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Chen S, Li Z, Voth GA. Acidic Conditions Impact Hydrophobe Transfer across the Oil-Water Interface in Unusual Ways. J Phys Chem B 2023; 127:3911-3918. [PMID: 37084419 PMCID: PMC10166083 DOI: 10.1021/acs.jpcb.3c00828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/09/2023] [Indexed: 04/23/2023]
Abstract
Molecular dynamics simulation and enhanced free energy sampling are used to study hydrophobic solute transfer across the water-oil interface with explicit consideration of the effect of different electrolytes: hydronium cation (hydrated excess proton) and sodium cation, both with chloride counterions (i.e., dissociated acid and salt, HCl and NaCl). With the Multistate Empirical Valence Bond (MS-EVB) methodology, we find that, surprisingly, hydronium can to a certain degree stabilize the hydrophobic solute, neopentane, in the aqueous phase and including at the oil-water interface. At the same time, the sodium cation tends to "salt out" the hydrophobic solute in the expected fashion. When it comes to the solvation structure of the hydrophobic solute in the acidic conditions, hydronium shows an affinity to the hydrophobic solute, as suggested by the radial distribution functions (RDFs). Upon consideration of this interfacial effect, we find that the solvation structure of the hydrophobic solute varies at different distances from the oil-liquid interface due to a competition between the bulk oil phase and the hydrophobic solute phase. Together with an observed orientational preference of the hydroniums and the lifetime of water molecules in the first solvation shell of neopentane, we conclude that hydronium stabilizes to a certain degree the dispersal of neopentane in the aqueous phase and eliminates any salting out effect in the acid solution; i.e., the hydronium acts like a surfactant. The present molecular dynamics study provides new insight into the hydrophobic solute transfer across the water-oil interface process, including for acid and salt solutions.
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Affiliation(s)
- Sijia Chen
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, The James Franck Institute, and Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Zhefu Li
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, The James Franck Institute, and Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, The James Franck Institute, and Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637, United States
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2
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Greene D, Qi R, Nguyen R, Qiu T, Luo R. Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. J Chem Inf Model 2019; 59:3041-3056. [PMID: 31145610 PMCID: PMC7197397 DOI: 10.1021/acs.jcim.9b00363] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new heterogeneous dielectric implicit membrane model, with respect to free energy simulations in explicit membrane and explicit water, and implemented it into the Amber software suite. This new model supersedes our previous uniform, single dielectric implicit membrane model by allowing the dielectric constant to vary with depth within the membrane. We calculated MMPBSA binding free energies for the human purinergic platelet receptor (P2Y12R) and two of the muscarinic acetylcholine receptors (M2R and M3R) bound to various antagonist ligands using both membrane models, and we found that the heterogeneous dielectric membrane model has a stronger correlation with experimental binding affinities compared to the older model under otherwise identical conditions. This improved membrane model increases the utility of MMPBSA calculations for the rational design and improvement of future drug candidates.
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3
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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4
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Lee BL, Kuczera K. Simulating the free energy of passive membrane permeation for small molecules. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1407029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas , Lawrence, KS, USA
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5
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Zahariev TK, Tadjer AV, Ivanova AN. Transfer of non-ionic surfactants across the water-oil interface: A molecular dynamics study. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Permeability across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2254-2265. [PMID: 27085977 DOI: 10.1016/j.bbamem.2016.03.032] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/22/2022]
Abstract
Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Braga C, Muscatello J, Lau G, Müller EA, Jackson G. Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface. J Chem Phys 2016; 144:044703. [DOI: 10.1063/1.4940137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Carlos Braga
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Jordan Muscatello
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Gabriel Lau
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Erich A. Müller
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - George Jackson
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
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8
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Local solubility of nonpolar molecules in the liquid–vapor interfaces of water and simple liquids. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Lakkaraju SK, Raman EP, Yu W, MacKerell AD. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:2281-2290. [PMID: 24932136 PMCID: PMC4053307 DOI: 10.1021/ct500201y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Indexed: 12/11/2022]
Abstract
![]()
Solute
sampling of explicit bulk-phase aqueous environments in
grand canonical (GC) ensemble simulations suffer from poor convergence
due to low insertion probabilities of the solutes. To address this,
we developed an iterative procedure involving Grand Canonical-like
Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Each iteration
involves GCMC of both the solutes and water followed by MD, with the
excess chemical potential (μex) of both the solute
and the water oscillated to attain their target concentrations in
the simulation system. By periodically varying the μex of the water and solutes over the GCMC-MD iterations, solute exchange
probabilities and the spatial distributions of the solutes improved.
The utility of the oscillating-μex GCMC-MD method
is indicated by its ability to approximate the hydration free energy
(HFE) of the individual solutes in aqueous solution as well as in
dilute aqueous mixtures of multiple solutes. For seven organic solutes:
benzene, propane, acetaldehyde, methanol, formamide, acetate, and
methylammonium, the average μex of the solutes and
the water converged close to their respective HFEs in both 1 M standard
state and dilute aqueous mixture systems. The oscillating-μex GCMC methodology is also able to drive solute sampling in
proteins in aqueous environments as shown using the occluded binding
pocket of the T4 lysozyme L99A mutant as a model system. The approach
was shown to satisfactorily reproduce the free energy of binding of
benzene as well as sample the functional group requirements of the
occluded pocket consistent with the crystal structures of known ligands
bound to the L99A mutant as well as their relative binding affinities.
