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  • 1.
    Cao, Xinrui
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ji, Yongfei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Department of Chemical Physics, University of Science and Technology of ChinaHefei, China.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Department of Chemical Physics, University of Science and Technology of ChinaHefei, China .
    Feasible Catalytic Strategy for Writing Conductive Nanoribbons on a Single-Layer Graphene Fluoride2014Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, nr 39, s. 22643-22648Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An accessible method for local reduction of graphene fluoride catalyzed by the Pt-coated nanotip with the assistance of a mixture of hydrogen and ethylene atmosphere is proposed and fully explored theoretically. Detailed mechanisms and roles of hydrogen and ethylene molecules in the cyclic reduction is discussed based on extensive first-principles calculations. It is demonstrated that the proposed cyclic reduction strategy is energetically favorable. This new strategy can be effectively applied in scanning probe lithography to fabricate electronic circuits at the nanoscale on graphene fluoride under mild conditions.

  • 2.
    Duan, Sai
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ai, Yue-Jie
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Roles of Plasmonic Excitation and Protonation on Photoreactions of p-Aminobenzenethiol on Ag Nanoparticles2014Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, nr 13, s. 6893-6902Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is increasing evidence that surface plasmons could catalyze photochemical reactions of organic molecules on metal surfaces. However, due to the complex interactions among the substrate, the adsorbate, the environment, and the incident light, the existence and the underlying mechanism of such catalytic processes have been under intense debate. Here we present a systematic first principles study on one of the most studied and controversial systems, namely, p-aminobenzenethiol (PATP) adsorbed on silver nanoparticles. Our calculations have confirmed that the observed surface-enhanced Raman scattering (SERS) bands at 1142, 1391, and 1440 cm(-1) of PATP on silver surfaces belong to its coupling reaction product, 4,4'-dimercaptoazobenzene (DMAB). It is found that the deprotonation or protonation of N atoms is the key initial step for the transformations between PATP and DMAB. The photodecomposition reaction from DMAB to PATP can occur only under the conditions that both proton transfer and plasmonic excitations have taken place. Moreover, in addition to the widely suggested hot-electron injection mechanism of plasmon, a new photochemical channel has been revealed in the decomposition of DMAB molecules under suitable incident light. This may open up an entire new type of chemical reaction in surface chemistry that we call plasmonic photochemistry. Our theoretical calculations provide consistent interpretations for the experimentally observed pH-,wavelength-,and electrode potential dependence of the SERS spectra of PATP/DMAB adsorbed on silver surfaces. Our findings highlight the important role of theoretical investigations for better understanding of complex processes involved in photochemical reaction of surface adsorbates.

  • 3.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical Study on Chemical Structures and Stability of Molecules in Metallic Junctions2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    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.

  • 4.
    Hu, Wei
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical modeling of surface and tip-enhanced Raman spectroscopies2017Inngår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 7, nr 2, artikkel-id UNSP e1293Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Raman spectroscopy is a powerful technique in molecular science because of the ability of providing vibrational 'finger-print'. The developments of the surfaceenhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have significantly improved the detection sensitivity and efficiency. However, they also introduce complications for the spectral assignments, for which advanced theoretical modeling has played an important role. Here we summarize some of our recent progresses for SERS and TERS, which generally combine both solid-state physics and quantum chemistry methods with two different schemes, namely the cluster model and the periodic boundary condition (PBC) model. In the cluster model, direct Raman spectra calculations are performed for the cluster taken from the accurate PBC structure. For PBC model, we have developed a quasianalytical approach that enables us to calculate the Raman spectra of entire system. Under the TERS condition, the non-uniformity of plasmonic field in real space can drastically alter the interaction between the molecule and the light. By taking into account the local distributions of the plasmonic field, a new interaction Hamiltonian is constructed and applied to model the super-high-resolution Raman images of a single molecule. It shows that the resonant Raman images reflect the transition density between ground and excited states, which are generally vibrational insensitive. The nonresonant Raman images, on the other hand, allow to visualize the atomic movement of individual vibrational modes in real space. The inclusion of non-uniformity of plasmonic field provides ample opportunities to discover new physics and new applications in the future. 

