1
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Ogrin P, Urbic T, Fennell CJ. Statistical-mechanical liquid theories reproduce anomalous thermodynamic properties of explicit two-dimensional water models. Phys Rev E 2022; 106:034115. [PMID: 36266898 PMCID: PMC10061499 DOI: 10.1103/physreve.106.034115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/12/2022] [Indexed: 11/07/2022]
Abstract
We have developed an analytical theory for a simple model of liquid water. We apply Wertheim's thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids to the rose model, which is among the simplest models of water. The particles interact through rose potentials for orientation dependent pairwise interactions. Modifying both the shape and range of a three-petal rose function, we construct an efficient and dynamical mimic of the two-dimensional (2D) Mercedes-Benz (MB) water model. The particles in 2D MB are 2D Lennard-Jones disks with three hydrogen bonding arms arranged symmetrically, resembling the Mercedes-Benz logo. Both models qualitatively predict both the anomalous properties of pure water and the anomalous solvation thermodynamics of nonpolar molecules. The IET is based on the orientationally averaged version of the Ornstein-Zernike equation. This is one of the main approximations in the present work. IET correctly predicts the pair correlation functions at high temperatures. Both TPT and IET are in semi-quantitative agreement with the Monte Carlo values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity. A major advantage of these theories is that they require orders of magnitude less computer time than the Monte Carlo simulations.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Christopher J. Fennell
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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2
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Tasnim T, Ryan C, Christensen ML, Fennell CJ, Pitre SP. Radical Perfluoroalkylation Enabled by a Catalytically Generated Halogen Bonding Complex and Visible Light Irradiation. Org Lett 2021; 24:446-450. [PMID: 34914870 DOI: 10.1021/acs.orglett.1c04139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploiting charge-transfer complexes in visible light-promoted single-electron redox reactions is a promising route for opening novel synthetic pathways, and catalytic approaches to complex formation are critical for facilitating this chemistry. This report describes the use of a substituted hydroquinone catalyst to promote radical perfluoroalkylation reactions. Mechanistic studies indicate that the reaction is initiated through formation of a visible light-absorbing halogen bonding complex between the hydroquinone catalyst and the perfluoroalkyl halide radical precursor.
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Affiliation(s)
- Tarannum Tasnim
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Calvin Ryan
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Miranda L Christensen
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Christopher J Fennell
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
| | - Spencer P Pitre
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, Oklahoma 74078, United States
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3
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Hayatifar A, Elifritz EA, Bloom MB, Pixley KM, Fennell CJ, Weinert CS. Direct amidation of acid fluorides using germanium amides. Dalton Trans 2021; 50:4490-4493. [PMID: 33877168 DOI: 10.1039/d1dt00754h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amide functional groups are an essential linkage that are found in peptides, proteins, and pharmaceuticals and new methods are constantly being sought for their formation. Here, a new method for their preparation is presented where germanium amides Ph3GeNR2 convert acid fluorides directly to amides. These germanium amides serve to abstract the fluorine atom of the acid fluoride and transfer their amide group -NR2 to the carbonyl carbon, and so function as amidation reagents.
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Affiliation(s)
- Ardalan Hayatifar
- Department of Chemistry, Oklahoma State University, 107 Physical Science, Stillwater, Oklahoma 74078, USA.
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4
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Fazelpour E, Fennell CJ. Interactive Molecular Model Assembly with 3D Printing. J Vis Exp 2020. [PMID: 32865537 DOI: 10.3791/61487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical laboratories and chemical education. Building on the long and successful history of physical modeling of molecular systems, we present select models along with a protocol to facilitate 3D printing of molecular structures that are able to do more than represent shape and connectivity. Models assembled as described incorporate dynamic aspects and degrees of freedom into saturated hydrocarbon structures. As a representative example, cyclohexane was assembled from parts printed and finished using different thermoplastics, and the resulting models retain their functionality at a variety of scales. The resulting structures show configurational space accessibility consistent with calculations and literature, and versions of these structures can be used as aids to illustrate concepts that are difficult to convey in other ways. This exercise enables us to evaluate successful printing protocols, make practical recommendations for assembly, and outline design principles for physical modeling of molecular systems. The provided structures, procedures, and results provide a foundation for individual manufacture and exploration of molecular structure and dynamics with 3D printing.