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Affiliation(s)
- Sirish Kaushik Lakkaraju
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - E Prabhu Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
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Wei C, Pohorille A. Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes: implications to the origins of life. ASTROBIOLOGY 2013; 13:177-188. [PMID: 23397957 DOI: 10.1089/ast.2012.0901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes was investigated by way of molecular dynamics simulations. Calculated permeability coefficients of membranes to aldopentoses, which exist predominantly in the pyranose form, are in a very good agreement with experimental results. The unexpected preferential permeation of ribose, compared to its diastereomers, found by Sacerdote and Szostak, is explained in terms of inter- and intramolecular interactions involving hydroxyl groups. In aqueous solution, these groups favor the formation of intermolecular hydrogen bonds with neighboring water molecules. Inside the membrane, however, they form intramolecular hydrogen bonds, which in ribose are arranged in a chain. In its diastereomers this chain is broken, which yields higher free energy barrier to transfer through membranes. Faster permeation of ribose would lead to its preferential accumulation inside cells if sugars were converted sufficiently quickly to nonpermeable derivatives. An estimate for the rate of such reaction was derived. Preferential accumulation of ribose would increase the probability of correct monomers' incorporation during synthesis of nucleic acids inside protocells. The same mechanism does not apply to nucleosides or their activated derivatives because sugars are locked in the furanose form, which contains fewer exocyclic hydroxyl groups than does pyranose. The results of this study underscore concerted early evolution of membranes and the biochemical processes that they encapsulated.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California 94035, USA
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11
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Cardenas AE, Jas GS, DeLeon KY, Hegefeld WA, Kuczera K, Elber R. Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics. J Phys Chem B 2012; 116:2739-50. [PMID: 22313494 PMCID: PMC3302722 DOI: 10.1021/jp2102447] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cellular transport machinery, such as channels and pumps, is working against the background of unassisted material transport through membranes. The permeation of a blocked tryptophan through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane is investigated to probe unassisted or physical transport. The transport rate is measured experimentally and modeled computationally. The time scale measured by parallel artificial membrane permeation assay (PAMPA) experiments is ~8 h. Simulations with the milestoning algorithm suggest mean first passage time (MFPT) of ~4 h and the presence of a large barrier at the center of the bilayer. A similar calculation with the solubility-diffusion model yields a MFPT of ~15 min. This permeation rate is 9 orders of magnitude slower than the permeation rate of only a tryptophan side chain (computed by us and others). This difference suggests critical dependence of transport time on permeant size and hydrophilicity. Analysis of the simulation results suggests that the permeant partially preserves hydrogen bonding of the peptide backbone to water and lipid molecules even when it is moving closer to the bilayer center. As a consequence, defects of the membrane structure are developed to assist permeation.
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Affiliation(s)
- Alfredo E Cardenas
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
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12
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Vorobyov I, Bennett WFD, Tieleman DP, Allen TW, Noskov S. The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers. J Chem Theory Comput 2012; 8:618-28. [PMID: 26596610 DOI: 10.1021/ct200417p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In spite of extensive research and use in medical practice, the precise molecular mechanism of volatile anesthetic action remains unknown. The distribution of anesthetics within lipid bilayers and potential targeting to membrane proteins is thought to be central to therapeutic function. Therefore, obtaining a molecular level understanding of volatile anesthetic partitioning into lipid bilayers is of vital importance to modern pharmacology. In this study we investigate the partitioning of the prototypical anesthetic, chloroform, into lipid bilayers and different organic solvents using molecular dynamics simulations with potential models ranging from simplified coarse-grained MARTINI to additive and polarizable CHARMM all-atom force fields. Many volatile anesthetics display significant inducible dipole moments, which correlate with their potency, yet the exact role of molecular polarizability in their stabilization within lipid bilayers remains unknown. We observe that explicit treatment of atomic polarizability makes it possible to accurately reproduce solvation free energies in solvents with different polarities, allowing for quantitative studies in heterogeneous molecular distributions, such as lipid bilayers. We calculate the free energy profiles for chloroform crossing lipid bilayers to reveal a role of polarizability in modulating chloroform partitioning thermodynamics via the chloroform-induced dipole moment and highlight competitive binding to the membrane core and toward the glycerol backbone that may have significant implications for understanding anesthetic action.
