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Fan X, Liu H, Anang E, Ren D. Effects of Electronegativity and Hydration Energy on the Selective Adsorption of Heavy Metal Ions by Synthetic NaX Zeolite. Materials (Basel) 2021; 14:ma14154066. [PMID: 34361261 PMCID: PMC8347618 DOI: 10.3390/ma14154066] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 12/03/2022]
Abstract
The adsorption capacity of synthetic NaX zeolite for Pb2+, Cd2+, Cu2+ and Zn2+ in single and multi-component systems were investigated. The effects of electronegativity and hydration energy on the selective adsorption, as well as potential selective adsorption mechanism of the NaX zeolite for Pb2+, Cd2+, Cu2+ and Zn2+ were also discussed. The maximum adsorption capacity order of the heavy metals in the single system was Pb2+ > Cd2+ > Cu2+ > Zn2+, and this could be related to their hydration energy and electronegativity. The values of the separation factors (α) and affinity constant (KEL) in different binary systems indicated that Pb2+ was preferentially adsorbed, and Zn2+ presented the lowest affinity for NaX zeolite. The selective adsorption capacities of the metals were in the order, Pb2+ > Cd2+ ≈ Cu2+ > Zn2+. The trend for the selective adsorption of NaX zeolite in ternary and quaternary systems was consistent with that in the binary systems. Pb2+ and Cu2+ reduced the stability of the Si-O-Al bonds and the double six-membered rings in the NaX framework, due to the high electronegativity of Pb2+ and Cu2+ than that of Al3+. The selective adsorption mechanism of NaX zeolite for the high electronegative metal ions could mainly result from the negatively charged O in the Si-O-Al structure of the NaX zeolite, hence heavy metal ions with high electronegativity display a strong affinity for the electron cloud of the oxygen atoms in the Si-O-Al. This study could evaluate the application and efficiency of zeolite in separating and recovering certain metal ions from industrial wastewater.
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Affiliation(s)
- Xianyuan Fan
- Department of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China; (X.F.); (E.A.); (D.R.)
- Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Hong Liu
- Department of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China; (X.F.); (E.A.); (D.R.)
- Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, China
- Correspondence: ; Tel.: +86-139-7148-8669
| | - Emmanuella Anang
- Department of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China; (X.F.); (E.A.); (D.R.)
| | - Dajun Ren
- Department of Resource and Environmental Engineering, Wuhan University of Science and Technology, Wuhan 430081, China; (X.F.); (E.A.); (D.R.)
- Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, China
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Chen LY. Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions. Front Phys 2020; 8:202. [PMID: 32542181 PMCID: PMC7295167 DOI: 10.3389/fphy.2020.00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249 U.S.A
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Abstract
Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.
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Affiliation(s)
- J Johnson
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - D A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - T Yamazaki
- Vancouver Prostate Centre, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - S Gusarov
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Dr., Edmonton, AB, T6G 2M9, Canada
| | - A Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Dr., Edmonton, AB, T6G 2M9, Canada
- Department of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering, 9211-116 Str., Edmonton, AB, T6G 1H9, Canada
| | - T Luchko
- Department of Physics and Astronomy, California State University, Northridge, CA 91330
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Andersson MP, Stipp SLS. Predicting hydration energies for multivalent ions. J Comput Chem 2014; 35:2070-5. [PMID: 25212881 DOI: 10.1002/jcc.23733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/03/2014] [Accepted: 08/23/2014] [Indexed: 01/13/2023]
Abstract
We have predicted the free energy of hydration for 40 monovalent and multivalent cations and anions using density functional theory and the implicit solvent model COnductor like Screening MOdel for Real Solvents (COSMO-RS) at the Becke-Perdew (BP)/Triple zeta valence with polarization functions (TZVP) level. Agreement with experimental data for monovalent and divalent ions is good and shows no significant systematic errors. Predictions are noticeably better than with standard COSMO. The agreement with experimental data for trivalent and tetravalent ions is slightly worse and shows systematic errors. Our results indicate that quantum chemical calculations combined with COSMO-RS solvent treatment is a reliable method for treating multivalent ions in solution, provided one hydration shell of explicit water molecules is included for metal cations. The accuracy is not high enough to allow absolute predictions of hydration energies but could be used to investigate trends for several ions, thanks to the low computational cost, in particular for ligand exchange reactions.
