1
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Kaiser S, Yue Z, Peng Y, Nguyen TD, Chen S, Teng D, Voth GA. Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package. J Phys Chem B 2024; 128:4959-4974. [PMID: 38742764 PMCID: PMC11129700 DOI: 10.1021/acs.jpcb.4c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.
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Affiliation(s)
- Scott Kaiser
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Zhi Yue
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yuxing Peng
- NVIDIA
Corporation, Santa
Clara, California 95051, United States
| | - Trung Dac Nguyen
- Research
Computing Center, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sijia Chen
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Da Teng
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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2
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Batista PR, Ducati LC, Autschbach J. Dynamic and relativistic effects on Pt-Pt indirect spin-spin coupling in aqueous solution studied by ab initio molecular dynamics and two- vs four-component density functional NMR calculations. J Chem Phys 2024; 160:114307. [PMID: 38497474 DOI: 10.1063/5.0196853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
Treating 195Pt nuclear magnetic resonance parameters in solution remains a considerable challenge from a quantum chemistry point of view, requiring a high level of theory that simultaneously takes into account the relativistic effects, the dynamic treatment of the solvent-solute system, and the dynamic electron correlation. A combination of Car-Parrinello molecular dynamics (CPMD) and relativistic calculations based on two-component zeroth order regular approximation spin-orbit Kohn-Sham (2c-ZKS) and four-component Dirac-Kohn-Sham (4c-DKS) Hamiltonians is performed to address the solvent effect (water) on the conformational changes and JPtPt1 coupling. A series of bridged PtIII dinuclear complexes [L1-Pt2(NH3)4(Am)2-L2]n+ (Am = α-pyrrolidonate and pivalamidate; L = H2O, Cl-, and Br-) are studied. The computed Pt-Pt coupling is strongly dependent on the conformational dynamics of the complexes, which, in turn, is correlated with the trans influence among axial ligands and with the angle N-C-O from the bridging ligands. The J-coupling is decomposed in terms of dynamic contributions. The decomposition reveals that the vibrational and explicit solvation contributions reduce JPtPt1 of diaquo complexes (L1 = L2 = H2O) in comparison to the static gas-phase magnitude, whereas the implicit solvation and bulk contributions correspond to an increase in JPtPt1 in dihalo (L1 = L2 = X-) and aquahalo (L1 = H2O; L2 = X-) complexes. Relativistic treatment combined with CPMD shows that the 2c-ZKS Hamiltonian performs as well as 4c-DKS for the JPtPt1 coupling.
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Affiliation(s)
- Patrick R Batista
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, SP, Brazil
| | - Lucas C Ducati
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000 São Paulo, SP, Brazil
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, USA
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3
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Villard J, Bircher MP, Rothlisberger U. Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder. Chem Sci 2024; 15:4434-4451. [PMID: 38516095 PMCID: PMC10952088 DOI: 10.1039/d3sc05828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.
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Affiliation(s)
- Justin Villard
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
| | - Martin P Bircher
- Computational and Soft Matter Physics, Universität Wien Wien A-1090 Austria
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne CH-1015 Switzerland
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4
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Zelovich T, Dekel DR, Tuckerman ME. Electrostatic Potential of Functional Cations as a Predictor of Hydroxide Diffusion Pathways in Nanoconfined Environments of Anion Exchange Membranes. J Phys Chem Lett 2024; 15:408-415. [PMID: 38179916 PMCID: PMC10801687 DOI: 10.1021/acs.jpclett.3c02800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Nanoconfined anion exchange membranes (AEMs) play a vital role in emerging electrochemical technologies. The ability to control dominant hydroxide diffusion pathways is an important goal in the design of nanoconfined AEMs. Such control can shorten hydroxide transport pathways between electrodes, reduce transport resistance, and enhance device performance. In this work, we propose an electrostatic potential (ESP) approach to explore the effect of the polymer electrolyte cation spacing on hydroxide diffusion pathways from a molecular perspective. By exploring cation ESP energy surfaces and validating outcomes through prior ab initio molecular dynamics simulations of nanoconfined AEMs, we find that we can achieve control over preferred hydroxide diffusion pathways by adjusting the cation spacing. The results presented in this work provide a unique and straightforward approach to predict preferential hydroxide diffusion pathways, enabling efficient design of highly conductive nanoconfined AEM materials for electrochemical technologies.
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Affiliation(s)
- Tamar Zelovich
- Department
of Chemistry, New York University (NYU), New York, New York 10003, United States
| | - Dario R. Dekel
- Wolfson
Department of Chemical Engineering, Technion
− Israel Institute of Technology, Haifa, 3200003, Israel
- Nancy
& Stephen Grand Technion Energy Program, Technion − Israel Institute of Technology, Haifa, 3200003, Israel
| | - Mark E. Tuckerman
- Department
of Chemistry, New York University (NYU), New York, New York 10003, United States
- Courant
Institute of Mathematical Sciences, New
York University (NYU), New York, New York 10012, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Rd. North, Shanghai 200062, China
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5
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Long Z, Tuckerman ME. Hydroxide Diffusion in Functionalized Cylindrical Nanopores as Idealized Models of Anion Exchange Membrane Environments: An Ab Initio Molecular Dynamics Study. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:2792-2804. [PMID: 36968146 PMCID: PMC10034739 DOI: 10.1021/acs.jpcc.2c05747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Anion exchange membranes (AEMs) have attracted significant interest for their applications in fuel cells and other electrochemical devices in recent years. Understanding water distributions and hydroxide transport mechanisms within AEMs is critical to improving their performance as concerns hydroxide conductivity. Recently, nanoconfined environments have been used to mimic AEM environments. Following this approach, we construct nanoconfined cylindrical pore structures using graphane nanotubes (GNs) functionalized with trimethylammonium cations as models of local AEM morphology. These structures were then used to investigate hydroxide transport using ab initio molecular dynamics (AIMD). The simulations showed that hydroxide transport is suppressed in these confined environments relative to the bulk solution although the mechanism is dominated by structural diffusion. One factor causing the suppressed hydroxide transport is the reduced proton transfer (PT) rates due to changes in hydroxide and water solvation patterns under confinement compared to bulk solution as well as strong interactions between hydroxide ions and the tethered cation groups.
