Yu Liu

University of California, Riverside, Riverside, California, United States

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Publications (13)44.6 Total impact

  • Yu Liu, Jianzhong Wu
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    ABSTRACT: Predicting the correct binding curves of H2(+) and H2 systems presents a great challenge in current applications of electronic density functional theory. Here we report a new functional for the exchange-correlation energy based on the weighted density approximation and the classical mapping method. With the exact sum rule for the exchange-correlation hole and accurate correlation functions of uniform electrons as the input, the new functional is free of delocalization and static correlation errors. It yields the exact results for any one-electron systems and the correct asymptotic limit of the binding energy between hydrogen atoms.
    Physical chemistry chemical physics : PCCP. 07/2014;
  • Jia Fu, Yu Liu, Jianzhong Wu
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    ABSTRACT: We report the performance of a classical density functional theory (CDFT) in the competition for the solvation free-energy category of the SAMPL4 blind prediction event. The theoretical calculations were carried out with the TIP3P water model and different combinations of solute configurations and molecular force fields. In comparison with the experimental data, the blind test yields an average unsigned error of 2.38 kcal/mol and the root mean square deviation of 2.99 kcal/mol. Whereas these numbers are significantly larger than the best results from explicit-solvent MD simulations, we find that the theoretical performance is sensitive to both the molecular force fields and solute configurations and that a comparable level of accuracy can be achieved by a judicious selection of the solute configurations and the force-field parameters. Most importantly, CDFT reduces the computational cost of MD simulation by almost 3 orders of magnitude, making it very attractive for large-scale hydration free-energy calculations (e.g., screening the aqueous solubility of drug-like molecules).
    Journal of Computer-Aided Molecular Design 03/2014; · 3.17 Impact Factor
  • Yu Liu, Jianzhong Wu
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    ABSTRACT: Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.
    The Journal of Chemical Physics 02/2014; 140(8):084103. · 3.12 Impact Factor
  • Yu Liu, Jia Fu, Jianzhong Wu
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    ABSTRACT: The classical density functional theory (DFT) is proposed as an efficient computational tool for high-throughput prediction of the solvation free energies of small molecules in liquid water under the ambient condition. With the solute molecules represented by the AMBER force field and the TIP3P model for the solvent, the new theoretical method predicts the hydration free energies of 500 neutral molecules with average unsigned errors of 0.96 and 1.04 kcal/mol in comparison with the experimental and simulation data, respectively. The DFT predictions are orders of magnitude faster than conventional molecular dynamics simulations, and the theoretical performance can be further improved by taking into account the molecular flexibility of large solutes.
    Journal of Physical Chemistry Letters 10/2013; 4(21):3687–3691. · 6.59 Impact Factor
  • Yu Liu, Jia Fu, Jianzhong Wu
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    ABSTRACT: We present an efficient computation procedure for rapid prediction of the self-diffusivity of gas molecules in nanoporous materials by a combination of the Knudsen model, Rosenfeld's excess entropy scaling method, and a classical density functional theory (DFT). The self-diffusivity conforms to the Knudsen model at low density, and the effects of intermolecular interactions at higher densities are accounted for by Rosenfeld's excess-entropy scaling method. The classical DFT provides a convenient way to calculate the excess entropy used in the scaling analysis. The hybrid computational procedure has been calibrated with MD simulation for the adsorption of H2, He, Ne and Ar gases in several nanoporous materials over a broad range of pressure. It predicts adsorption isotherms and different types of diffusion behavior in excellent agreement with the simulation results. While simulation of gas diffusion in nanoporous materials is extremely time consuming, the new procedure is computationally very efficient because it uses only single molecular and thermodynamic parameters.
    Langmuir 09/2013; · 4.38 Impact Factor
