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Philippi F, Goloviznina K, Gong Z, Gehrke S, Kirchner B, Pádua AAH, Hunt PA. Charge transfer and polarisability in ionic liquids: a case study. Phys Chem Chem Phys 2022; 24:3144-3162. [PMID: 35040843 DOI: 10.1039/d1cp04592j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and explanatory power of a classical MD simulation is inextricably linked to the underlying force field. A key aspect of the forcefield for ILs is the ability to recover charge based interactions. Our focus in this paper is on the description and recovery of charge transfer and polarisability effects, demonstrated through MD simulations of the widely used 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4C1im][NTf2] IL. We study the charge distributions generated by a range of ab initio methods, and present an interpolation method for determining atom-wise scaled partial charges. Two novel methods for determining the mean field (total) charge transfer from anion to cation are presented. The impact of using different charge models and different partial charge scaling (unscaled, uniformly scaled, atom-wise scaled) are compared to fully polarisable simulations. We study a range of Drude particle explicitly polarisable potentials and shed light on the performance of current approaches to counter known problems. It is demonstrated that small changes in the charge description and MD methodology can have a significant impact; biasing some properties, while leaving others unaffected within the structural and dynamic domains.
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Affiliation(s)
- Frederik Philippi
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, London W12 0BZ, UK
| | - Kateryna Goloviznina
- Laboratoire de Chimie, École Normale Supérieure de Lyon & CNRS, 69364 Lyon, France
| | - Zheng Gong
- Laboratoire de Chimie, École Normale Supérieure de Lyon & CNRS, 69364 Lyon, France
| | - Sascha Gehrke
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4+6, D-53115 Bonn, Germany.,Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| | - Agílio A H Pádua
- Laboratoire de Chimie, École Normale Supérieure de Lyon & CNRS, 69364 Lyon, France
| | - Patricia A Hunt
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, London W12 0BZ, UK.,School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand.
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2
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Egorov AV, Brodskaya EN, Laaksonen A. The Effect of Single-Atomic Ions on the Melting of Microscopic Ice Particles According to Molecular Dynamics Data. COLLOID JOURNAL 2018. [DOI: 10.1134/s1061933x1805006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Coons MP, Herbert JM. Quantum chemistry in arbitrary dielectric environments: Theory and implementation of nonequilibrium Poisson boundary conditions and application to compute vertical ionization energies at the air/water interface. J Chem Phys 2018; 148:222834. [DOI: 10.1063/1.5023916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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4
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Hunt PA. Quantum Chemical Modeling of Hydrogen Bonding in Ionic Liquids. Top Curr Chem (Cham) 2017; 375:59. [PMID: 28523638 PMCID: PMC5480408 DOI: 10.1007/s41061-017-0142-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/16/2017] [Indexed: 01/18/2023]
Abstract
Hydrogen bonding (H-bonding) is an important and very general phenomenon. H-bonding is part of the basis of life in DNA, key in controlling the properties of water and ice, and critical to modern applications such as crystal engineering, catalysis applications, pharmaceutical and agrochemical development. H-bonding also plays a significant role for many ionic liquids (IL), determining the secondary structuring and affecting key physical parameters. ILs exhibit a particularly diverse and wide range of traditional as well as non-standard forms of H-bonding, in particular the doubly ionic H-bond is important. Understanding the fundamental nature of the H-bonds that form within ILs is critical, and one way of accessing this information, that cannot be recovered by any other computational method, is through quantum chemical electronic structure calculations. However, an appropriate method and basis set must be employed, and a robust procedure for determining key structures is essential. Modern generalised solvation models have recently been extended to ILs, bringing both advantages and disadvantages. QC can provide a range of information on geometry, IR and Raman spectra, NMR spectra and at a more fundamental level through analysis of the electronic structure.
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Affiliation(s)
- Patricia A Hunt
- Imperial College of Science, Technology and Medicine, London, UK.
