Keli Han

Chinese Academy of Sciences, Peping, Beijing, China

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Publications (92)351.38 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The spontaneous and collision-assisted hydrogen-atom abstracting reaction (HA) dynamics of triplet benzil are investigated through the combination of transient absorption spectroscopy with TD-DFT calculations. HA dynamics exhibit a remarkable dependence on the hydrogen donor properties. The effects of the triplet-state hydrogen bonding on the reaction dynamics are illustrated. In particular, it is experimentally observed that strengthened triplet-state hydrogen bonding could accelerate the HA, whereas weakened triplet-state hydrogen bonding would postpone the HA. The triplet-state hydrogen bonding has great influences on the early stage of the HA reaction, while the bond dissociation energy of the hydrogen donors determines the subsequent reaction pathways. Protic solvents could sustain longer lifetimes of the excited-state intermediate formed after HA than non-protic solvents by 10 μs. This investigation provides insights into the HA dynamics and guidance to improve the product efficiency of photochemical reactions.
    Physical Chemistry Chemical Physics 07/2014; · 3.83 Impact Factor
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    ABSTRACT: In this article, the sensing mechanism of a fluorescence probe for hypochloric acid, NI-Se, has been investigated using experimental and theoretical methods. Based on the results of the steady-state and time-resolved emission spectra of NI-Se and its oxidized form NI-SeO, we suggested that there was twist internal charge transfer (TICT) state with faint fluorescence in NI-Se. Subsequently, the ground and excited state minimum geometries of NI-Se and NI-SeO were optimized with DFT/TD-DFT methods. The results demonstrated there was a twisting process in the excited state of NI-Se and that this twist process was induced by the nonbonding interaction between the Se and N atoms. In addition, the calculated spectra and molecular orbitals confirmed the charge transfer character of the TICT state in NI-Se. To further investigate the driving force behind the twist in NI-Se, we synthesized NI-O, which has no SeN nonbonding interaction, as a control sample. Herein, we also present the characterization, fluorescence properties and the optimized geometries of NI-O. Moreover, the results showed that SeN nonbonding interaction plays a significant role in the twisting process of NI-Se.
    Physical Chemistry Chemical Physics 01/2014; · 3.83 Impact Factor
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    ABSTRACT: This extensive theoretical study employed the spin‐flip density functional theory (SFDFT) method to investigate the photoisomerization of 11‐cis‐retinal protonated Schiff base (PSB11) and its minimal model tZt‐penta‐3,5‐dieniminium cation (PSB3). Our calculated results indicate that SFDFT can perform very well in describing the ground‐ and excited‐state geometries of PSB3 and PSB11. We located the conical intersection (CI) point and constructed the photoisomerization reaction path of PSB3 and PSB11 by using the SFDFT method. To further verify the SFDFT results, we computed the energy profiles along the constructed linearly interpolated internal coordinate (LIIC) pathways by using high‐level theoretical methods, such as the EOM‐CCSD, CR‐EOM‐CCSD(T), CASPT2, NEVPT2, and XMCQDPT2 methods. The SFDFT method predicts that the photoisomerization of PSB3 is barrierless, in accordance with previous complete‐active‐space self‐consistent‐field (CASSCF) results. However, an energy barrier is predicted along the LIIC pathways of PSB11. This finding is different from previous CASSCF results and may indicate that the photoisomerization of PSB11 in gas phase is similar to that in solution. However, the higher spin contamination of the SFDFT method in the vicinity of the CI point caused the located CI geometry to deviate from that of the real CI. In addition, the LIIC pathways are only approximations to the minimum energy path (MEP). Thus, further experimental and theoretical studies are needed to verify the existence of an energy barrier along the photoisomerization reaction path of PSB11 in gas phase. © 2013 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 01/2014; 35(2). · 3.84 Impact Factor
