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Ritter L, Tudor B, Hogan A, Pham T, Space B. PHAHST Potential: Modeling Sorption in a Dispersion-Dominated Environment. J Chem Theory Comput 2024; 20:5570-5582. [PMID: 38889276 DOI: 10.1021/acs.jctc.4c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
PHAHST (potentials with high accuracy, high speed, and transferability) is a recently developed force field that utilizes exponential repulsion, multiple dispersion terms, explicit many-body polarization, and many-body van der Waals interactions. The result is a systematic approach to force field development that is computationally practical. Here, PHAHST is employed in the simulation for rare gas uptake of krypton and xenon in the metal-organic material, HKUST-1. This material has shown promise in use as an adsorptive separating agent and presents a challenge to model due to the presence of heterogeneous interaction sorption surfaces, which include pores with readily accessible, open-metal sites that compete with dispersion-dominated pores. Such environments are difficult to simulate with commonly used empirical force fields, such as the Lennard-Jones (LJ) potential, which perform better when electrostatics are dominant in determining the nature of sorption and alone are incapable of modeling interactions with open-metal sites. The effectiveness of PHAHST is compared to the LJ potential in a series of mixed Kr-Xe gas simulations. It has been demonstrated that PHAHST compares favorably with experimental results, and the LJ potential is inadequate. Overall, we establish that force fields with physically grounded repulsion/dispersion terms are required in order to accurately model sorption, as these interactions are an important component of the energy. Furthermore, it is shown that the simple mixing rules work nearly quantitatively for the true pair potentials, while they are not transferable for effective potentials like LJ.
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Affiliation(s)
- Logan Ritter
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Brant Tudor
- John Hopkins School of Medicine, Anesthesiology and Critical Care Medicine, 601 Fifth Street S., Saint Petersburg, Florida 33701, United States
| | - Adam Hogan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Tony Pham
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Brian Space
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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Kříž K, van Maaren PJ, van der Spoel D. Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases. J Chem Theory Comput 2024; 20:2362-2376. [PMID: 38477573 DOI: 10.1021/acs.jctc.3c01257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25-30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, J. Am. Chem. Soc. 1992, 114, 7827-7843), a four-parameter Buckingham potential (Werhahn et al., Chem. Phys. Lett. 2015, 619, 133-138), or the three-parameter Morse potential (Morse, Phys. Rev. 1929, 34, 57-64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σij as ( 1 2 ( σ i 3 + σ j 3 ) ) 1 / 3 and one for the well-depth ϵij as ( 1 2 ( ϵ i - 2 + ϵ j - 2 ) ) - 1 / 2 . The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.
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Affiliation(s)
- Kristian Kříž
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
| | - Paul J van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
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Chowdhury P, Jha A, Bhandary D. Influence of Temperature-Guided SAM Growth on Wetting and Its Mass Transfer Models. J Phys Chem B 2023; 127:8208-8215. [PMID: 37703434 DOI: 10.1021/acs.jpcb.3c04173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The formation and growth of self-assembled monolayers (SAMs) composed of amphiphiles have garnered significant attention due to their diverse technical applications. This article reports the findings of molecular dynamics simulations aimed at elucidating the intricate relationship between the wetting behavior of amphiphiles, specifically n-alkanols, and the growth of their SAMs on a mica surface under varying temperature conditions. The investigation quantifies the structural characteristics of the formed SAMs, including density profiles, in-plane radial distribution functions, order parameters, and end-to-end length distributions of n-alkanol molecules within the SAM. Thermodynamic properties, such as the second virial coefficient and excess entropy, are examined in relation to temperature and time. The growth of the SAM is assessed by analyzing characteristic time scales at different temperatures and in-plane diffusion of n-alkanol molecules and utilizing classical theories of mass transfer to quantify the growth rate as a function of temperature. These results are then correlated with changes in the contact angle and spreading coefficient of n-alkanol droplets on the mica surface over time, providing insights into the impact of SAM growth on the wetting behavior and the mass transfer model of such systems.
