1
|
Nishikawa K. The Solution Chemistry of Mixing States Probed via Fluctuations: a Direct Description of Inhomogeneity in Mixing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Keiko Nishikawa
- Toyota Physical & Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| |
Collapse
|
2
|
Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
Collapse
Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| |
Collapse
|
3
|
Ploetz EA, Smith PE. Gas or Liquid? The Supercritical Behavior of Pure Fluids. J Phys Chem B 2019; 123:6554-6563. [DOI: 10.1021/acs.jpcb.9b04058] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, United States
| | - Paul E. Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, United States
| |
Collapse
|
4
|
Properties of Ion Complexes and Their Impact on Charge Transport in Organic Solvent-Based Electrolyte Solutions for Lithium Batteries: Insights from a Theoretical Perspective. BATTERIES-BASEL 2018. [DOI: 10.3390/batteries4040062] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrolyte formulations in standard lithium ion and lithium metal batteries are complex mixtures of various components. In this article, we review molecular key principles of ion complexes in multicomponent electrolyte solutions in regards of their influence on charge transport mechanisms. We outline basic concepts for the description of ion–solvent and ion–ion interactions, which can be used to rationalize recent experimental and numerical findings concerning modern electrolyte formulations. Furthermore, we discuss benefits and drawbacks of empirical concepts in comparison to molecular theories of solution for a more refined understanding of ion behavior in organic solvents. The outcomes of our discussion provide a rational for beneficial properties of ions, solvent, co-solvent and additive molecules, and highlight possible routes for further improvement of novel electrolyte solutions.
Collapse
|
5
|
Affiliation(s)
- Elizabeth A. Ploetz
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr North,
Kansas State University, Manhattan, Kansas 66506-0401,
USA
| | - Gayani N. Pallewela
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr North,
Kansas State University, Manhattan, Kansas 66506-0401,
USA
| | - Paul E. Smith
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr North,
Kansas State University, Manhattan, Kansas 66506-0401,
USA
| |
Collapse
|
6
|
Naleem N, Ploetz EA, Smith PE. Gaussian and non-Gaussian fluctuations in pure classical fluids. J Chem Phys 2017. [DOI: 10.1063/1.4977455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
| | - Elizabeth A. Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
| | - Paul E. Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
| |
Collapse
|
7
|
Reid JESJ, Gammons RJ, Slattery JM, Walker AJ, Shimizu S. Interactions in Water–Ionic Liquid Mixtures: Comparing Protic and Aprotic Systems. J Phys Chem B 2017; 121:599-609. [DOI: 10.1021/acs.jpcb.6b10562] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Joshua E. S. J. Reid
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
- TWI Ltd., Granta Park, Great Abington, Cambridge, CB21 6AL, U.K
| | - Richard J. Gammons
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K
| | - John M. Slattery
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K
| | - Adam J. Walker
- TWI Ltd., Granta Park, Great Abington, Cambridge, CB21 6AL, U.K
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| |
Collapse
|
8
|
Makarov DM, Egorov GI, Markarian SA, Kolker AM. Excess Gibbs Energy and Local Compositions in the Mixtures C2, C3 Alkane Diols and Triols with Water at Various Pressures. J SOLUTION CHEM 2016. [DOI: 10.1007/s10953-016-0524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Zemánková K, Troncoso J, Cerdeiriña CA, Romaní L, Anisimov MA. Hydrophobicity and thermodynamic response for aqueous solutions of amphiphiles. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Vafaei S, Tomberli B, Gray CG. McMillan-Mayer theory of solutions revisited: simplifications and extensions. J Chem Phys 2015; 141:154501. [PMID: 25338903 DOI: 10.1063/1.4897980] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
McMillan and Mayer (MM) proved two remarkable theorems in their paper on the equilibrium statistical mechanics of liquid solutions. They first showed that the grand canonical partition function for a solution can be reduced to one with an effectively solute-only form, by integrating out the solvent degrees of freedom. The total effective solute potential in the effective solute grand partition function can be decomposed into components which are potentials of mean force for isolated groups of one, two, three, etc., solute molecules. Second, from the first result, now assuming low solute concentration, MM derived an expansion for the osmotic pressure in powers of the solute concentration, in complete analogy with the virial expansion of gas pressure in powers of the density at low density. The molecular expressions found for the osmotic virial coefficients have exactly the same form as the corresponding gas virial coefficients, with potentials of mean force replacing vacuum potentials. In this paper, we restrict ourselves to binary liquid solutions with solute species A and solvent species B and do three things: (a) By working with a semi-grand canonical ensemble (grand with respect to solvent only) instead of the grand canonical ensemble used by MM, and avoiding graphical methods, we have greatly simplified the derivation of the first MM result, (b) by using a simple nongraphical method developed by van Kampen for gases, we have greatly simplified the derivation of the second MM result, i.e., the osmotic pressure virial expansion; as a by-product, we show the precise relation between MM theory and Widom potential distribution theory, and (c) we have extended MM theory by deriving virial expansions for other solution properties such as the enthalpy of mixing. The latter expansion is proving useful in analyzing ongoing isothermal titration calorimetry experiments with which we are involved. For the enthalpy virial expansion, we have also changed independent variables from semi-grand canonical, i.e., fixed {N(A), μ(B), V, T}, to those relevant to the experiment, i.e., fixed {N(A), N(B), p, T}, where μ denotes chemical potential, N the number of molecules, V the volume, p the pressure, and T the temperature.