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Affiliation(s)
- Martin P Andersson
- Department of Chemistry, Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
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Wang J, Cieplak P, Li J, Cai Q, Hsieh M, Luo R, Duan Y. Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization. J Phys Chem B 2012; 116:7088-101. [PMID: 22612331 PMCID: PMC3391542 DOI: 10.1021/jp3019759] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H(vap)), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H(vap) was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.
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Affiliation(s)
- Junmei Wang
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
| | - Piotr Cieplak
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Jie Li
- University of California at Davis Genome Center and Department of Biomedical Engineering, One Shields Avenue, Davis, CA 95616, USA
| | - Qin Cai
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - MengJuei Hsieh
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - Ray Luo
- University of California at Irvine, Molecular Biology and Biochemistry 3144 Natural Sciences I, Irvine, CA, USA 92697-3900
| | - Yong Duan
- University of California at Davis Genome Center and Department of Biomedical Engineering, One Shields Avenue, Davis, CA 95616, USA
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Smith SS, Steinle ED, Meyerhoff ME, Dawson DC. Cystic fibrosis transmembrane conductance regulator. Physical basis for lyotropic anion selectivity patterns. J Gen Physiol 1999; 114:799-818. [PMID: 10578016 PMCID: PMC2230651 DOI: 10.1085/jgp.114.6.799] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/1999] [Accepted: 11/01/1999] [Indexed: 12/01/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) Cl channel exhibits lyotropic anion selectivity. Anions that are more readily dehydrated than Cl exhibit permeability ratios (P(S)/P(Cl)) greater than unity and also bind more tightly in the channel. We compared the selectivity of CFTR to that of a synthetic anion-selective membrane [poly(vinyl chloride)-tridodecylmethylammonium chloride; PVC-TDMAC] for which the nature of the physical process that governs the anion-selective response is more readily apparent. The permeability and binding selectivity patterns of CFTR differed only by a multiplicative constant from that of the PVC-TDMAC membrane; and a continuum electrostatic model suggested that both patterns could be understood in terms of the differences in the relative stabilization of anions by water and the polarizable interior of the channel or synthetic membrane. The calculated energies of anion-channel interaction, derived from measurements of either permeability or binding, varied as a linear function of inverse ionic radius (1/r), as expected from a Born-type model of ion charging in a medium characterized by an effective dielectric constant of 19. The model predicts that large anions, like SCN, although they experience weaker interactions (relative to Cl) with water and also with the channel, are more permeant than Cl because anion-water energy is a steeper function of 1/r than is the anion-channel energy. These large anions also bind more tightly for the same reason: the reduced energy of hydration allows the net transfer energy (the well depth) to be more negative. This simple selectivity mechanism that governs permeability and binding acts to optimize the function of CFTR as a Cl filter. Anions that are smaller (more difficult to dehydrate) than Cl are energetically retarded from entering the channel, while the larger (more readily dehydrated) anions are retarded in their passage by "sticking" within the channel.
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Affiliation(s)
- Stephen S. Smith
- From the Department of Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Erich D. Steinle
- From the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Mark E. Meyerhoff
- From the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - David C. Dawson
- From the Department of Physiology, University of Michigan, Ann Arbor, Michigan 48109
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Abstract
Equilibrium quotients for the 1:1 complexes of dibenzo-30-crown-10 with Na(+), K(+), Rb(+), Cs(+), NH(4) (+), and T1(+) in methanol solution have been determined spectrophotometrically. The observed selectivity pattern is discussed in terms of the hydration energy of the cations and the cation-ligand binding energy. The rate of complex formation is diffusion-controlled. Relaxation amplitude data are consistent with a mechanism that involves conformational change of the crown compound.
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