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    ABSTRACT: Proper localization of newly synthesized proteins is essential to cellular function. Among different protein localization modes, the signal recognition particle (SRP) and SRP receptor (SR) constitute the conserved targeting machinery in all three life kingdoms and mediate about one third of the protein targeting reactions. Based on experimental and computational studies, a detailed molecular model is proposed to explain how this molecular machinery governs the efficiency and fidelity of protein localizations. In this targeting machinery, two distinct SRP GTPases are contained into the SRP and SR that are responsible to the interactions between SRP and SR. These two GTPases can interact with one another through a series of sequential and discrete interaction states that are the early intermediate formation, stable complex association, and GTPase activation. In contrast to canonical GTPases, a floppy and open conformation adopted in free SRP GTPases can facilitate efficient GTP/GDP exchange without the aid of any external factors. As the apo-form free SRP GTPases can adopt the conformational states of GDP- or GTP-bound form, the binding of GTP/GDP follows a mechanism of conformational selection. In the first step of complex formation, the two SRP GTPases can rapidly assemble into an unstable early intermediate by selecting and stabilizing one another's primed states from the equilibrium conformational ensemble. Subsequently, extensive inter- and intra-domain changes rearrange the early complex into a tight and closed state of stable complex through induced fit mechanism. Upon stable complex association, further tune of several important interaction networks activates the SRP GTPase for GTP hydrolysis. These different conformational states are coupled to corresponding protein targeting events, in which the complex formation deliveries the translating ribosome to the target membrane and the GTPase activation couples to the cargo release from SRP-SR machinery to the translocation channel. It is thus suggested that the SRP GTPases constitute a self-sufficient system to execute exquisite spatial and temporal control of the complex targeting process. The working mechanism of the SRP and SR provides a novel paradigm of how the protein machinery functions in controlling diverse biological processes efficiently and faithfully.
    Advances in experimental medicine and biology 01/2014; 805:385-409. · 1.83 Impact Factor
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    ABSTRACT: This extensive theoretical study employed the spin-flip density functional theory (SFDFT) method to investigate the photoisomerization of 11-cis-retinal protonated Schiff base (PSB11) and its minimal model tZt-penta-3,5-dieniminium cation (PSB3). Our calculated results indicate that SFDFT can perform very well in describing the ground- and excited-state geometries of PSB3 and PSB11. We located the conical intersection (CI) point and constructed the photoisomerization reaction path of PSB3 and PSB11 by using the SFDFT method. To further verify the SFDFT results, we computed the energy profiles along the constructed linearly interpolated internal coordinate (LIIC) pathways by using high-level theoretical methods, such as the EOM-CCSD, CR-EOM-CCSD(T), CASPT2, NEVPT2, and XMCQDPT2 methods. The SFDFT method predicts that the photoisomerization of PSB3 is barrierless, in accordance with previous complete-active-space self-consistent-field (CASSCF) results. However, an energy barrier is predicted along the LIIC pathways of PSB11. This finding is different from previous CASSCF results and may indicate that the photoisomerization of PSB11 in gas phase is similar to that in solution. However, the higher spin contamination of the SFDFT method in the vicinity of the CI point caused the located CI geometry to deviate from that of the real CI. In addition, the LIIC pathways are only approximations to the minimum energy path (MEP). Thus, further experimental and theoretical studies are needed to verify the existence of an energy barrier along the photoisomerization reaction path of PSB11 in gas phase. © 2013 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 11/2013; · 3.84 Impact Factor
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    ABSTRACT: A series of ratiometric probes based on heptamethine cyanine dyes for detecting hypochlorous acid have been developed. Here we present the synthesis, characterization and fluorescence properties of these probes. And it turns out that the probes are highly sensitive and selective toward hypochlorous acid. More importantly, the application in living cells for ratiometric imaging of hypochlorous acid has been achieved successfully.
    The Analyst 08/2013; · 4.23 Impact Factor
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    ABSTRACT: We have developed a near-infrared (NIR) reversible and ratiometric fluorescence sensor based on Se-BODIPY for the redox cycle between hypobromous acid oxidative stress and hydrogen sulfide repair. Real-time imaging shows that the probe is able to monitor intracellular HBrO/H2S redox cycle replacement.