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5
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Fennell CJ, Ghousifam N, Haseleu JM, Gappa-Fahlenkamp H. Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular Diffusion. J Phys Chem B 2018; 122:5599-5609. [PMID: 29510047 PMCID: PMC5985777 DOI: 10.1021/acs.jpcb.7b11846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We
present an atomistic level computational investigation of the
dynamics of a signaling protein, monocyte chemoattractant protein-1
(MCP-1), that explores how simulation geometry and solution ionic
strength affect the calculated diffusion coefficient. Using a simple
extension of noncubic finite size diffusion correction expressions,
it is possible to calculate experimentally comparable diffusion coefficients
that are fully consistent with those determined from cubic box simulations.
Additionally, increasing the concentration of salt in the solvent
environment leads to changes in protein dynamics that are not explainable
through changes in solvent viscosity alone. This work in accurate
computational determination of protein diffusion coefficients led
us to investigate molecular-weight-based predictors for biomolecular
diffusion. By introducing protein volume- and protein surface-area-based
extensions of traditional statistical relations connecting particle
molecular weight to diffusion, we find that protein solvent-excluded
surface area rather than volume works as a better geometric property
for estimating biomolecule Stokes radii. This work highlights the
considerations necessary for accurate computational determination
of biomolecule diffusivity and presents insight into molecular weight
relations for diffusion that could lead to new routes for estimating
protein diffusion beyond the traditional approaches.
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Affiliation(s)
| | | | - Jennifer M Haseleu
- Department of Chemistry , Saint Vincent College , Latrobe , Pennsylvania 15650 , United States
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6
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Singh K, Fennell CJ, Coutsias EA, Latifi R, Hartson S, Weaver JD. Light Harvesting for Rapid and Selective Reactions: Click Chemistry with Strain-Loadable Alkenes. Chem 2018. [DOI: 10.1016/j.chempr.2017.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev 2017; 117:12385-12414. [PMID: 28949513 PMCID: PMC5639468 DOI: 10.1021/acs.chemrev.7b00259] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 11/29/2022]
Abstract
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.
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Affiliation(s)
- Emiliano Brini
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Marivi Fernandez-Serra
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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8
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9
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Singh A, Fennell CJ, Weaver JD. Photocatalyst size controls electron and energy transfer: selectable E/ Z isomer synthesis via C-F alkenylation. Chem Sci 2016; 7:6796-6802. [PMID: 28042465 PMCID: PMC5134729 DOI: 10.1039/c6sc02422j] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/13/2016] [Indexed: 12/23/2022] Open
Abstract
Photocatalytic alkene synthesis can involve electron and energy transfer processes. The structure of the photocatalyst can be used to control the rate of the energy transfer, providing a mechanistic handle over the two processes. Jointly considering catalyst volume and emissive energy provides a highly sensitive strategy for predicting which mechanistic pathway will dominate. This model was developed en route to a photocatalytic Caryl-F alkenylation reaction of alkynes and highly-fluorinated arenes as partners. By judicious choice of photocatalyst, access to E- or Z-olefins was accomplished, even in the case of synthetically challenging trisubstituted alkenes. The generality and transferability of this model was tested by evaluating established photocatalytic reactions, resulting in shortened reaction times and access to complimentary Z-cinnamylamines in the photocatalytic [2 + 2] and C-H vinylation of amines, respectively. These results show that taking into account the size of the photocatalyst provides predictive ability and control in photochemical quenching events.
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Affiliation(s)
- A Singh
- Department of Chemistry , Oklahoma State University , Stillwater , OK 74078 , USA .
| | - C J Fennell
- Department of Chemistry , Oklahoma State University , Stillwater , OK 74078 , USA .
| | - J D Weaver
- Department of Chemistry , Oklahoma State University , Stillwater , OK 74078 , USA .