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Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - W F Drew Bennett
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - D Peter Tieleman
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
| | - Toby W Allen
- Department of Chemistry, University of California , Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sergei Noskov
- Department of Biological Sciences, University of Calgary , 2500 University Drive, Calgary, Canada, T2N 2N4
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13
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Subbotina JO, Johannes J, Lev B, Noskov SY. Halothane solvation in water and organic solvents from molecular simulations with new polarizable potential function. J Phys Chem B 2010; 114:6401-8. [PMID: 20411978 DOI: 10.1021/jp908339j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The partitioning of a substrate from one phase into another is a complex process with widespread applications: from chemical technology to the pharmaceutical industry. One particularly well-known and well-studied example is 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) trafficking through the lipid bilayer. Halothane is a model volatile anesthetic known to impact functions of model lipid bilayers, altering the structure and thickness upon its partitioning from the bulk phase. A number of theoretical and experimental investigations suggest the importance of electronic polarizability, determining a preference for halothane to partition in the interfacial systems as in lipid bilayers or binary solvents. The recently published protocol for the development of polarizable force fields based on the classical Drude model has provided fresh impetus to efforts directed at understanding the molecular principles governing complex thermodynamics of the hydrophobic hydration. Here, molecular simulations were combined with free energy simulations to study solvation of halothane in polarizable water and methanol. The absolute free energy of halothane solvation in different solvents (water, methanol, and n-hexane) has been evaluated for additive and polarizable models. It was found that both additive and polarizable models provide an adequate description of the halothane solvation in high-dielectric (polar) solvents such as water, but explicit accounting for electronic polarization is imperative for a correct description of the solvation thermodynamics in nonpolar systems. To study halothane dynamics in binary mixtures, all-atom molecular dynamics (MD) simulations for halothane-methanol mixtures in a wide range of concentrations were performed alongside an analysis of structural organization, dynamics, and thermodynamic properties to dissect the molecular determinants of the halothane solvation in polar and amphiphilic liquids such as methanol. Additionally, a theoretical test of the hypothesis on the weak hydrogen bonding of halothane and methanol in the condensed phase is provided, which was presented on the basis of spectroscopic analysis of the C-H vibrations in different gas-phase complexes. The simulations performed in the condensed phase suggest that hydrophobic interactions between halothane and methanol play a dominant role in preferential solvation.
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Affiliation(s)
- Julia O Subbotina
- Institute for BioComplexity and Informatics and Department for Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, Canada T2N 1N4
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14
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Shaytan AK, Ivanov VA, Shaitan KV, Khokhlov AR. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations. J Comput Chem 2010; 31:204-16. [DOI: 10.1002/jcc.21267] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Wei C, Pohorille A. Permeation of membranes by ribose and its diastereomers. J Am Chem Soc 2009; 131:10237-45. [PMID: 19621967 DOI: 10.1021/ja902531k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
It was recently found that ribose permeates membranes an order of magnitude faster than its diastereomers arabinose and xylose (Sacerdote, M. G.; Szostak, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6004). On this basis it was hypothesized that differences in membrane permeability to aldopentoses provide a mechanism for preferential delivery of ribose to primitive cells for subsequent selective incorporation into nucleotides and their polymers. However, the origins of these unusually large differences have not been well understood. We address this issue in molecular dynamics simulations combined with free energy calculations. It is found that the free energy of transferring ribose from water to the bilayer is lower by 1.5-2 kcal/mol than the barrier for transferring the other two aldopentoses. The calculated and measured permeability coefficients are in excellent agreement. The sugar structures that permeate the membrane are beta-pyranoses, with a possible contribution of the alpha-anomer for arabinose. The furanoid form of ribose is not substantially involved in permeation, even though it is non-negligibly populated in aqueous solution. The differences in free energy of transfer between ribose and arabinose or xylose are attributed, at least in part, to stronger highly cooperative, intramolecular interactions between consecutive exocyclic hydroxyl groups, which are stable in nonpolar media but rare in water. Water/hexadecane partition coefficients of the sugars obtained from separate molecular dynamics simulations correlate with the calculated permeability coefficients, in qualitative agreement with the Overton rule. The relevance of our calculations to understanding the origins of life is discussed.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Mail Stop 229-1, Moffett Field, California 94035, USA
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17
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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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18
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Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations. Proc Natl Acad Sci U S A 2009; 106:15119-24. [PMID: 19706896 DOI: 10.1073/pnas.0902778106] [Citation(s) in RCA: 248] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity is often characterized macroscopically by the droplet contact angle. Molecular signatures of hydrophobicity have, however, remained elusive. Successful theories predict a drying transition leading to a vapor-like region near large hard-sphere solutes and interfaces. Adding attractions wets the interface with local density increasing with attractions. Here we present extensive molecular simulation studies of hydration of realistic surfaces with a wide range of chemistries from hydrophobic (-CF(3), -CH(3)) to hydrophilic (-OH, -CONH(2)). We show that the water density near weakly attractive hydrophobic surfaces (e.g., -CF(3)) can be bulk-like or larger, and provides a poor quantification of surface hydrophobicity. In contrast, the probability of cavity formation or the free energy of binding of hydrophobic solutes to interfaces correlates quantitatively with the macroscopic wetting properties and serves as an excellent signature of hydrophobicity. Specifically, the probability of cavity formation is enhanced in the vicinity of hydrophobic surfaces, and water-water correlations correspondingly display characteristics similar to those near a vapor-liquid interface. Hydrophilic surfaces suppress cavity formation and reduce the water-water correlation length. Our results suggest a potentially robust approach for characterizing hydrophobicity of more complex and heterogeneous surfaces of proteins and biomolecules, and other nanoscopic objects.