    Chemical Communications 05/2013; · 6.38 Impact Factor
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    ABSTRACT: Oxidative C–H bond activation is a transformation of fundamental and practical interest, particularly if it can be carried out with high regio- and enantioselectivity. With nonheme iron oxygenases as inspiration (e.g., the Rieske oxygenases), a family of biomimetic nonheme iron complexes has been found to catalyze hydrocarbon oxidations by H2O2 via a postulated FeV(O)(OH) oxidant. Of particular interest is the Fe(S,S-PDP) catalyst discovered by White that, in the presence of acetic acid as an additive, performs selective C–H bond activation, even in complex organic molecules. The corresponding FeV(O)(OAc) species has been suggested as the key oxidant. We have carried out DFT studies to assess the viability of such an oxidant and discovered an alternative formulation. Theory reveals that the barrier for the formation of the putative FeV(O)(OAc) oxidant is too high for it to be feasible. Instead, a much lower barrier is found for the formation of a [(S,S-PDP)FeIII(κ2-peracetate)] species. In the course of C–H activation, this complex undergoes O–O bond homolysis to become a transient [(S,S-PDP)FeIV(O)(AcO·)] species that performs the efficient hydroxylation of alkanes. Thus, the acetic acid additive alters completely the nature of the high-valent oxidant, which remains disguised in the cyclic structure. This new mechanism can rationalize the many experimental observations associated with the oxidant formed in the presence of acetic acid, including the S = 1/2 EPR signal associated with the oxidant. These results further underscore the rich multioxidant scenario found in the mechanistic landscape for nonheme iron catalysts.
    ACS Catalysis 05/2013; 3(6):1334–1341. · 5.27 Impact Factor
  • Xueqin Pang, Keli Han, Qiang Cui
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    ABSTRACT: To facilitate computational study of proteins in the AlkB family and related α-ketoglutarate/Fe(II)-dependent dioxygenases, we have tested a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard-Jones parameters. Calculations for an AlkB active site model in the gas phase and ∼150 ns molecular dynamics (MD) simulations for two enzyme-dsDNA complexes (E. coli AlkB-dsDNA and ABH2-dsDNA) suggest that this simple modeling strategy provides a satisfactory description of structural properties of the Fe(II) site in AlkB enzymes, provided that care is exercised to control the binding mode of carboxylate (Asp) to the iron. MD simulations using the model for AlkB-dsDNA and ABH2-dsDNA systems find that although the structural features for the latter are overall in good agreement with the crystal structure, the dsDNA, and AlkB-dsDNA interface undergo substantial changes during the MD simulations from the crystal structure. Even for ABH2, new interactions form between a long loop region and dsDNA upon structural relaxation of the loop, supporting the role of this loop in DNA binding despite the lack of interactions between them in the crystal structure. Analysis of DNA backbone torsional distributions helps identify regions that adopt strained conformations. Collectively, the results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes; the simulations also provide additional insights regarding why AlkB and ABH2 prefer single-strand and double-strand DNA, respectively, as substrate. © 2013 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 05/2013; · 3.84 Impact Factor
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    ABSTRACT: The A2A adenosine receptor (A2A AR) is a unique G-protein coupled receptor (GPCR), because besides agonist, its antagonist could also lead to therapeutic relevance. Based on A2A AR-antagonist crystal structure, we have studied the binding mechanism of two distinct antagonists, ZM241385 and KW6002, and dynamic behaviors of A2A AR induced by antagonist binding. Key residues interacting with both antagonists and residues specifically binding to one of them are identified. ZM241385 specifically bound to S67(2.65) , M177(5.38) and N253(6.55) , while KW6002 binds to F62(2.60) , A81(3.29) and H264(7.29) . Moreover, interactions with L167(5.28) are found for both antagonists, which were not reported in agonist binding. The dynamic behaviors of antagonist bound holo-A2A ARs were found to be different from the apo-A2A AR in three typical functional switches, (i) the "ionic lock" was in equilibrium between formation and breakage in apo-A2A AR, but stayed broken in holo-A2A ARs; (ii) the "rotamer toggle switch", T88(3.36) /F242(6.44) /W246(6.48) , adopted different rotameric conformations in apo-A2A AR and holo-A2A ARs; (iii) apo-A2A AR preferred α-helical intracellular loop (IC)2 and flexible IC3, while holo-A2A ARs had a flexible IC2 and α-helical IC3. Our results indicated that antagonist binding induced different conformational rearrangements of these characteristic functional switches in apo-A2A AR and holo-A2A ARs. Proteins 2013. © 2013 Wiley Periodicals, Inc.