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5
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Xi E, Remsing RC, Patel AJ. Sparse Sampling of Water Density Fluctuations in Interfacial Environments. J Chem Theory Comput 2016; 12:706-13. [DOI: 10.1021/acs.jctc.5b01037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erte Xi
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard C. Remsing
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and
Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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6
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Ou SC, Cui D, Patel S. Molecular modeling of ions at interfaces: exploring similarities to hydrophobic solvation through the lens of induced aqueous interfacial fluctuations. Phys Chem Chem Phys 2016; 18:30357-30365. [DOI: 10.1039/c6cp04112d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion specific effects are ubiquitous in chemistry and biology.
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Affiliation(s)
- Shu-Ching Ou
- Sealy Center for Structural Biology and Molecular Biophysics
- University of Texas Medical Branch
- 301 University Boulevard
- Galveston
- USA
| | - Di Cui
- Department of Chemistry
- Temple University
- Philadelphia
- USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark
- USA
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7
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Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Holmberg N, Sammalkorpi M, Laasonen K. Ion Transport through a Water–Organic Solvent Liquid–Liquid Interface: A Simulation Study. J Phys Chem B 2014; 118:5957-70. [DOI: 10.1021/jp412162c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Nico Holmberg
- Department
of Chemistry, Aalto University, Aalto, Finland
| | | | - Kari Laasonen
- Department
of Chemistry, Aalto University, Aalto, Finland
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9
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Mayes HB, Tian J, Nolte MW, Shanks BH, Beckham GT, Gnanakaran S, Broadbelt LJ. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment. J Phys Chem B 2013; 118:1990-2000. [PMID: 24308866 DOI: 10.1021/jp409481f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering, Northwestern University , Evanston, Illinois 60208, United States
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Asmadi A, Kirchner T, Abdallah W, Fedorov MV, Stukan MR. Influence of the Drude charge value on the performance of polarisable water model: A test for microscopic and macroscopic parameters. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Ou S, Cui D, Patel S. Liquid-vapor interfacial properties of aqueous solutions of guanidinium and methyl guanidinium chloride: influence of molecular orientation on interface fluctuations. J Phys Chem B 2013; 117:11719-31. [PMID: 23937431 DOI: 10.1021/jp405862p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The guanidinium cation (C(NH2)3(+)) is a highly stable cation in aqueous solution due to its efficient solvation by water molecules and resonance stabilization of the charge. Its salts increase the solubility of nonpolar molecules ("salting-in") and decrease the ordering of water. It is one of the strongest denaturants used in biophysical studies of protein folding. We investigate the behavior of guanidinium and its derivative, methyl guanidinium (an amino acid analogue) at the air-water surface, using atomistic molecular dynamics (MD) simulations and calculation of potentials of mean force. Methyl guanidinium cation is less excluded from the air-water surface than guanidinium cation, but both cations show orientational dependence of surface affinity. Parallel orientations of the guanidinium ring (relative to the Gibbs dividing surface) show pronounced free energy minima in the interfacial region, while ring orientations perpendicular to the GDS exhibit no discernible surface stability. Calculations of surface fluctuations demonstrate that, near the air-water surface, the parallel-oriented cations generate significantly greater interfacial fluctuations compared to other orientations, which induces more long-ranged perturbations and solvent density redistribution. Our results suggest a strong correlation with induced interfacial fluctuations and ion surface stability. These results have implications for interpreting molecular-level, mechanistic action of this osmolyte's interaction with hydrophobic interfaces as they impact protein denaturation (solubilization).