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Jayasinghe M, Beck TL. Molecular Dynamics Simulations of the Structure and Thermodynamics of Carrier-Assisted Uranyl Ion Extraction. J Phys Chem B 2009; 113:11662-71. [DOI: 10.1021/jp903470n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manori Jayasinghe
- Department of Chemistry and Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221-0172
| | - Thomas L. Beck
- Department of Chemistry and Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221-0172
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20
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Rose D, Benjamin I. Free Energy of Transfer of Hydrated Ion Clusters from Water to an Immiscible Organic Solvent. J Phys Chem B 2009; 113:9296-303. [DOI: 10.1021/jp904470d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Daniel Rose
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
| | - Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064
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21
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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22
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Gupta A, Chauhan A, Kopelevich DI. Molecular transport across fluid interfaces: coupling between solute dynamics and interface fluctuations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:041605. [PMID: 18999437 DOI: 10.1103/physreve.78.041605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Indexed: 05/27/2023]
Abstract
We investigate the transport mechanism of a small hydrophobic solute molecule across two types of fluid interfaces, (i) an interface between two immiscible liquids and (ii) a surfactant-covered liquid-liquid interface. These systems are modeled by coarse-grained molecular dynamics simulations. It is demonstrated that the dynamics of the solute molecule near the interface significantly deviates from Markovian Brownian motion. Specifically, the correlation time of the random force acting on the solute strongly depends on the distance between the solute and the interface and increases by two orders of magnitude within a very narrow (less than 1 nm wide) region near the interface. The slow fluctuations of the random force in this narrow region are caused by capillary waves. The region location and width are determined by interface protrusions caused by attraction between the solute and the hydrophobic phase. We use results of molecular dynamics simulations to develop a stochastic model for the coupled solute-interface dynamics and estimate the rate of the solute transport across the interface. The observed phenomenon appears to be a general feature of mass transport across fluid or flexible membranes. The coupling between the solute transport and the interface fluctuations is the strongest in areas corresponding to a large free energy gradient or near a free energy barrier for the solute transport. This suggests a strong influence of the coupled solute-interface dynamics on the rate of mass transfer across interfaces.
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Affiliation(s)
- Ashish Gupta
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611-6005, USA
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Saito H, Shinoda W, Mikami M. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J Phys Chem B 2008; 112:11305-9. [DOI: 10.1021/jp801057k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroaki Saito
- Research Institute for Computational Sciences (RICS), Research Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan, and CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Wataru Shinoda
- Research Institute for Computational Sciences (RICS), Research Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan, and CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masuhiro Mikami
- Research Institute for Computational Sciences (RICS), Research Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan, and CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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24
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Matubayasi N, Shinoda W, Nakahara M. Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation. J Chem Phys 2008; 128:195107. [DOI: 10.1063/1.2919117] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Weis M, Kopáni M. Influence of vitamin C on alcohol binding to phospholipid monolayers. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2008; 37:893-901. [PMID: 18365189 DOI: 10.1007/s00249-008-0303-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 02/22/2008] [Accepted: 03/07/2008] [Indexed: 10/22/2022]
Abstract
The simple model of the biological membrane is provided by well-controlled lipid monolayers at the air-water interface. The Maxwell displacement current technique (MDC) provides novel approach to conformation study of the membrane models. The effect of alcohols is interaction with membrane molecules, mainly with the lipid head group and consequent changes in physical-chemical properties of the membrane. The aim of study is to detect changes in structural, electrical and mechanical properties of dipalmitoyl-phosphatidylcholine (DPPC) monolayer on the subphase of methanol-water and ethanol-water mixtures before and after addition of antioxidant agent, vitamin C. Monolayers properties are investigated by a surface pressure analysis (including mechanical properties evaluation) and the Maxwell displacement current measurement, the dipole moment projection calculation. Surface pressure-area isotherms show similar behaviour of the DPPC monolayer on alcohol-water mixtures independently on presence of vitamin C. Binding/adsorption process induces change of electron density distribution across monolayer and thus the molecular dipole moment. We observe small or negligible binding of methanol molecules on oxygen bonds of DPPC. Thus the antioxidant, vitamin C, has no significant effect. For ethanol-water mixtures is observed recovery of electrical properties in presence of antioxidant agent. We suppose that vitamin C regulates DPPC-ethanol molecules interaction.