    Proteins Structure Function and Bioinformatics 03/2013; · 3.34 Impact Factor
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    ABSTRACT: Based on a novel strategy for modulating the fluorescence of selenide and selenoxide, we have designed and developed a reversible fluorescent probe for hypochloric acid. And the synthesis, characterization, fluorescence properties, as well as the biological applications in living cells and animals, have all been described.
    Chemical Communications 02/2013; 49(24):2445-7. · 6.38 Impact Factor
  • Peiyu Zhang, Keli Han
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    ABSTRACT: An efficient GPUs version of time-dependent wave-packet code is developed for atom-diatom state-to-state reactive scattering processes. The propagation of wave-packet is entirely calculated on GPUs employing splitting operator method after preparation of the initial wave-packet on CPU. An additional splitting operator is introduced in rotational part of the Hamiltonian to decrease communication of GPUs without losing accuracy of state-to-state information. The code is tested to calculate differential cross sections of H+H2 reaction and state-resolved reaction probabilities of nonadiabatic triplet-singlet transitions of O(3P, 1D) + H2 for total angular momentum J = 0. The global speedups of 22.11, 38.80 and 44.80 are found comparing the parallel computation of one GPU, two GPUs by exact rotational operator, and two GPUs versions by approximate rotational operator with serial computation of CPU, respectively.
    The Journal of Physical Chemistry A 02/2013; · 2.77 Impact Factor
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    ABSTRACT: We present the synthesis, spectroscopic properties, and live-cell application of a new BODIPY (boron dipyrromethene) fluorescence probe BOD-Se based on selenoxide spirocyclization reaction for peroxynitrite detection. The probe employs BODIPY dye as fluorophore, and is integrated with a chemical peroxynitrite responsive organoselenium functional group. By using reactive diaryl selenide and modulating by intramolecular charge-transfer (ICT) process, the probe is employed for evaluating intracellular peroxynitrite level changes. Different intracellular peroxynitrite levels can be detected with BOD-Se by confocal microscopy experiments using mouse macrophage cell line RAW264.7.
    Dyes and Pigments 02/2013; 96(2):383–390. · 3.53 Impact Factor
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    ABSTRACT: We have developed a new reversible fluorescence probe MPhSe-BOD for the redox cycle process between hypochlorous acid and hydrogen sulfide in solution and in living cells. Confocal microscopy imaging using RAW264.7 cell lines shows that the probe has good cell membrane permeability, and can monitor intracellular HClO/H(2)S redox cycles continuously.
    Chemical Communications 12/2012; · 6.38 Impact Factor
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    ABSTRACT: A diselenide containing fluorescent probe based on a fluorescein scaffold for thiols was developed. The fluorescent probe exhibited rapid response, high selectivity and reversibility. Confocal fluorescence microscopy was used to visualize the redox changes mediated by thiols and reactive oxygen species in living HeLa cells.
    Chemical Communications 11/2012; · 6.38 Impact Factor
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    ABSTRACT: Ruthenium(II)-catalyzed redox-neutral annulative coupling of N-sulfonyl imines with alkynes has been achieved for the synthesis of indenamines, where a sulfonamide cocatalyst is necessary.