  • 5.
    Hu, Wei
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China, China.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhang, Guangping
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ma, Yong
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tian, Guangjun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Hefei National Laboratory for Physical Sciences, Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, China.
    Quasi-Analytical Approach for Modeling of Surface-Enhanced Raman Scattering2015Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, nr 52, s. 28992-28998Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Surface-enhanced Raman scattering has become a powerful analytical tool for the characterization of molecules adsorbed on metal surfaces. The lack of reliable computational methods to accurately assign the complicated Raman spectra has hampered its practical applications. We propose here a quasi-analytical method that allows for the effective evaluation of Raman tensors in periodic systems based on density functional perturbation theory and the finite-difference approach. Its applicability has been validated by simulating Raman spectra of 4,4’-bipyridine (4,4’-bpy) in various conditions. The calculated Raman spectra of isolated 4,4’-bpy as well as its adsorption on flat gold surfaces nicely reproduce their experimental counterparts. The same method has also been successfully applied to a more complicated system, namely 4,4’-bpy inside gold nano junctions. By comparing with the in situ experimental spectra, four interfacial configurations are identified, which are further verified by the good agreement between the simulated charge transfer properties and the experimental measurements. These results indicate that the proposed low-cost quasi-analytical method can provide accurate interpretation for the experimentally measured surface-enhanced Raman spectra and unambiguously determine the structures of the molecules on metal surfaces.

  • 6.
    Hu, Wei
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China, China.
    Tian, Guangjun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Lin, L. -L
    Ma, Yong
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Shandong Normal University, China.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China, China.
    Vibrational identification for conformations of trans-1,2-bis (4-pyridyl) ethylene in gold molecular junctions2015Inngår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 453-454, s. 20-25Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The surface-enhanced Raman scattering (SERS) spectroscopy and inelastic electron tunneling spectroscopy (IETS) are employed to study trans-1,2-bis (4-pyridyl) ethylene (BPE)/gold system. Both junction and complex forms are considered for the SERS simulations. It is predicted that the peak at 1581 cm-1 is more intense in the junction forms than that in the complex forms. Time dependent density functional theory calculations show that the relative intensity is mainly controlled by the excitation energy derivative respect to the normal modes, and the total intensity is governed by the excitation energy of the excited states. The CH bending modes dominate the IET spectra when BPE adsorbed on the flat gold surfaces. While, the pyridyl ring deformation modes are more active when BPE adsorbed on the edge of the gold clusters. For BPE adsorbed on the tip of gold clusters, the pyridyl ring and CC stretching modes show significant contribution to the IET spectra.

  • 7.
    Hu, Wei
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China.
    Zhang, Guang-Ping
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fu, Qiang
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China.
    Molecular Design to Enhance the Thermal Stability of a Photo Switchable Molecular Junction Based on Dimethyldihydropyrene and Cyclophanediene Isomerization2015Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, nr 21, s. 11468-11474Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Photoswitchable molecular devices based on dimethyldihydropyrene (DHP) and cyclophanediene (CPD) isomers in gold junctions have been systematically studied by using first-principles calculations. The reaction pathways for the forth- and back-isomerization between DHP and CPD have been explored. It is found that along the ground state, the calculated barrier for the back-isomerization from CPD to DHP is as high as 23.2 kcal/mol. The forth- and back-isomerization on excited state was found to be much easier compared to that on the ground state. Our calculations have shown that the same conclusions about the reaction pathways can be drawn for the DHP/CPD derivatives that were experimentally studied. It is revealed that the thermal stability of the molecular switch can be significantly enhanced when certain substitutions are employed. A desirable substitution that gives a larger ON/OFF ratio and higher thermal stability is proposed for these isomeric systems. We have also found that the electrode distance has a huge impact on the electron transport properties, as well as the switching performance, of these junctions, which nicely explains some puzzling experimental observations.

  • 8. Li, Debing
    et al.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO).
    Zhang, Junqiao
    Shi, Hui
    Chen, Qu
    Sun, Tianyang
    Liang, Lijun
    Wang, Qian
    Separation of Hydrogen Gas from Coal Gas by Graphene Nanopores2015Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 119, nr 45, s. 25559-25565Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We designed a series of porous graphene as the separation membrane for hydrogen gas in coal gas. The permeation process of different gas molecules (H-2, CO, CH4, and H2S) in porous graphene was evaluated under the atmospheric pressure and high pressure conditions. Our results indicate the hydrogen permeability and selectivity could be tuned by the size and the shape of the porous graphene. For graphene with bigger pores, the selectivity for hydrogen gas could decrease. In the porous graphene with same pore area, the hydrogen gas selectivity could be affected by the shape of the pore. The potential of mean force (PMF) of different gases to pass through a good separation candidate was calculated. The order of PMF for different gases to pass through the good separation candidate is H-2 < CO < CH4 approximate to H2S, which is also confirmed by the first-principle density function theory (DFT) calculation.