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    ABSTRACT: Direct correlation functions (DCFs) play a pivotal role in the applications of classical density functional theory (DFT) to addressing the thermodynamic properties of inhomogeneous systems beyond the local-density or mean-field approximations. Whereas numerous studies have been dedicated to the radial distribution functions of liquid water - the most important solvent on earth, relatively little attention has been given to the site-site DCFs. The water DCFs are long-ranged and difficult to calculate directly by simulation, and the predictions from conventional liquid-state theories have been rarely calibrated. Here we report a computational procedure for accurate evaluation of the site-site DCFs of liquid water based on three popular molecular models (viz., SPC, SPC∕E, and TIP3P). The numerical results provide a benchmark for calibration of conventional liquid-state theories and fresh insights into development of new DFT methods. We show that: (1) the long-range behavior of the site-site DCFs depends on both the molecular model and the thermodynamic condition; (2) the asymptotic limit of DCFs at large distance does not follow the mean-spherical approximation (MSA); (3) individual site-site DCFs are long ranged (∼40 nm) but a summation of all DCF pairs exhibits only short-range behavior (∼1 nm or a few water diameters); (4) the site-site bridge correlation functions behave as the DCFs, i.e., they are also long-ranged while the summation of all bridge correlation functions is short ranged. Our analytical and numerical analyses of the DCFs provide some simple strategies for possible improvement of the numerical performance of conventional liquid-state theories.
    The Journal of Chemical Physics 08/2013; 139(6):064509. · 3.12 Impact Factor
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    Yu Liu, Jianzhong Wu
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    ABSTRACT: At ambient conditions the intermolecular correlation in liquid water is generally believed to be short ranged as shown in the atomic pair distribution functions (PDFs) obtained from scattering experiments or from theoretical predictions. However, atom-atom PDFs provide only a partial description of the higher dimensional intermolecular correlation function that depends on both the positions and orientations of water molecules. Here we study the atomic PDFs of liquid water as well as the angular correlation function (ACF) using a classical density functional theory. We demonstrate that, different from the PDFs, the ACF exhibits long-range oscillatory decay extending up to tens of molecular diameters. The theoretical predictions are in good agreement with molecular simulations and corroborate recent experimental results from the second harmonic light scattering experiments.
    The Journal of Chemical Physics 07/2013; 139(4):041103. · 3.12 Impact Factor
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    ABSTRACT: We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.
    Journal of Chemical Theory and Computation 03/2013; 9(4):1896–1908. · 5.39 Impact Factor
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    ABSTRACT: A molecular thermodynamic model is developed to examine crowding effect on DNA melting. Each pair of nucleotides in double-stranded DNA and each nucleotide in single-stranded DNA are represented by two types of charged Lennard-Jones segments, respectively. Water molecules are mimicked explicitly as spherical particles, embedded in a dielectric continuum. Crowders with varying concentration, size, interaction strength, and chain length are considered. For DNA with a sequence of A(20), the melting temperature is predicted to increase by 1 K in the presence of Ficoll70 and by 7.5 K in the presence of Ficoll70-polyvinyl pyrrolidone360 mixture. The predictions agree well with experimental data. Furthermore, the melting temperature is found to increase with increasing crowder size, but reduce with increasing interaction strength and crowder length. The predicted changes of Gibbs energy, entropy and enthalpy are consistent with experimentally measured values. The study reveals that DNA melting in a crowded environment is influenced by both entropic and enthalpic effects.
    Physical Chemistry Chemical Physics 10/2012; 14(44):15400-5. · 3.83 Impact Factor
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    ABSTRACT: A reaction density functional theory (R-DFT) is developed for chemical reactions in confined space by integrating reaction thermodynamics and DFT for chain fluids. The theory is applied to investigate DNA melting in slit pores, with nucleotides represented by coarse-grained charged Lennard-Jones particles. Three types of slit pores are considered for DNA melting: repulsive pore, attractive pore, and under electric field. In repulsive pores, the melting temperature increases slightly with reducing pore width, and the increase magnitude is nearly the same for DNA of different chain lengths. The double-strand DNA (dsDNA) and single-strand DNA (ssDNA) are located in the slit center, particularly for long DNA due to the effect of configuration entropy. In attractive pores, the melting temperature increases with increasing wall-fluid interaction. The DNA chains are preferentially adsorbed near the slit walls with a strong wall-fluid interaction. Under electric field, the melting temperature increases slightly and is more distinct for shorter DNA.