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Affiliation(s)
- Zhuoran Long
- Department
of Chemistry, New York University, New York, New York10003, United States
| | - Mark E. Tuckerman
- Department
of Chemistry, New York University, New York, New York10003, United States
- Courant
Institute of Mathematical Science, New York
University, New York, New York10012, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai200062, China
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6
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Nachaki EO, Leonik FM, Kuroda DG. Effect of the N-Alkyl Side Chain on the Amide-Water Interactions. J Phys Chem B 2022; 126:8290-8299. [PMID: 36219826 DOI: 10.1021/acs.jpcb.2c04988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amide-water interactions influence the structure and functions of amide-based systems, such as proteins and homopolymers. In particular, the N-alkylation of the amide unit appears to play a critical role in defining the interactions of the amide group. Previous studies have linked the thermal behavior of amide-based polymers to the nature of their N-alkyl side chain. However, the connection between the chemical structure of the N-alkyl and the hydration of the amide remains elusive. In this study, the solvation structure and dynamics of amides, having differing N-alkyl groups, are investigated using a combination of linear and nonlinear infrared spectroscopies and computational methods. Interestingly, the dynamics of the amide local environment do not slow down as the N-alkyl side chain becomes bulkier, but rather speeds up. Computational calculations confirm the hydration dynamics and assign the effect to smaller amplitude and faster rotations of the bulkier group. It is also observed experimentally that the hydrogen-bond making and breaking between water and the amide carbonyl do not directly relate to the size of the N-alkyl side chain. The bulkier N-isopropyl substituent presents significantly slower chemical exchange dynamics than smaller chains (ethyl and methyl), but the two small groups do not present a major difference. The hydrogen-bond making and breaking disparities and similarities among groups are well modeled by the theory demonstrating that the N-alkyl group affects the amide hydration structure and dynamics via a steric effect. In summary, the results presented here show that the size of the N-substituted alkyl group significantly influences the hydration dynamics of amides and stress the importance of considering this effect on much larger systems, such as polymers.
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Affiliation(s)
- Ernest O Nachaki
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Fedra M Leonik
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
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7
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Jung KA, Markland TE. 2D spectroscopies from condensed phase dynamics: Accessing third-order response properties from equilibrium multi-time correlation functions. J Chem Phys 2022; 157:094111. [DOI: 10.1063/5.0107087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopies provides access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, Centroid Molecular Dynamics (CMD) and Ring Polymer Molecular Dynamics (RPMD) naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.
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8
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Biswas A, Mallik BS. Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations. J Phys Chem A 2022; 126:5134-5147. [PMID: 35900106 DOI: 10.1021/acs.jpca.2c03387] [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
We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
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9
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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10
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Herrero C, Pauletti M, Tocci G, Iannuzzi M, Joly L. Connection between water's dynamical and structural properties: Insights from ab initio simulations. Proc Natl Acad Sci U S A 2022; 119:e2121641119. [PMID: 35588447 PMCID: PMC9173753 DOI: 10.1073/pnas.2121641119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/12/2022] [Indexed: 01/25/2023] Open
Abstract
SignificanceFirst-principles calculations, which explicitly account for the electronic structure of matter, can shed light on the molecular structure and dynamics of water in its supercooled state. In this work, we use density functional theory, which relies on a functional to describe electronic exchange and correlations, to evaluate which functional best describes the temperature evolution of bulk water transport coefficients. We also assess the validity of the Stokes-Einstein relation for all the functionals in the temperature range studied, and explore the link between structure and dynamics. Based on these results, we show how transport coefficients can be computed from structural descriptors, which require shorter simulation times to converge, and we point toward strategies to develop better functionals.
