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| 2. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
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Tidskriftsartikel (refereegranskat)abstract
- The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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| 3. |
- 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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| 4. |
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| 5. |
- Hu, Wei, 1985-
(författare)
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Theoretical Study on Chemical Structures and Stability of Molecules in Metallic Junctions
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, we focus on the structural identification of the interface using surface enhanced Raman spectroscopy (SERS) and inelastic electron tunnelling scattering (IETS). Two different molecular junctions, namely gold/ trans-1,2-bis (4-pyridyl) ethylene/gold junction and gold/4,4'-bipyridine/gold junctions in various conditions were studied and the corresponding configurations were determined. The enhancement in SERS was also studied by employing the time-dependent density functional theory. Furthermore, we studied some properties of the interface, such as the stability of the adsorbates and charge transfer properties of molecular junctions. The decrease in the stability of molecules was found when adsorbed on metallic surface and trapped in metallic junctions. Our studies explained several puzzles and by rational design, more stable molecular devices were obtained.
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| 6. |
- Ai, Yuejie, 1982-, et al.
(författare)
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Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:10, s. 2366-2377
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Tidskriftsartikel (refereegranskat)abstract
- We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.
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| 7. |
- Fu, Qiang, et al.
(författare)
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Understanding the concept of randomness in inelastic electron tunneling excitations
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:38, s. 12012-12023
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Tidskriftsartikel (refereegranskat)abstract
- Inelastic electron tunneling excitation has been realized in the last decade as an effective way to probe reliably detailed atomic structures and control precisely behaviors of surface adsorbates at a single molecule level. A good understanding of rich and complex processes on the surface under inelastic electron excitations is of great importance, not only from a fundamental scientific point of view but also for potential practical applications. In this perspective paper, we give an overview of recent developments on excitations and characterizations of inelastic electron tunneling processes in surface adsorbates and molecular junctions. Special attention has been paid to the understanding of the randomness of the processes. A recently proposed general statistical model is introduced which has resolved a long-standing puzzle concerning the experimentally observed non-integer power law relationship between the rate of molecular conformation changes and the tunneling current. The success of the new model is highlighted by its applications for molecular switches.
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| 8. |
- Fu, Ying, et al.
(författare)
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Multiple-photon spectrum of CdS semiconductor quantum dot for bioimaging
- 2006
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Ingår i: Thin Solid Films. - : Elsevier BV. - 0040-6090 .- 1879-2731. ; 515:2, s. 842-845
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Tidskriftsartikel (refereegranskat)abstract
- We study the dynamic processes of multiple-photon absorption and emission in a semiconductor quantum dot. By the non-perturbative time-dependent Schrodinger equation, it is shown that electrons in the quantum dot can be optically excited from the valence band to the conduction band via multiphoton processes, leaving holes in the valence band. The radiative recombination of the conduction-band electrons with the valence-band holes results in optical emission of a single photon having an energy which is larger than the input photon energy, resulting in the high-photon-energy luminescence from the quantum dot activated by low-energy photons to emit radiation in the visible optical regime for bioimaging application.
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| 9. |
- Hua, Weijie, et al.
(författare)
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Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis : Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:41, s. 13214-13222
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Tidskriftsartikel (refereegranskat)abstract
- In this work we highlight the potential of NEXAFS-near-edge X-ray absorption fine structure-analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (pi*(1)) and amine (pi*(2)) nitrogen absorption bands with a characteristic energy difference (Delta). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around +/- 0.4-0.5 eV change of Delta, to the spectra due to a switch of single-double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Delta, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing "compressed" and "expanded" models. or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2-0.3 angstrom can result in the reduction of Delta by 0.2-0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create "blocks" in the pi-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens More distinguishable with a larger Delta. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.
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| 10. |
- Hua, Weijie, et al.
(författare)
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Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:20, s. 7016-7021
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Tidskriftsartikel (refereegranskat)abstract
- In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG)center dot poly(dC) and poly(dA)center dot poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.
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