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10
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Paranahewage SS, Gierhart CS, Fennell CJ. Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields. J Comput Aided Mol Des 2016; 30:1059-1065. [PMID: 27573982 PMCID: PMC5206264 DOI: 10.1007/s10822-016-9950-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/21/2016] [Indexed: 11/05/2022]
Abstract
Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nature of the force fields. Here, we report on an application of such calculations in the SAMPL5 experiment that also involves an effort in balancing solute and solvent interactions via their expected static dielectric constants. This strategy performs well with respect to predictive accuracy and correlation with unknown experimental values. We follow this by performing a series of retrospective investigations which highlight the potential importance of proper balancing in these systems, and we use a null hypothesis analysis to explore potential biases in the comparisons with experiment. The collective findings indicate that considerations of force field compatibility through dielectric behavior is a potential strategy for future improvements in transfer processes between disparate environments.
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Affiliation(s)
| | - Cassidy S Gierhart
- Department of Chemical Engineering, Oklahoma State University, Stillwater, OK, 74078, USA
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11
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Affiliation(s)
- Hamid Mortazavian
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Christopher J. Fennell
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Frank D. Blum
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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12
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Affiliation(s)
- Hamid Mortazavian
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Christopher J. Fennell
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Frank D. Blum
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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13
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Fennell CJ, Gezelter JD. Computational Free Energy Studies of a New Ice Polymorph Which Exhibits Greater Stability than Ice Ih. J Chem Theory Comput 2015; 1:662-7. [PMID: 26641688 DOI: 10.1021/ct050005s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The absolute free energies of several ice polymorphs were calculated using thermodynamic integration. These polymorphs are predicted by computer simulations using a variety of common water models to be stable at low pressures. A recently discovered ice polymorph that has as yet only been observed in computer simulations (Ice-i) was determined to be the stable crystalline state for all the water models investigated. Phase diagrams were generated, and phase coexistence lines were determined for all of the known low-pressure ice structures. Additionally, potential truncation was shown to play a role in the resulting shape of the free energy landscape.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - J Daniel Gezelter
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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14
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Li L, Fennell CJ, Dill KA. Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. J Chem Phys 2015; 141:22D518. [PMID: 25494789 DOI: 10.1063/1.4900890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We are interested in the free energies of transferring nonpolar solutes into aqueous NaCl solutions with salt concentrations upwards of 2 M, the Hofmeister regime. We use the semi-explicit assembly (SEA) computational model to represent these electrolyte solutions. We find good agreement with experiments (Setschenow coefficients) on 43 nonpolar and polar solutes and with TIP3P explicit-solvent simulations. Besides being much faster than explicit solvent calculations, SEA is more accurate than the PB models we tested, successfully capturing even subtle salt effects in both the polar and nonpolar components of solvation. We find that the salt effects are mainly due to changes in the cost of forming nonpolar cavities in aqueous NaCl solutions, and not mainly due to solute-ion electrostatic interactions.
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Affiliation(s)
- Libo Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, People's Republic of China
| | | | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, and Departments of Physics and Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Drechsel NJD, Fennell CJ, Dill KA, Villà-Freixa J. TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives. J Chem Theory Comput 2014; 10:4121-4132. [PMID: 25221446 PMCID: PMC4159216 DOI: 10.1021/ct5002818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 12/01/2022]
Abstract
We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called TRIFORCE, reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application.