Collapse
Affiliation(s)
- Shaghayegh Vafaei
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Bruno Tomberli
- Department of Physics, Capilano University, Vancouver, British Columbia V7J3H5, Canada
| | - C G Gray
- Department of Physics, University of Guelph, Guelph, Ontario N1G2W1, Canada
| |
Collapse
|
11
|
Ploetz EA, Smith PE. Particle and Energy Pair and Triplet Correlations in Liquids and Liquid Mixtures from Experiment and Simulation. J Phys Chem B 2015; 119:7761-77. [DOI: 10.1021/acs.jpcb.5b00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, United States
| |
Collapse
|
12
|
Ploetz EA, Smith PE. Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures. J Chem Phys 2015; 142:094504. [PMID: 25747091 PMCID: PMC4352168 DOI: 10.1063/1.4913514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/12/2015] [Indexed: 11/15/2022] Open
Abstract
Kirkwood-Buff or Fluctuation Solution Theory can be used to provide experimental pair fluctuations, and/or integrals over the pair distribution functions, from experimental thermodynamic data on liquid mixtures. Here, this type of approach is used to provide triplet and quadruplet fluctuations, and the corresponding integrals over the triplet and quadruplet distribution functions, in a purely thermodynamic manner that avoids the use of structure factors. The approach is then applied to binary mixtures of water + methanol and benzene + methanol over the full composition range under ambient conditions. The observed correlations between the different species vary significantly with composition. The magnitude of the fluctuations and integrals appears to increase as the number of the most polar molecule involved in the fluctuation or integral also increases. A simple physical picture of the fluctuations is provided to help rationalize some of these variations.
Collapse
Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| |
Collapse
|
13
|
Ploetz EA, Karunaweera S, Smith PE. Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for pure liquids. J Chem Phys 2015; 142:044502. [PMID: 25637990 PMCID: PMC4312347 DOI: 10.1063/1.4905562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/22/2014] [Indexed: 11/14/2022] Open
Abstract
Fluctuation solution theory has provided an alternative view of many liquid mixture properties in terms of particle number fluctuations. The particle number fluctuations can also be related to integrals of the corresponding two body distribution functions between molecular pairs in order to provide a more physical picture of solution behavior and molecule affinities. Here, we extend this type of approach to provide expressions for higher order triplet and quadruplet fluctuations, and thereby integrals over the corresponding distribution functions, all of which can be obtained from available experimental thermodynamic data. The fluctuations and integrals are then determined using the International Association for the Properties of Water and Steam Formulation 1995 (IAPWS-95) equation of state for the liquid phase of pure water. The results indicate small, but significant, deviations from a Gaussian distribution for the molecules in this system. The pressure and temperature dependence of the fluctuations and integrals, as well as the limiting behavior as one approaches both the triple point and the critical point, are also examined.
Collapse
Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| |
Collapse
|
14
|
Reid JESJ, Walker AJ, Shimizu S. Residual water in ionic liquids: clustered or dissociated? Phys Chem Chem Phys 2015; 17:14710-8. [DOI: 10.1039/c5cp01854d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A rigorous statistical thermodynamic theory clarifies how residual water molecules interact in three dialkylimidazolium ionic liquids.
Collapse
Affiliation(s)
- Joshua E. S. J. Reid
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| | | | - Seishi Shimizu
- York Structural Biology Laboratory
- Department of Chemistry
- University of York
- York YO10 5DD
- UK
| |
Collapse
|
15
|
Makarov DM, Egorov GI. Analysis of the pressure effect on the local composition in a water-alkanol mixture using Kirkwood-Buff integrals. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476614020103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Piazza R, Buzzaccaro S, Secchi E, Parola A. On the general concept of buoyancy in sedimentation and ultracentrifugation. Phys Biol 2013; 10:045005. [DOI: 10.1088/1478-3975/10/4/045005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
17
|
Ploetz EA, Smith PE. Local Fluctuations in Solution: Theory and Applications. ADVANCES IN CHEMICAL PHYSICS 2013; 153:311-372. [PMID: 24683278 DOI: 10.1002/9781118571767.ch4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
18
|
Jiao Y, Smith PE. Fluctuation theory of molecular association and conformational equilibria. J Chem Phys 2011; 135:014502. [PMID: 21744905 DOI: 10.1063/1.3601342] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
General expressions relating the effects of pressure, temperature, and composition on solute association and conformational equilibria using the fluctuation theory of solutions are provided. The expressions are exact and can be used to interpret experimental or computer simulation data for any multicomponent mixture involving molecules of any size and character at any composition. The relationships involve particle-particle, particle-energy, and energy-energy correlations within local regions in the vicinity of each species involved in the equilibrium. In particular, it is demonstrated that the results can be used to study peptide and protein association or aggregation, protein denaturation, and protein-ligand binding. Exactly how the relevant fluctuating properties may be obtained from experimental or computer simulation data are also outlined. It is shown that the enthalpy, heat capacity, and compressibility differences associated with the equilibrium process can, in principle, be obtained from a single simulation. Fluctuation based expressions for partial molar heat capacities, thermal expansions, and isothermal compressibilities are also provided.
Collapse
Affiliation(s)
- Yuanfang Jiao
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
| | | |
Collapse
|