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| 2. |
- 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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| 3. |
- Ai, Yuejie, et al.
(författare)
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Hydrophobicity and Hydrophilicity Balance Determines Shape Selectivity of Suzuki Coupling Reactions Inside Pd@meso-SiO2 Nanoreactor
- 2016
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 120:19, s. 10244-10251
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Tidskriftsartikel (refereegranskat)abstract
- Molecular sorting and catalysis directed by shape selectivity have been extensively applied in porous extended frameworks for a low-carbon, predictable, renewable component of modern industry. A comprehensive understanding of the underlying recognition mechanism toward different shapes is unfortunately still missing, owing to the lack of structural and dynamic information under operating conditions. We demonstrate here that such difficulties can be overcome by state-of-the-art molecular dynamics simulations which provide atomistic details that are not accessible experimentally, as exemplified by our interpretation for the experimentally observed aggregation induced shape selectivity for Suzuki C-C coupling reaction catalyzed by Pd particles in mesoporous silica. It is found that both aggregation ability and aggregating pattern of the reactants play the decisive role in controlling the shape selectivity, which are in turn determined by the balance between the hydrophobicity and hydrophilicity of the reactants, or in other words, by the balance between the noncovalent hydrogen bonding interaction and van der Waals forces. A general rule that allows prediction of the shape selectivity of a reactant has been proposed and verified against experiments. We show that molecular modeling is a powerful tool for rational design of new mesoporous systems and for the control of catalytic reactions that are important for the petrochemical industry.
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| 4. |
- Ai, Yuejie, et al.
(författare)
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Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase
- 2010
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Ingår i: The Journal of Physical Chemistry Letters. - U. S. A. : American Chemical Society. - 1948-7185. ; 1, s. 743-747
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Tidskriftsartikel (refereegranskat)abstract
- The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADH− in DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADH− in DNA photolyase
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| 5. |
- 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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| 6. |
- Chen, Zhe, et al.
(författare)
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Ruthenium/Graphene-like Layered Carbon Composite as an Efficient Hydrogen Evolution Reaction Electrocatalyst
- 2016
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 8:51, s. 35132-35137
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Tidskriftsartikel (refereegranskat)abstract
- Efficient water splitting through electrocatalysis has been studied extensively in modern energy devices, while the development of catalysts with activity and stability comparable to those of Pt is still a great challenge. In this work, we successfully developed a facile route to synthesize graphene-like layered carbon (GLC) from a layered silicate template. The obtained GLC has layered structure similar to that of the template and can be used as support to load ultrasmall Ru nanoparticles on it in supercritical water. The specific structure and surface properties of GLC enable Ru nanoparticles to disperse highly uniformly on it even at a large loading amount (62 wt %). When the novel Ru/GLC was used as catalyst on a glass carbon electrode for hydrogen evolution reaction (HER) in a 0.5 M H2SO4 solution, it exhibits an extremely low onset potential of only 3 mV and a small Tafel slope of 46 mV/decade. The outstanding performance proved that Ru/GLC is highly active catalyst for HER, comparable with transition-metal dichalcogenides or selenides. As the price of ruthenium is much lower than platinum, our study shows that Ru/GLC might be a promising candidate as an HER catalyst in future energy applications.
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| 7. |
- Ma, Yong, et al.
(författare)
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The equilibrium geometry of A@C60 : A test case for conventional density functional theory
- 2014
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 591, s. 312-316
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Tidskriftsartikel (refereegranskat)abstract
- Potential energy surfaces (PESs) along the reaction pathway towards the center of CC bond between two six membered rings for ten different endohedral fullerenes A@C60 (A = H, C, O, S, N, P, He, Ne, Ar, Kr) have been studied by density functional theory (DFT) and Hartree-Fock (HF) method. The results show that no suitable method can consistently describe the interaction between atom A and carbon cage. The dispersion corrected DFT methods fail to describe the equilibrium geometry and PES of the complexes with light atoms. Nevertheless, the inclusion of the dispersion stabilizes the system as reflected by interaction energies (IEs) between atom A and C60.
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| 8. |
- Tan, Chuang, et al.
(författare)
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Direct Determination of Resonance Energy Transfer in Photolyase : Structural Alignment for the Functional State
- 2014
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 118:45, s. 10522-10530
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Tidskriftsartikel (refereegranskat)abstract
- Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH, and the corresponding orientation factors (kappa(2)) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.
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| 9. |
- Yu, Shujun, et al.
(författare)
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Macroscopic, Spectroscopic, and Theoretical Investigation for the Interaction of Phenol and Naphthol on Reduced Graphene Oxide
- 2017
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 51:6, s. 3278-3286
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Tidskriftsartikel (refereegranskat)abstract
- Interaction of phenol and naphthol with reduced graphene oxide (rGO), and their competitive behavior on rGO were examined by batch experiments, spectroscopic analysis and theoretical calculations. The batch sorption showed that the removal percentage of phenol or naphthol on rGO in bisolute systems was significantly lower than those of phenol or naphthol in single-solute systems. However, the overall sorption capacity of rGO in bisolute system was higher than single-solute system, indicating that the rGO was a very suitable material for the simultaneous elimination of organic pollutants from aqueous solutions. The interaction mechanism was mainly pi-pi interactions and hydrogen bonds, which was evidenced by FTIR, Raman and theoretical calculation. FTIR and Raman showed that a blue shift of C=C and -OH stretching modes and the enhanced intensity ratios of I-D/I-G after phenols sorption. The theoretical calculation indicated that the total hydrogen bond numbers, diffusion constant and solvent accessible surface area of naphthol were higher than those of phenol, indicating higher sorption affinity of rGO for naphthol as compared to phenol. These findings were valuable for elucidating the interaction mechanisms between phenols and graphene-based materials, and provided an essential start in simultaneous removal of organics from wastewater.
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| 10. |
- Yu, Shujun, et al.
(författare)
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Spectroscopic and theoretical studies on the counterion effect of Cu(II) ion and graphene oxide interaction with titanium dioxide
- 2016
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Ingår i: ENVIRONMENTAL SCIENCE-NANO. - : Royal Society of Chemistry. - 2051-8153 .- 2051-8161. ; 3:6, s. 1361-1368
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Tidskriftsartikel (refereegranskat)abstract
- With the widespread use of graphene oxide (GO), it is inevitable that part of GO is released into the environment and co-exist with heavy metal ions as contaminants and is likely to be co-adsorbed on minerals and oxides. This study, for the first time, demonstrates the individual and mutual removal mechanism of GO and Cu(II) on titanium dioxide (TiO2) by batch experiments, spectroscopic analysis and density functional theory (DFT) computations. Electrostatic interaction and hydrogen bonding are the dominant modes of GO sorption onto TiO2, and the interaction of Cu(II) with TiO2 is mainly dominated by inner-sphere surface complexation. The presence of Cu(II) enhances GO coagulation on TiO2 and vice versa. The experimental results are further verified by DFT sorption energy (Es) calculations in the order (TiO2-GO)-Cu > TiO2-GO for GO interaction and (TiO2-GO)-Cu > TiO2-Cu for Cu(II) interaction. The mutual interaction is favorable for the simultaneous removal of GO and heavy metal ions by surface complexation between Cu(II) and oxygen-containing functional groups. These findings might facilitate better understanding of the co-removal behavior of carbon nanomaterials and heavy metal ions on oxides, which is crucial to decreasing the environmental toxicity of pollutants in the natural environment.
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