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Affiliation(s)
- Prateek Chowdhury
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) Varanasi, Varanasi, UP 221005, India
| | - Ayush Jha
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) Varanasi, Varanasi, UP 221005, India
| | - Debdip Bhandary
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU) Varanasi, Varanasi, UP 221005, India
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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5
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Adaptive intermolecular interaction parameters for accurate Mixture Density Functional Theory calculations. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paul S, Torsi R, Robinson JA, Momeni K. Effect of the Substrate on MoS 2 Monolayer Morphology: An Integrated Computational and Experimental Study. ACS APPLIED MATERIALS & INTERFACES 2022; 14:18835-18844. [PMID: 35421302 DOI: 10.1021/acsami.2c03471] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Synthesis of two-dimensional materials, specifically transition metal dichalcogenides (TMDs), with controlled lattice orientations is a major barrier to their industrial applications. Controlling the orientation of as-grown TMDs is critical for preventing the formation of grain boundaries, thus reaching their maximum mechanical and optoelectronic performance. Here, we investigated the role of the substrate's crystallinity in the growth orientation of 2D materials using reactive molecular dynamics (MD) simulations and verified with experimental growth using the chemical vapor deposition (CVD) technique. We considered MoS2 as our model material and investigated its growth on crystalline and amorphous silica and sapphire substrates. We revealed the role of the substrate's energy landscape on the orientation of as-grown TMDs, where the presence of monolayer-substrate energy barriers perpendicular to the streamlines hinder the detachment of precursor nuclei from the substrate. We show that MoS2 monolayers with controlled orientations could not be grown on the SiO2 substrate and revealed that amorphization of the substrate changes the intensity and equilibrium distance of monolayer-substrate interactions. Our simulations indicate that 0° rotated MoS2 is the most favorable configuration on a sapphire substrate, consistent with our experimental results. The experimentally validated computational results and insight presented in this study pave the way for the high-quality synthesis of TMDs for high-performance electronic and optoelectronic devices.
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Affiliation(s)
- Shiddartha Paul
- Department of Mechanical Engineering, The University of Alabama, Tuscaloosa, Alabama 35401, United States
| | - Riccardo Torsi
- 2D Crystal Consortium, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joshua A Robinson
- 2D Crystal Consortium, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for 2D and Layered Materials, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kasra Momeni
- Department of Mechanical Engineering, The University of Alabama, Tuscaloosa, Alabama 35401, United States
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Yan H, Xu X, Li P, He P, Peng Q, Ding C. Aluminum Doping Effect on Surface Structure of Silver Ultrathin Films. MATERIALS (BASEL, SWITZERLAND) 2022; 15:648. [PMID: 35057365 PMCID: PMC8781137 DOI: 10.3390/ma15020648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022]
Abstract
Ultrathin silver films with low loss in the visible and near-infrared spectrum range have been widely used in the fields of metamaterials and optoelectronics. In this study, Al-doped silver films were prepared by the magnetron sputtering method and were characterized by surface morphology, electrical conductivity, and light transmittance analyses. Molecular dynamics simulations and first-principles density functional theory calculations were applied to study the surface morphologies and migration pathway for the formation mechanisms in Al-doped silver films. The results indicate that the migration barrier of silver on a pristine silver surface is commonly lower than that of an Al-doped surface, revealing that the aluminum atoms in the doping site decrease the surface mobility and are conducive to the formation of small islands of silver. When the islands are dense, they coalesce into a single layer, leading to a smoother surface. This might be the reason for the observably lower 3D growth mode of silver on an Al-doped silver surface. Our results with electronic structure insights on the mechanism of the Al dopants on surface morphologies might benefit the quality control of the silver thin films.
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Affiliation(s)
- Han Yan
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (H.Y.); (X.X.); (C.D.)
| | - Xiong Xu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (H.Y.); (X.X.); (C.D.)
| | - Peng Li
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (H.Y.); (X.X.); (C.D.)
| | - Peijie He
- School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072, China;
| | - Qing Peng
- Physics Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
- K.A. CARE Energy Research & Innovation Center at Dhahran, Dhahran 31261, Saudi Arabia
- Hydrogen and Energy Storage Center, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Can Ding
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (H.Y.); (X.X.); (C.D.)