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Affiliation(s)
- Cecilia Herrero
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Michela Pauletti
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland
| | - Gabriele Tocci
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland
| | - Marcella Iannuzzi
- Department of Chemistry, Universität Zürich, 8057 Zürich, Switzerland
| | - Laurent Joly
- Univ Lyon, Univ Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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11
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Yang Y, Peltier CR, Zeng R, Schimmenti R, Li Q, Huang X, Yan Z, Potsi G, Selhorst R, Lu X, Xu W, Tader M, Soudackov AV, Zhang H, Krumov M, Murray E, Xu P, Hitt J, Xu L, Ko HY, Ernst BG, Bundschu C, Luo A, Markovich D, Hu M, He C, Wang H, Fang J, DiStasio RA, Kourkoutis LF, Singer A, Noonan KJT, Xiao L, Zhuang L, Pivovar BS, Zelenay P, Herrero E, Feliu JM, Suntivich J, Giannelis EP, Hammes-Schiffer S, Arias T, Mavrikakis M, Mallouk TE, Brock JD, Muller DA, DiSalvo FJ, Coates GW, Abruña HD. Electrocatalysis in Alkaline Media and Alkaline Membrane-Based Energy Technologies. Chem Rev 2022; 122:6117-6321. [PMID: 35133808 DOI: 10.1021/acs.chemrev.1c00331] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly alkaline fuel cells and water electrolyzers. Anion exchange (alkaline) membrane fuel cells (AEMFCs) enable the use of nonprecious electrocatalysts for the sluggish oxygen reduction reaction (ORR), relative to proton exchange membrane fuel cells (PEMFCs), which require Pt-based electrocatalysts. However, the hydrogen oxidation reaction (HOR) kinetics is significantly slower in alkaline media than in acidic media. Understanding these phenomena requires applying theoretical and experimental methods to unravel molecular-level thermodynamics and kinetics of hydrogen and oxygen electrocatalysis and, particularly, the proton-coupled electron transfer (PCET) process that takes place in a proton-deficient alkaline media. Extensive electrochemical and spectroscopic studies, on single-crystal Pt and metal oxides, have contributed to the development of activity descriptors, as well as the identification of the nature of active sites, and the rate-determining steps of the HOR and ORR. Among these, the structure and reactivity of interfacial water serve as key potential and pH-dependent kinetic factors that are helping elucidate the origins of the HOR and ORR activity differences in acids and bases. Additionally, deliberately modulating and controlling catalyst-support interactions have provided valuable insights for enhancing catalyst accessibility and durability during operation. The design and synthesis of highly conductive and durable alkaline membranes/ionomers have enabled AEMFCs to reach initial performance metrics equal to or higher than those of PEMFCs. We emphasize the importance of using membrane electrode assemblies (MEAs) to integrate the often separately pursued/optimized electrocatalyst/support and membranes/ionomer components. Operando/in situ methods, at multiscales, and ab initio simulations provide a mechanistic understanding of electron, ion, and mass transport at catalyst/ionomer/membrane interfaces and the necessary guidance to achieve fuel cell operation in air over thousands of hours. We hope that this Review will serve as a roadmap for advancing the scientific understanding of the fundamental factors governing electrochemical energy conversion in alkaline media with the ultimate goal of achieving ultralow Pt or precious-metal-free high-performance and durable alkaline fuel cells and related technologies.
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Affiliation(s)
- Yao Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Cheyenne R Peltier
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rui Zeng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Roberto Schimmenti
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Qihao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Huang
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Zhifei Yan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Georgia Potsi
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ryan Selhorst
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xinyao Lu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Weixuan Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mariel Tader
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Hanguang Zhang
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mihail Krumov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ellen Murray
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Pengtao Xu
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy Hitt
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Linxi Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Colin Bundschu
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Aileen Luo
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Danielle Markovich
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Meixue Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Cheng He
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Hongsen Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jiye Fang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Lena F Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Andrej Singer
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kevin J T Noonan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Li Xiao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Lin Zhuang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Bryan S Pivovar
- Chemical and Materials Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Piotr Zelenay
- Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique Herrero
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Juan M Feliu
- Instituto de Electroquímica, Universidad de Alicante, Alicante E-03080, Spain
| | - Jin Suntivich
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Emmanuel P Giannelis
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | | | - Tomás Arias
- Department of Physics, Cornell University, Ithaca, New York 14853, United States
| | - Manos Mavrikakis
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas E Mallouk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Joel D Brock
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - David A Muller
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
| | - Francis J DiSalvo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Geoffrey W Coates
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Héctor D Abruña
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Center for Alkaline Based Energy Solutions (CABES), Cornell University, Ithaca, New York 14853, United States
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12
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Computer simulation study of ion-water and water-water hydrogen bonds in sulfuric acid solutions at low temperatures. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Das B, Chandra A. Ab Initio Molecular Dynamics Study of Aqueous Solutions of Magnesium and Calcium Nitrates: Hydration Shell Structure, Dynamics and Vibrational Echo Spectroscopy. J Phys Chem B 2022; 126:528-544. [PMID: 35001626 DOI: 10.1021/acs.jpcb.1c08545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio molecular dynamics simulations are performed to study the hydration shell structure, dynamics, and vibrational echo spectroscopy of aqueous Mg(NO3)2 and Ca(NO3)2 solutions. The hydration shell structure is probed through calculations of various ion-ion and ion-water radial and spatial distribution functions. On the dynamical side, calculations have been made for the hydrogen bond dynamics of hydration shells and also residence dynamics and lifetimes of water in different solvation environments. Subsequently, we looked at the dynamics of frequency fluctuations of OD modes of heavy water in different hydration environments. Specifically, the temporal decay of spectral observables of two-dimensional infrared (2DIR) spectroscopy, three pulse echo peak shift (3PEPS) measurements and also of time correlations of frequency fluctuations are calculated to investigate the dynamics of vibrational spectral diffusion of water in different hydration environments in these solutions. The OD stretch frequencies of water molecules in the vicinity of both divalent cations are found to be red-shifted and also fluctuating at a slower rate than other water molecules present in the solutions. The Mg2+ ions are found to be strongly hydrated which can be linked to their lower tendency to form contact ion-pairs and essentially no water exchange between the cationic hydration shells and bulk during the time scale of the current simulations. The stronger hydration of Mg2+ ions make their hydration shells structurally and dynamically more rigid and make the dynamics of hydrogen bonds and vibrational spectral diffusion, as revealed through spectral observables of 2DIR and 3PEPS slower than that for the Ca2+ ions. The structural and spectral dynamics of water molecules outside the cationic solvation shells in the Mg(NO3)2 solution are also found to be relatively slower than that of the Ca(NO3)2 solution and pure water which show the effects of stronger electric fields of Mg2+ ions extending beyond their first hydration shells. Also, water molecules in the hydration shells of the NO3- ions are found to relax at a slower rate in the Mg(NO3)2 solution which manifests the effect countercations have on anionic hydration shells for divalent metal nitrate solutions.