  • 9. Liang, L.
    et al.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Xue, Z.
    Shen, J. -W
    Theoretical study on the interaction of nucleotides on two-dimensional atomically thin graphene and molybdenum disulfide2017Inngår i: FlatChem, ISSN 2452-2627, Vol. 2, s. 8-14Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work, the interaction between single nucleotide and polynucleotides composed of different nucleotides and two-dimensional (2D) materials (graphene and MoS2) were investigated through first principles calculations and molecular dynamics (MD) simulation. The binding energy strength between single nucleotide and graphene is G &gt; C &gt; A &gt; T, and it is G &gt; A &gt; C &gt; T between single nucleotide and MoS2, derived from density function density (DFT) calculations. The binding strength between polynucleotide and graphene is A6 &gt; G6 &gt; T6 &gt; C6, and the order is G6 &gt; A6 &gt; C6 &gt; T6 of binding strength between polynucleotide and MoS2, calculated from molecular dynamics simulation. The average binding free energy for different single nucleotide A, T, C, G (polynucleotides A6, T6, C6, G6) on graphene sheet is −4.17 kcal/mol (-10.04 kcal/mol), and it is about −2.29 kcal/mol (-2.24 kcal/mol) on MoS2 surface. The binding strength for different single nucleotide (polynucleotides) on graphene sheets is around 2 times (4 times) stronger than that between nucleotide (polynucleotides) and MoS2 surface. The different absorption strength of nucleotides on these two-dimensional materials may be utilized for different promising applications.

  • 10. Liang, Lijun
    et al.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhang, Zhisen
    Shen, Jia-Wei
    Theoretic Study on Dispersion Mechanism of Boron Nitride Nanotubes by Polynucleotides2016Inngår i: SCIENTIFIC REPORTS, ISSN 2045-2322, Vol. 6, artikkel-id 39747Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Due to the unique electrical and mechanical properties of boron nitride nanotubes (BNNT), BNNT has been a promising material for many potential applications, especially in biomedical field. Understanding the dispersion of BNNT in aqueous solution by biomolecules is essential for its use in biomedical applications. In this study, BNNT wrapped by polynucleotides in aqueous solution was investigated by molecular dynamics (MD) simulations. Our results demonstrated that the BNNT wrapped by polynucleotides could greatly hinder the aggregation of BNNTs and improve the dispersion of BNNTs in aqueous solution. Dispersion of BNNTs with the assistance of polynucleotides is greatly affected by the wrapping manner of polynucleotides on BNNT, which mainly depends on two factors: the type of polynucleotides and the radius of BNNT. The interaction between polynucleotides and BNNT(9, 9) is larger than that between polynucleotides and BNNT(5, 5), which leads to the fact that dispersion of BNNT(9, 9) is better than that of BNNT(5, 5) with the assistance of polynucleotides in aqueous solution. Our study revealed the molecular-level dispersion mechanism of BNNT with the assistance of polynucleotides in aqueous solution. It shades a light on the understanding of dispersion of single wall nanotubes by biomolecules.

  • 11.
    Ma, Yong
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Song, Xiu-neng
    Wang, Chuan-kui
    Density Functional Theory Study on Raman Spectra of Rhodamine Molecules in Different Forms2014Inngår i: Chinese Journal of Chemical Physics, ISSN 1674-0068, Vol. 27, nr 3, s. 291-296Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rhodamine molecules are one of the most used dyes for applications related to Raman spectroscopy. We have systematically studied Raman spectra of Rhodamine 60, Rhodamine 123, and Rhodamine B (RhB) molecules using density functional theory. It is found that with BP86 functional the calculated Raman spectra of cationic Rhodamine molecules are in good agreement with corresponding experimental spectra in aqueous solution. It is shown that the involvement of the counter ion, chlorine, and the specific hydrogen bonds has noticeable effects on the Raman spectra of RhB that can partially explain the observed difference between Raman spectra of RhB in solution and on gold surfaces. It also indicates that an accurate description of surface enhanced Raman scattering for Rhodamine molecules on metal surface still requires to take into account the changes induced by the interfacial interactions.