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Priyadarsini A, Mallik BS. Comparative first principles-based molecular dynamics study of catalytic mechanism and reaction energetics of water oxidation reaction on 2D-surface. J Comput Chem 2021; 42:1138-1149. [PMID: 33851446 DOI: 10.1002/jcc.26528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/02/2023]
Abstract
The study of the water-splitting process, which can proceed in 2e- as well as 4e- pathway, reveals that the process is entirely an uphill process, and the third step, that is, the oxooxo bond formation is the rate-determining step. The kinetic barrier of the oxygen evolution reaction (OER) on the 2D material catalysts in the presence of explicit solvents is scarcely studied. Here, we investigate the dynamics of the OER on the undoped graphene and the activation energy barrier of each step using first principles molecular dynamics simulations. Here we provide a detailed analysis of the kinetics of all the 4e- transfer steps of OER on the graphene surface. We also compare the accuracy of one of the density functional theory (DFT) functionals and density functional based tight binding (DFTB) method in explaining the OER steps. The comparative study reveals that DFTB can be used for performing metadynamics simulations quipped with much less computational cost than DFT functionals. By both Perdew-Burke-Ernzerhof and DFTB methods, the third step is revealed to be the rate-determining step with an energy barrier of 21.19 ± 0.51 and 20.23 ± 0.20 kcal mol-1 , respectively. DFTB gives an impression of being successful in predicting the energy barriers of OER in 4e- transfer pathway and comparable to the DFT method, and we would like to extend the use of DFTB for further studies with a sizable and complex system.
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Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
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Molecular simulations of the adsorption and separation of hydrogen sulfide, carbon dioxide, methane, and nitrogen and their binary mixtures (H 2S/CH 4), (CO 2/CH 4) on NUM-3a metal-organic frameworks. J Mol Model 2021; 27:133. [PMID: 33893884 DOI: 10.1007/s00894-021-04709-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 02/10/2021] [Indexed: 10/21/2022]
Abstract
In this work, the adsorptions of carbon dioxide, methane, nitrogen, and hydrogen sulfide and the separation of their binary mixtures into NUM-3a Metal-Organic Framework (MOF) were studied through Grand Canonical Monte Carlo (GCMC) simulation method. The simulated pure gas uptakes using three generic force fields (UFF, Dreiding, and OPLS) at 298 K were compared with the experimental values. The accuracy of the applied force fields for each gas was compared with the experimental isotherms and discussed. Our results show that OPLS has the best accuracy in the case of methane while Dreiding was the best for CO2 and N2. Simulated gas uptakes indicated that H2S was more adsorbed by NUM-3a than CO2, CH4, and N2. The calculated adsorption selectivity of NUM-3a for the binary mixtures of CH4 with H2S is larger than that of CO2. NUM-3a possess more affinity for H2S and CO2 than for CH4, where it may be a promising adsorbent material for separating carbon dioxide and hydrogen sulfide from methane. Furthermore, the most probable sites for the adsorption of the studied gases on the NUM-3a were investigated. The heats of adsorptions, as well as Henry's law constants, were also calculated, and it was in line with the observed gas adsorptions. The most preferred sites for the adsorption of carbon dioxide and hydrogen sulfide are the carboxyl groups and inside the channels and around the metal centers. However, methane and nitrogen are mainly accumulating in the channels' s apexes of NUM-3a around the metal center.
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Tian Z, Yan H, Peng Q, Guo LJ, Zhou S, Ding C, Li P, Luo Q. Atomistic Insights into Aluminum Doping Effect on Surface Roughness of Deposited Ultra-Thin Silver Films. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:E158. [PMID: 33435138 PMCID: PMC7826873 DOI: 10.3390/nano11010158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
Ultra-thin and continuous metallic silver films are attracting growing interest due to the applications in flexible transparent conducting electrodes. The surface morphology and structure of silver film are very important for its electrical resistivity and optical loss. Therefore, roughness control is essential for the production of ultra-thin metallic electrode film. We have investigated the effect of aluminum doping on the improvement of surface morphology of ultra-thin silver films using molecular dynamics simulations. Al-doped silver films showed smaller surface roughness than pure silver films at various substrate temperatures. When the temperature of the substrate was 600 K, the roughness of Al-doped silver film first decreased, and then increased with the increase of the incident velocity of silver atoms. Silver atoms were more likely to agglomerate on the surface of the substrate after adding aluminum atoms, as aluminum dopants promoted the immobilization of silver atoms on SiO2 substrate due to the anchoring effect. The smoother surface could be attributable to the reduced mean free path of silver due to the cage effect by the aluminum dopant.