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Affiliation(s)
- Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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14
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Priyadarsini A, Mallik BS. Amphiphilicity of Intricate Layered Graphene/g-C 3N 4 Nanosheets. J Phys Chem B 2021; 125:11697-11708. [PMID: 34664957 DOI: 10.1021/acs.jpcb.1c05609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hybrid heterostructure of the tri-s-triazine form of graphitic carbon nitride (g-C3N4), a stable two-dimensional material, results from intricate layer formation with graphene. In this material, g-C3N4, an amphiphilic material, stabilizes Pickering emulsions as an emulsifier and can effectively disperse graphene. Due to the various technological applications of the hybrid nanosheets in an aqueous environment, it is essential to study the interaction of water molecules with graphene and g-C3N4 (Gr/g-C3N4)-combined heterostructure. Although few studies have been performed signifying the water orientation in the interfacial layer, we find that there is a lack of detailed studies using various dynamical and structural properties of the interfacial water molecules. The interface of the Gr/g-C3N4 hybrid structure, one of the rarely found amphiphilic interfaces (on the g-C3N3 side), is appropriate for exploring the water affinity due to the availability of heterogeneous interfacial aqueous interactions. We adopted classical molecular dynamics simulations using two models for water molecules to study the structure and dynamics of an aqueous interface. We have correlated the structural properties to dynamics and spectral properties to understand the overall behavior of the amphiphilic interface. Our results branch into two significant hydrogen bond (HB) properties in HB count and HB strength among the water molecules in the different layers. The HB counts in the different layers of water are correlated using the average distance distribution (PrO4), tetrahedral order parameters, HB donor/acceptor count, and total HBs per water molecule. A conspicuous difference is found in the HB count and related dynamics of the system. The HB lifetime and diffusion coefficient hint at the equivalent strength of HBs in the different layers. All the findings conclude that the amphiphilicity of the Gr/g-C3N4 interface can help in understanding various interfacial physical and chemical processes.
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Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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15
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Batista PR, Penna TC, Ducati LC, Correra TC. p-Aminobenzoic acid protonation dynamics in an evaporating droplet by ab initio molecular dynamics. Phys Chem Chem Phys 2021; 23:19659-19672. [PMID: 34524295 DOI: 10.1039/d1cp01495a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protonation equilibria are known to vary from the bulk to microdroplet conditions, which could induce many chemical and physical phenomena. Protonated p-aminobenzoic acid (PABA + H+) can be considered a model for probing the protonation dynamics in an evaporating droplet, as its protonation equilibrium is highly dependent on the formation conditions from solution via atmospheric pressure ionization sources. Experiments using diverse experimental techniques have shown that protic solvents allow formation of the O-protomer (PABA protonated in the carboxylic acid group) stable in the gas phase, while aprotic solvents yield the N-protomer (protonated in the amino group) that is the most stable protomer in solution. In this work, we explore the protonation equilibrium of PABA solvated by different numbers of water molecules (n = 0 to 32) using ab initio molecular dynamics. For n = 8-32, the protonation is either at the NH2 group or in the solvent network. The solvent network interacts with the carboxylic acid group, but there is no complete proton transfer to form the O-protomer. For smaller clusters, however, solvent-mediated proton transfers to the carboxylic acid were observed, both via the Grotthuss mechanism and the vehicle or shuttle mechanism (for n = 1 and 2). Thermodynamic considerations allowed a description of the origins of the kinetic trapping effect, which explains the observation of the solution structure in the gas phase. This effect likely occurs in the final evaporation steps, which are outside the droplet size range covered by previous classical molecular dynamics simulations of charged droplets. These results may be considered relevant in determining the nature of the species observed in the ubiquitous ESI based mass spectrometry analysis, and in general for droplet chemistry, explaining how protonation equilibria are drastically changed from bulk to microdroplet conditions.
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Affiliation(s)
- Patrick R Batista
- Department of Fundamental Chemistry, Institute of Chemistry - University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, Brazil.
| | - Tatiana C Penna
- Department of Fundamental Chemistry, Institute of Chemistry - University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, Brazil.
| | - Lucas C Ducati
- Department of Fundamental Chemistry, Institute of Chemistry - University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, Brazil.
| | - Thiago C Correra
- Department of Fundamental Chemistry, Institute of Chemistry - University of São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, Brazil.
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16
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Yao Y, Kanai Y. Nuclear Quantum Effect and Its Temperature Dependence in Liquid Water from Random Phase Approximation via Artificial Neural Network. J Phys Chem Lett 2021; 12:6354-6362. [PMID: 34231366 DOI: 10.1021/acs.jpclett.1c01566] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report structural and dynamical properties of liquid water described by the random phase approximation (RPA) correlation together with the exact exchange energy (EXX) within density functional theory. By utilizing thermostated ring polymer molecular dynamics, we examine the nuclear quantum effects and their temperature dependence. We circumvent the computational limitation of performing direct first-principles molecular dynamics simulation at this high level of electronic structure theory by adapting an artificial neural network model. We show that the EXX+RPA level of theory accurately describes liquid water in terms of both dynamical and structural properties.