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Affiliation(s)
- M Weis
- Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 81219, Bratislava, Slovakia
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26
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MacCallum JL, Tieleman DP. Chapter 8 Interactions between Small Molecules and Lipid Bilayers. CURRENT TOPICS IN MEMBRANES 2008. [DOI: 10.1016/s1063-5823(08)00008-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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27
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Asthagiri D, Ashbaugh HS, Piryatinski A, Paulaitis ME, Pratt LR. Non-van der Waals Treatment of the Hydrophobic Solubilities of CF4. J Am Chem Soc 2007; 129:10133-40. [PMID: 17661465 DOI: 10.1021/ja071037n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A quasi-chemical theory implemented on the basis of molecular simulation is derived and tested for the hydrophobic hydration of CF4(aq). The theory formulated here subsumes a van der Waals treatment of solvation and identifies contributions to the hydration free energy of CF4(aq) that naturally arise from chemical contributions defined by quasi-chemical theory and fluctuation contributions analogous to Debye-Hückel or random phase approximations. The resulting Gaussian statistical thermodynamic model avoids consideration of hypothetical drying-then-rewetting problems and is physically reliable in these applications as judged by the size of the fluctuation contribution. The specific results here confirm that unfavorable tails of binding energy distributions reflect few-body close solute-solvent encounters. The solvent near-neighbors are pushed by the medium into unfavorable interactions with the solute, in contrast to the alternative view that a preformed interface is pulled by the solute-solvent attractive interactions into contact with the solute. The polyatomic model of CF4(aq) studied gives a satisfactory description of the experimental solubilities including the temperature dependence. The proximal distributions evaluated here for polyatomic solutes accurately reconstruct the observed distributions of water near these molecules which are nonspherical. These results suggest that drying is not an essential consideration for the hydrophobic solubilities of CF4, or of C(CH3)4 which is more soluble.
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Affiliation(s)
- D Asthagiri
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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28
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Delgado-Buscalioni R, De Fabritiis G, Coveney PV. Determination of the chemical potential using energy-biased sampling. J Chem Phys 2007; 123:054105. [PMID: 16108629 DOI: 10.1063/1.2000244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An energy-biased method to evaluate ensemble averages requiring test-particle insertion is presented. The method is based on biasing the sampling within the subdomains of the test-particle configurational space with energies smaller than a given value freely assigned. These energy wells are located via unbiased random insertion over the whole configurational space and are sampled using the so-called Hit-and-Run algorithm, which uniformly samples compact regions of any shape immersed in a space of arbitrary dimensions. Because the bias is defined in terms of the energy landscape it can be exactly corrected to obtain the unbiased distribution. The test-particle energy distribution is then combined with the Bennett relation for the evaluation of the chemical potential. We apply this protocol to a system with relatively small probability of low-energy test-particle insertion, liquid argon at high density and low temperature, and show that the energy-biased Bennett method is around five times more efficient than the standard Bennett method. A similar performance gain is observed in the reconstruction of the energy distribution.
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Affiliation(s)
- R Delgado-Buscalioni
- Departamento Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, Paseo Senda del Rey 9, Madrid 28040, Spain.
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29
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Lukacova V, Peng M, Fanucci G, Tandlich R, Hinderliter A, Maity B, Manivannan E, Cook GR, Balaz S. Drug-membrane interactions studied in phospholipid monolayers adsorbed on nonporous alkylated microspheres. ACTA ACUST UNITED AC 2007; 12:186-202. [PMID: 17218665 PMCID: PMC2896050 DOI: 10.1177/1087057106297063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Characterization of interactions with phospholipids is an integral part of the in vitro profiling of drug candidates because of the roles the interactions play in tissue accumulation and passive diffusion. Currently used test systems may inadequately emulate the bilayer core solvation properties (immobilized artificial membranes [IAM]), suffer from potentially slow transport of some chemicals (liposomes in free or immobilized forms), and require a tedious separation (if used for free liposomes). Here the authors introduce a well-defined system overcoming these drawbacks: nonporous octadecylsilica particles coated with a self-assembled phospholipid monolayer. The coating mimics the structure of the headgroup region, as well as the thickness and properties of the hydrocarbon core, more closely than IAM. The monolayer has a similar transition temperature pattern as the corresponding bilayer. The particles can be separated by filtration or a mild centrifugation. The partitioning equilibria of 81 tested chemicals were dissected into the headgroup and core contributions, the latter using the alkane/water partition coefficients. The deconvolution allowed a successful prediction of the bilayer/water partition coefficients with the standard deviation of 0.26 log units. The plate-friendly assay is suitable for high-throughput profiling of drug candidates without sacrificing the quality of analysis or details of the drug-phospholipid interactions.
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Affiliation(s)
- Viera Lukacova
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105, USA
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30
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31
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Xiang TX, Anderson BD. Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv Drug Deliv Rev 2006; 58:1357-78. [PMID: 17092601 DOI: 10.1016/j.addr.2006.09.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 09/04/2006] [Indexed: 11/21/2022]
Abstract
Computational methods to predict drug permeability across biomembranes prior to synthesis are increasingly desirable to minimize the investment in drug design and development. Significant progress in molecular dynamics (MD) simulation methodologies applied to lipid bilayer membranes, for example, is making it possible to move beyond characterization of the membranes themselves to explore various thermodynamic and kinetic processes governing membrane binding and transport. Such methods are also likely to be directly applicable to the design and optimization of liposomal delivery systems. MD simulations are particularly valuable in addressing issues that are difficult to explore in laboratory experiments due to the heterogeneity of lipid bilayer membranes at the molecular level. Insights emerging from MD simulations are contributing to an understanding of which regions within bilayers are most and least favored by solutes at equilibrium as the solute structure is varied, local diffusivities of permeants, and the origin of the amplified selectivity to permeant size imposed by lipid bilayer membranes, particularly as changes in composition increase acyl chain ordering.