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Affiliation(s)
- Zhong Tian
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (Z.T.); (C.D.); (P.L.)
| | - Han Yan
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (Z.T.); (C.D.); (P.L.)
| | - Qing Peng
- Physics Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
- K.A.CARE Energy Research & Innovation Center at Dhahran, Dhahran 31261, Saudi Arabia
| | - Lin Jay Guo
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Shengjun Zhou
- School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072, China;
| | - Can Ding
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (Z.T.); (C.D.); (P.L.)
| | - Peng Li
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, Wuhan 430070, China; (Z.T.); (C.D.); (P.L.)
| | - Qi Luo
- School of Sciences, Wuhan University of Technology, Wuhan 430070, China;
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Ozcelik HG, Satiroglu E, Barisik M. Size dependent influence of contact line pinning on wetting of nano-textured/patterned silica surfaces. NANOSCALE 2020; 12:21376-21391. [PMID: 33078810 DOI: 10.1039/d0nr05392a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wetting behavior on a heterogeneous surface undergoes contact angle hysteresis as the droplet stabilized at a metastable state with a contact angle significantly different from its equilibrium value due to contact line pinning. However, there is a lack of consensus on how to calculate the influence of pinning forces. In general, the pinning effect can be characterized as (i) microscopic behavior when a droplet is pinned and the contact angle increases/decreases as the droplet volume increases/decreases and (ii) macroscopic behavior as the pinning effects decrease and ultimately, disappear with the increase of the droplet size. The current work studied both behaviors using molecular dynamics (MD) simulation with more than 300 different size water droplets on silica surfaces with three different patterns across two different wetting conditions. Results showed that the contact angle increases linearly with increasing droplet volume through the microscopic behavior, while the droplet is pinned on top of a certain number of patterns. When we normalized the droplet size with the corresponding pattern size, we observed a "wetting similarity" that linear microscopic contact angle variations over different size heterogeneities continuously line up. This shows that the pinning force remains constant and the resulting pinning effects are scalable by the size ratio between the droplet and pattern, independent of the size-scale. The slope of these microscopic linear variations decreases with an increase in the droplet size as observed through the macroscopic behavior. We further found a universal behavior in the variation of the corresponding pinning forces, independent of the wetting condition. In macroscopic behavior, pinning effects become negligible and the contact angle reaches the equilibrium value of the corresponding surface when the diameter of the free-standing droplet is approximately equal to 24 times the size of the surface structure. We found that the pinning effect is scalable with the droplet volume, not the size of the droplet base.
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Affiliation(s)
- H Gokberk Ozcelik
- Department of Mechanical Engineering, Izmir Institute of Technology, Izmir, 35430, Turkey.
| | - Ezgi Satiroglu
- Department of Energy Systems Engineering, Izmir Institute of Technology, Izmir, 35430, Turkey
| | - Murat Barisik
- Department of Mechanical Engineering, Izmir Institute of Technology, Izmir, 35430, Turkey.
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Khalili AA, Yeganegi S. Computational study of the effect of functionalization on natural gas components separation and adsorption in NUM-3a MOF. J Mol Graph Model 2020; 101:107731. [PMID: 32931982 DOI: 10.1016/j.jmgm.2020.107731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
The upgrading of natural gas on the pristine and functionalized NUM-3a -X (X = -Cl, -NH2, -F) were studied using Monte Carlo simulations in the grand canonical ensemble (GCMC). The equilibrium structures of the functionalized NUM-3a-X were found and confirmed by the quantum mechanical DFT methods. At first, the adsorptions of the components of the natural gas, CH4, CO2, H2S and N2 as pure gases in the pristine MOF were calculated, utilizing the common force fields for the MOFs and compared with the available experimental data to find out the best performing ones for the simulation of adsorption of the studied gases. Based on the obtained results, NUM-3a -Cl showed the highest uptake for the pure gases. Also, we found that the adsorption of CO2 on NUM-3a -X (X = -Cl, -NH2, -F) is higher than that of other gases. Furthermore, our GCMC simulations revealed that the inclusion of functional groups increases the CO2 selectivity in binary mixtures. In addition, the selectivity of NUM-3a-Cl for CO2 was found to be higher than that the other studied MOFs. The simulated CO2 selectivity were in the order of CO2/N2 > CO2/CH4. Our results indicated that the inclusion of electron withdrawing functional groups can enhance the performance of a MOF for CO2 separation applications. In addition, the isosteric heats of adsorption and Henry's law coefficients were studied.
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Affiliation(s)
- Azita Amouzad Khalili
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Saeid Yeganegi
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran.