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Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Durham, North Carolina 27599, United States
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17
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Biswas A, Mallik BS. Dynamics of Ionic Liquid through Intrinsic Vibrational Probes Using the Dispersion-Corrected DFT Functionals. J Phys Chem B 2021; 125:6994-7008. [PMID: 34142827 DOI: 10.1021/acs.jpcb.1c04960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
First principles molecular dynamics simulations have been utilized to study the spectral properties of the protic ionic liquid, methylammonium formate (MAF). All simulations were performed using density functional theory (DFT) and various van der Waals-corrected exchange-correlation functionals. We calculated the vibrational stretch frequency distributions, determined the time-frequency correlations of the intrinsic vibrational probes, the N-H and C-O modes in MAF, and the frequency-structure correlations. We also estimated the average hydrogen-bond lifetimes and orientation dynamics to capture the ultrafast spectral response. The spectroscopic signature of the N-H stretching vibrations using the Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals displays a spectral shift in the lower frequency side, suggesting stronger hydrogen-bonding interactions represented by the gradient approximation functionals than the van der Waals (vdW)-corrected simulations. The carboxylate frequency profiles with the dispersion-corrected representations are almost similar without a significant difference in the normalized distributions. Besides, the COO stretching frequencies at the peak maxima positions of the PBE functionals exhibit a lesser deviation from the experimental data. Spectral diffusion dynamics of the intrinsic vibrational probes on the cationic and anionic sites of the ionic liquid proceed through a short time relaxation of the intact hydrogen bonds followed by an intermediate time constant and a longer time decay indicating the switchover of hydrogen bonds. Dispersion-corrected atom-centered one-electron potential (DCACP) correction added to the BLYP system slows down the picosecond time scales of frequency correlation and the time constants of rotational motion, lengthening the overall system dynamics. The observed trends in the time-dependent decays of frequency fluctuations and the orientation autocorrelation functions correlate with the structural interactions in liquid MAF and hydrogen-bond dynamics. In this study, we examine the predictions made by different density functional treatments comparing the results of the uncorrected BLYP and PBE representations with the semiempirical vdW methods of Grimme and matching our calculated data with the experimental observations.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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18
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Batista PR, Ducati LC, Autschbach J. Solvent effect on the 195Pt NMR properties in pyridonate-bridged Pt III dinuclear complex derivatives investigated by ab initio molecular dynamics and localized orbital analysis. Phys Chem Chem Phys 2021; 23:12864-12880. [PMID: 34075921 DOI: 10.1039/d0cp05849a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ab initio molecular dynamics investigation of the solvent effect (water) on the structural parameters, 195Pt NMR spin-spin coupling constants (SSCCs) and chemical shifts of a series of pyridonate-bridged PtIII dinuclear complexes is performed using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations. The indirect solvent effect (via structural changes) has a dramatic effect on the 1JPtPt SSCCs. The complexes exhibit a strong trans influence in solution, where the Pt-Pt bond lengthens with increasing axial ligand σ-donor strength. In the diaqua complex, where the solvent effect is more pronounced, the SSCCs averaged for CPMD configurations with explicit plus implicit solvation agree much better with the experimental data, while the calculations for static geometry and CPMD unsolvated configurations show large deviations with respect to experiment. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of 1JPtPt and 195Pt chemical shifts. An analysis of 1JPtPt in terms of localized and canonical orbitals shows that the SSCCs are driven by changes in the s-character of the natural atomic orbitals of Pt atoms, which affect the 'Fermi contact' mechanism.
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Affiliation(s)
- Patrick R Batista
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil.
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19
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Zelovich T, Tuckerman ME. OH - and H 3O + Diffusion in Model AEMs and PEMs at Low Hydration: Insights from Ab Initio Molecular Dynamics. MEMBRANES 2021; 11:355. [PMID: 34066142 PMCID: PMC8151131 DOI: 10.3390/membranes11050355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/25/2021] [Accepted: 05/06/2021] [Indexed: 11/27/2022]
Abstract
Fuel cell-based anion-exchange membranes (AEMs) and proton exchange membranes (PEMs) are considered to have great potential as cost-effective, clean energy conversion devices. However, a fundamental atomistic understanding of the hydroxide and hydronium diffusion mechanisms in the AEM and PEM environment is an ongoing challenge. In this work, we aim to identify the fundamental atomistic steps governing hydroxide and hydronium transport phenomena. The motivation of this work lies in the fact that elucidating the key design differences between the hydroxide and hydronium diffusion mechanisms will play an important role in the discovery and determination of key design principles for the synthesis of new membrane materials with high ion conductivity for use in emerging fuel cell technologies. To this end, ab initio molecular dynamics simulations are presented to explore hydroxide and hydronium ion solvation complexes and diffusion mechanisms in the model AEM and PEM systems at low hydration in confined environments. We find that hydroxide diffusion in AEMs is mostly vehicular, while hydronium diffusion in model PEMs is structural. Furthermore, we find that the region between each pair of cations in AEMs creates a bottleneck for hydroxide diffusion, leading to a suppression of diffusivity, while the anions in PEMs become active participants in the hydronium diffusion, suggesting that the presence of the anions in model PEMs could potentially promote hydronium diffusion.
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Affiliation(s)
- Tamar Zelovich
- Department of Chemistry, New York University (NYU), New York 10003, NY, USA
| | - Mark E. Tuckerman
- Department of Chemistry, New York University (NYU), New York 10003, NY, USA
- Courant Institute of Mathematical Sciences, New York University (NYU), New York, NY 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Rd. North, Shanghai 200062, China
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20
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Yue S, Muniz MC, Calegari Andrade MF, Zhang L, Car R, Panagiotopoulos AZ. When do short-range atomistic machine-learning models fall short? J Chem Phys 2021; 154:034111. [DOI: 10.1063/5.0031215] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Shuwen Yue
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Maria Carolina Muniz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | | | - Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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21
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Han B, Isborn CM, Shi L. Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models. J Chem Theory Comput 2021; 17:889-901. [PMID: 33405925 DOI: 10.1021/acs.jctc.0c01102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.
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Affiliation(s)
- Bowen Han
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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22
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Li M, Chen L, Gui L, Cao S, Liu D, Zhao G, Ding M, Yan J, Wang D. Born–Oppenheimer molecular dynamics simulations on structures of high-density and low-density water: a comparison of the SCAN meta-GGA and PBE GGA functionals. Phys Chem Chem Phys 2021; 23:2298-2304. [DOI: 10.1039/d0cp05707j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using Born–Oppenheimer ab initio molecular dynamics (BOAIMD) simulations, the high-density water (HDW) and low-density water (LDW) structures based on SCAN meta-GGA are compared with those based on PBE GGA.