  • 12. Mohammed, Abdelsalam
    et al.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Andersson, Per Ola
    Lundquist, Margaretha
    Landström, Lars
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Cluster approximations of chemically enhanced molecule-surface Raman spectra: The case of trans-1,2-bis (4-pyridyl) ethylene (BPE) on gold2013Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 581, s. 70-73Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The system, trans-1,2-bis (4-pyridyl) ethylene (BPE) on a Au substrate, is used to examine the applicability of cluster approximations for chemically enhanced molecule-surface Raman spectra. Different size of Au clusters, and adsorption sites, as well as different functionals were studied. In addition, the relative intensity of the two dominant modes of the theoretical spectra have been calculated for the different cluster sizes and adsorption sites. It was found that already a Au-20 cluster leads to excellent agreement with experimentally recorded spectra.

  • 13. Sun, Xuan
    et al.
    Chen, Weiwei
    Liang, Lijun
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Wang, Huanhuan
    Pang, Zhenfeng
    Ye, Yuxun
    Hu, Xiurong
    Wang, Qi
    Kong, Xueqian
    Jin, Yizheng
    Lei, Ming
    Construction of Electron Transfer Network by Self-Assembly of Self-n-Doped Fullerene Ammonium Iodide2016Inngår i: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 28, nr 23, s. 8726-8731Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Construction of pi-conjugation network in ordered fullerenes by self-assembly remains challenging for improving their optoelectronic performance and developing advanced materials. Here, we present a layered stacking of self-n-doped fullerene ammonium iodide (PCBANI) through a delicate balance among iodide anion-C-60 pi, electrostatic, and C-60 pi-pi interactions to construct an unprecedented supra molecular system. X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and computational modeling are carried out to clarify the structure. Remarkably, the formation of intermolecular iodide anion pi interactions between iodide and the surrounded fullerene cores yields an iodide-linked C-60 pi-pi two-dimensional (2-D) network. Consequently, the ordered and tightly packed fullerenes sandwiching iodide could facilitate electron transfer along the network system. Comparative devices incorporating the disordered films show dramatically decreased current densities and manifest the importance of the pi-extended network for electron transfer. This work provides a key strategy to control the packing of ordered electron-transport materials to suppress defect formation. Moreover, engineering self-assembly of self-n-doped fullerenes with novel architectures, such as nanowire, nanotube, and nanoparticle would yield new functionalities that are suitable for photovoltaic devices, nanoelectronics, etc.

  • 14.
    Tian, Guangjun
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhang, Guang-Ping
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hu, Wei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. University of Science and Technology of China, China.
    The effect of Duschinsky rotation on charge transport properties of molecular junctions in the sequential tunneling regime2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 35, s. 23007-23016Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present here a systematic theoretical study on the effect of Duschinsky rotation on charge transport properties of molecular junctions in the sequential tunneling regime. In the simulations we assume that only two electronic charging states each coupled to a two dimensional vibrational potential energy surface (PES) are involved in the transport process. The Duschinsky rotation effect is accounted by varying the rotational angle between the two sets of displaced PESs. Both harmonic potential and anharmonic Morse potential have been considered for the cases of the intermediate to strong electron-vibration couplings. Our calculations show that the inclusion of the Duschinsky rotation effect can significantly change the charge transport properties of a molecular junction. Such an effect makes the otherwise symmetric Coulomb diamond become asymmetric in harmonic potentials. Depending on the angle of the rotation, the low bias current could be significantly suppressed or enhanced. This effect is particularly prominent in the Franck-Condon (FC) blockade regime where the electron-vibration coupling is strong. These changes are caused by the variation of the FC factors which are closely related to the rotational angle between the two sets of PESs involved in the charge transport process. For a molecular junction with Morse potentials, the changes caused by Duschinsky rotation are much more complicated. Both the amplitude and shape of the Coulomb diamond are closely dependent on the rotational angle in the whole range from 0 to 2 pi. One interesting result is that with a rotation angle of pi (and also pi/2 for certain cases) symmetric Coulomb diamonds can even be formed from the intrinsically asymmetric Morse potential. These results could be important for the interpretation of experimental observations.

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