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Fatehi M, Mohebbi A, Moradi A. Understanding the structural, dynamic and thermodynamic properties of 5-Nonylsalicylaldoxime: Molecular dynamics and experimental studies. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J Comput Aided Mol Des 2018; 33:133-203. [DOI: 10.1007/s10822-018-0111-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 10/27/2022]
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15
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Haghbakhsh R, Parvaneh K, Esmaeilzadeh F. New models for the binary interaction parameters of nitrogen–alkanes mixtures based on the cubic equations of state. CHEM ENG COMMUN 2018. [DOI: 10.1080/00986445.2017.1423475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Reza Haghbakhsh
- School of Chemical and Petroleum Engineering, Oil and Gas Thermodynamics Research Laboratory, Shiraz University, Shiraz, Iran
| | - Khalil Parvaneh
- School of Chemical and Petroleum Engineering, Oil and Gas Thermodynamics Research Laboratory, Shiraz University, Shiraz, Iran
| | - Feridun Esmaeilzadeh
- School of Chemical and Petroleum Engineering, Oil and Gas Thermodynamics Research Laboratory, Shiraz University, Shiraz, Iran
- Department of Chemical and Petroleum Engineering, School of Chemical and Petroleum Engineering, Enhanced Oil and Gas Recovery Institute, Advanced Research Group for Gas Condensate Recovery, Shiraz University, Shiraz, Iran
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16
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Thermal boundary resistance between the polycrystalline graphene and the amorphous SiO2 substrate. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Wei L, Li P, Tang K. Iterative combining rules for the van der Waals potentials of mixed rare gas systems. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Liu B, Tang X, Fang W, Li X, Zhang J, Zhang Z, Shen Y, Yan Y, Sun X, He J. Molecular dynamics study of di-CF4 based reverse micelles in supercritical CO 2. Phys Chem Chem Phys 2016; 18:29156-29163. [PMID: 27730238 DOI: 10.1039/c6cp04253h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Reverse micelles (RMs) in supercritical CO2 (scCO2) are promising alternatives for organic solvents, especially when both polar and non-polar components are involved. Fluorinated surfactants, particularly double-chain fluorocarbon surfactants, are able to form well-structured RMs in scCO2. The inherent self-assembly mechanisms of surfactants in scCO2 are still subject to discussion. In this study, molecular dynamics simulations are performed to investigate the self-aggregation behavior of di-CF4 based RMs in scCO2, and stable and spherical RMs are formed. The dynamics process and the self-assembly structure in the RMs reveal a three-step mechanism to form the RMs, that is, small RMs, rod-like RMs and fusion of the rod-like RMs. Hydrogen-bonds between headgroups and water molecules, and salt bridges linking Na+ ions, headgroups and water molecules enhance the interfacial packing efficiency of the surfactant. The results show that di-CF4 molecules have a high surfactant coverage at the RM interface, implying a high CO2-philicity. This mainly results from bending of the short chain (C-COO-CH2-(CF2)3-CF3) due to the flexible carboxyl group. The microscopic insight provided in this study is helpful in understanding surfactant self-assembly phenomena and designing new CO2-philic surfactants.
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Affiliation(s)
- Bing Liu
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China. and NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Xinpeng Tang
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Wenjing Fang
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Xiaoqi Li
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Jun Zhang
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Zhiliang Zhang
- NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
| | - Yue Shen
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Youguo Yan
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Xiaoli Sun
- School of Science, China University of Petroleum, Qingdao 266580, Shandong, China.
| | - Jianying He
- NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, 7491, Norway.
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19
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Horta BAC, Merz PT, Fuchs PFJ, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set. J Chem Theory Comput 2016; 12:3825-50. [DOI: 10.1021/acs.jctc.6b00187] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Pascal T. Merz
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Patrick F. J. Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jozica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Chemistry,
Biology and Pharmacy Information Center, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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20
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Shi J, Zhang Y, Sun K, Fang L. Effect of water film on the plastic deformation of monocrystalline copper. RSC Adv 2016. [DOI: 10.1039/c6ra17126e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effect of a water film on the plastic deformation behavior and mechanism of monocrystalline copper are studied by molecular dynamics simulations.
