the molecular mechanisms of photocatalytic reactions are rare. This thesis is devoted to investigate several typical photocatalytic reactions on the surfaces of the most popular photocatalysis TiO2 with density functional theory. We start our study with the characterization of both the free and trapped hole on the surface generated by the light. The oxidation of physisorbed H2O molecule by the hole trapped at bridge oxygen on rutile TiO2(110) surface has been studied. The hole is found to transferto the molecule via the anti-bonding orbital as a result of the hybridization between the hole orbital and the HOMO of the molecule. The energy and symmetry mismatching between the trapped hole orbital and the HOMO of the molecule explains why the trapped hole cannot directly transfer to the chemisorbed H2O molecule. On the other hand, we have found that the chemisorbed H2O moleculecan be more efficiently oxidized by the free hole with a lower barrier and higher reaction energy compared to the oxidation by the trapped hole. In this reaction, the free hole is transferred to the chemisorbed H2O after the dissociation. This is different from the oxidation of chemisorbed H2O on anatase TiO2(101) surface by free hole, in which the hole is transferred concertedly with the dissociation of themolecule. In order to understand the hole scavenger ability of organic molecules, the oxidation of three small organic molecules (CH3OH, HCOOH and HCOH) onanatase TiO2(101) surface has been systematically investigated. The concerted hole and proton transfer is found for all these molecules. The calculations suggestthat both kinetic and thermodynamic effects need to be considered to correctly describe the hole transfer process. The order of hole scavenging power is found tofollow: HCOH > HCOOH > CH3OH > H2O, which agrees well with experiments. Photo-selective catalytic reduction of the NO by NH3 and the photooxidationof CO by O2 are closely related to the environment application. Both reactionsinvolve the formation and/or breaking of non R–H bonds. The mechanism for the photoreduction of NO proposed by experiment has been verified by our calculations.The role of the hole is to oxidize the adsorbed NH3 into ·NH2 radical, which canform a NH2NO complex with a gaseous NO molecule easily. The photooxidation of CO by O2 is the first multi-step photoreaction we ever studied. By combining thepotential energy surfaces at the ground and excited state we have found that thehole and electron both take part in the reaction. A molecular mechanism which is in consistent with various experiments is proposed. These studies show that density functional theory is a powerful tool for studying the photocatalytic reaction. Apparently, more work needs to be done in orderto improve the performance of the existing materials and to design new ones thatcan take advantage of the solar light more efficiently
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| 9. |
- Li, Junfeng, 1982-
(författare)
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Theoretical Studies on Vibrationally Resolved Optical Spectra of Polycyclic Aromatic Molecules
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Polycyclic aromatic molecules are of great interest owing to their many important applications in chemistry and have therefore been the focus of investigations for over half a century with spectroscopic techniques. This thesis is devoted to the modeling of vibrationally resolved optical spectra of polycyclic aromatic molecules. The general goal is to demonstrate the importance of nuclear motion on the electronic spectra and provide reliable spectral assignments and spectral fingerprints to distinguish different molecular isomers that are often not possible to be identified by experiments alone. In this thesis, four sets of polycyclic aromatic molecules have been systematically studied by using quantum chemistry methods. The simulated vibronic spectra are in good agreement with their experimental counterparts, which enables to provide correct reassignments for the electronic spectra.
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| 10. |
- LI, Xiao-Fei, 1973-
(författare)
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Electron and Spin Transport in Graphene-Based Nanodevices
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is devoted to the multi-scale modeling of electron and spin transport in graphene-based nanodevices. Several devices with fascinating structures and attractive properties have been designed by means of state-of-the-art computational methods, which include ab-initio molecular dynamics (MD) simulations for the geometry, density functional theory (DFT) for the electronic structure, and non-equilibrium Green’s functions (NEGF) for carriers transport properties.Poly-crystalline graphenes offer ample opportunities to make devices with desirable properties. We have systematically studied a type of poly-crystalline graphene constructed by zigzag and armchair graphene nanoribbons (ZGNR and AGNR). It is found that the choice of the supercells in modeling with periodic boundary conditions (PBC) has strong implications on the electronic and magnetic properties of such hybrid systems. A model with minimal lattice mismatch is obtained, which could be regarded as the most appropriate model for hybrid GNRs. With this model, it is revealed that the hybrid GNR is of ferromagnetism with a high Curie temperature. We have then designed armchair/zigzag graphene nanoribbon heterojunctions (AGNR|ZGNR) with a well-defined conductance oscillation and rectification behavior. It is shown that the resonance or nonresonance of the frontier orbitals between AGNR and ZGNR is the source of the oscillation and the asymmetric structure is the root of the rectification. A high rectification ratio can be achieved by tuning the width of ZGNR to enhance the asymmetric character of transmission function and to minimize the backward current.The electron transport properties of graphene can be modified by hydrogenation strips (HSs) formed from the absorbed hydrogen atoms. We have designed a new graphene nanoribbon that has zigzag-edged HSs placed at its middle region. It is found that the HS can electrically separate the GNR into sub-GNRs and each HS introduces two spin-polarized conducting edge-like states around the Fermi level. This leads to a significant enhancement of the conductance and the spinpolarization. We have also found that by introducing embedding a short sp3-edged section into the sp2-edged ZGNRs or a short sp2-edged section into the sp3-edged ZGNRs, the orbital symmetry mismatch between these two sections can induce the opening of the conductance energy gap in ZGNRs over a wide energy region. This simple strategy explains many unexplained experimental results and offers a simple strategy to design GNRs with a proper energy gap.We have also carefully examined the spin-polarization of chiral GNRs with reconstructed (2,1)-edges. It is found that the unsaturated (2,1)-edged chiral GNRs can possess strong current polarizations (nearly 100%) and a striking negative differential resistance (NDR) behavior.
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