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Affiliation(s)
- Mengli Li
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Lu Chen
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Lirong Gui
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Shuo Cao
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Di Liu
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Gang Zhao
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Mingcui Ding
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Jinliang Yan
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
| | - Dehua Wang
- School of Physics and Optoelectronic Engineering
- Ludong University
- Yantai 264025
- P. R. China
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23
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Biswas A, Mallik BS. Ultrafast Aqueous Dynamics in Concentrated Electrolytic Solutions of Lithium Salt and Ionic Liquid. J Phys Chem B 2020; 124:9898-9912. [DOI: 10.1021/acs.jpcb.0c06221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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24
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Song J, Wang L, Zhang L, Wu W, Gao Z. First-principles molecular dynamics studying the solidification of Ti-6Al-4V alloy. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Yadav S, Chandra A. Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study. J Phys Chem B 2020; 124:7194-7204. [PMID: 32706258 DOI: 10.1021/acs.jpcb.0c02221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed ab initio molecular dynamics simulation of a nitrite ion in water to investigate the structural and dynamical properties of its hydration shell. The nitrite ion is found to exhibit strong asymmetry toward hydrogen bonding due to its two different types of hydrogen bond acceptor sites. This difference is better captured through further partitioning of the hydration shell into its proximal and distal regions. The frequency shifts of the stretch modes of hydration shell water reveal that the nitrogen site forms a stronger hydrogen bond than its oxygen sites with the latter forming hydrogen bonds, which are similar in strength to that between a pair of water molecules. The escape dynamics of water from the hydration shell is found to be rather slow, which seems to classify the nitrite ion as a structure-maker. However, the dynamics of orientational and hydrogen bond relaxation reveal a faster mobility of water molecules in the hydration shell than bulk water in spite of strong ion-water interactions. It is found that the nitrite ion can hold water molecules in its solvation shell and still make them rotate fast in its vicinity through switching of their hydrogen bonds between its nitrogen and oxygen acceptor sites. The dipole moment of the solute in water is also calculated in the present study.
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Affiliation(s)
- Sushma Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
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26
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Yao Y, Kanai Y. Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional. J Chem Phys 2020; 153:044114. [DOI: 10.1063/5.0012815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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27
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Priyadarsini A, Dasari S, Mallik BS. Thermophysical Properties and Angular Jump Dynamics of Water: A Comparative DFT and DFT-Dispersion-Based Molecular Dynamics Study. J Phys Chem A 2020; 124:6039-6049. [DOI: 10.1021/acs.jpca.0c02909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi 502285, Sangareddy, Telangana, India
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28
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Tang F, Ohto T, Sun S, Rouxel JR, Imoto S, Backus EHG, Mukamel S, Bonn M, Nagata Y. Molecular Structure and Modeling of Water-Air and Ice-Air Interfaces Monitored by Sum-Frequency Generation. Chem Rev 2020; 120:3633-3667. [PMID: 32141737 PMCID: PMC7181271 DOI: 10.1021/acs.chemrev.9b00512] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Indexed: 12/26/2022]
Abstract
From a glass of water to glaciers in Antarctica, water-air and ice-air interfaces are abundant on Earth. Molecular-level structure and dynamics at these interfaces are key for understanding many chemical/physical/atmospheric processes including the slipperiness of ice surfaces, the surface tension of water, and evaporation/sublimation of water. Sum-frequency generation (SFG) spectroscopy is a powerful tool to probe the molecular-level structure of these interfaces because SFG can specifically probe the topmost interfacial water molecules separately from the bulk and is sensitive to molecular conformation. Nevertheless, experimental SFG has several limitations. For example, SFG cannot provide information on the depth of the interface and how the orientation of the molecules varies with distance from the surface. By combining the SFG spectroscopy with simulation techniques, one can directly compare the experimental data with the simulated SFG spectra, allowing us to unveil the molecular-level structure of water-air and ice-air interfaces. Here, we present an overview of the different simulation protocols available for SFG spectra calculations. We systematically compare the SFG spectra computed with different approaches, revealing the advantages and disadvantages of the different methods. Furthermore, we account for the findings through combined SFG experiments and simulations and provide future challenges for SFG experiments and simulations at different aqueous interfaces.
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Affiliation(s)
- Fujie Tang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shumei Sun
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physical Chemistry, University of Vienna, Währinger Strasse 42, 1090 Vienna, Austria
| | - Jérémy R. Rouxel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Sho Imoto
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Ellen H. G. Backus
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physical Chemistry, University of Vienna, Währinger Strasse 42, 1090 Vienna, Austria
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Physics, State Key Laboratory of Surface Physics and Key Laboratory
of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
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29
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Roy VP, Kubarych KJ. A simple lattice Monte Carlo simulation to model interfacial and crowded water rearrangements. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Biswas A, Mallik BS. Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112524] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Biswas A, Mallik BS. Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell. RSC Adv 2020. [DOI: 10.1039/c9ra10521b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
| | - Bhabani S. Mallik
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
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32
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Zhong K, Yu CC, Dodia M, Bonn M, Nagata Y, Ohto T. Vibrational mode frequency correction of liquid water in density functional theory molecular dynamics simulations with van der Waals correction. Phys Chem Chem Phys 2020; 22:12785-12793. [DOI: 10.1039/c9cp06335h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We develop a frequency correction scheme for the stretch and bending modes of liquid water, which substantially improves the prediction of the vibrational spectra.