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Affiliation(s)
- Junqin Shi
- State Key Laboratory for Mechanical Behavior of Materials
- Xi’an Jiaotong University
- Xi’an
- China
| | - Yanan Zhang
- State Key Laboratory for Mechanical Behavior of Materials
- Xi’an Jiaotong University
- Xi’an
- China
| | - Kun Sun
- State Key Laboratory for Mechanical Behavior of Materials
- Xi’an Jiaotong University
- Xi’an
- China
| | - Liang Fang
- State Key Laboratory for Mechanical Behavior of Materials
- Xi’an Jiaotong University
- Xi’an
- China
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21
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22
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Determination of Transport Properties of Dilute Binary Mixtures Containing Carbon Dioxide through Isotropic Pair Potential Energies. Chin J Chem Eng 2014. [DOI: 10.1016/s1004-9541(14)60018-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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24
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Cioce CR, McLaughlin K, Belof JL, Space B. A Polarizable and Transferable PHAST N2 Potential for Use in Materials Simulation. J Chem Theory Comput 2013; 9:5550-7. [DOI: 10.1021/ct400526a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Christian R. Cioce
- Department
of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, Florida 33620-5250, United States
| | - Keith McLaughlin
- Department
of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, Florida 33620-5250, United States
| | - Jonathan L. Belof
- Lawrence
Livermore National Laboratory, 7000 East Ave., Livermore, California 94550, United States
| | - Brian Space
- Department
of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, Florida 33620-5250, United States
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25
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Barisik M, Beskok A. Wetting characterisation of silicon (1,0,0) surface. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.758854] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Torres E, DiLabio GA. Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods. J Chem Theory Comput 2013; 9:3342-9. [DOI: 10.1021/ct4003114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edmanuel Torres
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan
Drive, Edmonton, Alberta, Canada T6G 2M9
- Faculty of Basic Sciences, Universidad Technológica de Bolívar,
Cartagena, Colombia
| | - Gino A. DiLabio
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan
Drive, Edmonton, Alberta, Canada T6G 2M9
- Department
of Physics, University of Alberta, Edmonton
Alberta, Canada T6G
2E1
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27
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Cabrales-Navarro FA, Gómez-Ballesteros JL, Balbuena PB. Molecular dynamics simulations of metal-organic frameworks as membranes for gas mixtures separation. J Memb Sci 2013. [DOI: 10.1016/j.memsci.2012.10.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Mohammad-Aghaie D, Papari MM, Zargari F. Modeling Transport Properties of N 2–Noble Gas Mixtures at Low and Moderate Densities. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20110329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Polarisable multipolar electrostatics from the machine learning method Kriging: an application to alanine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1137-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Ren P, Wu C, Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput 2011; 7:3143-3161. [PMID: 22022236 PMCID: PMC3196664 DOI: 10.1021/ct200304d] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chuanjie Wu
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
| | - Jay W. Ponder
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
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31
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Reif MM, Hünenberger PH. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water. J Chem Phys 2011; 134:144104. [DOI: 10.1063/1.3567022] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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32
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Bauer BA, Zhong Y, Meninger DJ, Davis JE, Patel S. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models. J Mol Graph Model 2011; 29:876-87. [PMID: 21414823 PMCID: PMC3070209 DOI: 10.1016/j.jmgm.2010.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 09/17/2010] [Accepted: 09/23/2010] [Indexed: 11/15/2022]
Abstract
We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.
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Affiliation(s)
- Brad A. Bauer
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - Yang Zhong
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - David J. Meninger
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
- Department of Physics and Astronomy University of Delaware Newark, DE 19716
| | - Joseph E. Davis
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
| | - Sandeep Patel
- Department of Chemistry and Biochemistry 238 Brown Laboratory University of Delaware Newark, DE 19716
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33
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Mejía SM, Mills MJL, Shaik MS, Mondragon F, Popelier PLA. The dynamic behavior of a liquid ethanol–water mixture: a perspective from quantum chemical topology. Phys Chem Chem Phys 2011; 13:7821-33. [DOI: 10.1039/c0cp02869j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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34
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Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:201-49. [DOI: 10.1007/128_2011_164] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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Dai CF, Chang RY. Molecular dynamics simulation of formation and control of nanodroplets in piezoelectric nanoejection systems. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.484022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Zhu X, MacKerell AD. Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. J Comput Chem 2010; 31:2330-41. [PMID: 20575015 PMCID: PMC2923574 DOI: 10.1002/jcc.21527] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins.
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Affiliation(s)
- Xiao Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, 20 Penn Street, Baltimore, Maryland 21201
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37
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Baker CM, Lopes PEM, Zhu X, Roux B, MacKerell AD. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput 2010; 6:1181-1198. [PMID: 20401166 PMCID: PMC2853947 DOI: 10.1021/ct9005773] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.