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Affiliation(s)
- Nils J. D. Drechsel
- Computational
Biochemistry and Biophysics Laboratory,
Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, C/Doctor Aiguader, 88, 08003 Barcelona, Catalunya, Spain
- Laufer
Center for Physical and Quantitative Biology, Stony Brook University, Stony
Brook, New York 11794-5252, United States
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology and Departments of Physics
and Chemistry, Stony Brook University, Stony Brook, New York 11794-5252, United States
| | - Jordi Villà-Freixa
- Computational
Biochemistry and Biophysics Laboratory,
Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, C/Doctor Aiguader, 88, 08003 Barcelona, Catalunya, Spain
- Escola
Politècnica Superior, Universitat
de Vic—Universitat Central de Catalunya, C/de la Laura, 13, 08500 Vic, Catalunya, Spain
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16
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Fennell CJ, Wymer KL, Mobley DL. A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. J Phys Chem B 2014; 118:6438-46. [PMID: 24702668 PMCID: PMC4064691 DOI: 10.1021/jp411529h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a simple optimization strategy for incorporating experimental dielectric response information on neat liquids in classical molecular models of alcohol. Using this strategy, we determine simple and transferable hydroxyl modulation rules that, when applied to an existing molecular parameter set, result in a newly dielectric corrected (DC) parameter set. We applied these rules to the general Amber force field (GAFF) to form an initial set of GAFF-DC parameters, and we found this to lead to significant improvement in the calculated dielectric constant and hydration free energy values for a wide variety of small molecule alcohol models. Tests of the GAFF-DC parameters in the SAMPL4 blind prediction event for hydration show these changes improve agreement with experiment. Surprisingly, these simple modifications also outperform detailed quantum mechanical electric field calculations using a self-consistent reaction field environment coupling term. This work provides a potential benchmark for future developments in methods for representing condensed-phase environments in electronic structure calculations.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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17
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Abstract
We perform extensive molecular dynamics (MD) simulations between pairs of ions of various diameters (2-5.5 Å in increments of 0.5 Å) and charge (+1 or -1) interacting in explicit water (TIP3P) under ambient conditions. We extract their potentials of mean force (PMFs). We develop an interpolation scheme, called i-PMF, that is capable of capturing the full set of PMFs for arbitrary combinations of ion sizes ranging from 2 to 5.5 Å. The advantage of the interpolation process is computational cost. Whereas it can take 100 h to simulate each PMF by MD, we can compute an equivalently accurate i-PMF in seconds. This process may be useful for rapid and accurate calculation of the strengths of salt bridges and the effects of bridging waters in biomolecular simulations. We also find that our data is consistent with Collins' "law of matching affinities" of ion solubilities: small-small or large-large ion pairs are poorly soluble in water, whereas small-large are highly soluble.
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Affiliation(s)
- Miha Lukšič
- Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794-5252, United States
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18
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Li L, Dill KA, Fennell CJ. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. J Comput Aided Mol Des 2014; 28:259-64. [PMID: 24474161 DOI: 10.1007/s10822-014-9712-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/16/2014] [Indexed: 12/14/2022]
Abstract
Here, we test a method, called semi-explicit assembly (SEA), that computes the solvation free energies of molecules in water in the SAMPL4 blind test challenge. SEA was developed with the intention of being as accurate as explicit-solvent models, but much faster to compute. It is accurate because it uses pre-simulations of simple spheres in explicit solvent to obtain structural and thermodynamic quantities, and it is fast because it parses solute free energies into regionally additive quantities. SAMPL4 provided us the opportunity to make new tests of SEA. Our tests here lead us to the following conclusions: (1) The newest version, called Field-SEA, which gives improved predictions for highly charged ions, is shown here to perform as well as the earlier versions (dipolar and quadrupolar SEA) on this broad blind SAMPL4 test set. (2) We find that both the past and present SEA models give solvation free energies that are as accurate as TIP3P. (3) Using a new approach for force field parameter optimization, we developed improved hydroxyl parameters that ensure consistency with neat-solvent dielectric constants, and found that they led to improved solvation free energies for hydroxyl-containing compounds in SAMPL4. We also learned that these hydroxyl parameters are not just fixing solvent exposed oxygens in a general sense, and therefore do not improve predictions for carbonyl or carboxylic-acid groups. Other such functional groups will need their own independent optimizations for potential improvements. Overall, these tests in SAMPL4 indicate that SEA is an accurate, general and fast new approach to computing solvation free energies.
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Affiliation(s)
- Libo Li
- Departments of Chemistry and Physics, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
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19
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Abstract
![]()
Previous
work describes a computational solvation model called semi-explicit
assembly (SEA). The SEA water model computes the free energies of
solvation of nonpolar and polar solutes in water with good efficiency
and accuracy. However, SEA gives systematic errors in the solvation
free energies of ions and charged solutes. Here, we describe field-SEA,
an improved treatment that gives accurate solvation free energies
of charged solutes, including monatomic and polyatomic ions and model
dipeptides, as well as nonpolar and polar molecules. Field-SEA is
computationally inexpensive for a given solute because explicit-solvent
model simulations are relegated to a precomputation step and because
it represents solvating waters in terms of a solute’s free-energy
field. In essence, field-SEA approximates the physics of explicit-model
simulations within a computationally efficient framework. A key finding
is that an atom’s solvation shell inherits characteristics
of a neighboring atom, especially strongly charged neighbors. Field-SEA
may be useful where there is a need for solvation free-energy computations
that are faster than explicit-solvent simulations and more accurate
than traditional implicit-solvent simulations for a wide range of
solutes.