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Affiliation(s)
- Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Center for Excellence in Nanoscience
- School of Chemistry and Materials Science
- University of Science and Technology of China
| | - Chun-Chieh Yu
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Mayank Dodia
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research
- Ackermannweg 10
- 55128 Mainz
- Germany
| | - Tatsuhiko Ohto
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
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33
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Liu X, Cheng K, Jia G. Investigation of nonlinear dielectric response of DMSO-methanol mixture by molecular dynamics simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Bakó I, Daru J, Pothoczki S, Pusztai L, Hermansson K. Effects of H-bond asymmetry on the electronic properties of liquid water – An AIMD analysis. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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35
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36
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Biswas A, Priyadarsini A, Mallik BS. Dynamics and Spectral Response of Water Molecules around Tetramethylammonium Cation. J Phys Chem B 2019; 123:8753-8766. [DOI: 10.1021/acs.jpcb.9b05466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
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37
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Pothoczki S, Pusztai L, Bakó I. Molecular Dynamics Simulation Studies of the Temperature-Dependent Structure and Dynamics of Isopropanol–Water Liquid Mixtures at Low Alcohol Content. J Phys Chem B 2019; 123:7599-7610. [DOI: 10.1021/acs.jpcb.9b05631] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Szilvia Pothoczki
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly-Thege M. út 29-33, H-1121 Budapest, Hungary
| | - László Pusztai
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly-Thege M. út 29-33, H-1121 Budapest, Hungary
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Imre Bakó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
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38
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Philips A, Autschbach J. Proton NMR relaxation from molecular dynamics: intramolecular and intermolecular contributions in water and acetonitrile. Phys Chem Chem Phys 2019; 21:26621-26629. [DOI: 10.1039/c9cp04976b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accurate 1H NMR relaxation rates for protons in pure water and acetonitrile are computed via ab initio and force field molecular dynamics. Dipole–dipole and spin-rotation mechanisms are considered.
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Affiliation(s)
- Adam Philips
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
| | - Jochen Autschbach
- Department of Chemistry
- University at Buffalo
- State University of New York
- Buffalo
- USA
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39
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McDonnell MT, Keffer DJ. Reactive molecular dynamics simulations of an excess proton in polyethylene glycol-water solutions. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1557328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - David J. Keffer
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN, USA
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40
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Liu J, Zhang JZH, He X. Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab Initio Molecular Dynamics. J Phys Chem B 2018; 122:10202-10209. [PMID: 30351119 DOI: 10.1021/acs.jpcb.8b09513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ion-specific effects at the water/air interface represent a fundamentally essential topic of research, and high-level ab initio simulations are still demanding to reveal the microscopic picture of the interactions between ions and water at the solvation interface. In this work, we present a fragment-based ab initio molecular dynamics (AIMD) simulation of sodium halide solution droplet (in a neutral mixture of Na+, F-, Cl-, and Br- ions) at the MP2/aug-cc-pVDZ level. We show that the studied halide ions exhibit surface preference in the order (F- < Cl- < Br-) which is in accordance with the experimental observation. The resulting potential of mean force (PMF) for Br- produces a distinct minimum at the water/air interface, while the minimum of the PMF for F- appears in the bulk region. The ion-pairing interactions between halide anions and Na+ cations are characterized, and it reveals that the specific solvent-separated ion pairs (SIPs) are more preferred than the direct contact ion pairs (CIPs). The transition between different types of SIPs is observed. Other structural and dynamical properties of ions and ion-hydration shells are investigated. These results provide broader and new physical insights for understanding the ion-specific behavior in interfacial solvation at the atomistic level.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China.,Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
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41
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König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules 2018; 23:E2695. [PMID: 30347691 PMCID: PMC6222909 DOI: 10.3390/molecules23102695] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/01/2022] Open
Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Hangzhou 310024, China.
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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42
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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43
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Shi Y, Scheiber H, Khaliullin RZ. Contribution of the Covalent Component of the Hydrogen-Bond Network to the Properties of Liquid Water. J Phys Chem A 2018; 122:7482-7490. [PMID: 30157633 DOI: 10.1021/acs.jpca.8b06857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yifei Shi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A0B8, Canada
| | - Hayden Scheiber
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A0B8, Canada
| | - Rustam Z. Khaliullin
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A0B8, Canada
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44
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Zhou M, Cheng K, Sun H, Jia G. Investigation of Nonlinear Output-Input Microwave Power of DMSO-Ethanol Mixture by Molecular Dynamics Simulation. Sci Rep 2018; 8:7186. [PMID: 29739957 PMCID: PMC5940686 DOI: 10.1038/s41598-018-21846-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/06/2018] [Indexed: 11/14/2022] Open
Abstract
The nonlinear response of output-input microwave power for DMSO-ethanol mixture, which was exhibited as the direct evidence of non-thermal effect in experiment, was investigated by molecular dynamics simulation. Effects of microwave field on the mixture were evaluated from the alteration in structure, transport, hydrogen bonding dynamics and intermolecular interaction energy. Increasing the strength of the microwave field did not lead to any markedly conformational change, but decrease the diffusion coefficient. Prolonged hydrogen bonding lifetimes, which caused by the redistribution of microwave energy, was also detected. Distinct threshold effect was observed, which was consistent with the behavior in the experiment.
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Affiliation(s)
- Min Zhou
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, 610101, China
| | - Ke Cheng
- College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu, 610103, China
| | - Haoran Sun
- College of Optoelectronic Technology, Chengdu University of Information Technology, Chengdu, 610103, China
| | - Guozhu Jia
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, 610101, China.
