Yingdi Jin

The University of Hong Kong, Hong Kong, Hong Kong

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Publications (5)30.9 Total impact

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    Yingdi Jin · Xingxing Li · Jinlong Yang
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    ABSTRACT: A serial of two dimensional titanium and zirconium trichalcogenides nanosheets MX3 (M=Ti, Zr; X=S, Se, Te) are investigated based on first-principles calculations. The evaluated low cleavage energy indicates that stable two dimensional monolayers can be exfoliated from their bulk crystals in experiment. Electronic studies reveal very rich electronic properties in these monolayers, including metallic TiTe3 and ZrTe3, direct band gap semiconductor TiS3 and indirect band gap semiconductors TiSe3, ZrS3 and ZrSe3. The band gaps of all the semiconductors are between 0.57~1.90 eV, which implies their potential applications in nano-electronics. And the calculated effective masses demonstrate highly anisotropic conduction properties for all the semiconductors. Optically, TiS3 and TiSe3 monolayers exhibit good light absorption in the visible and near-infrared region respectively, indicating their potential applications in optical devices. In particular, the highly anisotropic optical absorption of TiS3 monolayer suggests it could be used in designing nano optical waveguide polarizers.
    Physical Chemistry Chemical Physics 02/2015; 17(28). DOI:10.1039/C5CP02813B · 4.20 Impact Factor
  • Yang Liu · Xiaoli Fan · Yingdi Jin · Xiangqian Hu · Hao Hu
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    ABSTRACT: Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.
    Journal of Chemical Theory and Computation 07/2013; 9(9):4257-4265. DOI:10.1021/ct400406v · 5.31 Impact Factor
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    ABSTRACT: Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum-mechanical and molecular-mechanical subsystems. Instead, classical Lennard-Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long-range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations. However, we show here that the LJ potential cannot correctly describe subtle details of the electron density of the QM subsystem because of the neglect of Pauli repulsions between the QM and MM subsystems. The inaccurate electron density subsequently affects the calculation of electronic and magnetic properties of the QM subsystem. To explicitly consider Pauli interactions with QM/MM methods, we propose a method to use empirical effective potentials on the MM atoms. The test case of the binding energy and magnetic properties of a water dimer shows promising results for the general application of effective potentials to mimic Pauli repulsions in QM/MM calculations. © 2013 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 07/2013; 34(27). DOI:10.1002/jcc.23401 · 3.60 Impact Factor
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    ABSTRACT: We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.
    Physical Chemistry Chemical Physics 04/2012; 14(21):7700-9. DOI:10.1039/c2cp23714h · 4.20 Impact Factor
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    ABSTRACT: By first-principles theory we study the nearly free electron (NFE) states of carbon and boron nitride nanotubes. In addition to the well-known π* bands, we found a series of one-dimensional (1D) NFE bands with on-axis spatial distributions, which resemble atomic orbitals projected onto a plane. These bands are 1D counterparts of the recently discovered superatom orbitals of 0D fullerenes. In addition to the previously reported lowest energy NFE state with the angular quantum number l = 0 corresponding to s atomic orbital character, we find higher energy NFE bands with l > 0 corresponding to the p, d, etc., orbitals. We show that these atom-like states of nanotubes originate from the many-body screening, which is responsible for the image potential of the parent two-dimensional (2D) graphene or BN sheets. With a model potential that combines the short-range exchange-correlation and the long-range Coulomb interactions, we reproduce the energies and radial wave function profiles of the NFE states from the density functional theory calculations. When the nanotube radius exceeds the radial extent on NFE states, the NFE state energies converge to those of image potential states of the parent 2D molecular sheets. To explore possible applications in molecular electronics that take advantage of the NFE properties of nanotube building blocks, we investigate the modification of NFE states by transverse electric fields, alkali metal encapsulation, and lateral and concentric nanotube dimerization.
    Nano Letters 11/2010; 10(12). DOI:10.1021/nl1023854 · 13.59 Impact Factor