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Affiliation(s)
- Tian-Xiang Xiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
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32
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Trogdon G, Murray JS, Concha MC, Politzer P. Molecular surface electrostatic potentials and anesthetic activity. J Mol Model 2006; 13:313-8. [PMID: 17024409 DOI: 10.1007/s00894-006-0145-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2005] [Revised: 07/31/2006] [Indexed: 10/24/2022]
Abstract
General anesthetics apparently act through weak, noncovalent and reversible interactions with certain sites in appropriate brain proteins. As a means of gaining insight into the factors underlying anesthetic potency, we have analyzed the computed electrostatic potentials V (S)(r) on the surfaces of 20 molecules with activities that vary between zero and high. Our results are fully consistent with, and help to interpret, what has been observed experimentally. We find that an intermediate level of internal charge separation is required; this is measured by Pi, the average absolute deviation of V (S)(r), and the approximate window is 7 < Pi < 13 kcal mol(-1). This fits in well with the fact that anesthetics need to be lipid soluble, but also to have some degree of hydrophilicity. We further show that polyhalogenated alkanes and ethers, which include the most powerful known anesthetics, have strong positive potentials, V (S,max), associated with their hydrogens, chlorines and bromines (but not fluorines). These positive sites may impede the functioning of key brain proteins, for example by disrupting their normal hydrogen-bond patterns. It has indeed been recognized for some time that the most active polyhalogenated alkanes and ethers contain hydrogens usually in combination with chlorines and/or bromines.
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Affiliation(s)
- Gavin Trogdon
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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33
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Vemparala S, Saiz L, Eckenhoff RG, Klein ML. Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles. Biophys J 2006; 91:2815-25. [PMID: 16877515 PMCID: PMC1578482 DOI: 10.1529/biophysj.106.085324] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations have been performed to investigate the partitioning of the volatile anesthetic halothane from an aqueous phase into a coexisting hydrated bilayer, composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipids, with embedded alpha-helical peptide bundles based on the membrane-bound portions of the alpha- and delta-subunits, respectively, of nicotinic acetylcholine receptor. In the molecular dynamics simulations halothane molecules spontaneously partitioned into the DOPC bilayer and then preferentially occupied regions close to lipid headgroups. A single halothane molecule was observed to bind to tyrosine (Tyr-277) residue in the alpha-subunit, an experimentally identified specific binding site. The binding of halothane attenuated the local loop dynamics of alpha-subunit and significantly influenced global concerted motions suggesting anesthetic action in modulating protein function. Steered molecular dynamics calculations on a single halothane molecule partitioned into a DOPC lipid bilayer were performed to probe the free energy profile of halothane across the lipid-water interface and rationalize the observed spontaneous partitioning. Partitioned halothane molecules affect the hydrocarbon chains of the DOPC lipid, by lowering of the hydrocarbon tilt angles. The anesthetic molecules also caused a decrease in the number of peptide-lipid contacts. The observed local and global effects of anesthetic binding on protein motions demonstrated in this study may underlie the mechanism of action of anesthetics at a molecular level.
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Affiliation(s)
- Satyavani Vemparala
- Department of Chemistry and Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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34
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Won A, Oh I, Liao M, Sonner JM, Harris RA, Laster MJ, Brosnan R, Trudell JR, Eger EI. The Minimum Alveolar Anesthetic Concentration of 2-, 3-, and 4-Alcohols and Ketones in Rats: Relevance to Anesthetic Mechanisms. Anesth Analg 2006; 102:1419-26. [PMID: 16632820 DOI: 10.1213/01.ane.0000204258.00676.98] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Meyer-Overton hypothesis predicts that anesthetic potency correlates inversely with lipophilicity; e.g., MAC times the olive oil/gas partition coefficient equals a constant of approximately 1.82 +/- 0.56 atm (mean +/- sd) for conventional inhaled anesthetics. MAC is the minimum alveolar concentration of anesthetic required to eliminate movement in response to a noxious stimulus in 50% of subjects. In contrast to conventional inhaled anesthetics, MAC times the olive oil/gas partition coefficient for normal alcohols from methanol through octanol equals a constant one tenth as large as that for conventional inhaled anesthetics. The alcohol (C-OH) group causes a great affinity of alcohols to water, and the C-OH may tether the alcohol at the hydrophobic-hydrophilic interface where anesthetics are thought to act. We hypothesized that the position of the C-OH group determined potency, perhaps by governing the maximum extent to which the acyl portion of the molecule might extend into a hydrophobic phase. Using the same reasoning, we added studies of ketones with similar numbers of carbon atoms between the C=O group and the terminal methyl group. The results for both alcohols and ketones showed the predicted correlation, but the correlation was no better than that with carbon chain length regardless of the placement of the oxygen. The oil/gas partition coefficient predicted potency as well as, or better than, either chain length or oxygen placement. Hydrophilicity, as indicated by the saline/gas partition coefficient, also seemed to influence potency.