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45
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Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T. Advanced Potential Energy Surfaces for Molecular Simulation. J Phys Chem B 2018; 120:9811-32. [PMID: 27513316 DOI: 10.1021/acs.jpcb.6b06414] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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Affiliation(s)
| | - Henry A Boateng
- Department of Mathematics, Bates College , 2 Andrews Road, Lewiston, Maine 04240, United States
| | - Richard T Bradshaw
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.,Faculty of Applied Physics and Mathematics, Gdansk University of Technology , 80-223 Gdansk, Poland
| | | | | | - Jason Swails
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States
| | - Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States
| | - Peter Eastman
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Lee-Ping Wang
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Jonathan W Essex
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ilian T Todorov
- STFC Daresbury Laboratory , Keckwick Lane, Daresbury, Warrington WA4 4AD, United Kingdom
| | - Mark E Tuckerman
- NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai , Shanghai 200062, China
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46
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Śmiechowski M. Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water. J Phys Chem B 2018. [PMID: 29513989 DOI: 10.1021/acs.jpcb.7b11334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques can extract important information from the computed IR spectra of aqueous solutions of BF4- and PF6-, interesting weakly coordinating anions that have been known for a long time to alter the IR spectrum of water in an unusual manner. The distance-dependent spectra of both ions are analyzed using the spectral similarity method that provides a quantitative picture of both the spectrum of the solute-affected solvent and the number of solvent molecules thus altered. We find, in accordance with previous experiments, a considerable blue shift of the νOH stretching band of liquid water by 264 cm-1 for BF4- and 306 cm-1 for PF6-, with the affected numbers being 3.7 and 4.2, respectively. Considering also the additional information on solute-solvent dipolar couplings delivered by radially and spatially resolved IR spectra, the computational IR spectroscopy based on AIMD simulations is shown to be a viable predictive tool with strong interpretative power.
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Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty , Gdańsk University of Technology , Narutowicza 11/12 , 80-233 Gdańsk , Poland
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47
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Machida M, Kato K, Shiga M. Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations. J Chem Phys 2018; 148:102324. [DOI: 10.1063/1.5000091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Masahiko Machida
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Koichiro Kato
- Mizuho Information and Research Institute, Inc., 2-3, Kandanishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency (JAEA), 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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48
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Liu J, He X, Zhang JZH, Qi LW. Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory. Chem Sci 2018; 9:2065-2073. [PMID: 29675248 PMCID: PMC5885775 DOI: 10.1039/c7sc04205a] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
An accurate and efficient ab initio molecular dynamics (AIMD) simulation of liquid water was made possible using the fragment-based approach (J. F. Liu, X. He and J. Z. H. Zhang, Phys. Chem. Chem. Phys., 2017, 19, 11931-11936). In this study, we advance the AIMD simulations using the fragment-based coupled cluster (CC) theory, more accurately revealing the structural and dynamical properties of liquid water under ambient conditions. The results show that the double-donor hydrogen-bond configurations in liquid water are nearly in balance with the single-donor configurations, with a slight bias towards the former. Our observation is in contrast to the traditional tetrahedral water structure. The hydrogen-bond switching dynamics in liquid water are very fast, with a hydrogen-bond life time of around 0.78 picoseconds, determined using AIMD simulation at the CCD/aug-cc-pVDZ level. This time scale is remarkably shorter than the ∼3.0 picoseconds that is commonly obtained from traditional nonpolarized force fields and density functional theory (DFT) based first-principles simulations. Additionally, the obtained radial distribution functions, triplet oxygen angular distribution, diffusion coefficient, and the dipole moment of the water molecule are uniformly in good agreement with the experimental observations. The current high-level AIMD simulation sheds light on the understanding of the structural and dynamical properties of liquid water.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
| | - Xiao He
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
| | - John Z H Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry , NYU Shanghai , Shanghai , 200062 , China
- Department of Chemistry , New York University , New York , NY 10003 , USA
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines , Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing , 210009 , China .
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Sharma B, Chandra A. Born-Oppenheimer Molecular Dynamics Simulations of a Bromate Ion in Water Reveal Its Dual Kosmotropic and Chaotropic Behavior. J Phys Chem B 2018; 122:2090-2101. [PMID: 29376361 DOI: 10.1021/acs.jpcb.7b09300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvation structure and dynamics of a bromate (BrO3-) ion in water are studied by means of Born-Oppenheimer molecular dynamics simulations at two different temperatures using the Becke-Lee-Yang-Parr functional with Grimme D3 dispersion corrections. The bromate ion possesses a pyramidal structure, and it has two types of solvation sites, namely, the bromine and oxygen atoms. We have looked at different radial and orientational distributions of water molecules around the bromate ion and also investigated their hydrogen bonding properties. The solvation structure of the bromate ion is also compared with that of the iodate (IO3-) ion, which is structurally rather similar to the bromate ion and was found to have some unusual solvation properties in water. It is found that the bromate ion follows a similar trend as that followed by the iodate ion as far as the solvation structure is concerned. However, the effect of the former on surrounding water is found to be much weaker than that of the latter. On the dynamical side, we have looked at diffusion, residence dynamics, and also the orientational and hydrogen bond relaxation of water molecules around the BrO3- ion and compared them with those of the bulk. Dynamical results are presented for both H2O and D2O around the BrO3- ion. Interpretation of the dynamical results in terms of structure-making (kosmotropic)/-breaking (chaotropic) properties of the BrO3- ion reveals that the bromine atom of this ion acts as a water structure breaker, whereas the three oxygens act as water structure makers. Thus, in spite of being a single ion, the bromate ion has dual characteristics and the experimentally observed kosmotropic ability of this ion is actually a trade-off between a chaotropic site (the bromine atom) and three kosmotropic sites (three oxygen atoms) that are present in the ion.
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Affiliation(s)
- Bikramjit Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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Roy Choudhuri J, Chandra A. Effects of dispersion interactions on the structure, polarity, and dynamics of liquid-vapor interface of an aqueous NaCl solution: Results of first principles simulations at room temperature. J Chem Phys 2018; 148:024702. [DOI: 10.1063/1.5005951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jyoti Roy Choudhuri
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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