    Organic Letters 10/2012; · 6.14 Impact Factor
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    ABSTRACT: The ground and excited state geometries, the excitation and emission energies for a series of fluorescein derivatives in aqueous solutions have been investigated using time-dependent density functional theory (TD-DFT) with B3LYP and a long-range corrected CAM-B3LYP functional. The RI-CC2 method was employed to confirm the CAM-B3LYP results. As far as we know, the excited state geometries for a series of fluorescein derivatives were optimized for the first time, and the conformational changes upon photoexcitation were discussed. Importantly, the previous proposed photo induced electron transfer (PeT) mechanism for dictating the fluorescence quantum yield (Φ(fl)) of fluorescein derivatives was not fully supported by our calculations. Internal conversion may still be the most likely mechanism for dictating the Φ(fl) of fluorescein derivatives, which indicates a need for further experimental and theoretical studies on the excited state dynamics of fluorescein derivatives.
    Physical Chemistry Chemical Physics 10/2012; 14(43):15191-8. · 3.83 Impact Factor
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    ABSTRACT: Subpicosecond fluorescence depletion spectroscopy (FDS) was used to measure the solvation dynamics of coumarin 153 (C153) in methanol. The FDS mechanisms were discussed. A quasi-continuous model was used to describe the solvational relaxation of excited states. The perturbations of the probe pulse on the excited sample system, including up-conversion and stimulated emission, were sufficiently discussed. For a probe molecule used in the FDS experiment, ensuring that the up-conversion perturbation can be negligible is important. FDS was found to be a good technique for measuring the solvation dynamics of C153 in methanol.
    Journal of Luminescence 09/2012; 132(9):2275–2280. · 2.14 Impact Factor
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    ABSTRACT: NH and N-protected isoquinolones undergo Rh(III)-catalyzed oxidative olefination at the 8-position. Complementary redox-neutral olefination of such isoquinolones using internal alkynes was achieved under ruthenium catalysis.
    Organic Letters 07/2012; 14(16):4166-9. · 6.14 Impact Factor
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    ABSTRACT: We describe the synthesis, properties, and application of two reversible fluorescent probes, mCy-TemOH and Cy-TemOH, for HOBr sensing and imaging in live cells. The two probes contain a hydroxylamine functional group for the monitoring of HOBr oxidation/ascorbic acid reduction events. Confocal fluorescence microscopy has established the HOBr detection in live-cells.
    Chemical Communications 06/2012; 48(62):7735-7. · 6.38 Impact Factor

Publication Stats

627 Citations
351.38 Total Impact Points

Institutions

  • 1998–2014
    • Chinese Academy of Sciences
      • • State Key Laboratory of Molecular Reaction Dynamics
      • • Dalian Institute of Chemical Physics
      Peping, Beijing, China
  • 2011–2013
    • Dalian Institute of Chemical Physics
      Lü-ta-shih, Liaoning, China
  • 1991–2013
    • Northeast Institute of Geography and Agroecology
      • • State Key Laboratory of Molecular Reaction Dynamics
      • • Dalian Institute of Chemical Physics
      Beijing, Beijing Shi, China
    • Shandong University
      Chi-nan-shih, Shandong Sheng, China
  • 2000–2012
    • Dalian University of Technology
      • • School of Chemical Engineering
      • • Department of Chemistry
      • • State Key Laboratory of Fine Chemicals
      • • Department of Physics
      Dalian, Liaoning, China
    • University of Jinan (Jinan, China)
      Chi-nan-shih, Shandong Sheng, China
  • 2010
    • The Scripps Research Institute
      • Department of Chemistry
      La Jolla, California, United States
  • 2006
    • Technical Institute of Physics and Chemistry
      Peping, Beijing, China
    • Ludong University
      Shan-tang, Jiangxi Sheng, China
    • Lund University
      • Department of Physical Chemistry
      Lund, Skane, Sweden