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Affiliation(s)
- Albert Won
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94143-0464, USA
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35
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Lukacova V, Peng M, Tandlich R, Hinderliter A, Balaz S. Partitioning of organic compounds in phases imitating the headgroup and core regions of phospholipid bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:1869-74. [PMID: 16460120 PMCID: PMC2896065 DOI: 10.1021/la052187j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Solvation free energies of drugs, peptides, and other small molecules in the core and headgroup regions of phospholipid bilayers determine their conformations, accumulation, and transport properties. The transfer free energy includes the energy terms for the formation of a cavity for the solute, the interactions of the solute with phospholipids, electrostatic interactions of the solute with the membrane, and dipole potentials and entropy terms. The interaction energies with phospholipids can be estimated by correlating the partitioning in surrogate solvent systems and in the bilayer. As the headgroup surrogate, we use diacetylphosphatidylcholine (DAcPC), the acetylated headgroup of the most abundant mammalian phospholipid, phosphatidylcholine, which forms a homogeneous solution with acceptable viscosity when mixed with water in ratios similar to those in the fully hydrated bilayer. The two-phase system of n-hexadecane (C16) as the core surrogate and hydrated DAcPC was used to monitor partitioning of 16 nonionizable compounds. On the bilogarithmic scale, the C16/DAcPC partition coefficients correlate neither with those in the C16/water and 1-octanol/water systems nor with their difference, which is frequently used as a parameter of hydrogen bonding for prediction of the bilayer location of the solutes. The C16/DAcPC system provides a satisfactory emulation of the solvation properties of the bilayer regions, as reflected in correct predictions of the bilayer location for those of the studied chemicals, for which this information is available.
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Affiliation(s)
- Viera Lukacova
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Ming Peng
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Roman Tandlich
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Anne Hinderliter
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
| | - Stefan Balaz
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105
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36
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Chang TM, Dang LX. Recent Advances in Molecular Simulations of Ion Solvation at Liquid Interfaces. Chem Rev 2005; 106:1305-22. [PMID: 16608182 DOI: 10.1021/cr0403640] [Citation(s) in RCA: 234] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tsun-Mei Chang
- Department of Chemistry, University of Wisconsin-Parkside, 900 Wood Road, Box 2000, Kenosha, Wisconsin 53141, USA
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37
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Patel HA, Garde S, Keblinski P. Thermal resistance of nanoscopic liquid-liquid interfaces: dependence on chemistry and molecular architecture. NANO LETTERS 2005; 5:2225-31. [PMID: 16277458 DOI: 10.1021/nl051526q] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water-organic liquid, water-surfactant, surfactant-organic liquid, is relatively high (in the range of 65-370 MW/m2 K) compared to that for solid-liquid interfaces ( approximately 10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid-liquid interfaces.
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Affiliation(s)
- Harshit A Patel
- The Howard P. Isermann Department of Chemical & Biological Engineering and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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38
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Pohorille A, Schweighofer K, Wilson MA. The origin and early evolution of membrane channels. ASTROBIOLOGY 2005; 5:1-17. [PMID: 15711166 DOI: 10.1089/ast.2005.5.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The origin and early evolution of ion channels are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly greater complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Bacteria, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.
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Affiliation(s)
- Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California 94035, USA.
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39
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Kuznetsova T, Kvamme B. Grand Canonical Molecular Dynamic Simulations For Polar Systems. CHEM ENG COMMUN 2005. [DOI: 10.1080/00986440590473416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Saladino AC, Tang P. Optimization of Structures and LJ Parameters of 1-Chloro-1,2,2-trifluorocyclobutane and 1,2-Dichlorohexafluorocyclobutane. J Phys Chem A 2004. [DOI: 10.1021/jp046662i] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander C. Saladino
- Department of Anesthesiology and Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Pei Tang
- Department of Anesthesiology and Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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41
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Bemporad D, Luttmann C, Essex JW. Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area. Biophys J 2004; 87:1-13. [PMID: 15240439 PMCID: PMC1304332 DOI: 10.1529/biophysj.103.030601] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2003] [Accepted: 02/04/2004] [Indexed: 11/18/2022] Open
Abstract
Cell membrane permeation is required for most drugs to reach their biological target, and understanding this process is therefore crucial for rational drug design. Recent molecular dynamics simulations have studied the permeation of eight small molecules through a phospholipid bilayer. Unlike experiments, atomistic simulations allow the direct calculation of diffusion and partition coefficients of solutes at different depths inside a lipid membrane. Further analyses of the simulations suggest that solute diffusion is less size-dependent and solute partitioning more size-dependent than was commonly thought.