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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13
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14
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Ou S, Hu Y, Patel S, Wan H. Spherical monovalent ions at aqueous liquid-vapor interfaces: interfacial stability and induced interface fluctuations. J Phys Chem B 2013; 117:11732-42. [PMID: 24032752 DOI: 10.1021/jp406001b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ion-specific interfacial behaviors of monovalent halides impact processes such as protein denaturation, interfacial stability, and surface tension modulation, and as such, their molecular and thermodynamic underpinnings garner much attention. We use molecular dynamics simulations of monovalent anions in water to explore effects on distant interfaces. We observe long-ranged ion-induced perturbations of the aqueous environment, as suggested by experiment and theory. Surface stable ions, characterized as such by minima in potentials of mean force computed using umbrella sampling MD simulations, induce larger interfacial fluctuations compared to nonsurface active species, conferring more entropy approaching the interface. Smaller anions and cations show no interfacial potential of mean force minima. The difference is traced to hydration shell properties of the anions, and the coupling of these shells with distant solvent. The effects correlate with the positions of the anions in the Hofmeister series (acknowledging variations in force field ability to recapitulate essential underlying physics), suggesting how differences in induced, nonlocal perturbations of interfaces may be related to different specific-ion effects in dilute biophysical and nanomaterial systems.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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15
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Stern AC, Baer MD, Mundy CJ, Tobias DJ. Thermodynamics of iodide adsorption at the instantaneous air-water interface. J Chem Phys 2013; 138:114709. [PMID: 23534655 DOI: 10.1063/1.4794688] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We performed molecular dynamics simulations using both polarizable and non-polarizable force fields to study the adsorption of iodide to the air-water interface. A novel aspect of our analysis is that the progress of ion adsorption is measured as the distance from the instantaneous interface, which is defined by a coarse-graining scheme proposed recently by Willard and Chandler ["Instantaneous liquid interfaces," J. Phys. Chem. B 114, 1954-1958 (2010)]. Referring structural and thermodynamic quantities to the instantaneous interface unmasks molecular-scale details that are obscured by thermal fluctuations when the same quantities are referred to an average measure of the position of the interface, such as the Gibbs dividing surface. Our results suggest that an ion adsorbed at the interface resides primarily in the topmost water layer, and the interfacial location of the ion is favored by enthalpy and opposed by entropy.
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Affiliation(s)
- Abraham C Stern
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA.
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16
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Ou S, Patel S. Temperature dependence and energetics of single ions at the aqueous liquid-vapor interface. J Phys Chem B 2013; 117:6512-23. [PMID: 23537166 DOI: 10.1021/jp401243m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate temperature-dependence of free energetics with two single halide anions, I(-) and Cl(-), crossing the aqueous liquid-vapor interface through molecular dynamics simulations. The result shows that I(-) has a modest surface stability of 0.5 kcal/mol at 300 K and the stability decreases as the temperature increases, indicating the surface adsorption process for the anion is entropically disfavored. In contrast, Cl(-) shows no such surface state at all temperatures. Decomposition of free energetics reveals that water-water interactions provide a favorable enthalpic contribution, while the desolvation of ion induces an increase in free energy. Calculations of surface fluctuations demonstrate that I(-) generates significantly greater interfacial fluctuations compared to Cl(-). The fluctuation is attributed to the malleability of the solvation shells, which allows for more long-ranged perturbations and solvent density redistribution induced by I(-) as the anion approaches the liquid-vapor interface. The increase in temperature of the solvent enhances the inherent thermally excited fluctuations and consequently reduces the relative contribution from anion to surface fluctuations, which is consistent with the decrease in surface stability of I(-). Our results indicate a strong correlation with induced interfacial fluctuations and anion surface stability; moreover, resulting temperature dependent behavior of induced fluctuations suggests the possibility of a critical level of induced fluctuations associated with surface stability.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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17
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Stukan MR, Asmadi A, Abdallah W. Bulk properties of SWM4-NDP water model at elevated temperature and pressure. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2012.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Neyt JC, Wender A, Lachet V, Ghoufi A, Malfreyt P. Prediction of the concentration dependence of the surface tension and density of salt solutions: atomistic simulations using Drude oscillator polarizable and nonpolarizable models. Phys Chem Chem Phys 2013; 15:11679-90. [DOI: 10.1039/c3cp50904d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Baer MD, Mundy CJ. An ab initio approach to understanding the specific ion effect. Faraday Discuss 2013; 160:89-101; discussion 103-20. [DOI: 10.1039/c2fd20113e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4787-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Bauer BA, Ou S, Patel S. Role of spatial ionic distribution on the energetics of hydrophobic assembly and properties of the water/hydrophobe interface. Phys Chem Chem Phys 2012; 14:1892-906. [PMID: 22231014 DOI: 10.1039/c1cp20839j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present results from all-atom molecular dynamics simulations of large-scale hydrophobic plates solvated in NaCl and NaI salt solutions. As observed in studies of ions at the air-water interface, the density of iodide near the water-plate interface is significantly enhanced relative to chloride and in the bulk. This allows for the partial hydration of iodide while chloride remains more fully hydrated. In 1 M solutions, iodide directly pushes the hydrophobes together (contributing -2.51 kcal mol(-1)) to the PMF. Chloride, however, strengthens the water-induced contribution to the PMF by ~-2.84 kcal mol(-1). These observations are enhanced in 3 M solutions, consistent with the increased ion density in the vicinity of the hydrophobes. The different salt solutions influence changes in the critical hydrophobe separation distance and characteristic wetting/dewetting transitions. These differences are largely influenced by the ion-specific expulsion of iodide from bulk water. Results of this study are of general interest to the study of ions at interfaces and may lend insight to the mechanisms underlying the Hofmeister series.