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Affiliation(s)
- Libo Li
- Laufer Center for Physical and Quantitative Biology, and Departments of Physics and Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
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20
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Urbič T, Fennell CJ, Dill KA. A microscopic theory of solvation of monoions. Acta Chim Slov 2012; 59:554-558. [PMID: 24061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
The solvation free energies of ions are often computed using continuum theories, like the Born model. The Born model has the disadvantages that to fit experimental data, ionic radii are taken as adjustable parameters and you need to know the dielectric constant. We present here a more microscopic treatment for computing the free energies of ion solvation in water. Like the Born model, it gives an expression that is simple and can be computed quickly, but unlike the Born model, it uses true ionic radii and does not require inputting a dielectric constant. We show that the present model gives predictions for the free energies of transfer of alkali and halide ions into water that are in excellent agreement with recent experimentally derived estimates.
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21
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Abstract
Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations--water, carbon tetrachloride, chloroform, and dichloromethane. Normally, such solvent models are parametrized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parametrizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parametrizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations.
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Affiliation(s)
- Christopher J Fennell
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA.
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Fennell CJ, Kehoe CW, Dill KA. Accurate Solutions with the Semi-Explicit Assembly Water Model. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Kehoe CW, Fennell CJ, Dill KA. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J Comput Aided Mol Des 2011; 26:563-8. [PMID: 22205387 DOI: 10.1007/s10822-011-9536-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/14/2011] [Indexed: 11/28/2022]
Abstract
We report here a test of the Semi-Explicit Assembly (SEA) model in the solvation free energy category of the SAMPL3 blind prediction event (summer 2011). We tested how dependent the SEA results are on the chosen force field by performing calculations with both the General Amber and OPLS force fields. We compared our SEA results with full molecular dynamics simulations in explicit solvent. Of the 20 submissions, our SEA/OPLS results gave the second smallest RMS errors in free energies compared to experiments. SEA gives results that are very similar to those of its underlying force field and explicit solvent model. Hence, while the SEA water modeling approach is much faster than explicit solvent simulations, its predictions appear to be just as accurate.
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Affiliation(s)
- Charles W Kehoe
- Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA 94158, USA
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Affiliation(s)
- David L. Mobley
- Department of Chemistry, University of New Orleans, New Orleans, LA
| | - Janene R. Baker
- Department of Chemistry, University of New Orleans, New Orleans, LA
| | - Alan E. Barber
- Department of Biopharmaceutical Science, University of California, San Francisco, CA
| | | | - Ken A. Dill
- Laufer Center, Stony Brook University, Stony Brook, NY
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Abstract
We consider the free energies of solvating molecules in water. Computational modeling usually involves either detailed explicit-solvent simulations, or faster computations, which are based on implicit continuum approximations or additivity assumptions. These simpler approaches often miss microscopic physical details and non-additivities present in experimental data. We review explicit-solvent modeling that identifies the physical bases for the errors in the simpler approaches. One problem is that water molecules that are shared between two substituent groups often behave differently than waters around each substituent individually. One manifestation of non-additivities is that solvation free energies in water can depend not only on surface area or volume, but on other properties, such as the surface curvature. We also describe a new computational approach, called Semi-Explicit Assembly, that aims to repair these flaws and capture more of the physics of explicit water models, but with computational efficiencies approaching those of implicit-solvent models.