    The Journal of Physical Chemistry B 02/2011; 115(8):1848-55. · 3.61 Impact Factor
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    ABSTRACT: In this work, a recently developed density functional theory in three-dimensional space was extended to the adsorption of gas mixtures. Weighted density approximations to the excess free energy with different weighting functions were adopted for both repulsive and attractive contributions. An equation of state for hard-sphere mixtures and a modified Benedict-Webb-Rubin equation for Lennard-Jones mixtures were used to estimate the excess free energy of a uniform fluid. The theory was applied to the adsorption of CO(2)/CH(4) and CO(2)/N(2) mixtures in two metal-organic frameworks: ZIF-8 and Zn(2)(BDC)(2)(ted). To validate the theoretical predictions, grand canonical Monte Carlo simulations were also conducted. The predicted adsorption and selectivity from DFT were found to agree well with the simulation results. CO(2) has stronger adsorption than CH(4) and N(2), particularly in Zn(2)(BDC)(2)(ted). The selectivity of CO(2) over CH(4) or N(2) increases with increasing pressure as attributed to the cooperative interactions of adsorbed CO(2) molecules. The composition of the gas mixture exhibits a significant effect on adsorption but not on selectivity.
    The Journal of Physical Chemistry B 02/2010; 114(8):2820-7. · 3.61 Impact Factor
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    ABSTRACT: A weighted density functional theory is developed for Yukawa chain fluids confined in a nanoslit. The excess free-energy functional is separated into repulsive and attractive contributions. A simple Heaviside function is used as the weighting function to calculate the weighted density in both contributions. The excess free-energy functional of repulsive interaction is calculated by the equation of state developed by Liu et al., while the contribution to excess free-energy functional by attractive interaction is calculated using the statistical associating fluids theory for chain molecules with attractive potentials of variable range. For pure fluids, the predicted density profiles near the nanoslit wall are in good agreement with simulations. The effect of cut-off introduced in the weighting function for the attractive part is examined; in addition, the surface excess and partition coefficient are calculated. The density profiles are also predicted for mixtures of two Yukawa chain fluids with different chain lengths, hard-core diameters, fluid–fluid and wall–fluid interactions. This work reveals that it is important to decompose the excess free-energy functional into repulsive and attractive contributions, and a simple weighting function can be used for both contributions.
    Molecular Simulation 01/2010; 36(4):291-301. · 1.06 Impact Factor
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    ABSTRACT: A density functional theory (DFT) is developed in three-dimensional nanoconfined space and applied for H(2) storage in metal-organic frameworks. Two different weighting functions based on the weighted density approximation (WDA) are adopted, respectively, for the repulsive and attractive contributions to the excess free energy. The Carnahan-Starling equation and a modified Benedicit-Webb-Rubin equation are used to calculate the excess free energy of uniform fluid. To compare with DFT predictions, grand canonical Monte Carlo simulations are carried out separately. For H(2) adsorption in MOF-5 and ZIF-8, the isotherms predicted from the DFT agree well with simulation and experiment results, and the DFT is found to be superior to the mean-field-approximation (MFA)-based theory. The adsorption energies and isosteric heats predicted are also in accord with simulation results. From the predicted density contours, the DFT shows that the preferential adsorption sites are the corners of metal clusters in MOF-5 and the top of organic linkers in ZIF-8, consistent with simulation and experimental observations.
    The Journal of Physical Chemistry B 09/2009; 113(36):12326-31. · 3.61 Impact Factor

Publication Stats

7 Citations
44.60 Total Impact Points

Institutions

  • 2013
    • University of California, Riverside
      Riverside, California, United States
  • 2010–2013
    • East China University of Science and Technology
      • School of Chemistry and Molecular Engineering
      Shanghai, Shanghai Shi, China
  • 2009
    • National University of Singapore
      • Department of Chemical & Biomolecular Engineering
      Singapore, Singapore