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Affiliation(s)
- Brad A Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Abstract
Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy.
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Bauer BA, Zhong Y, Meninger DJ, Davis JE, Patel S. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models. J Mol Graph Model 2011; 29:876-87. [PMID: 21414823 PMCID: PMC3070209 DOI: 10.1016/j.jmgm.2010.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 09/17/2010] [Accepted: 09/23/2010] [Indexed: 11/15/2022]
Abstract
We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.
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Affiliation(s)
- Brad A. Bauer
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - Yang Zhong
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - David J. Meninger
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
- Department of Physics and Astronomy University of Delaware Newark, DE 19716
| | - Joseph E. Davis
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - Sandeep Patel
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
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25
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Yamamoto T, Ohnishi S. Molecular dynamics study on helium nanobubbles in water. Phys Chem Chem Phys 2011; 13:16142-5. [DOI: 10.1039/c1cp22018g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Feng H, Zhou J, Lu X, Fichthorn KA. Communication: Molecular dynamics simulations of the interfacial structure of alkali metal fluoride solutions. J Chem Phys 2010; 133:061103. [DOI: 10.1063/1.3478520] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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27
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Lev B, Zhang R, de la Lande A, Salahub D, Noskov SY. The QM-MM interface for CHARMM-deMon. J Comput Chem 2010; 31:1015-23. [PMID: 20027641 DOI: 10.1002/jcc.21387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi-particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force-field (CHARMM27) or a polarizable force-field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual-thermostat method and the VV2 integrator to run molecular dynamics simulations.
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Affiliation(s)
- Bogdan Lev
- Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
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Bauer BA, Patel S. Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4-point with charge dependent polarizability (TIP4P-QDP) water. J Chem Phys 2010; 132:024713. [PMID: 20095700 PMCID: PMC2821151 DOI: 10.1063/1.3269673] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 11/09/2009] [Indexed: 01/01/2023] Open
Abstract
We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)]; this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl(-), Br(-), and I(-) exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 A(3) for TIP4P-QDP versus 1.1 A(3) (TIP4P-FQ) and 0.87 A(3) (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal (and within the interfacial region) so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields.
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Affiliation(s)
- Brad A Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Lopes PEM, Roux B, MacKerell AD. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc 2009; 124:11-28. [PMID: 20577578 PMCID: PMC2888514 DOI: 10.1007/s00214-009-0617-x] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.
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Affiliation(s)
- Pedro E. M. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
| | - Benoit Roux
- Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago 929 E. 57th St. Chicago, IL 60637
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21230, USA
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On the fluctuations that drive small ions toward, and away from, interfaces between polar liquids and their vapors. Proc Natl Acad Sci U S A 2009; 106:15125-30. [PMID: 19720991 DOI: 10.1073/pnas.0905168106] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Contrary to the expectations from classic theories of ion solvation, spectroscopy and computer simulations of the liquid-vapor interface of aqueous electrolyte solutions suggest that ions little larger than a water molecule can prefer to reside near the liquid's surface. Here we advance the view that such affinity originates in a competition between strong opposing forces, primarily due to volume exclusion and dielectric polarization, that are common to all dense polar liquids. We present evidence for this generic mechanism from computer simulations of (i) water and (ii) a Stockmayer fluid near its triple point. In both cases, we show that strong surface enhancement of small ions, obtained by tuning solutes' size and charge, can be accentuated or suppressed by modest changes in either of those parameters. Statistics of solvent polarization, when the ion is held at and above the Gibbs dividing surface, highlight a basic deficiency in conventional models of dielectric response, namely, the neglect of interfacial flexibility. By distorting the solution's boundary, an ion experiences fluctuations in electrostatic potential and in electric field whose magnitudes attenuate much more gradually (as the ion is removed from the liquid phase) than for a quiescent planar interface. As one consequence, the collective responses that determine free energies of solvation can resolve very differently in nonuniform environments than in bulk. We show that this persistence of electric-field fluctuations additionally shapes the sensitivity of solute distributions to ion polarizability.