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38
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Dai CF, Chang RY. Molecular dynamics simulation of thread break-up and formation of droplets in nanoejection system. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802430745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Mohammad-Aghaie D, Papari MM, Moghadasi J, Haghighi B. Assessment of the Effect of Mixing Rules on Transport Properties of Gas Mixtures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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40
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41
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Anisimov VM, Vorobyov IV, Roux B, MacKerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput 2007; 3:1927-1946. [PMID: 18802495 PMCID: PMC2542883 DOI: 10.1021/ct700100a] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O(alcohol)-O(water) LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.
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Affiliation(s)
- Victor M. Anisimov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
| | - Igor V. Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
| | - Benoît Roux
- Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago 929 E. 57 St. Chicago, IL 60637
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
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42
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Lenart PJ, Panagiotopoulos AZ. Tracing the Critical Loci of Binary Fluid Mixtures Using Molecular Simulation. J Phys Chem B 2006; 110:17200-6. [PMID: 16928018 DOI: 10.1021/jp0630931] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monte Carlo simulations are used to trace the critical loci for a number of binary mixtures. In particular, we use grand canonical Monte Carlo (GCMC) simulations with histogram reweighting and mixed-field finite-size scaling to determine the mixture critical lines. Two different classes of criticality are investigated. A mixture of methane and ethane displays type I criticality, exhibiting continuous mixing between the two species across the entire composition range. A methane-water mixture shows type IIIb criticality, with a discontinuity in the critical locus. Quantitative agreement is found between simulation and experimental critical loci for the methane-ethane system using no adjustable parameters for interactions in the mixture. For the water-methane system, we investigate the effect of the combining rules for the intermolecular interaction between the two species on the mixture critical locus. We also investigate several potentials for methane: a nonpolar exponential-6, an octopolar fixed partial charge, and a polarizable fluctuating charge model. Qualitative agreement between simulations and experiments is found for all potentials, but none are able to quantitatively capture the abrupt increase in the critical temperature as methane is added to the system.
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Affiliation(s)
- Philip J Lenart
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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Borodin O, Smith GD. Development of Many−Body Polarizable Force Fields for Li-Battery Components: 1. Ether, Alkane, and Carbonate-Based Solvents. J Phys Chem B 2006; 110:6279-92. [PMID: 16553446 DOI: 10.1021/jp055079e] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.
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Affiliation(s)
- Oleg Borodin
- Department of Materials Science & Engineering, University of Utah, Salt Lake City, Utah 84112, USA.
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van 't Hof A, Peters CJ, de Leeuw SW. An advanced Gibbs-Duhem integration method: Theory and applications. J Chem Phys 2006; 124:054906. [PMID: 16468917 DOI: 10.1063/1.2137706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The conventional Gibbs-Duhem integration method is very convenient for the prediction of phase equilibria of both pure components and mixtures. However, it turns out to be inefficient. The method requires a number of lengthy simulations to predict the state conditions at which phase coexistence occurs. This number is not known from the outset of the numerical integration process. Furthermore, the molecular configurations generated during the simulations are merely used to predict the coexistence condition and not the liquid- and vapor-phase densities and mole fractions at coexistence. In this publication, an advanced Gibbs-Duhem integration method is presented that overcomes above-mentioned disadvantage and inefficiency. The advanced method is a combination of Gibbs-Duhem integration and multiple-histogram reweighting. Application of multiple-histogram reweighting enables the substitution of the unknown number of simulations by a fixed and predetermined number. The advanced method has a retroactive nature; a current simulation improves the predictions of previously computed coexistence points as well. The advanced Gibbs-Duhem integration method has been applied for the prediction of vapor-liquid equilibria of a number of binary mixtures. The method turned out to be very convenient, much faster than the conventional method, and provided smooth simulation results. As the employed force fields perfectly predict pure-component vapor-liquid equilibria, the binary simulations were very well suitable for testing the performance of different sets of combining rules. Employing Lorentz-Hudson-McCoubrey combining rules for interactions between unlike molecules, as opposed to Lorentz-Berthelot combining rules for all interactions, considerably improved the agreement between experimental and simulated data.
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Affiliation(s)
- A van 't Hof
- Physical Chemistry and Molecular Thermodynamics, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
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