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Abstract
We present a new approach to computer modeling of solvation free energies of oil in water. In Semi-Explicit Assembly, we first precompute structural and thermal properties of TIP3P waters around different Lennard-Jones spheres. This tabulated information is then used to compute the nonpolar solvation properties of arbitrary solutes. By accumulating interactions from whole regions of the solute molecule, Semi-Explicit Assembly more properly accounts for effects of solute shape and solves problems that appear as nonadditivities in traditional gammaA approaches. Semi-Explicit Assembly involves little parameter fitting because the solute and water properties are taken from existing force fields. We tested the predictions on alkanes, alkynes, linear and planar polyaromatic hydrocarbons, and on a diverse set of 504 molecules previously explored by explicit solvent simulations. We found that not all hydrocarbons are the same. Hydrocarbons have "hot spots", places where first-shell waters interact more strongly with the molecule than at other locations. For example, waters are more attracted to hover over hydrocarbon rings than at the edges. By accounting for these collective regional effects, Semi-Explicit Assembly approaches the physical accuracies of explicit solvent models in computing nonpolar solvation free energies, but because of the precomputations and the regional additivities, it is nearly as fast to compute as gammaA methods.
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Affiliation(s)
- Christopher J. Fennell
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143
| | - Charlie Kehoe
- Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, CA 94143
| | - Ken A. Dill
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143
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Fennell CJ, Bizjak A, Vlachy V, Dill KA, Sarupria S, Rajamani S, Garde S. Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions. J Phys Chem B 2009. [DOI: 10.1021/jp908484v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Using classical molecular dynamics simulations, we study ion-ion interactions in water. We study the potentials of mean force (PMF) for the full set of alkali halide ion pairs, and in each case, we test different parameter sets for modeling both the water and the ions. Altogether, we compared 300 different PMFs. We also calculate association equilibrium constants (KA) and compare them to two types of experiments. Of additional interest here was the proposition of Collins called the "law of matching water affinities", where the relative affinity of ions in solution depends on the matching of cation and anion sizes. From observations on the relative depths of the free energies of the contact ion pair (CIP) and the solvent-shared ion pair (SIP), along with related solvent structure analyses, we find a good correlation with this proposition: small-small and large-large should associate in water, and small-large should be more dissociated.
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Affiliation(s)
- Christopher J Fennell
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA.
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Abstract
We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
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Fennell CJ, Gezelter JD. Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. J Chem Phys 2007; 124:234104. [PMID: 16821904 DOI: 10.1063/1.2206581] [Citation(s) in RCA: 331] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate pairwise electrostatic interaction methods and show that there are viable computationally efficient (O(N)) alternatives to the Ewald summation for typical modern molecular simulations. These methods are extended from the damped and cutoff-neutralized Coulombic sum originally proposed by Wolf et al. [J. Chem. Phys. 110, 8255 (1999)]. One of these, the damped shifted force method, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. Comparisons were performed with this and other pairwise methods against the smooth particle-mesh Ewald summation to see how well they reproduce the energetics and dynamics of a variety of molecular simulations.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry/Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Meineke MA, Vardeman CF, Lin T, Fennell CJ, Gezelter JD. OOPSE: an object-oriented parallel simulation engine for molecular dynamics. J Comput Chem 2005; 26:252-71. [PMID: 15614795 DOI: 10.1002/jcc.20161] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.
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Affiliation(s)
- Matthew A Meineke
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556-5670, USA
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Fennell CJ, Gezelter JD. On the structural and transport properties of the soft sticky dipole and related single-point water models. J Chem Phys 2004; 120:9175-84. [PMID: 15267854 DOI: 10.1063/1.1697381] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The density maximum and temperature dependence of the self-diffusion constant were investigated for the soft sticky dipole (SSD) water model and two related reparametrizations of this single-point model. A combination of microcanonical and isobaric-isothermal molecular dynamics simulations was used to calculate these properties, both with and without the use of reaction field to handle long-range electrostatics. The isobaric-isothermal simulations of the melting of both ice-Ih and ice-Ic showed a density maximum near 260 K. In most cases, the use of the reaction field resulted in calculated densities which were significantly lower than experimental densities. Analysis of self-diffusion constants shows that the original SSD model captures the transport properties of experimental water very well in both the normal and supercooled liquid regimes. We also present our reparametrized versions of SSD for use both with the reaction field or without any long-range electrostatic corrections. These are called the SSD/RF and SSD/E models, respectively. These modified models were shown to maintain or improve upon the experimental agreement with the structural and transport properties that can be obtained with either the original SSD or the density-corrected version of the original model (SSD1). Additionally, a novel low-density ice structure is presented which appears to be the most stable ice structure for the entire SSD family.
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Affiliation(s)
- Christopher J Fennell
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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