Qi Wu

City University of Hong Kong, Chiu-lung, Kowloon City, Hong Kong

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Publications (6)21.52 Total impact

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    ABSTRACT: Arabidopsis thaliana UV RESISTANCE LOCUS8 (UVR8) has been identified as a photoreceptor for ultraviolet-B (UV-B). Tryptophan (Trp) residues have been shown to play a critical role in the response to UV-B irradiation in UVR8. In this work, we explore the spectroscopic behaviors of Trps in different protein environments of the UVR8 structure using the time-dependent density functional tight-binding (TD-DFTB) scheme. We show that W233 exhibits the longest absorption wavelength, highlighting its potential as a terminal Trp chromophore in UV-B harvesting antenna. Our electronic and optical property analyses using various amino acid models support the important roles of W285 and W233 in sensing UV-B light at longer absorption wavelengths (~290 nm). We also provide evidence for the specific function ofW94 in absorption at the longest wavelengths (305.8 nm in cluster II and 304.5 nm in cluster III). To these findings, we also add information about the influence of the arginine and aspartic acid residues surrounding the Trp pyramid on the particular absorption bands (280~300 nm) that are characteristic of the UV-B photoreceptor.
    No preview · Article · Mar 2015 · Physical Chemistry Chemical Physics
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    ABSTRACT: UVB from sunlight is an important environmental signal for plants. In Arabidopsis thaliana, the UVB signal is perceived by photoreceptor AtUVR8, which undergoes light-induced dimer dissociation. Crystallographic and mutational studies have identified two tryptophan residues at the dimer interface that are crucial for UVB responses. However, the molecular events leading up to dimer dissociation remain elusive. We applied dynamic crystallography to capture light-induced structural changes in photoactive AtUVR8 crystals. Here we report two intermediate structures at 1.67 Å resolution. At the epicentre of UVB signalling, concerted motions associated with Trp 285/Trp 233 lead to ejection of a water molecule, which weakens a network of hydrogen bonds and salt bridges at the dimer interface. Partial opening of the β-propeller structure, due to thermal relaxation of conformational strains originating in the epicentre, further disrupts the dimer interface and leads to dissociation. These dynamic crystallographic observations provide structural insights into the photo-perception and signalling mechanism of UVR8.
    Full-text · Article · Jan 2015
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    ABSTRACT: The size-dependent optical properties of silicon nanosheets (SiNSs) are investigated using the time-dependent density functional based tight-binding method (TD-DFTB). Evidence for the formation of self-trapped exciton states in SiNSs is provided by examining the localization properties in terms of the characteristic size of the electronic excitations. We show that the frontier molecular orbitals in the first excited state are highly localized in the central stretched Si-Si bond of the NSs due to structural relaxation, which leads to a significant red-shift of the optical gaps. For SiNSs, the boundary length and local structure of the central section in SiNSs influence the spatial extent of self-trapped excitons in the first excited state. The first excited states are observed to be spatially less localized for SiNSs with a longer boundary length. The distribution of electronic density perturbation is diverse in the case of central Si-6 or a single Si-Si bond, thereby leading to different spatial confinement of structural relaxation. In contrast with zero- and one-dimensional Si nanomaterials, the two-dimensional SiNSs show a highly localized exciton when the width is less than 2 nm, which suggests it as a candidate for exploring the characteristics of exciton self-trapping.
    No preview · Article · Sep 2014 · The Journal of Physical Chemistry C
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    ABSTRACT: To promote possible applications of graphene in molecular identification based on stacking effects, in particular in recognizing aromatic amino acids and even sequencing nucleobases in life sciences, we comprehensively study the interaction between graphene segments and different cyclic organic hydrocarbons including benzene (C6H6), cyclohexane (C6H12), benzyne (C6H4), cyclohexene (C6H10), 1,3-cyclohexadiene (C6H8(1)) and 1,4-cyclohexadiene (C6H8(2)), using the density-functional tight-binding (DFTB) method. Interestingly, we find obviously different characteristics in Raman vibrational and ultraviolet visible absorption spectra of the small molecules adsorbed on the graphene sheet. Specifically, we find that both spectra involve clearly different characteristic peaks, belonging to the different small molecules upon adsorption, with the ones of ionized molecules being more substantial. Further analysis shows that the adsorptions are almost all due to the presence of dispersion energy in neutral cases and involve charge transfer from the graphene to the small molecules. In contrast, the main binding force in the ionic adsorption systems is the electronic interaction. The results present clear signatures that can be used to recognize different kinds of aromatic hydrocarbon rings on graphene sheets. We expect that our findings will be helpful for designing molecular recognition devices using graphene.
    Full-text · Article · Sep 2013 · Nanoscale
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    ABSTRACT: Silicon is the leading semiconductor material in microelectronic industry. Owing to the large surface to volume ratio, low-dimensional Si nanostructures, for instance, silicon quantum dots exhibit diverse electronic and optical properties. Passivating the surface of Si nanostructures by a suitable species is thereby required to stabilize and engineer the dot properties in different environment. Recent theoretical advances in the investigation of the excited state properties of silicon quantum dots (QDs) are reviewed in this article. The theoretical calculations reveal that the excited state relaxation is prevalent in hydrogenated silicon nanoparticles. Stokes shift due to structure relaxation in the excited state varies with the particle size. It is therefore desirable to minimize Stokes shift for the purpose of maximizing its quantum yield or efficiency in photoluminescence applications. Consequently, surface functionalization by a suitable species turns out to be the most effective avenue. Determination of proper passivating agent is of outmost importance to satisfy the practical necessity. All these intermingled factors are briefly addressed in this article.
    No preview · Article · Jun 2013 · Journal of Cluster Science
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    ABSTRACT: We report possible cage-like nanostructures formed by a representative amino acid, serine octamers and decamers, determined by binding energy calculations and molecular dynamic simulations using the density functional tight-binding method. We used the l-handed serine to construct complex conformers linked by hydrogen bonds. We found the structures linked by -COOH···O=C- to be the most stable conformers and the calculation of the vibrational modes of complexes further illustrated this result. We attempted to apply our cage-like structures to the delivery of C(20) and cycloserine as model molecules. Our results may shed light on the design of cage-like biocompatible complexes for drug delivery.
    Full-text · Article · May 2012 · Organic & Biomolecular Chemistry

Publication Stats

21 Citations
21.52 Total Impact Points


  • 2012-2015
    • City University of Hong Kong
      • Department of Physics and Materials Science
      Chiu-lung, Kowloon City, Hong Kong
  • 2014
    • The University of Hong Kong
      Hong Kong, Hong Kong
  • 2013
    • Beijing Computational Science Research Center
      Peping, Beijing, China