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Davis JE, Patel S. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J Phys Chem B 2009; 113:9183-96. [PMID: 19526999 PMCID: PMC2746983 DOI: 10.1021/jp901088g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modeled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, head group orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties.
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Affiliation(s)
- Joseph E. Davis
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Ho MH, Klein ML, Kuo IFW. Bulk and interfacial aqueous fluoride: an investigation via first principles molecular dynamics. J Phys Chem A 2009; 113:2070-4. [PMID: 19173578 PMCID: PMC2765570 DOI: 10.1021/jp808735x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Using first principles molecular dynamics simulation, we have studied a fluoride anion embedded in a periodically replicated water slab composed of 215 water molecules to mimic both bulk and interfacial solvation. In contrast to some recent experiments, our findings suggest that there are only small structural changes for fluoride and its first solvation shell in the bulk. Moreover, the presence of fluoride does not significantly alter the rotational dynamics of nearby water. In addition, we have computed the molecular dipole moments using Wannier centers. At the interface, the presence of fluoride increases the molecular dipole moments of nearby water molecules, whereas in the bulk, the dipole moments for water appear to be essentially invariant to the presence of fluoride in the vicinity. Previous studies of the air-water interface have showed interfacial water to have higher average HOMO energies and, thus, likely to be more prone to electrophilic attack. With the addition of fluoride, the most likely reactive site for electrophilic reactions shifts to the anion. This finding could explain the known large increase in reaction rates for heterogeneous process of interest in atmospheric science. The reactive properties of other anions near the air-water interface are of general interest in heterogeneous chemistry and can be elucidated using a similar type of analysis, as performed here for the fluoride anion.
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Affiliation(s)
- Ming-Hsun Ho
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323
| | - Michael L. Klein
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323
| | - I-F. William Kuo
- Chemical Sciences Division, Lawrence Livermore National Laboratory P.O. Box 808, Livermore, CA 94551
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Bauer BA, Warren GL, Patel S. Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface. J Chem Theory Comput 2009; 5:359-373. [PMID: 23133341 PMCID: PMC3488353 DOI: 10.1021/ct800320f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.(1) that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å(3) and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm(3) at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are anticipated in regions with both liquid and vapor character, interfacial simulations of TIP4P-QDP were performed and compared to TIP4P-FQ, a static polarizability analog. Despite similar features in density profiles such as the position of the GDS and interfacial width, enhanced dipole moments are observed for the TIP4P-QDP interface and onset of the vapor phase. Water orientational profiles show an increased preference (over TIP4P-FQ) in the orientation of the permanent dipole vector of the molecule within the interface; an enhanced z-induced dipole moment directly results from this preference. Hydrogen bond formation is lower, on average, in the bulk for TIP4P-QDP than TIP4P-FQ. However, the average number of hydrogen bonds formed by TIP4P-QDP in the interface exceeds that of TIP4P-FQ, and observed hydrogen bond networks extend further into the gaseous region. The TIP4P-QDP interfacial potential, calculated to be -11.98(±0.08) kcal/mol, is less favorable than that for TIP4P-FQ by approximately 2% as a result of a diminished quadrupole contribution. Surface tension is calculated within a 1.3% reduction from the experimental value. Results reported demonstrate TIP4P-QDP as a model comparable to the popular TIP4P-FQ while accounting for a physical effect previously neglected by other water models. Further refinements to this model, as well as future applications are discussed.
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Affiliation(s)
- Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - G. Lee Warren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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