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Affiliation(s)
- D Bemporad
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
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42
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Shinoda W, Mikami M, Baba T, Hato M. Molecular Dynamics Study on the Effects of Chain Branching on the Physical Properties of Lipid Bilayers: 2. Permeability. J Phys Chem B 2004. [DOI: 10.1021/jp035998+] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Bemporad D, Essex JW, Luttmann C. Permeation of Small Molecules through a Lipid Bilayer: A Computer Simulation Study. J Phys Chem B 2004. [DOI: 10.1021/jp035260s] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Abstract
Enthalpy-entropy noncompensation characterizes the relative changes in the hydration thermodynamic functions upon "transforming" ethane into fluoromethane, chloromethane, bromomethane, and iodomethane. An analysis grounded on a simple statistical mechanical theory of hydration allows a plausible rationalization of such enthalpy-entropy noncompensation. It is shown that increasing the strength of solute-water attractive interactions modifying the chemical nature of a part of the solute molecule, but not its size, is a largely noncompensating process for the hydration of noncharged and nonhydrogen bonding species, and dominates the compensating contribution coming from the reorganization of water H bonds.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Universita del Sannio, Via Port'Arsa, 11-82100 Benevento, Italy.
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45
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Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys 2004; 120:3563-78. [PMID: 15268518 DOI: 10.1063/1.1642607] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The efficiencies of two recently developed methods for calculating free energy changes along a generalized coordinate in a system are discussed in the context of other, related approaches. One method is based on Jarzynski's identity [Phys. Rev. Lett. 78, 2690 (1997)]. The second method relies on thermodynamic integration of the average force and is called the adaptive biasing force method [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)]. Both methods are designed such that the system evolves along the chosen coordinate(s) without experiencing free energy barriers and they require calculating the instantaneous, unconstrained force acting on this coordinate using the formula derived by Darve and Pohorille. Efficiencies are analyzed by comparing analytical estimates of statistical errors and by considering two numerical examples-internal rotation of hydrated 1,2-dichloroethane and transfer of fluoromethane across a water-hexane interface. The efficiencies of both methods are approximately equal in the first but not in the second case. During transfer of fluoromethane the system is easily driven away from equilibrium and, therefore, the performance of the method based on Jarzynski's identity is poor.
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46
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De Fabritiis G, Delgado-Buscalioni R, Coveney PV. Energy controlled insertion of polar molecules in dense fluids. J Chem Phys 2004; 121:12139-42. [PMID: 15606230 DOI: 10.1063/1.1835957] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of freedom of the molecule, combining steepest-descent and Newton-Raphson steps which embed information on the average sizes of the potential energy wells obtained from prior inspection of the liquid structure. We perform a molecular dynamics simulation of a liquid water shell which demonstrates that the method enables fast and energy-controlled water molecule insertion in aqueous environments. The algorithm finds low energy configurations of incoming water molecules around three orders of magnitude faster than direct random insertion. This method represents an important step towards dynamic simulations of open systems and it may also prove useful for energy-biased ensemble average calculations of the chemical potential.
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Affiliation(s)
- Gianni De Fabritiis
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ London, United Kingdom.
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47
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Koubi L, Saiz L, Tarek M, Scharf D, Klein ML. Influence of Anesthetic and Nonimmobilizer Molecules on the Physical Properties of a Polyunsaturated Lipid Bilayer. J Phys Chem B 2003. [DOI: 10.1021/jp035169o] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laure Koubi
- Center for Molecular Modeling and Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, NIST Center for Neutron Research, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Gaithersburg, Maryland 20899-8562, Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche C.N.R.S./U.H.P. No. 7565, Universite Henri PoincaréNancy I, B.P. 239, F-54506 Vandoeuvre-lès
| | - Leonor Saiz
- Center for Molecular Modeling and Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, NIST Center for Neutron Research, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Gaithersburg, Maryland 20899-8562, Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche C.N.R.S./U.H.P. No. 7565, Universite Henri PoincaréNancy I, B.P. 239, F-54506 Vandoeuvre-lès
| | - Mounir Tarek
- Center for Molecular Modeling and Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, NIST Center for Neutron Research, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Gaithersburg, Maryland 20899-8562, Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche C.N.R.S./U.H.P. No. 7565, Universite Henri PoincaréNancy I, B.P. 239, F-54506 Vandoeuvre-lès
| | - Daphna Scharf
- Center for Molecular Modeling and Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, NIST Center for Neutron Research, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Gaithersburg, Maryland 20899-8562, Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche C.N.R.S./U.H.P. No. 7565, Universite Henri PoincaréNancy I, B.P. 239, F-54506 Vandoeuvre-lès
| | - Michael L. Klein
- Center for Molecular Modeling and Chemistry Department, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, NIST Center for Neutron Research, Materials Science and Engineering Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Gaithersburg, Maryland 20899-8562, Equipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche C.N.R.S./U.H.P. No. 7565, Universite Henri PoincaréNancy I, B.P. 239, F-54506 Vandoeuvre-lès
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Patel HA, Nauman EB, Garde S. Molecular structure and hydrophobic solvation thermodynamics at an octane–water interface. J Chem Phys 2003. [DOI: 10.1063/1.1605942] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Jedlovszky P, Varga I, Gilányi T. Adsorption of apolar molecules at the water liquid–vapor interface: A Monte Carlo simulations study of the water-n-octane system. J Chem Phys 2003. [DOI: 10.1063/1.1581848] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zhang X, Steel WH, Walker RA. Probing Solvent Polarity across Strongly Associating Solid/Liquid Interfaces Using Molecular Rulers. J Phys Chem B 2003. [DOI: 10.1021/jp022067+] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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